Writing R Extensions

Version 4.4.0 Under development (2024-02-13)

R Core Team
This manual is for R, version 4.4.0 Under development (2024-02-13).
Copyright c 1999–2023 R Core Team
Permission is granted to make and distribute verbatim copies of this manual provided
the copyright notice and this permission notice are preserved on all copies.
Permission is granted to copy and distribute modified versions of this manual under
the conditions for verbatim copying, provided that the entire resulting derived work
is distributed under the terms of a permission notice identical to this one.
Permission is granted to copy and distribute translations of this manual into an-
other language, under the above conditions for modified versions, except that this
permission notice may be stated in a translation approved by the R Core Team.
 i

Table of Contents

Acknowledgements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

1 Creating R packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.1 Package structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.1.1 The DESCRIPTION file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.1.2 Licensing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.1.3 Package Dependencies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
1.1.3.1 Suggested packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
1.1.4 The INDEX file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
1.1.5 Package subdirectories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
1.1.6 Data in packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
1.1.7 Non-R scripts in packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
1.1.8 Specifying URLs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
1.2 Configure and cleanup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
1.2.1 Using Makevars. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
1.2.1.1 OpenMP support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
1.2.1.2 Using pthreads . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
1.2.1.3 Compiling in sub-directories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
1.2.2 Configure example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
1.2.3 Using modern Fortran code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
1.2.4 Using C++ code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
1.2.5 C standards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
1.2.6 Using cmake . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
1.3 Checking and building packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
1.3.1 Checking packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
1.3.2 Building package tarballs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
1.3.3 Building binary packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
1.4 Writing package vignettes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
1.4.1 Encodings and vignettes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
1.4.2 Non-Sweave vignettes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
1.5 Package namespaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
1.5.1 Specifying imports and exports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
1.5.2 Registering S3 methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
1.5.3 Load hooks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
1.5.4 useDynLib . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
1.5.5 An example. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
1.5.6 Namespaces with S4 classes and methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
1.6 Writing portable packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
1.6.1 PDF size . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
1.6.2 Check timing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
1.6.3 Encoding issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
1.6.4 Portable C and C++ code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
1.6.4.1 Common symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
1.6.4.2 C++17 issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
1.6.5 Portable Fortran code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
1.6.6 Binary distribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
1.7 Diagnostic messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
1.8 Internationalization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
 ii

1.8.1 C-level messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

1.8.2 R messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
1.8.3 Preparing translations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
1.9 CITATION files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
1.10 Package types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
1.10.1 Frontend . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
1.11 Services . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

2 Writing R documentation files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80

2.1 Rd format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
2.1.1 Documenting functions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
2.1.2 Documenting data sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
2.1.3 Documenting S4 classes and methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
2.1.4 Documenting packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
2.2 Sectioning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
2.3 Marking text . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
2.4 Lists and tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
2.5 Cross-references . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
2.6 Mathematics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
2.7 Figures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
2.8 Insertions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
2.9 Indices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
2.10 Platform-specific documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
2.11 Conditional text . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
2.12 Dynamic pages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
2.13 User-defined macros . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
2.14 Encoding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
2.15 Processing documentation files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
2.16 Editing Rd files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97

3 Tidying and profiling R code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98

3.1 Tidying R code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
3.2 Profiling R code for speed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
3.3 Profiling R code for memory use . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
3.3.1 Memory statistics from Rprof . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
3.3.2 Tracking memory allocations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
3.3.3 Tracing copies of an object . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
3.4 Profiling compiled code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
3.4.1 Profiling on Linux . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
3.4.1.1 perf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
3.4.1.2 oprofile and operf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
3.4.1.3 sprof . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
3.4.2 Profiling on macOS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
3.4.3 Profiling on Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
 iii

4 Debugging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
4.1 Browsing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
4.2 Debugging R code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
4.3 Checking memory access . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
4.3.1 Using gctorture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
4.3.2 Using valgrind . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
4.3.3 Using the Address Sanitizer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
4.3.3.1 Using the Leak Sanitizer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
4.3.4 Using the Undefined Behaviour Sanitizer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
4.3.5 Other analyses with ‘clang’ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
4.3.6 Other analyses with ‘gcc’ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
4.3.7 Using ‘Dr. Memory’ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
4.3.8 Fortran array bounds checking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
4.4 Debugging compiled code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
4.4.1 Finding entry points in dynamically loaded code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
4.4.2 Inspecting R objects when debugging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
4.4.3 Debugging on macOS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
4.5 Using Link-time Optimization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120

5 System and foreign language interfaces . . . . . . . . . . . . . . . . . . . . 123

5.1 Operating system access . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
5.2 Interface functions .C and .Fortran . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
5.3 dyn.load and dyn.unload. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
5.4 Registering native routines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
5.4.1 Speed considerations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
5.4.2 Example: converting a package to use registration . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
5.4.3 Linking to native routines in other packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
5.5 Creating shared objects. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
5.6 Interfacing C++ code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
5.6.1 External C++ code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
5.7 Fortran I/O . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
5.8 Linking to other packages. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
5.8.1 Unix-alikes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
5.8.2 Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
5.9 Handling R objects in C . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
5.9.1 Handling the effects of garbage collection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
5.9.2 Allocating storage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
5.9.3 Details of R types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
5.9.4 Attributes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
5.9.5 Classes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
5.9.6 Handling lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
5.9.7 Handling character data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
5.9.8 Finding and setting variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
5.9.9 Some convenience functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
5.9.9.1 Semi-internal convenience functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
5.9.10 Named objects and copying . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
5.10 Interface functions .Call and .External . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
5.10.1 Calling .Call . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
5.10.2 Calling .External . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
5.10.3 Missing and special values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
5.11 Evaluating R expressions from C . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
 iv

5.11.1 Zero-finding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155

5.11.2 Calculating numerical derivatives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156
5.12 Parsing R code from C . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
5.12.1 Accessing source references . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
5.13 External pointers and weak references . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
5.13.1 An example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
5.14 Vector accessor functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
5.15 Character encoding issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163

6 The R API: entry points for C code . . . . . . . . . . . . . . . . . . . . . . . 165

6.1 Memory allocation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
6.1.1 Transient storage allocation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
6.1.2 User-controlled memory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166
6.2 Error signaling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
6.2.1 Error signaling from Fortran . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
6.3 Random number generation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
6.3.1 Random-number generation from Fortran . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
6.4 Missing and IEEE special values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
6.5 Printing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
6.5.1 Printing from Fortran . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
6.6 Calling C from Fortran and vice versa . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
6.6.1 Fortran character strings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
6.6.2 Fortran LOGICAL. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
6.6.3 Passing functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
6.7 Numerical analysis subroutines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
6.7.1 Distribution functions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
6.7.2 Mathematical functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
6.7.3 Numerical Utilities. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
6.7.4 Mathematical constants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
6.8 Optimization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
6.9 Integration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
6.10 Utility functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
6.11 Re-encoding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
6.12 Condition handling and cleanup code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
6.13 Allowing interrupts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
6.14 Platform and version information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
6.15 Inlining C functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
6.16 Controlling visibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
6.17 Using these functions in your own C code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
6.18 Organization of header files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187

7 Generic functions and methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189

7.1 Adding new generics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190

8 Linking GUIs and other front-ends to R . . . . . . . . . . . . . . . . . . . 191

8.1 Embedding R under Unix-alikes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
8.1.1 Compiling against the R library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
8.1.2 Setting R callbacks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
8.1.3 Registering symbols. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
8.1.4 Meshing event loops . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
 v

8.1.5 Threading issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197

8.2 Embedding R under Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
8.2.1 Using (D)COM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
8.2.2 Calling R.dll directly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
8.2.3 Finding R HOME . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201

Function and variable index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203

Concept index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 208

 1

Acknowledgements
The contributions to early versions of this manual by Saikat DebRoy (who wrote the first draft
of a guide to using .Call and .External) and Adrian Trapletti (who provided information on
the C++ interface) are gratefully acknowledged.
 2

1 Creating R packages
Packages provide a mechanism for loading optional code, data and documentation as needed.
The R distribution itself includes about 30 packages.
In the following, we assume that you know the library() command, including its lib.loc
argument, and we also assume basic knowledge of the R CMD INSTALL utility. Otherwise, please
look at R’s help pages on
?library
?INSTALL
before reading on.
For packages which contain code to be compiled, a computing environment including a num-
ber of tools is assumed; the “R Installation and Administration” manual describes what is
needed for each OS.
Once a source package is created, it must be installed by the command R CMD INSTALL. See
Section “Add-on-packages” in R Installation and Administration.
Other types of extensions are supported (but rare): See Section 1.10 [Package types], page 79.
Some notes on terminology complete this introduction. These will help with the reading of
this manual, and also in describing concepts accurately when asking for help.
A package is a directory of files which extend R, a source package (the master files of a
package), or a tarball containing the files of a source package, or an installed package, the
result of running R CMD INSTALL on a source package. On some platforms (notably macOS and
Windows) there are also binary packages, a zip file or tarball containing the files of an installed
package which can be unpacked rather than installing from sources.
A package is not1 a library. The latter is used in two senses in R documentation.
• A directory into which packages are installed, e.g. /usr/lib/R/library: in that sense it is
sometimes referred to as a library directory or library tree (since the library is a directory
which contains packages as directories, which themselves contain directories).
• That used by the operating system, as a shared, dynamic or static library or (especially on
Windows) a DLL, where the second L stands for ‘library’. Installed packages may contain
compiled code in what is known on Unix-alikes as a shared object and on Windows as a DLL.
The concept of a shared library (dynamic library on macOS) as a collection of compiled code
to which a package might link is also used, especially for R itself on some platforms. On
most platforms these concepts are interchangeable (shared objects and DLLs can both be
loaded into the R process and be linked against), but macOS distinguishes between shared
objects (extension .so) and dynamic libraries (extension .dylib).
There are a number of well-defined operations on source packages.
• The most common is installation which takes a source package and installs it in a library
using R CMD INSTALL or install.packages.
• Source packages can be built. This involves taking a source directory and creating a tarball
ready for distribution, including cleaning it up and creating PDF/HTML documentation
from any vignettes it may contain. Source packages (and most often tarballs) can be checked,
when a test installation is done and tested (including running its examples); also, the
contents of the package are tested in various ways for consistency and portability.
• Compilation is not a correct term for a package. Installing a source package which contains
C, C++ or Fortran code will involve compiling that code. There is also the possibility of
‘byte’ compiling the R code in a package (using the facilities of package compiler): nowadays
1
although this is a persistent mis-usage. It seems to stem from S, whose analogues of R’s packages were officially
known as library sections and later as chapters, but almost always referred to as libraries.
Chapter 1: Creating R packages 3

this is enabled by default for all packages. So compiling a package may come to mean byte-
compiling its R code.
• It used to be unambiguous to talk about loading an installed package using library(),
but since the advent of package namespaces this has been less clear: people now often talk
about loading the package’s namespace and then attaching the package so it becomes visible
on the search path. Function library performs both steps, but a package’s namespace can
be loaded without the package being attached (for example by calls like splines::ns).
The concept of lazy loading of code or data is mentioned at several points. This is part of
the installation, always selected for R code but optional for data. When used the R objects of
the package are created at installation time and stored in a database in the R directory of the
installed package, being loaded into the session at first use. This makes the R session start up
faster and use less (virtual) memory. (For technical details, see Section “Lazy loading” in R
Internals.)
CRAN is a network of WWW sites holding the R distributions and contributed code, espe-
cially R packages. Users of R are encouraged to join in the collaborative project and to submit
their own packages to CRAN: current instructions are linked from https://CRAN.R-project.
org/banner.shtml#submitting.

1.1 Package structure

The sources of an R package consist of a subdirectory containing the files DESCRIPTION and
NAMESPACE, and the subdirectories R, data, demo, exec, inst, man, po, src, tests, tools and
vignettes (some of which can be missing, but which should not be empty). The package
subdirectory may also contain files INDEX, configure, cleanup, LICENSE, LICENCE and NEWS.
Other files such as INSTALL (for non-standard installation instructions), README/README.md2 , or
ChangeLog will be ignored by R, but may be useful to end users. The utility R CMD build may
add files in a build directory (but this should not be used for other purposes).
Except where specifically mentioned,3 packages should not contain Unix-style ‘hidden’
files/directories (that is, those whose name starts with a dot).
The DESCRIPTION and INDEX files are described in the subsections below. The NAMESPACE
file is described in the section on Section 1.5 [Package namespaces], page 48.
The optional files configure and cleanup are (Bourne) shell scripts which are, respectively,
executed before and (if option --clean was given) after installation on Unix-alikes, see Sec-
tion 1.2 [Configure and cleanup], page 20. The analogues on Windows are configure.win and
cleanup.win. Since R 4.2.0 on Windows, configure.ucrt and cleanup.ucrt are supported
and take precedence over configure.win and cleanup.win. They can hence be used to provide
content specific to UCRT or Rtools42 and newer, if needed, but the support for .ucrt files may
be removed in future when building packages from source on the older versions of R will no
longer be needed, and hence the files may be renamed back to .win.
For the conventions for files NEWS and ChangeLog in the GNU project see https://www.gnu.
org/prep/standards/standards.html#Documentation.
The package subdirectory should be given the same name as the package. Because some file
systems (e.g., those on Windows and by default on macOS) are not case-sensitive, to maintain
portability it is strongly recommended that case distinctions not be used to distinguish different

2
This seems to be commonly used for a file in ‘markdown’ format. Be aware that most users of R will not
know that, nor know how to view such a file: platforms such as macOS and Windows do not have a default
viewer set in their file associations. The CRAN package web pages render such files in HTML: the converter
used expects the file to be encoded in UTF-8.
3
currently, top-level files .Rbuildignore and .Rinstignore, and vignettes/.install_extras.
Chapter 1: Creating R packages 4

packages. For example, if you have a package named foo, do not also create a package named
Foo.
To ensure that file names are valid across file systems and supported operating systems, the
ASCII control characters as well as the characters ‘"’, ‘*’, ‘:’, ‘/’, ‘<’, ‘>’, ‘?’, ‘\’, and ‘|’ are not
allowed in file names. In addition, files with names ‘con’, ‘prn’, ‘aux’, ‘clock$’, ‘nul’, ‘com1’ to
‘com9’, and ‘lpt1’ to ‘lpt9’ after conversion to lower case and stripping possible “extensions”
(e.g., ‘lpt5.foo.bar’), are disallowed. Also, file names in the same directory must not differ
only by case (see the previous paragraph). In addition, the basenames of ‘.Rd’ files may be used
in URLs and so must be ASCII and not contain %. For maximal portability filenames should only
contain only ASCII characters not excluded already (that is A-Za-z0-9._!#$%&+,;=@^(){}'[]
— we exclude space as many utilities do not accept spaces in file paths): non-English alphabetic
characters cannot be guaranteed to be supported in all locales. It would be good practice to
avoid the shell metacharacters (){}'[]$~: ~ is also used as part of ‘8.3’ filenames on Windows.
In addition, packages are normally distributed as tarballs, and these have a limit on path lengths:
for maximal portability 100 bytes.
A source package if possible should not contain binary executable files: they are not portable,
and a security risk if they are of the appropriate architecture. R CMD check will warn about them4
unless they are listed (one filepath per line) in a file BinaryFiles at the top level of the package.
Note that CRAN will not accept submissions containing binary files even if they are listed.
The R function package.skeleton can help to create the structure for a new package: see
its help page for details.

1.1.1 The DESCRIPTION file

The DESCRIPTION file contains basic information about the package in the following format:

Package: pkgname
Version: 0.5-1
Date: 2015-01-01
Title: My First Collection of Functions
Authors@R: c(person("Joe", "Developer", role = c("aut", "cre"),
email = "[email protected]"),
person("Pat", "Developer", role = "aut"),
person("A.", "User", role = "ctb",
email = "[email protected]"))
Author: Joe Developer [aut, cre],
Pat Developer [aut],
A. User [ctb]
Maintainer: Joe Developer <[email protected]>
Depends: R (>= 3.1.0), nlme
Suggests: MASS
Description: A (one paragraph) description of what
the package does and why it may be useful.
License: GPL (>= 2)
URL: https://www.r-project.org, http://www.another.url
BugReports: https://pkgname.bugtracker.url

The format is that of a version of a ‘Debian Control File’ (see the help for ‘read.dcf’ and
https://www.debian.org/doc/debian-policy/ch-controlfields.html: R does not require
encoding in UTF-8 and does not support comments starting with ‘#’). Fields start with an
ASCII name immediately followed by a colon: the value starts after the colon and a space. Con-
tinuation lines (for example, for descriptions longer than one line) start with a space or tab.
Field names are case-sensitive: all those used by R are capitalized.

4
false positives are possible, but only a handful have been seen so far.
Chapter 1: Creating R packages 5

For maximal portability, the DESCRIPTION file should be written entirely in ASCII — if this
is not possible it must contain an ‘Encoding’ field (see below).
Several optional fields take logical values: these can be specified as ‘yes’, ‘true’, ‘no’ or
‘false’: capitalized values are also accepted.
The ‘Package’, ‘Version’, ‘License’, ‘Description’, ‘Title’, ‘Author’, and ‘Maintainer’
fields are mandatory, all other fields are optional. Fields ‘Author’ and ‘Maintainer’ can be
auto-generated from ‘Authors@R’, and may be omitted if the latter is provided: however if they
are not ASCII we recommend that they are provided.
The mandatory ‘Package’ field gives the name of the package. This should contain only
(ASCII) letters, numbers and dot, have at least two characters and start with a letter and not
end in a dot. If it needs explaining, this should be done in the ‘Description’ field (and not the
‘Title’ field).
The mandatory ‘Version’ field gives the version of the package. This is a sequence of at
least two (and usually three) non-negative integers separated by single ‘.’ or ‘-’ characters. The
canonical form is as shown in the example, and a version such as ‘0.01’ or ‘0.01.0’ will be
handled as if it were ‘0.1-0’. It is not a decimal number, so for example 0.9 < 0.75 since 9 <
75.
The mandatory ‘License’ field is discussed in the next subsection.
The mandatory ‘Title’ field should give a short description of the package. Some package
listings may truncate the title to 65 characters. It should use title case (that is, use capitals
for the principal words: tools::toTitleCase can help you with this), not use any markup,
not have any continuation lines, and not end in a period (unless part of . . . ). Do not repeat
the package name: it is often used prefixed by the name. Refer to other packages and external
software in single quotes, and to book titles (and similar) in double quotes.
The mandatory ‘Description’ field should give a comprehensive description of what the
package does. One can use several (complete) sentences, but only one paragraph. It should be
intelligible to all the intended readership (e.g. for a CRAN package to all CRAN users). It is good
practice not to start with the package name, ‘This package’ or similar. As with the ‘Title’ field,
double quotes should be used for quotations (including titles of books and articles), and single
quotes for non-English usage, including names of other packages and external software. This field
should also be used for explaining the package name if necessary. URLs should be enclosed in
angle brackets, e.g. ‘<https://www.r-project.org>’: see also Section 1.1.8 [Specifying URLs],
page 20.
The mandatory ‘Author’ field describes who wrote the package. It is a plain text field intended
for human readers, but not for automatic processing (such as extracting the email addresses of
all listed contributors: for that use ‘Authors@R’). Note that all significant contributors must be
included: if you wrote an R wrapper for the work of others included in the src directory, you
are not the sole (and maybe not even the main) author.
The mandatory ‘Maintainer’ field should give a single name followed by a valid (RFC 2822)
email address in angle brackets. It should not end in a period or comma. This field is what is
reported by the maintainer function and used by bug.report. For a CRAN package it should
be a person, not a mailing list and not a corporate entity: do ensure that it is valid and will
remain valid for the lifetime of the package.
Note that the display name (the part before the address in angle brackets) should be enclosed
in double quotes if it contains non-alphanumeric characters such as comma or period. (The
current standard, RFC 5322, allows periods but RFC 2822 did not.)
Both ‘Author’ and ‘Maintainer’ fields can be omitted if a suitable ‘Authors@R’ field is given.
This field can be used to provide a refined and machine-readable description of the package
“authors” (in particular specifying their precise roles), via suitable R code. It should create
Chapter 1: Creating R packages 6

an object of class "person", by either a call to person or a series of calls (one per “author”)
concatenated by c(): see the example DESCRIPTION file above. The roles can include ‘"aut"’
(author) for full authors, ‘"cre"’ (creator) for the package maintainer, and ‘"ctb"’ (contribu-
tor) for other contributors, ‘"cph"’ (copyright holder, which should be the legal name for an
institution or corporate body), among others. See ?person for more information. Note that no
role is assumed by default. Auto-generated package citation information takes advantage of this
specification. The ‘Author’ and ‘Maintainer’ fields are auto-generated from it if needed when
building5 or installing.
An optional ‘Copyright’ field can be used where the copyright holder(s) are not the authors.
If necessary, this can refer to an installed file: the convention is to use file inst/COPYRIGHTS.
The optional ‘Date’ field gives the release date of the current version of the package. It is
strongly recommended6 to use the ‘yyyy-mm-dd’ format conforming to the ISO 8601 standard.
The ‘Depends’, ‘Imports’, ‘Suggests’, ‘Enhances’, ‘LinkingTo’ and
‘Additional_repositories’ fields are discussed in a later subsection.
Dependencies external to the R system should be listed in the ‘SystemRequirements’ field,
possibly amplified in a separate README file. This includes specifying a non-default C++ standard
and the need for GNU make.
The ‘URL’ field may give a list of URLs separated by commas or whitespace, for example
the homepage of the author or a page where additional material describing the software can be
found. These URLs are converted to active hyperlinks in CRAN package listings. See Section 1.1.8
[Specifying URLs], page 20.
The ‘BugReports’ field may contain a single URL to which bug reports about the package
should be submitted. This URL will be used by bug.report instead of sending an email to the
maintainer. A browser is opened for a ‘http://’ or ‘https://’ URL. To specify another email
address for bug reports, use ‘Contact’ instead: however bug.report will try to extract an email
address (preferably from a ‘mailto:’ URL or enclosed in angle brackets) from ‘BugReports’.
Base and recommended packages (i.e., packages contained in the R source distribution or
available from CRAN and recommended to be included in every binary distribution of R) have
a ‘Priority’ field with value ‘base’ or ‘recommended’, respectively. These priorities must not
be used by other packages.
A ‘Collate’ field can be used for controlling the collation order for the R code files in a
package when these are processed for package installation. The default is to collate according to
the ‘C’ locale. If present, the collate specification must list all R code files in the package (tak-
ing possible OS-specific subdirectories into account, see Section 1.1.5 [Package subdirectories],
page 13) as a whitespace separated list of file paths relative to the R subdirectory. Paths con-
taining white space or quotes need to be quoted. An OS-specific collation field (‘Collate.unix’
or ‘Collate.windows’) will be used in preference to ‘Collate’.
The ‘LazyData’ logical field controls whether the R datasets use lazy-loading. A ‘LazyLoad’
field was used in versions prior to 2.14.0, but now is ignored.
The ‘KeepSource’ logical field controls if the package code is sourced using keep.source =
TRUE or FALSE: it might be needed exceptionally for a package designed to always be used with
keep.source = TRUE.
The ‘ByteCompile’ logical field controls if the package R code is to be byte-compiled on
installation: the default is to byte-compile. This can be overridden by installing with flag
--no-byte-compile.

5
at least if this is done in a locale which matches the package encoding.
6
and required by CRAN, so checked by R CMD check --as-cran.
Chapter 1: Creating R packages 7

The ‘UseLTO’ logical field is used to indicate if source code in the package7 is to be compiled
with Link-Time Optimization (see Section 4.5 [Using Link-time Optimization], page 120) if R was
installed with --enable-lto (default true) or --enable-lto=R (default false) (or on Windows if
LTO_OPT is set in MkRules). This can be overridden by the flags --use-LTO and --no-use-LTO.
LTO is said to give most size and performance improvements for large and complex (heavily
templated) C++ projects.
The ‘StagedInstall’ logical field controls if package installation is ‘staged’, that is done to
a temporary location and moved to the final location when successfully completed. This field
was introduced in R 3.6.0 and it true by default: it is considered to be a temporary measure
which may be withdrawn in future.
The ‘ZipData’ logical field has been ignored since R 2.13.0.
The ‘Biarch’ logical field is used on Windows to select the INSTALL option --force-biarch
for this package.
The ‘BuildVignettes’ logical field can be set to a false value to stop R CMD build from
attempting to build the vignettes, as well as preventing8 R CMD check from testing this. This
should only be used exceptionally, for example if the PDFs include large figures which are not
part of the package sources (and hence only in packages which do not have an Open Source
license).
The ‘VignetteBuilder’ field names (in a comma-separated list) packages that provide an en-
gine for building vignettes. These may include the current package, or ones listed in ‘Depends’,
‘Suggests’ or ‘Imports’. The utils package is always implicitly appended. See Section 1.4.2
[Non-Sweave vignettes], page 48, for details. Note that if, for example, a vignette has engine
‘knitr::rmarkdown’, then knitr (https://CRAN.R-project.org/package=knitr) provides the
engine but both knitr and rmarkdown (https://CRAN.R-project.org/package=rmarkdown)
are needed for using it, so both these packages need to be in the ‘VignetteBuilder’ field and at
least suggested (as rmarkdown is only suggested by knitr, and hence not available automatically
along with it). Many packages using knitr (https://CRAN.R-project.org/package=knitr)
also need the package formatR (https://CRAN.R-project.org/package=formatR) which it
suggests and so the user package needs to do so too and include this in ‘VignetteBuilder’.
If the DESCRIPTION file is not entirely in ASCII it should contain an ‘Encoding’ field specifying
an encoding. This is used as the encoding of the DESCRIPTION file itself and of the R and
NAMESPACE files, and as the default encoding of .Rd files. The examples are assumed to be in
this encoding when running R CMD check, and it is used for the encoding of the CITATION file.
Only encoding names latin1 and and UTF-8 are known to be portable. (Do not specify an
encoding unless one is actually needed: doing so makes the package less portable. If a package
has a specified encoding, you should run R CMD build etc in a locale using that encoding.)
The ‘NeedsCompilation’ field should be set to "yes" if the package contains native code
which needs to be compiled, otherwise "no" (when the package could be installed from source
on any platform without additional tools). This is used by install.packages(type = "both")
in R >= 2.15.2 on platforms where binary packages are the norm: it is normally set by R CMD
build or the repository assuming compilation is required if and only if the package has a src
directory.
The ‘OS_type’ field specifies the OS(es) for which the package is intended. If present, it
should be one of unix or windows, and indicates that the package can only be installed on a
platform with ‘.Platform$OS.type’ having that value.
The ‘Type’ field specifies the type of the package: see Section 1.10 [Package types], page 79.

7
without a src/Makefile* file.
8
But it is checked for Open Source packages by R CMD check --as-cran.
Chapter 1: Creating R packages 8

One can add subject classifications for the content of the package using the fields
‘Classification/ACM’ or ‘Classification/ACM-2012’ (using the Computing Classification
System of the Association for Computing Machinery, https://www.acm.org/publications/
class-2012; the former refers to the 1998 version), ‘Classification/JEL’ (the Journal of
Economic Literature Classification System, https://www.aeaweb.org/econlit/jelCodes.
php, or ‘Classification/MSC’ or ‘Classification/MSC-2010’ (the Mathematics Subject
Classification of the American Mathematical Society, https://mathscinet.ams.org/msc/
msc2010.html; the former refers to the 2000 version). The subject classifications should be
comma-separated lists of the respective classification codes, e.g., ‘Classification/ACM: G.4,
H.2.8, I.5.1’.
A ‘Language’ field can be used to indicate if the package documentation is not in English: this
should be a comma-separated list of standard (not private use or grandfathered) IETF language
tags as currently defined by RFC 5646 (https://www.rfc-editor.org/rfc/rfc5646, see also
https://en.wikipedia.org/wiki/IETF_language_tag), i.e., use language subtags which in
essence are 2-letter ISO 639-1 (https://en.wikipedia.org/wiki/ISO_639-1) or 3-letter ISO
639-3 (https://en.wikipedia.org/wiki/ISO_639-3) language codes.
An ‘RdMacros’ field can be used to hold a comma-separated list of packages from which
the current package will import Rd macro definitions. These package should also be listed in
‘Imports’ (or ‘Depends’). The macros in these packages will be imported after the system
macros, in the order listed in the ‘RdMacros’ field, before any macro definitions in the current
package are loaded. Macro definitions in individual .Rd files in the man directory are loaded last,
and are local to later parts of that file. In case of duplicates, the last loaded definition will be
used.9 Both R CMD Rd2pdf and R CMD Rdconv have an optional flag --RdMacros=pkglist. The
option is also a comma-separated list of package names, and has priority over the value given in
DESCRIPTION. Packages using Rd macros should depend on R 3.2.0 or later.
Note: There should be no ‘Built’ or ‘Packaged’ fields, as these are added by the
package management tools.
There is no restriction on the use of other fields not mentioned here (but using other cap-
italizations of these field names would cause confusion). Fields Note, Contact (for contacting
the authors/developers10 ) and MailingList are in common use. Some repositories (including
CRAN and R-forge) add their own fields.

1.1.2 Licensing
Licensing for a package which might be distributed is an important but potentially complex
subject.
It is very important that you include license information! Otherwise, it may not even be
legally correct for others to distribute copies of the package, let alone use it.
The package management tools use the concept of ‘free or open source software’ (FOSS, e.g.,
https://en.wikipedia.org/wiki/FOSS) licenses: the idea being that some users of R and its
packages want to restrict themselves to such software. Others need to ensure that there are no
restrictions stopping them using a package, e.g. forbidding commercial or military use. It is a
central tenet of FOSS software that there are no restrictions on users nor usage.
Do not use the ‘License’ field for information on copyright holders: if needed, use a
‘Copyright’ field.
The mandatory ‘License’ field in the DESCRIPTION file should specify the license of the pack-
age in a standardized form. Alternatives are indicated via vertical bars. Individual specifications
must be one of
9
Duplicate definitions may trigger a warning: see Section 2.13 [User-defined macros], page 95.
10
bug.report will try to extract an email address from a Contact field if there is no BugReports field.
Chapter 1: Creating R packages 9

• One of the “standard” short specifications

GPL-2 GPL-3 LGPL-2 LGPL-2.1 LGPL-3 AGPL-3 Artistic-2.0
BSD_2_clause BSD_3_clause MIT
as made available via https://www.R-project.org/Licenses/ and contained in subdirec-
tory share/licenses of the R source or home directory.
• The names or abbreviations of other licenses contained in the license data base in file
share/licenses/license.db in the R source or home directory, possibly (for versioned
licenses) followed by a version restriction of the form ‘(op v)’ with ‘op’ one of the com-
parison operators ‘<’, ‘<=’, ‘>’, ‘>=’, ‘==’, or ‘!=’ and ‘v’ a numeric version specification
(strings of non-negative integers separated by ‘.’), possibly combined via ‘,’ (see below for
an example). For versioned licenses, one can also specify the name followed by the version,
or combine an existing abbreviation and the version with a ‘-’.
Abbreviations GPL and LGPL are ambiguous and usually11 taken to mean any version of the
license: but it is better not to use them.
• One of the strings ‘file LICENSE’ or ‘file LICENCE’ referring to a file named LICENSE or
LICENCE in the package (source and installation) top-level directory.
• The string ‘Unlimited’, meaning that there are no restrictions on distribution or use other
than those imposed by relevant laws (including copyright laws).
Multiple licences can be specified separated by ‘|’ (surrounded by spaces) in which case the user
can choose any of the alternatives.
If a package license restricts a base license (where permitted, e.g., using GPL-3 or AGPL-3
with an attribution clause), the additional terms should be placed in file LICENSE (or LICENCE),
and the string ‘+ file LICENSE’ (or ‘+ file LICENCE’, respectively) should be appended to the
corresponding individual license specification (preferably with the ‘+’ surrounded by spaces).
Note that several commonly used licenses do not permit restrictions: this includes GPL-2 and
hence any specification which includes it.
Examples of standardized specifications include
License: GPL-2
License: LGPL (>= 2.0, < 3) | Mozilla Public License
License: GPL-2 | file LICENCE
License: GPL (>= 2) | BSD_3_clause + file LICENSE
License: Artistic-2.0 | AGPL-3 + file LICENSE
Please note in particular that “Public domain” is not a valid license, since it is not recognized
in some jurisdictions.
Please ensure that the license you choose also covers any dependencies (including system
dependencies) of your package: it is particularly important that any restrictions on the use of
such dependencies are evident to people reading your DESCRIPTION file.
Fields ‘License_is_FOSS’ and ‘License_restricts_use’ may be added by repositories
where information cannot be computed from the name of the license. ‘License_is_FOSS: yes’
is used for licenses which are known to be FOSS, and ‘License_restricts_use’ can have values
‘yes’ or ‘no’ if the LICENSE file is known to restrict users or usage, or known not to. These are
used by, e.g., the available.packages filters.
The optional file LICENSE/LICENCE contains a copy of the license of the package. To avoid
any confusion only include such a file if it is referred to in the ‘License’ field of the DESCRIPTION
file.
Whereas you should feel free to include a license file in your source distribution, please do
not arrange to install yet another copy of the GNU COPYING or COPYING.LIB files but refer to
11
CRAN expands them to e.g. GPL-2 | GPL-3.
Chapter 1: Creating R packages 10

the copies on https://www.R-project.org/Licenses/ and included in the R distribution (in

directory share/licenses). Since files named LICENSE or LICENCE will be installed, do not use
these names for standard license files. To include comments about the licensing rather than the
body of a license, use a file named something like LICENSE.note.
A few “standard” licenses are rather license templates which need additional information to
be completed via ‘+ file LICENSE’ (with the ‘+’ surrounded by spaces). Where the additional
information is ‘COPYRIGHT HOLDER’, this must give the actual legal entities (not something vague
like ‘Name-of-package authors’): if more than one they should be listed in decreasing order of
contribution.

1.1.3 Package Dependencies

The ‘Depends’ field gives a comma-separated list of package names which this package depends
on. Those packages will be attached before the current package when library or require is
called. Each package name may be optionally followed by a comment in parentheses specifying
a version requirement. The comment should contain a comparison operator, whitespace and a
valid version number, e.g. ‘MASS (>= 3.1-20)’.
The ‘Depends’ field can also specify a dependence on a certain version of R — e.g., if the
package works only with R version 4.0.0 or later, include ‘R (>= 4.0)’ in the ‘Depends’ field.
(As here, trailing zeroes can be dropped and it is recommended that they are.) You can also
require a certain SVN revision for R-devel or R-patched, e.g. ‘R (>= 2.14.0), R (>= r56550)’
requires a version later than R-devel of late July 2011 (including released versions of 2.14.0).
It makes no sense to declare a dependence on R without a version specification, nor on the
package base: this is an R package and package base is always available.
A package or ‘R’ can appear more than once in the ‘Depends’ field, for example to give upper
and lower bounds on acceptable versions.
It is inadvisable to use a dependence on R with patchlevel (the third digit) other than
zero. Doing so with packages which others depend on will cause the other packages to become
unusable under earlier versions in the series, and e.g. versions 4.x.1 are widely used throughout
the Northern Hemisphere academic year.
Both library and the R package checking facilities use this field: hence it is an error to use
improper syntax or misuse the ‘Depends’ field for comments on other software that might be
needed. The R INSTALL facilities check if the version of R used is recent enough for the package
being installed, and the list of packages which is specified will be attached (after checking version
requirements) before the current package.
The ‘Imports’ field lists packages whose namespaces are imported from (as specified in the
NAMESPACE file) but which do not need to be attached. Namespaces accessed by the ‘::’ and
‘:::’ operators must be listed here, or in ‘Suggests’ or ‘Enhances’ (see below). Ideally this
field will include all the standard packages that are used, and it is important to include S4-using
packages (as their class definitions can change and the DESCRIPTION file is used to decide which
packages to re-install when this happens). Packages declared in the ‘Depends’ field should not
also be in the ‘Imports’ field. Version requirements can be specified and are checked when the
namespace is loaded.
The ‘Suggests’ field uses the same syntax as ‘Depends’ and lists packages that are not neces-
sarily needed. This includes packages used only in examples, tests or vignettes (see Section 1.4
[Writing package vignettes], page 45), and packages loaded in the body of functions. E.g., sup-
pose an example12 from package foo uses a dataset from package bar. Then it is not necessary
to have bar use foo unless one wants to execute all the examples/tests/vignettes: it is useful to

12
even one wrapped in \donttest.
Chapter 1: Creating R packages 11

have bar, but not necessary. Version requirements can be specified but should be checked by
the code which uses the package.
Finally, the ‘Enhances’ field lists packages “enhanced” by the package at hand, e.g., by pro-
viding methods for classes from these packages, or ways to handle objects from these packages (so
several packages have ‘Enhances: chron’ because they can handle datetime objects from chron
(https://CRAN.R-project.org/package=chron) even though they prefer R’s native datetime
functions). Version requirements can be specified, but are currently not used. Such packages
cannot be required to check the package: any tests which use them must be conditional on the
presence of the package. (If your tests use e.g. a dataset from another package it should be in
‘Suggests’ and not ‘Enhances’.)
The general rules are
• A package should be listed in only one of these fields.
• Packages whose namespace only is needed to load the package using library(pkgname)
should be listed in the ‘Imports’ field and not in the ‘Depends’ field. Packages listed in
import or importFrom directives in the NAMESPACE file should almost always be in ‘Imports’
and not ‘Depends’.
• Packages that need to be attached to successfully load the package using library(pkgname)
must be listed in the ‘Depends’ field.
• All packages that are needed13 to successfully run R CMD check on the package must be
listed in one of ‘Depends’ or ‘Suggests’ or ‘Imports’. Packages used to run examples
or tests conditionally (e.g. via if(require(pkgname))) should be listed in ‘Suggests’ or
‘Enhances’. (This allows checkers to ensure that all the packages needed for a complete
check are installed.)
• Packages needed to use datasets from the package should be in ‘Imports’: this includes
those needed to define S4 classes used.
In particular, packages providing “only” data for examples or vignettes should be listed in
‘Suggests’ rather than ‘Depends’ in order to make lean installations possible.
Version dependencies in the ‘Depends’ and ‘Imports’ fields are used by library when it
loads the package, and install.packages checks versions for the ‘Depends’, ‘Imports’ and (for
dependencies = TRUE) ‘Suggests’ fields.
It is important that the information in these fields is complete and accurate: it is for example
used to compute which packages depend on an updated package and which packages can safely
be installed in parallel.
This scheme was developed before all packages had namespaces (R 2.14.0 in October 2011),
and good practice changed once that was in place.
Field ‘Depends’ should nowadays be used rarely, only for packages which are intended to
be put on the search path to make their facilities available to the end user (and not to the
package itself): for example it makes sense that a user of package latticeExtra (https://
CRAN.R-project.org/package=latticeExtra) would want the functions of package lattice
(https://CRAN.R-project.org/package=lattice) made available.
Almost always packages mentioned in ‘Depends’ should also be imported from in the
NAMESPACE file: this ensures that any needed parts of those packages are available when some
other package imports the current package.
13
This includes all packages directly called by library and require calls, as well as data obtained via
data(theirdata, package = "somepkg") calls: R CMD check will warn about all of these. But there are subtler
uses which it may not detect: e.g. if package A uses package B and makes use of functionality in package B
which uses package C which package B suggests or enhances, then package C needs to be in the ‘Suggests’
list for package A. Nor will undeclared uses in included files be reported, nor unconditional uses of packages
listed under ‘Enhances’. R CMD check --as-cran will detect more of the subtler uses.
Chapter 1: Creating R packages 12

The ‘Imports’ field should not contain packages which are not imported from (via the
NAMESPACE file or :: or ::: operators), as all the packages listed in that field need to be installed
for the current package to be installed. (This is checked by R CMD check.)
R code in the package should call library or require only exceptionally. Such calls are
never needed for packages listed in ‘Depends’ as they will already be on the search path. It used
to be common practice to use require calls for packages listed in ‘Suggests’ in functions which
used their functionality, but nowadays it is better to access such functionality via :: calls.
A package that wishes to make use of header files in other packages to compile its C/C++ code
needs to declare them as a comma-separated list in the field ‘LinkingTo’ in the DESCRIPTION
file. For example
LinkingTo: link1, link2
The ‘LinkingTo’ field can have a version requirement which is checked at installation.
Specifying a package in ‘LinkingTo’ suffices if these are C/C++ headers containing source
code or static linking is done at installation: the packages do not need to be (and usually should
not be) listed in the ‘Depends’ or ‘Imports’ fields. This includes CRAN package BH (https://
CRAN.R-project.org/package=BH) and almost all users of RcppArmadillo (https://CRAN.
R-project.org/package=RcppArmadillo) and RcppEigen (https://CRAN.R-project.org/
package=RcppEigen). Note that ‘LinkingTo’ applies only to installation: if a packages wishes
to use headers to compile code in tests or vignettes the package providing them needs to be
listed in ‘Suggests’ or perhaps ‘Depends’.
For another use of ‘LinkingTo’ see Section 5.4.3 [Linking to native routines in other packages],
page 133.
The ‘Additional_repositories’ field is a comma-separated list of repository URLs where
the packages named in the other fields may be found. It is currently used by R CMD check to
check that the packages can be found, at least as source packages (which can be installed on any
platform).

1.1.3.1 Suggested packages

Note that someone wanting to run the examples/tests/vignettes may not have a suggested
package available (and it may not even be possible to install it for that platform). The
recommendation used to be to make their use conditional via if(require("pkgname")):
this is OK if that conditioning is done in examples/tests/vignettes, although using
if(requireNamespace("pkgname")) is preferred, if possible.
However, using require for conditioning in package code is not good practice as it alters the
search path for the rest of the session and relies on functions in that package not being masked
by other require or library calls. It is better practice to use code like
if (requireNamespace("rgl", quietly = TRUE)) {
rgl::plot3d(...)
} else {
## do something else not involving rgl.
}
Note the use of rgl:: as that object would not necessarily be visible (and if it is, it need not
be the one from that namespace: plot3d occurs in several other packages). If the intention is
to give an error if the suggested package is not available, simply use e.g. rgl::plot3d.
If the conditional code produces print output, function withAutoprint can be useful.
Note that the recommendation to use suggested packages conditionally in tests does also ap-
ply to packages used to manage test suites: a notorious example was testthat (https://CRAN.
R-project.org/package=testthat) which in version 1.0.0 contained illegal C++ code and hence
could not be installed on standards-compliant platforms.
Chapter 1: Creating R packages 13

Some people have assumed that a ‘recommended’ package in ‘Suggests’ can safely be used
unconditionally, but this is not so. (R can be installed without recommended packages, and
which packages are ‘recommended’ may change.)
As noted above, packages in ‘Enhances’ must be used conditionally and hence objects within
them should always be accessed via ::.
On most systems, R CMD check can be run with only those packages declared in ‘Depends’
and ‘Imports’ by setting environment variable _R_CHECK_DEPENDS_ONLY_=true, whereas setting
_R_CHECK_SUGGESTS_ONLY_=true also allows suggested packages, but not those in ‘Enhances’
nor those not mentioned in the DESCRIPTION file. It is recommended that a package is checked
with each of these set, as well as with neither.
WARNING: Be extremely careful if you do things which would be run at installation time
depending on whether suggested packages are available or not—this includes top-level code in
R code files, .onLoad functions and the definitions of S4 classes and methods. The problem is
that once a namespace of a suggested package is loaded, references to it may be captured in
the installed package (most commonly in S4 methods), but the suggested package may not be
available when the installed package is used (which especially for binary packages might be on
a different machine). Even worse, the problems might not be confined to your package, for the
namespaces of your suggested packages will also be loaded whenever any package which imports
yours is installed and so may be captured there.

1.1.4 The INDEX file

The optional file INDEX contains a line for each sufficiently interesting object in the package,
giving its name and a description (functions such as print methods not usually called explicitly
might not be included). Normally this file is missing and the corresponding information is auto-
matically generated from the documentation sources (using tools::Rdindex()) when installing
from source.
The file is part of the information given by library(help = pkgname).
Rather than editing this file, it is preferable to put customized information about the package
into an overview help page (see Section 2.1.4 [Documenting packages], page 87) and/or a vignette
(see Section 1.4 [Writing package vignettes], page 45).

1.1.5 Package subdirectories

The R subdirectory contains R code files, only. The code files to be installed must start with an
ASCII (lower or upper case) letter or digit and have one of the extensions14 .R, .S, .q, .r, or .s.
We recommend using .R, as this extension seems to be not used by any other software. It should
be possible to read in the files using source(), so R objects must be created by assignments.
Note that there need be no connection between the name of the file and the R objects created
by it. Ideally, the R code files should only directly assign R objects and definitely should not
call functions with side effects such as require and options. If computations are required to
create objects these can use code ‘earlier’ in the package (see the ‘Collate’ field) plus functions
in the ‘Depends’ packages provided that the objects created do not depend on those packages
except via namespace imports.
Extreme care is needed if top-level computations are made to depend on availability or not of
other packages. In particular this applies to setMethods and setClass calls. Nor should they
depend on the availability of external resources such as downloads.
Two exceptions are allowed: if the R subdirectory contains a file sysdata.rda (a
saved image of one or more R objects: please use suitable compression as suggested by
14
Extensions .S and .s arise from code originally written for S(-PLUS), but are commonly used for assembler
code. Extension .q was used for S, which at one time was tentatively called QPE.
Chapter 1: Creating R packages 14

tools::resaveRdaFiles, and see also the ‘SysDataCompression’ DESCRIPTION field.) this

will be lazy-loaded into the namespace environment – this is intended for system datasets that
are not intended to be user-accessible via data. Also, files ending in ‘.in’ will be allowed in
the R directory to allow a configure script to generate suitable files.
Only ASCII characters (and the control characters tab, form feed, LF and CR) should be
used in code files. Other characters are accepted in comments15 , but then the comments may
not be readable in e.g. a UTF-8 locale. Non-ASCII characters in object names will normally16
fail when the package is installed. Any byte will be allowed in a quoted character string but
‘\uxxxx’ escapes should be used for non-ASCII characters. However, non-ASCII character strings
may not be usable in some locales and may display incorrectly in others.
Various R functions in a package can be used to initialize and clean up. See Section 1.5.3
[Load hooks], page 50.
The man subdirectory should contain (only) documentation files for the objects in the package
in R documentation (Rd) format. The documentation filenames must start with an ASCII (lower
or upper case) letter or digit and have the extension .Rd (the default) or .rd. Further, the names
must be valid in ‘file://’ URLs, which means17 they must be entirely ASCII and not contain
‘%’. See Chapter 2 [Writing R documentation files], page 80, for more information. Note that all
user-level objects in a package should be documented; if a package pkg contains user-level objects
which are for “internal” use only, it should provide a file pkg-internal.Rd which documents all
such objects, and clearly states that these are not meant to be called by the user. See e.g. the
sources for package grid in the R distribution. Note that packages which use internal objects
extensively should not export those objects from their namespace, when they do not need to be
documented (see Section 1.5 [Package namespaces], page 48).
Having a man directory containing no documentation files may give an installation error.
The man subdirectory may contain a subdirectory named macros; this will contain source for
user-defined Rd macros. (See Section 2.13 [User-defined macros], page 95.) These use the Rd
format, but may not contain anything but macro definitions, comments and whitespace.
The R and man subdirectories may contain OS-specific subdirectories named unix or windows.
The sources and headers for the compiled code are in src, plus optionally a file Makevars
or Makefile (or for use on Windows, with extension .win or .ucrt). When a package is
installed using R CMD INSTALL, make is used to control compilation and linking into a shared
object for loading into R. There are default make variables and rules for this (determined when
R is configured and recorded in R_HOME/etcR_ARCH/Makeconf), providing support for C, C++,
fixed- or free-form Fortran, Objective C and Objective C++18 with associated extensions .c, .cc
or .cpp, .f, .f90 or .f95,19 .m, and .mm, respectively. We recommend using .h for headers,
also for C++20 or Fortran include files. (Use of extension .C for C++ is no longer supported.)
Files in the src directory should not be hidden (start with a dot), and hidden files will under
some versions of R be ignored.
It is not portable (and may not be possible at all) to mix all these languages in a single
package. Because R itself uses it, we know that C and fixed-form Fortran can be used together,
and mixing C, C++ and Fortran usually work for the platform’s native compilers.
15
but they should be in the encoding declared in the DESCRIPTION file.
16
This is true for OSes which implement the ‘C’ locale: Windows’ idea of the ‘C’ locale uses the WinAnsi charset.
17
More precisely, they can contain the English alphanumeric characters and the symbols ‘$ - _ . + ! ' ( ) , ;
= &’.
18
either or both of which may not be supported on particular platforms. Their main use is on macOS, but
unfortunately recent versions of the macOS SDK have removed much of the support for Objective C v1.0 and
Objective C++.
19
This is not accepted by the Intel Fortran compiler.
20
Using .hpp is not guaranteed to be portable.
Chapter 1: Creating R packages 15

If your code needs to depend on the platform there are certain defines which can used in C
or C++. On all Windows builds (even 64-bit ones) ‘_WIN32’ will be defined: on 64-bit Windows
builds also ‘_WIN64’. On macOS ‘__APPLE__’ is defined21 ; for an ‘Apple Silicon’ platform, test
for both ‘__APPLE__’ and ‘__arm64__’.
The default rules can be tweaked by setting macros22 in a file src/Makevars (see Section 1.2.1
[Using Makevars], page 25). Note that this mechanism should be general enough to eliminate the
need for a package-specific src/Makefile. If such a file is to be distributed, considerable care
is needed to make it general enough to work on all R platforms. If it has any targets at all, it
should have an appropriate first target named ‘all’ and a (possibly empty) target ‘clean’ which
removes all files generated by running make (to be used by ‘R CMD INSTALL --clean’ and ‘R CMD
INSTALL --preclean’). There are platform-specific file names on Windows: src/Makevars.win
takes precedence over src/Makevars and src/Makefile.win must be used. Since R 4.2.0,
src/Makevars.ucrt takes precedence over src/Makevars.win and src/Makefile.ucrt takes
precedence over src/Makefile.win. src/Makevars.ucrt and src/Makefile.ucrt will be ig-
nored by earlier versions of R, and hence can be used to provide content specific to UCRT or
Rtools42 and newer, but the support for .ucrt files may be removed in the future when building
packages from source on the older versions of R will no longer be needed, and hence the files
may be renamed back to .win. Some make programs require makefiles to have a complete final
line, including a newline.
A few packages use the src directory for purposes other than making a shared object (e.g.
to create executables). Such packages should have files src/Makefile and src/Makefile.win
or src/Makefile.ucrt (unless intended for only Unix-alikes or only Windows). Note that on
Unix such makefiles are included after R_HOME/etc/R_ARCH/Makeconf so all the usual R macros
and make rules are available – for example C compilation will by default use the C compiler
and flags with which R was configured. This also applies on Windows as from R 4.3.0: packages
intended to be used with earlier versions should include that file themselves.
The order of inclusion of makefiles for a package which does not have a src/Makefile file is
Unix-alike Windows
src/Makevars src/Makevars.ucrt, src/Makevars.win
R_HOME/etc/R_ARCH/Makeconf R_HOME/etc/R_ARCH/Makeconf
R_MAKEVARS_SITE, R_HOME/etc/R_ R_MAKEVARS_SITE, R_HOME/etc/R_
ARCH/Makevars.site ARCH/Makevars.site
R_HOME/share/make/shlib.mk R_HOME/share/make/winshlib.mk
R_MAKEVARS_USER, ~/.R/Makevars-platform, R_MAKEVARS_USER, ~/.R/Makevars.ucrt,
~/.R/Makevars ~/.R/Makevars.win64,
~/.R/Makevars.win
For those which do, it is
R_HOME/etc/R_ARCH/Makeconf R_HOME/etc/R_ARCH/Makeconf
R_MAKEVARS_SITE, R_HOME/etc/R_ R_MAKEVARS_SITE, R_HOME/etc/R_
ARCH/Makevars.site ARCH/Makevars.site
src/Makefile src/Makefile.ucrt, src/Makefile.win
R_MAKEVARS_USER, ~/.R/Makevars-platform, R_MAKEVARS_USER, ~/.R/Makevars.ucrt,
~/.R/Makevars ~/.R/Makevars.win64,
~/.R/Makevars.win
Items in capitals are environment variables: those separated by commas are alternatives looked
for in the order shown.
21
There is also ‘__APPLE_CC__’, but that indicates a compiler with Apple-specific features not the OS, although
for historical reasons is is defined by LLVM clang. It is used in Rinlinedfuns.h.
22
the POSIX terminology, called ‘make variables’ by GNU make.
Chapter 1: Creating R packages 16

In very special cases packages may create binary files other than the shared objects/DLLs
in the src directory. Such files will not be installed in a multi-architecture setting since R CMD
INSTALL --libs-only is used to merge multiple sub-architectures and it only copies shared
objects/DLLs. If a package wants to install other binaries (for example executable programs),
it should provide an R script src/install.libs.R which will be run as part of the installation
in the src build directory instead of copying the shared objects/DLLs. The script is run in a
separate R environment containing the following variables: R_PACKAGE_NAME (the name of the
package), R_PACKAGE_SOURCE (the path to the source directory of the package), R_PACKAGE_DIR
(the path of the target installation directory of the package), R_ARCH (the arch-dependent part
of the path, often empty), SHLIB_EXT (the extension of shared objects) and WINDOWS (TRUE on
Windows, FALSE elsewhere). Something close to the default behavior could be replicated with
the following src/install.libs.R file:
files <- Sys.glob(paste0("*", SHLIB_EXT))
dest <- file.path(R_PACKAGE_DIR, paste0('libs', R_ARCH))
dir.create(dest, recursive = TRUE, showWarnings = FALSE)
file.copy(files, dest, overwrite = TRUE)
if(file.exists("symbols.rds"))
file.copy("symbols.rds", dest, overwrite = TRUE)
On the other hand, executable programs could be installed along the lines of
execs <- c("one", "two", "three")
if(WINDOWS) execs <- paste0(execs, ".exe")
if ( any(file.exists(execs)) ) {
dest <- file.path(R_PACKAGE_DIR, paste0('bin', R_ARCH))
dir.create(dest, recursive = TRUE, showWarnings = FALSE)
file.copy(execs, dest, overwrite = TRUE)
}
Note the use of architecture-specific subdirectories of bin where needed. (Executables should
installed under a bin directory and not under libs. It is good practice to check that they can
be executed as part of the installation script, so a broken package is not installed.)
The data subdirectory is for data files: See Section 1.1.6 [Data in packages], page 17.
The demo subdirectory is for R scripts (for running via demo()) that demonstrate some of
the functionality of the package. Demos may be interactive and are not checked automatically,
so if testing is desired use code in the tests directory to achieve this. The script files must
start with a (lower or upper case) letter and have one of the extensions .R or .r. If present, the
demo subdirectory should also have a 00Index file with one line for each demo, giving its name
and a description separated by a tab or at least three spaces. (This index file is not generated
automatically.) Note that a demo does not have a specified encoding and so should be an ASCII
file (see Section 1.6.3 [Encoding issues], page 66). Function demo() will use the package encoding
if there is one, but this is mainly useful for non-ASCII comments.
The contents of the inst subdirectory will be copied recursively to the installation directory.
Subdirectories of inst should not interfere with those used by R (currently, R, data, demo, exec,
libs, man, help, html and Meta, and earlier versions used latex, R-ex). The copying of the
inst happens after src is built so its Makefile can create files to be installed. To exclude
files from being installed, one can specify a list of exclude patterns in file .Rinstignore in the
top-level source directory. These patterns should be Perl-like regular expressions (see the help
for regexp in R for the precise details), one per line, to be matched case-insensitively against
the file and directory paths, e.g. doc/.*[.]png$ will exclude all PNG files in inst/doc based
on the extension.
Note that with the exceptions of INDEX, LICENSE/LICENCE and NEWS, information files at the
top level of the package will not be installed and so not be known to users of Windows and macOS
Chapter 1: Creating R packages 17

compiled packages (and not seen by those who use R CMD INSTALL or install.packages() on
the tarball). So any information files you wish an end user to see should be included in inst.
Note that if the named exceptions also occur in inst, the version in inst will be that seen in
the installed package.
Things you might like to add to inst are a CITATION file for use by the citation function,
and a NEWS.Rd file for use by the news function. See its help page for the specific format
restrictions of the NEWS.Rd file.
Another file sometimes needed in inst is AUTHORS or COPYRIGHTS to specify the authors or
copyright holders when this is too complex to put in the DESCRIPTION file.
Subdirectory tests is for additional package-specific test code, similar to the specific tests
that come with the R distribution. Test code can either be provided directly in a .R (or .r as
from R 3.4.0) file, or via a .Rin file containing code which in turn creates the corresponding
.R file (e.g., by collecting all function objects in the package and then calling them with the
strangest arguments). The results of running a .R file are written to a .Rout file. If there is a
corresponding23 .Rout.save file, these two are compared, with differences being reported but
not causing an error. The directory tests is copied to the check area, and the tests are run with
the copy as the working directory and with R_LIBS set to ensure that the copy of the package
installed during testing will be found by library(pkg_name). Note that the package-specific
tests are run in a vanilla R session without setting the random-number seed, so tests which use
random numbers will need to set the seed to obtain reproducible results (and it can be helpful
to do so in all cases, to avoid occasional failures when tests are run).
If directory tests has a subdirectory Examples containing a file pkg-Ex.Rout.save, this is
compared to the output file for running the examples when the latter are checked. Reference
output should be produced without having the --timings option set (and note that --as-cran
sets it).
If reference output is included for examples, tests or vignettes do make sure that it is fully
reproducible, as it will be compared verbatim to that produced in a check run, unless the
‘IGNORE_RDIFF’ markup is used. Things which trip up maintainers include displayed version
numbers from loading other packages, printing numerical results to an unreproducibly high
precision and printing timings. Another trap is small values which are in fact rounding error
from zero: consider using zapsmall.
Subdirectory exec could contain additional executable scripts the package needs, typically
scripts for interpreters such as the shell, Perl, or Tcl. NB: only files (and not directories) under
exec are installed (and those with names starting with a dot are ignored), and they are all
marked as executable (mode 755, moderated by ‘umask’) on POSIX platforms. Note too that
this is not suitable for executable programs since some platforms (including Windows) support
multiple architectures using the same installed package directory.
Subdirectory po is used for files related to localization: see Section 1.8 [Internationalization],
page 76.
Subdirectory tools is the preferred place for auxiliary files needed during configuration, and
also for sources need to re-create scripts (e.g. M4 files for autoconf: some prefer to put those
in a subdirectory m4 of tools).

1.1.6 Data in packages

The data subdirectory is for data files, either to be made available via lazy-loading or for loading
using data(). (The choice is made by the ‘LazyData’ field in the DESCRIPTION file: the default
23
The best way to generate such a file is to copy the .Rout from a successful run of R CMD check. If you
want to generate it separately, do run R with options --vanilla --no-echo and with environment variable
LANGUAGE=en set to get messages in English. Be careful not to use output with the option --timings (and
note that --as-cran sets it).
Chapter 1: Creating R packages 18

is not to do so.) It should not be used for other data files needed by the package, and the
convention has grown up to use directory inst/extdata for such files.
Data files can have one of three types as indicated by their extension: plain R code (.R or
.r), tables (.tab, .txt, or .csv, see ?data for the file formats, and note that .csv is not the
standard24 CSV format), or save() images (.RData or .rda). The files should not be hidden
(have names starting with a dot). Note that R code should be if possible “self-sufficient” and
not make use of extra functionality provided by the package, so that the data file can also be
used without having to load the package or its namespace: it should run as silently as possible
and not change the search() path by attaching packages or other environments.
Images (extensions .RData25 or .rda) can contain references to the namespaces of packages
that were used to create them. Preferably there should be no such references in data files,
and in any case they should only be to packages listed in the Depends and Imports fields, as
otherwise it may be impossible to install the package. To check for such references, load all
the images into a vanilla R session, run str() on all the datasets, and look at the output of
loadedNamespaces().
Particular care is needed where a dataset or one of its components is of an S4 class, especially
if the class is defined in a different package. First, the package containing the class definition
has to be available to do useful things with the dataset, so that package must be listed in
Imports or Depends (even if this gives a check warning about unused imports). Second, the
definition of an S4 class can change, and often is unnoticed when in a package with a different
author. So it may be wiser to use the .R form and use that to create the dataset object when
needed (loading package namespaces but not attaching them by using requireNamespace(pkg,
quietly = TRUE) and using pkg:: to refer to objects in the namespace).
If you are not using ‘LazyData’ and either your data files are large or e.g., you use data/foo.R
scripts to produce your data, loading your namespace, you can speed up installation by providing
a file datalist in the data subdirectory. This should have one line per topic that data() will
find, in the format ‘foo’ if data(foo) provides ‘foo’, or ‘foo: bar bah’ if data(foo) provides
‘bar’ and ‘bah’. R CMD build will automatically add a datalist file to data directories of over
1Mb, using the function tools::add_datalist.
Tables (.tab, .txt, or .csv files) can be compressed by gzip, bzip2 or xz, optionally with
additional extension .gz, .bz2 or .xz.
If your package is to be distributed, do consider the resource implications of large datasets
for your users: they can make packages very slow to download and use up unwelcome amounts
of storage space, as well as taking many seconds to load. It is normally best to distribute large
datasets as .rda images prepared by save(, compress = TRUE) (the default). Using bzip2 or
xz compression will usually reduce the size of both the package tarball and the installed package,
in some cases by a factor of two or more.
Package tools has a couple of functions to help with data images: checkRdaFiles reports
on the way the image was saved, and resaveRdaFiles will re-save with a different type of
compression, including choosing the best type for that particular image.
Many packages using ‘LazyData’ will benefit from using a form of compression other than
gzip in the installed lazy-loading database. This can be selected by the --data-compress
option to R CMD INSTALL or by using the ‘LazyDataCompression’ field in the DESCRIPTION file.
Useful values are bzip2, xz and the default, gzip: value none is also accepted. The only way to
discover which is best is to try them all and look at the size of the pkgname/data/Rdata.rdb
file. A function to do that (quoting sizes in KB) is
CheckLazyDataCompression <- function(pkg)
24
e.g. https://www.rfc-editor.org/rfc/rfc4180.
25
People who have trouble with case are advised to use .rda as a common error is to refer to abc.RData as
abc.Rdata!
Chapter 1: Creating R packages 19

{
pkg_name <- sub("_.*", "", pkg)
lib <- tempfile(); dir.create(lib)
zs <- c("gzip", "bzip2", "xz")
res <- integer(3); names(res) <- zs
for (z in zs) {
opts <- c(paste0("--data-compress=", z),
"--no-libs", "--no-help", "--no-demo", "--no-exec", "--no-test-load")
install.packages(pkg, lib, INSTALL_opts = opts, repos = NULL, quiet = TRUE)
res[z] <- file.size(file.path(lib, pkg_name, "data", "Rdata.rdb"))
}
ceiling(res/1024)
}
(applied to a source package without any ‘LazyDataCompression’ field). R CMD check will warn
if it finds a pkgname/data/Rdata.rdb file of more than 5MB without ‘LazyDataCompression’
being set. If you see that, run CheckLazyDataCompression() and set the field – to gzip in the
unlikely event26 that is the best choice.
The analogue for sysdata.rda is field ‘SysDataCompression’: the default is xz for files
bigger than 1MB otherwise gzip.
Lazy-loading is not supported for very large datasets (those which when serialized exceed
2GB, the limit for the format on 32-bit platforms).

1.1.7 Non-R scripts in packages

Code which needs to be compiled (C, C++, Fortran . . . ) is included in the src subdirectory and
discussed elsewhere in this document.
Subdirectory exec could be used for scripts for interpreters such as the shell, BUGS,
JavaScript, Matlab, Perl, php (amap (https://CRAN.R-project.org/package=amap)),
Python or Tcl (Simile (https://CRAN.R-project.org/package=Simile)), or even R.
However, it seems more common to use the inst directory, for example WriteXLS/inst/Perl,
NMF/inst/m-files, RnavGraph/inst/tcl, RProtoBuf/inst/python and emdbook/inst/BUGS
and gridSVG/inst/js.
Java code is a special case: except for very small programs, .java files should be byte-
compiled (to a .class file) and distributed as part of a .jar file: the conventional location
for the .jar file(s) is inst/java. It is desirable (and required under an Open Source license)
to make the Java source files available: this is best done in a top-level java directory in the
package—the source files should not be installed.
If your package requires one of these interpreters or an extension then this should be de-
clared in the ‘SystemRequirements’ field of its DESCRIPTION file. (Users of Java most often do
so via rJava (https://CRAN.R-project.org/package=rJava), when depending on/importing
that suffices unless there is a version requirement on Java code in the package.)
Windows and Mac users should be aware that the Tcl extensions ‘BWidget’ and ‘Tktable’
(which have sometimes been included in the Windows27 and macOS R installers) are extensions
and do need to be declared (and that ‘Tktable’ is less widely available than it used to be,
including not in the main repositories for major Linux distributions). ‘BWidget’ needs to be
installed by the user on other OSes. This is fairly easy to do: first find the Tcl search path:
library(tcltk)
strsplit(tclvalue('auto_path'), " ")[[1]]
26
For all the CRAN packages tested, either gz or bzip2 provided a very substantial reduction in installed size.
27
‘BWidget’ still is on Windows but ‘Tktable’ was not in R 4.0.0.
Chapter 1: Creating R packages 20

then download the sources from https://sourceforge.net/projects/tcllib/files/

BWidget/ and in a terminal run something like
tar xf bwidget-1.9.14.tar.gz
sudo mv bwidget-1.9.14 /usr/local/lib
substituting a location on the Tcl search path for /usr/local/lib if needed. (If no location on
that search path is writeable, you will need to add one each time ‘BWidget’ is to be used with
tcltk::addTclPath().)
To (silently) test for the presence of ‘Tktable’ one can use
library(tcltk)
have_tktable <- !isFALSE(suppressWarnings(tclRequire('Tktable')))
Installing ‘Tktable’ needs a C compiler and the Tk headers (not necessarily installed
with Tcl/Tk). At the time of writing the latest sources (from 2008) were available from
https://sourceforge.net/projects/tktable/files/tktable/2.10/Tktable2.10.tar.gz/
download, but needed patching for current Tk (8.6.11, but not 8.6.10) – a patch can be found
at https://www.stats.ox.ac.uk/pub/bdr/Tktable/. For a system installation of Tk you
may need to install Tktable as ‘root’ as on e.g. Fedora all the locations on auto_path are
owned by ‘root’.

1.1.8 Specifying URLs

URLs in many places in the package documentation will be converted to clickable hyperlinks in
at least some of their renderings. So care is needed that their forms are correct and portable.
The full URL should be given, including the scheme (often ‘http://’ or ‘https://’) and a
final ‘/’ for references to directories.
Spaces in URLs are not portable and how they are handled does vary by HTTP server and
by client. There should be no space in the host part of an ‘http://’ URL, and spaces in the
remainder should be encoded, with each space replaced by ‘%20’.
Other characters may benefit from being encoded: see the help on URLencode().
The canonical URL for a CRAN package is
https://cran.r-project.org/package=pkgname
and not a version starting ‘https://cran.r-project.org/web/packages/pkgname’.

1.2 Configure and cleanup

Note that most of this section is specific to Unix-alikes: see the comments later on about the
Windows port of R.
If your package needs some system-dependent configuration before installation you can in-
clude an executable (Bourne28 shell script configure in your package which (if present) is
executed by R CMD INSTALL before any other action is performed. This can be a script created
by the Autoconf mechanism, but may also be a script written by yourself. Use this to detect if
28
The script should only assume a POSIX-compliant /bin/sh – see https://pubs.opengroup.org/onlinepubs/
9699919799/utilities/V3_chap02.html. In particular bash extensions must not be used, and not all R
platforms have a bash command, let alone one at /bin/bash. All known shells used with R support the
use of backticks, but not all support ‘$(cmd)’. However, real-world shells are not fully POSIX-compliant and
omissions and idiosyncrasies need to be worked around—which Autoconf will do for you. Arithmetic expansion
is a known issue: see https://www.gnu.org/software/autoconf/manual/autoconf.html#Portable-Shell
for this and others. Some checks can be done by the checkbashisms Perl script at https://sourceforge.
net/projects/checkbaskisms/files, also available in most Linux distributions in a package named either
‘devscripts’ or ‘devscripts-checkbashisms’: a later version can be extracted from Debian sources such as
the most recent tar.xz in https://deb.debian.org/debian/pool/main/d/devscripts/ and has been needed
for recent versions of Perl.
Chapter 1: Creating R packages 21

any nonstandard libraries are present such that corresponding code in the package can be dis-
abled at install time rather than giving error messages when the package is compiled or used. To
summarize, the full power of Autoconf is available for your extension package (including variable
substitution, searching for libraries, etc.). Background and useful tips on Autoconf and related
tools (including pkg-config described below) can be found at https://autotools.info/.
A configure script is run in an environment which has all the environment variables set for
an R session (see R_HOME/etc/Renviron) plus R_PACKAGE_NAME (the name of the package), R_
PACKAGE_DIR (the path of the target installation directory of the package, a temporary location
for staged installs) and R_ARCH (the arch-dependent part of the path, often empty).
Under a Unix-alike only, an executable (Bourne shell) script cleanup is executed as the last
thing by R CMD INSTALL if option --clean was given, and by R CMD build when preparing the
package for building from its source.
As an example consider we want to use functionality provided by a (C or Fortran) library
foo. Using Autoconf, we can create a configure script which checks for the library, sets variable
HAVE_FOO to TRUE if it was found and to FALSE otherwise, and then substitutes this value into
output files (by replacing instances of ‘@HAVE_FOO@’ in input files with the value of HAVE_FOO).
For example, if a function named bar is to be made available by linking against library foo (i.e.,
using -lfoo), one could use
AC_CHECK_LIB(foo, fun, [HAVE_FOO=TRUE], [HAVE_FOO=FALSE])
AC_SUBST(HAVE_FOO)
......
AC_CONFIG_FILES([foo.R])
AC_OUTPUT
in configure.ac (assuming Autoconf 2.50 or later).
The definition of the respective R function in foo.R.in could be
foo <- function(x) {
if(!@HAVE_FOO@)
stop("Sorry, library 'foo' is not available")
...
From this file configure creates the actual R source file foo.R looking like
foo <- function(x) {
if(!FALSE)
stop("Sorry, library 'foo' is not available")
...
if library foo was not found (with the desired functionality). In this case, the above R code
effectively disables the function.
One could also use different file fragments for available and missing functionality, respectively.
You will very likely need to ensure that the same C compiler and compiler flags are used in
the configure tests as when compiling R or your package. Under a Unix-alike, you can achieve
this by including the following fragment early in configure.ac (before calling AC_PROG_CC or
anything which calls it)
: ${R_HOME=`R RHOME`}
if test -z "${R_HOME}"; then
echo "could not determine R_HOME"
exit 1
fi
CC=`"${R_HOME}/bin/R" CMD config CC`
CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
Chapter 1: Creating R packages 22

(Using ‘${R_HOME}/bin/R’ rather than just ‘R’ is necessary in order to use the correct version
of R when running the script as part of R CMD INSTALL, and the quotes since ‘${R_HOME}’ might
contain spaces.)
If your code does load checks (for example, to check for an entry point in a library or to run
code) then you will also need
LDFLAGS=`"${R_HOME}/bin/R" CMD config LDFLAGS`
Packages written with C++ need to pick up the details for the C++ compiler and switch the
current language to C++ by something like
CXX=`"${R_HOME}/bin/R" CMD config CXX`
if test -z "$CXX"; then
AC_MSG_ERROR([No C++ compiler is available])
fi
CXXFLAGS=`"${R_HOME}/bin/R" CMD config CXXFLAGS`
CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
AC_LANG(C++)
The latter is important, as for example C headers may not be available to C++ programs or may
not be written to avoid C++ name-mangling. Note that an R installation is not required to have
a C++ compiler so ‘CXX’ may be empty. If the package specifies a non-default C++ standard, use
the config variable names (such as CXX17) appropriate to the standard, but still set CXX and
CXXFLAGS.
You can use R CMD config to get the value of the basic configuration variables, and also the
header and library flags necessary for linking a front-end executable program against R, see R
CMD config --help for details. If you do, it is essential that you use both the command and the
appropriate flags, so that for example ‘CC’ must always be used with ‘CFLAGS’ and (for code to be
linked into a shared library) ‘CPICFLAGS’. For Fortran, be careful to use ‘FC FFLAGS FPICFLAGS’
for fixed-form Fortran and ‘FC FCFLAGS FPICFLAGS’ for free-form Fortran.
As from R 4.3.0, variables
CC CFLAGS CXX CXXFLAGS CPPFLAGS LDFLAGS FC FCFLAGS
are set in the environment (if not already set) when configure is called from R CMD INSTALL, in
case the script forgets to set them as described above. This includes making use of the selected
C standard (but not the C++ standard as that is selected at a later stage by R CMD SHLIB).
To check for an external BLAS library using the AX_BLAS macro from the official Autoconf
Macro Archive29 , one can use
FC=`"${R_HOME}/bin/R" CMD config FC`
FCLAGS=`"${R_HOME}/bin/R" CMD config FFLAGS`
AC_PROG_FC
FLIBS=`"${R_HOME}/bin/R" CMD config FLIBS`
AX_BLAS([], AC_MSG_ERROR([could not find your BLAS library], 1))
Note that FLIBS as determined by R must be used to ensure that Fortran code works on all R
platforms.
N.B.: If the configure script creates files, e.g. src/Makevars, you do need a cleanup script
to remove them. Otherwise R CMD build may ship the files that are created. For example,
package RODBC (https://CRAN.R-project.org/package=RODBC) has
#!/bin/sh

rm -f config.* src/Makevars src/config.h

29
https://www.gnu.org/software/autoconf-archive/ax_blas.html. If you include macros from that archive
you need to arrange for them to be included in the package sources for use by autoreconf.
Chapter 1: Creating R packages 23

As this example shows, configure often creates working files such as config.log. If you use
a hand-crafted script rather than one created by autoconf, it is highly recommended that you
log its actions to file config.log.
If your configure script needs auxiliary files, it is recommended that you ship them in a tools
directory (as R itself does).
You should bear in mind that the configure script will not be used on Windows systems.
If your package is to be made publicly available, please give enough information for a user
on a non-Unix-alike platform to configure it manually, or provide a configure.win script (or
configure.ucrt) to be used on that platform. (Optionally, there can be a cleanup.win script
(or cleanup.ucrt). Both should be shell scripts to be executed by ash, which is a mini-
mal version of Bourne-style sh. As from R 4.2.0, bash is used. When configure.win (or
configure.ucrt) is run the environment variables R_HOME (which uses ‘/’ as the file separa-
tor), R_ARCH and R_ARCH_BIN will be set. Use R_ARCH to decide if this is a 64-bit build (its
value there is ‘/x64’) and to install DLLs to the correct place (${R_HOME}/libs${R_ARCH}).
Use R_ARCH_BIN to find the correct place under the bin directory, e.g. ${R_HOME}/bin${R_
ARCH_BIN}/Rscript.exe. If a configure.win script does compilation (including calling R CMD
SHLIB), most of the considerations above apply.
As the scripts on Windows are executed as sh ./configure.win and similar, any ’shebang’
first line (such as #! /bin/bash) is treated as a comment.
In some rare circumstances, the configuration and cleanup scripts need to know the location
into which the package is being installed. An example of this is a package that uses C code
and creates two shared object/DLLs. Usually, the object that is dynamically loaded by R is
linked against the second, dependent, object. On some systems, we can add the location of this
dependent object to the object that is dynamically loaded by R. This means that each user does
not have to set the value of the LD_LIBRARY_PATH (or equivalent) environment variable, but
that the secondary object is automatically resolved. Another example is when a package installs
support files that are required at run time, and their location is substituted into an R data
structure at installation time. The names of the top-level library directory (i.e., specifiable via
the ‘-l’ argument) and the directory of the package itself are made available to the installation
scripts via the two shell/environment variables R_LIBRARY_DIR and R_PACKAGE_DIR. Addition-
ally, the name of the package (e.g. ‘survival’ or ‘MASS’) being installed is available from the
environment variable R_PACKAGE_NAME. (Currently the value of R_PACKAGE_DIR is always ${R_
LIBRARY_DIR}/${R_PACKAGE_NAME}, but this used not to be the case when versioned installs
were allowed. Its main use is in configure.win (or configure.ucrt) scripts for the installation
path of external software’s DLLs.) Note that the value of R_PACKAGE_DIR may contain spaces
and other shell-unfriendly characters, and so should be quoted in makefiles and configure scripts.
One of the more tricky tasks can be to find the headers and libraries of external software. One
tool which is increasingly available on Unix-alikes (but not by default30 on macOS) to do this
is pkg-config. The configure script will need to test for the presence of the command itself 31
(see for example package tiff (https://CRAN.R-project.org/package=tiff)), and if present it
can be asked if the software is installed, of a suitable version and for compilation/linking flags
by e.g.
$ pkg-config --exists 'libtiff-4 >= 4.1.0' --print-errors # check the status
$ pkg-config --modversion libtiff-4
4.3.0
30
but it is available on the machines used to produce the CRAN binary packages: however as Apple does not
ship .pc files for its system libraries such as expat, libcurl, libxml2, sqlite3 and ‘zlib’, it may well not
find information on these. Some substitutes are available from https://github.com/R-macos/recipes/tree/
master/stubs/pkgconfig-darwin and are installed on the CRAN package builders.
31
It is not wise to check the version of pkg-config as it is sometimes a link to pkgconf, a separate project with
a different version series.
Chapter 1: Creating R packages 24

$ pkg-config --cflags libtiff-4

-I/usr/local/include
$ pkg-config --libs libtiff-4
-L/usr/local/lib -ltiff
$ pkg-config --static --libs libtiff-4
-L/usr/local/lib -ltiff -lwebp -llzma -ljpeg -lz
Note that pkg-config --libs gives the information required to link against the default version32
of that library (usually the dynamic one), and pkg-config --static --libs may be needed if
the static library is to be used.
Static libraries are commonly used on macOS (and Windows) to facilitate bundling external
software with binary distributions of packages. This means that portable (source) packages
need to allow for this. It is not safe to just use pkg-config --static --libs, as that will often
include further libraries that are not necessarily installed on the user’s system (or maybe only
the versioned library such as libjbig.so.2.1 is installed and not libjbig.so which would be
needed to use -ljbig sometimes included in pkg-config --static --libs libtiff-4).
Another issue is that pkg-config --exists may not be reliable. It checks not only that the
‘module’ is available but all of the dependencies, including those in principle needed for static
linking. (XQuartz 2.8.x only distributed dynamic libraries and not some of the .pc files needed
for --exists.)
Sometimes the name by which the software is known to pkg-config is not what one might
expect (e.g. ‘libxml-2.0’ even for 2.9.x). To get a complete list use
pkg-config --list-all | sort
Some external software provides a -config command to do a similar job to pkg-config,
including
curl-config freetype-config gdal-config geos-config
gsl-config iodbc-config libpng-config nc-config
pcre-config pcre2-config xml2-config xslt-config
(curl-config is for libcurl not curl. nc-config is for netcdf.) Most have an option to use
static libraries.
N.B. These commands indicate what header paths and libraries are needed, but they do not
obviate the need to check that the recipes they give actually work. (This is especially necessary
for platforms which use static linking.)
If using Autoconf it is good practice to include all the Autoconf sources in the package (and
required for an Open Source package and tested by R CMD check --as-cran). This will include
the file configure.ac33 in the top-level directory of the package. If extensions written in m4 are
needed, these should be included under the directory tools and included from configure.ac
via e.g.,
m4_include([tools/ax_pthread.m4])
Alternatively, Autoconf can be asked to search all .m4 files in a directory by including something
like34
AC_CONFIG_MACRO_DIR([tools/m4])
One source of such extensions is the ‘Autoconf Archive’ (https://www.gnu.org/software/
autoconf-archive/. It is not safe to assume this is installed on users’ machines, so the exten-
sion should be shipped with the package (taking care to comply with its licence).
32
but not all projects get this right when only a static library is installed, so it is often necessary to try in turn
pkg-config --libs and pkg-config --static --libs.
33
a decade ago Autoconf used configure.in: this is still accepted but should be renamed and autoreconf as
used by R CMD check --as-cran will report as such.
34
For those using autoconf 2.70 or later there is also AC_CONFIG_MACRO_DIRS which allows multiple directories
to be specified.
Chapter 1: Creating R packages 25

1.2.1 Using Makevars

Sometimes writing your own configure script can be avoided by supplying a file Makevars: also
one of the most common uses of a configure script is to make Makevars from Makevars.in.
A Makevars file is a makefile and is used as one of several makefiles by R CMD SHLIB (which
is called by R CMD INSTALL to compile code in the src directory). It should be written if at
all possible in a portable style, in particular (except for Makevars.win and Makevars.ucrt)
without the use of GNU extensions.
The most common use of a Makevars file is to set additional preprocessor options (for example
include paths and definitions) for C/C++ files via PKG_CPPFLAGS, and additional compiler flags
by setting PKG_CFLAGS, PKG_CXXFLAGS or PKG_FFLAGS, for C, C++ or Fortran respectively (see
Section 5.5 [Creating shared objects], page 134).
N.B.: Include paths are preprocessor options, not compiler options, and must be set in
PKG_CPPFLAGS as otherwise platform-specific paths (e.g. ‘-I/usr/local/include’) will take
precedence. PKG_CPPFLAGS should contain ‘-I’, ‘-D’, ‘-U’ and (where supported) ‘-include’
and ‘-pthread’ options: everything else should be a compiler flag. The order of flags matters,
and using ‘-I’ in PKG_CFLAGS or PKG_CXXFLAGS has led to hard-to-debug platform-specific errors.
Makevars can also be used to set flags for the linker, for example ‘-L’ and ‘-l’ options, via
PKG_LIBS.
When writing a Makevars file for a package you intend to distribute, take care to ensure that
it is not specific to your compiler: flags such as -O2 -Wall -pedantic (and all other -W flags:
for the Oracle compilers these were used to pass arguments to compiler phases) are all specific
to GCC (and compilers such as clang which aim to be options-compatible with it).
Also, do not set variables such as CPPFLAGS, CFLAGS etc.: these should be settable by users
(sites) through appropriate personal (site-wide) Makevars files. See Section “Customizing pack-
age compilation” in R Installation and Administration,
There are some macros35 which are set whilst configuring the building of R itself and
are stored in R_HOME/etcR_ARCH/Makeconf. That makefile is included as a Makefile after
Makevars[.win], and the macros it defines can be used in macro assignments and make com-
mand lines in the latter. These include
FLIBS A macro containing the set of libraries need to link Fortran code. This may need to
be included in PKG_LIBS: it will normally be included automatically if the package
contains Fortran source files in the src directory.
BLAS_LIBS
A macro containing the BLAS libraries used when building R. This may need to
be included in PKG_LIBS. Beware that if it is empty then the R executable will
contain all the double-precision and double-complex BLAS routines, but no single-
precision nor complex routines. If BLAS_LIBS is included, then FLIBS also needs to
be36 included following it, as most BLAS libraries are written at least partially in
Fortran. However, it can be omitted if the package contains Fortran source code as
that will add FLIBS to the link line.
LAPACK_LIBS
A macro containing the LAPACK libraries (and paths where appropriate) used when
building R. This may need to be included in PKG_LIBS. It may point to a dynamic
library libRlapack which contains the main double-precision LAPACK routines as
well as those double-complex LAPACK routines needed to build R, or it may point
35
in POSIX parlance: GNU make calls these ‘make variables’.
36
at least on Unix-alikes: the Windows build currently resolves such dependencies to a static Fortran library
when Rblas.dll is built.
Chapter 1: Creating R packages 26

to an external LAPACK library, or may be empty if an external BLAS library also

contains LAPACK.
[libRlapack includes all the double-precision LAPACK routines which were current
in 2003 and a few more recent ones: a list of which routines are included is in file
src/modules/lapack/README. Note that an external LAPACK/BLAS library need
not do so, as some were ‘deprecated’ (and not compiled by default) in LAPACK
3.6.0 in late 2015.]
For portability, the macros BLAS_LIBS and FLIBS should always be included after
LAPACK_LIBS (and in that order).
SAFE_FFLAGS
A macro containing flags which are needed to circumvent over-optimization of
FORTRAN code: it is might be ‘-g -O2 -ffloat-store’ or ‘-g -O2 -msse2
-mfpmath=sse’ on ‘ix86’ platforms using gfortran. Note that this is not an
additional flag to be used as part of PKG_FFLAGS, but a replacement for FFLAGS.
See the example later in this section.
Setting certain macros in Makevars will prevent R CMD SHLIB setting them: in particular if
Makevars sets ‘OBJECTS’ it will not be set on the make command line. This can be useful in
conjunction with implicit rules to allow other types of source code to be compiled and included
in the shared object. It can also be used to control the set of files which are compiled, either by
excluding some files in src or including some files in subdirectories. For example
OBJECTS = 4dfp/endianio.o 4dfp/Getifh.o R4dfp-object.o
Note that Makevars should not normally contain targets, as it is included before the de-
fault makefile and make will call the first target, intended to be all in the default makefile.
If you really need to circumvent that, use a suitable (phony) target all before any actual
targets in Makevars.[win]: for example package fastICA (https://CRAN.R-project.org/
package=fastICA) used to have
PKG_LIBS = @BLAS_LIBS@

SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FFLAGS)

all: $(SHLIB)

slamc.o: slamc.f
$(FC) $(SLAMC_FFLAGS) -c -o slamc.o slamc.f
needed to ensure that the LAPACK routines find some constants without infinite looping. The
Windows equivalent was
all: $(SHLIB)

slamc.o: slamc.f
$(FC) $(SAFE_FFLAGS) -c -o slamc.o slamc.f
(since the other macros are all empty on that platform, and R’s internal BLAS was not used).
Note that the first target in Makevars will be called, but for back-compatibility it is best named
all.
If you want to create and then link to a library, say using code in a subdirectory, use something
like
.PHONY: all mylibs

all: $(SHLIB)
$(SHLIB): mylibs
Chapter 1: Creating R packages 27

mylibs:
(cd subdir; $(MAKE))
Be careful to create all the necessary dependencies, as there is no guarantee that the dependencies
of all will be run in a particular order (and some of the CRAN build machines use multiple
CPUs and parallel makes). In particular,
all: mylibs
does not suffice. GNU make does allow the construct
.NOTPARALLEL: all
all: mylibs $(SHLIB)
but that is not portable. dmake and pmake allow the similar .NO_PARALLEL, also not portable:
some variants of pmake accept .NOTPARALLEL as an alias for .NO_PARALLEL.
Note that on Windows it is required that Makevars[.win, .ucrt] does create a DLL: this
is needed as it is the only reliable way to ensure that building a DLL succeeded. If you want
to use the src directory for some purpose other than building a DLL, use a Makefile.win or
Makefile.ucrt file.
It is sometimes useful to have a target ‘clean’ in Makevars, Makevars.win or Makevars.ucrt:
this will be used by R CMD build to clean up (a copy of) the package sources. When it is run by
build it will have fewer macros set, in particular not $(SHLIB), nor $(OBJECTS) unless set in
the file itself. It would also be possible to add tasks to the target ‘shlib-clean’ which is run
by R CMD INSTALL and R CMD SHLIB with options --clean and --preclean.
Avoid the use of default (also known as ‘implicit’ rules) in makefiles, as these are make-
specific. Even when mandated by POSIX – GNU make does not comply and this has broken
package installation.
An unfortunately common error is to have
all: $(SHLIB) clean
which asks make to clean in parallel with compiling the code. Not only does this lead to hard-
to-debug installation errors, it wipes out all the evidence of any error (from a parallel make
or not). It is much better to leave cleaning to the end user using the facilities in the previous
paragraph.
If you want to run R code in Makevars, e.g. to find configuration information, please do
ensure that you use the correct copy of R or Rscript: there might not be one in the path at all,
or it might be the wrong version or architecture. The correct way to do this is via
"$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" filename
"$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e 'R expression'
where $(R_ARCH_BIN) is only needed currently on Windows.
Environment or make variables can be used to select different macros for Intel 64-bit code or
code for other architectures, for example (GNU make syntax, allowed on Windows)
ifeq "$(WIN)" "64"
PKG_LIBS = value for 64-bit Intel Windows
else
PKG_LIBS = value for unknown Windows architectures
endif
On Windows there is normally a choice between linking to an import library or directly to
a DLL. Where possible, the latter is much more reliable: import libraries are tied to a specific
toolchain, and in particular on 64-bit Windows two different conventions have been commonly
used. So for example instead of
PKG_LIBS = -L$(XML_DIR)/lib -lxml2
Chapter 1: Creating R packages 28

one can use

PKG_LIBS = -L$(XML_DIR)/bin -lxml2
since on Windows -lxxx will look in turn for
libxxx.dll.a
xxx.dll.a
libxxx.a
xxx.lib
libxxx.dll
xxx.dll
where the first and second are conventionally import libraries, the third and fourth often static
libraries (with .lib intended for Visual C++), but might be import libraries. See for example
https://sourceware.org/binutils/docs-2.20/ld/WIN32.html#WIN32.
The fly in the ointment is that the DLL might not be named libxxx.dll, and in fact on
32-bit Windows there is a libxml2.dll whereas on one build for 64-bit Windows the DLL is
called libxml2-2.dll. Using import libraries can cover over these differences but can cause
equal difficulties.
If static libraries are available they can save a lot of problems with run-time finding of DLLs,
especially when binary packages are to be distributed and even more when these support both
architectures. Where using DLLs is unavoidable we normally arrange (via configure.win or
configure.ucrt) to ship them in the same directory as the package DLL.

1.2.1.1 OpenMP support

There is some support for packages which wish to use OpenMP37 . The make macros
SHLIB_OPENMP_CFLAGS
SHLIB_OPENMP_CXXFLAGS
SHLIB_OPENMP_FFLAGS
are available for use in src/Makevars, src/Makevars.win or Makevars.ucrt. Include the
appropriate macro in PKG_CFLAGS, PKG_CXXFLAGS and so on, and also in PKG_LIBS (but see
below for Fortran). C/C++ code that needs to be conditioned on the use of OpenMP can
be used inside #ifdef _OPENMP: note that some toolchains used for R (including Apple’s for
macOS38 and some others using clang39 ) have no OpenMP support at all, not even omp.h.
For example, a package with C code written for OpenMP should have in src/Makevars the
lines
PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS)
PKG_LIBS = $(SHLIB_OPENMP_CFLAGS)
Note that the macro SHLIB_OPENMP_CXXFLAGS applies to the default C++ compiler and not
necessarily to the C++17/20/23 compiler: users of the latter should do their own configure
checks. If you do use your own checks, make sure that OpenMP support is complete by compiling
and linking an OpenMP-using program: on some platforms the runtime library is optional and
on others that library depends on other optional libraries.
Some care is needed when compilers are from different families which may use different
OpenMP runtimes (e.g. clang vs GCC including gfortran, although it is often possible to use
the clang runtime with GCC but not vice versa: however gfortran >= 9 may generate calls
37
https://www.openmp.org/, https://en.wikipedia.org/wiki/OpenMP, https://hpc-tutorials.llnl.gov/
openmp/
38
There are somewhat fragile workarounds: see https://mac.r-project.org/openmp/.
39
Default builds of LLVM clang 3.8.0 and later have support for OpenMP, but the libomp run-time library
may not be installed.
Chapter 1: Creating R packages 29

not in the clang runtime). For a package with Fortran code using OpenMP the appropriate
lines are
PKG_FFLAGS = $(SHLIB_OPENMP_FFLAGS)
PKG_LIBS = $(SHLIB_OPENMP_CFLAGS)
as the C compiler will be used to link the package code. There are platforms on which this
does not work for some OpenMP-using code and installation will fail. Since R >= 3.6.2 the best
alternative for a package with only Fortran sources using OpenMP is to use
USE_FC_TO_LINK =
PKG_FFLAGS = $(SHLIB_OPENMP_FFLAGS)
PKG_LIBS = $(SHLIB_OPENMP_FFLAGS)
in src/Makevars, src/Makevars.win or Makevars.ucrt. Note however, that when this is
used $(FLIBS) should not be included in PKG_LIBS since it is for linking Fortran-compiled code
by the C compiler.
Common platforms may inline all OpenMP calls and so tolerate the omission of the OpenMP
flag from PKG_LIBS, but this usually results in an installation failure with a different compiler or
compilation flags. So cross-check that e.g. -fopenmp appears in the linking line in the installation
logs.
It is not portable to use OpenMP with more than one of C, C++ and Fortran in a single
package since it is not uncommon that the compilers are of different families.
For portability, any C/C++ code using the omp_* functions should include the omp.h header:
some compilers (but not all) include it when OpenMP mode is switched on (e.g. via flag
-fopenmp).
There is nothing40 to say what version of OpenMP is supported: version 4.0 (and much of 4.5
or 5.0) is supported by recent versions of the Linux and Windows platforms, but portable pack-
ages cannot assume that end users have recent versions. Apple clang on macOS has no OpenMP
support. https://www.openmp.org/resources/openmp-compilers-tools/ gives some idea of
what compilers support what versions. Note that support for Fortran compilers is often less up-
to-date and that page suggests it is unwise to rely on a version later than 3.1. Which introduced
a Fortran OpenMP module, so Fortran users of OpenMP should include
use omp_lib
Rarely, using OpenMP with clang on Linux generates calls in libatomic, resulting in loading
messages like
undefined symbol: __atomic_compare_exchange
undefined symbol: __atomic_load
The workaround is to link with -latomic (having checked it exists).
The performance of OpenMP varies substantially between platforms. The Windows im-
plementation has substantial overheads, so is only beneficial if quite substantial tasks are run
in parallel. Also, on Windows new threads are started with the default41 FPU control word,
so computations done on OpenMP threads will not make use of extended-precision arithmetic
which is the default for the main process.
Do not include these macros unless your code does make use of OpenMP (possibly for C++
via included external headers): this can result in the OpenMP runtime being linked in, threads
being started, . . . .
Calling any of the R API from threaded code is ‘for experts only’ and strongly discouraged.
Many functions in the R API modify internal R data structures and might corrupt these data
40
In most implementations the _OPENMP macro has value a date which can be mapped to an OpenMP version:
for example, value 201307 is the date of version 4.0 (July 2013). However this may be used to denote the
latest version which is partially supported, not that which is fully implemented.
41
Windows default, not MinGW-w64 default.
Chapter 1: Creating R packages 30

structures if called simultaneously from multiple threads. Most R API functions can signal
errors, which must only happen on the R main thread. Also, external libraries (e.g. LAPACK)
may not be thread-safe.
Packages are not standard-alone programs, and an R process could contain more than one
OpenMP-enabled package as well as other components (for example, an optimized BLAS) mak-
ing use of OpenMP. So careful consideration needs to be given to resource usage. OpenMP
works with parallel regions, and for most implementations the default is to use as many threads
as ‘CPUs’ for such regions. Parallel regions can be nested, although it is common to use only
a single thread below the first level. The correctness of the detected number of ‘CPUs’ and the
assumption that the R process is entitled to use them all are both dubious assumptions. One
way to limit resources is to limit the overall number of threads available to OpenMP in the R
process: this can be done via environment variable OMP_THREAD_LIMIT, where implemented.42
Alternatively, the number of threads per region can be limited by the environment variable
OMP_NUM_THREADS or API call omp_set_num_threads, or, better, for the regions in your code as
part of their specification. E.g. R uses43
#pragma omp parallel for num_threads(nthreads) ...
That way you only control your own code and not that of other OpenMP users.
Note that setting environment variables to control OpenMP is implementation-dependent and
may need to be done outside the R process or before any use of OpenMP (which might be by
another process or R itself). Also, implementation-specific variables such as KMP_THREAD_LIMIT
might take precedence.

1.2.1.2 Using pthreads

There is no direct support for the POSIX threads (more commonly known as pthreads): by
the time we considered adding it several packages were using it unconditionally so it seems that
nowadays it is universally available on POSIX operating systems (hence not Windows).
For reasonably recent versions of gcc and clang the correct specification is
PKG_CPPFLAGS = -pthread
PKG_LIBS = -pthread
(and the plural version is also accepted on some systems/versions). For other platforms the
specification is
PKG_CPPFLAGS = -D_REENTRANT
PKG_LIBS = -lpthread
(and note that the library name is singular). This is what -pthread does on all known current
platforms (although earlier versions of OpenBSD used a different library name).
For a tutorial see https://hpc-tutorials.llnl.gov/posix/.
POSIX threads are not normally used on Windows, which has its own native concepts of
threads. However, there are two projects implementing pthreads on top of Windows, pthreads-
w32 and winpthreads (part of the MinGW-w64 project).
Whether Windows toolchains implement pthreads is up to the toolchain provider. A make
variable SHLIB_PTHREAD_FLAGS is available for use in src/Makevars.win or Makevars.ucrt:
this should be included in both PKG_CPPFLAGS (or the Fortran compiler flags) and PKG_LIBS.
The presence of a working pthreads implementation cannot be unambiguously determined
without testing for yourself: however, that ‘_REENTRANT’ is defined44 in C/C++ code is a good
indication.
42
Which it was at the time of writing with GCC, Intel and Clang compilers. The count may include the thread
running the main process.
43
Be careful not to declare nthreads as const int: the Oracle compiler required it to be ‘an lvalue’.
44
some Windows toolchains had the typo ‘_REENTRANCE’ instead.
Chapter 1: Creating R packages 31

Note that not all pthreads implementations are equivalent as parts are optional (see
https://pubs.opengroup.org/onlinepubs/009695399/basedefs/pthread.h.html): for ex-
ample, macOS lacks the ‘Barriers’ option.
See also the comments on thread-safety and performance under OpenMP: on all known R
platforms OpenMP is implemented via pthreads and the known performance issues are in the
latter.

1.2.1.3 Compiling in sub-directories

Package authors fairly often want to organize code in sub-directories of src, for example if they
are including a separate piece of external software to which this is an R interface.
One simple way is simply to set OBJECTS to be all the objects that need to be compiled,
including in sub-directories. For example, CRAN package RSiena (https://CRAN.R-project.
org/package=RSiena) has
SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.cpp model/*/*.cpp model/*/*/*.cpp)

OBJECTS = siena07utilities.o siena07internals.o siena07setup.o siena07models.o $(SOURCES:.cpp=.o)

One problem with that approach is that unless GNU make extensions are used, the source
files need to be listed and kept up-to-date. As in the following from CRAN package lossDev
(https://CRAN.R-project.org/package=lossDev):
OBJECTS.samplers = samplers/ExpandableArray.o samplers/Knots.o \
samplers/RJumpSpline.o samplers/RJumpSplineFactory.o \
samplers/RealSlicerOV.o samplers/SliceFactoryOV.o samplers/MNorm.o
OBJECTS.distributions = distributions/DSpline.o \
distributions/DChisqrOV.o distributions/DTOV.o \
distributions/DNormOV.o distributions/DUnifOV.o distributions/RScalarDist.o
OBJECTS.root = RJump.o

OBJECTS = $(OBJECTS.samplers) $(OBJECTS.distributions) $(OBJECTS.root)

Where the subdirectory is self-contained code with a suitable makefile, the best approach is
something like
PKG_LIBS = -LCsdp/lib -lsdp $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

$(SHLIB): Csdp/lib/libsdp.a

Csdp/lib/libsdp.a:
@(cd Csdp/lib && $(MAKE) libsdp.a \
CC="$(CC)" CFLAGS="$(CFLAGS) $(CPICFLAGS)" AR="$(AR)" RANLIB="$(RANLIB)")
Note the quotes: the macros can contain spaces, e.g. CC = "gcc -m64 -std=gnu99". Several
authors have forgotten about parallel makes: the static library in the subdirectory must be
made before the shared object ($(SHLIB)) and so the latter must depend on the former. Others
forget the need45 for position-independent code.
We really do not recommend using src/Makefile instead of src/Makevars, and as the
example above shows, it is not necessary.

1.2.2 Configure example

It may be helpful to give an extended example of using a configure script to create a
src/Makevars file: this is based on that in the RODBC (https://CRAN.R-project.org/
package=RODBC) package.
The configure.ac file follows: configure is created from this by running autoconf in the
top-level package directory (containing configure.ac).
AC_INIT([RODBC], 1.1.8) dnl package name, version

45
A few OSes (AIX, Windows) do not need special flags for such code, but most do—although compilers will
often generate PIC code when not asked to do so.
Chapter 1: Creating R packages 32

dnl A user-specifiable option

odbc_mgr=""
AC_ARG_WITH([odbc-manager],
AC_HELP_STRING([--with-odbc-manager=MGR],
[specify the ODBC manager, e.g. odbc or iodbc]),
[odbc_mgr=$withval])

if test "$odbc_mgr" = "odbc" ; then

AC_PATH_PROGS(ODBC_CONFIG, odbc_config)
fi

dnl Select an optional include path, from a configure option

dnl or from an environment variable.
AC_ARG_WITH([odbc-include],
AC_HELP_STRING([--with-odbc-include=INCLUDE_PATH],
[the location of ODBC header files]),
[odbc_include_path=$withval])
RODBC_CPPFLAGS="-I."
if test [ -n "$odbc_include_path" ] ; then
RODBC_CPPFLAGS="-I. -I${odbc_include_path}"
else
if test [ -n "${ODBC_INCLUDE}" ] ; then
RODBC_CPPFLAGS="-I. -I${ODBC_INCLUDE}"
fi
fi

dnl ditto for a library path

AC_ARG_WITH([odbc-lib],
AC_HELP_STRING([--with-odbc-lib=LIB_PATH],
[the location of ODBC libraries]),
[odbc_lib_path=$withval])
if test [ -n "$odbc_lib_path" ] ; then
LIBS="-L$odbc_lib_path ${LIBS}"
else
if test [ -n "${ODBC_LIBS}" ] ; then
LIBS="-L${ODBC_LIBS} ${LIBS}"
else
if test -n "${ODBC_CONFIG}"; then
odbc_lib_path=`odbc_config --libs | sed s/-lodbc//`
LIBS="${odbc_lib_path} ${LIBS}"
fi
fi
fi

dnl Now find the compiler and compiler flags to use

: ${R_HOME=`R RHOME`}
if test -z "${R_HOME}"; then
echo "could not determine R_HOME"
exit 1
fi
CC=`"${R_HOME}/bin/R" CMD config CC`
CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`

if test -n "${ODBC_CONFIG}"; then

RODBC_CPPFLAGS=`odbc_config --cflags`
fi
CPPFLAGS="${CPPFLAGS} ${RODBC_CPPFLAGS}"

dnl Check the headers can be found

AC_CHECK_HEADERS(sql.h sqlext.h)
if test "${ac_cv_header_sql_h}" = no ||
test "${ac_cv_header_sqlext_h}" = no; then
AC_MSG_ERROR("ODBC headers sql.h and sqlext.h not found")
Chapter 1: Creating R packages 33

fi

dnl search for a library containing an ODBC function

if test [ -n "${odbc_mgr}" ] ; then
AC_SEARCH_LIBS(SQLTables, ${odbc_mgr}, ,
AC_MSG_ERROR("ODBC driver manager ${odbc_mgr} not found"))
else
AC_SEARCH_LIBS(SQLTables, odbc odbc32 iodbc, ,
AC_MSG_ERROR("no ODBC driver manager found"))
fi

dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they are defined.
AC_CHECK_TYPES([SQLLEN, SQLULEN], , , [# include <sql.h>])
dnl for unixODBC header
AC_CHECK_SIZEOF(long, 4)

dnl substitute RODBC_CPPFLAGS and LIBS

AC_SUBST(RODBC_CPPFLAGS)
AC_SUBST(LIBS)
AC_CONFIG_HEADERS([src/config.h])
dnl and do substitution in the src/Makevars.in and src/config.h
AC_CONFIG_FILES([src/Makevars])
AC_OUTPUT
where src/Makevars.in would be simply
PKG_CPPFLAGS = @RODBC_CPPFLAGS@
PKG_LIBS = @LIBS@
A user can then be advised to specify the location of the ODBC driver manager files by
options like (lines broken for easier reading)
R CMD INSTALL \
--configure-args='--with-odbc-include=/opt/local/include \
--with-odbc-lib=/opt/local/lib --with-odbc-manager=iodbc' \
RODBC
or by setting the environment variables ODBC_INCLUDE and ODBC_LIBS.

1.2.3 Using modern Fortran code

R assumes that source files with extension .f are fixed-form Fortran 90 (which includes Fortran
77), and passes them to the compiler specified by macro ‘FC’. The Fortran compiler will also
accept free-form Fortran 90/95 code with extension .f90 or (most46 ) .f95.
The same compiler is used for both fixed-form and free-form Fortran code (with different
file extensions and possibly different flags). Macro PKG_FFLAGS can be used for package-specific
flags: for the un-encountered case that both are included in a single package and that different
flags are needed for the two forms, macro PKG_FCFLAGS is also available for free-form Fortran.
The code used to build R allows a ‘Fortran 90’ compiler to be selected as ‘FC’, so platforms
might be encountered which only support Fortran 90. However, Fortran 95 is supported on all
known platforms.
Most compilers specified by ‘FC’ will accept Fortran 2003, 2008 or 2018 code: such code
should still use file extension .f90. Most current platforms use gfortran where you might
need to include -std=f2003, -std=f2008 or (from version 8) -std=f2018 in PKG_FFLAGS or
PKG_FCFLAGS: the default is ‘GNU Fortran’, currently Fortran 2018 (but Fortran 95 prior to
gfortran 8) with non-standard extensions. The other compilers in current use (LLVM’s flang-
new and Intel’s ifx) default to Fortran 2018.
It is good practice to describe a Fortran version requirement in DESCRIPTION’s
‘SystemRequirements’ field.
46
Intel compilers do not by default but this is worked around when using packages without a src/Makefile.
Chapter 1: Creating R packages 34

Modern versions of Fortran support modules, whereby compiling one source file creates a
module file which is then included in others. (Module files typically have a .mod extension: they
do depend on the compiler used and so should never be included in a package.) This creates a
dependence which make will not know about and often causes installation with a parallel make
to fail. Thus it is necessary to add explicit dependencies to src/Makevars to tell make the
constraints on the order of compilation. For example, if file iface.f90 creates a module ‘iface’
used by files cmi.f90 and dmi.f90 then src/Makevars needs to contain something like
cmi.o dmi.o: iface.o
Note that it is not portable (although some platforms do accept it) to define a module of the
same name in multiple source files.

1.2.4 Using C++ code

R can be built without a C++ compiler although one is available (but not necessarily installed)
on all known R platforms. As from R 4.0.0 a C++ compiler will be selected only if it conforms to
the 2011 standard (‘C++11’). A minor update47 (‘C++14’) was published in December 2014 and
was used by default as from R 4.1.0 if supported. Further revisions ‘C++17’ (in December 2017)
and ‘C++20’ (with many new features in December 2020) have been published since. The next
revision, ‘C++23’, is expected in 2023/4 and several compilers already have extensive partial
support for the current drafts.
The default standard for compiling R packages was changed to C++17 in R 4.3.0 if supported,
and from R 4.4.0 only a C++17 compiler will be selected as the default C++ compiler.
What standard a C++ compiler aims to support can be hard to determine: the value48 of __
cplusplus may help but some compilers use it to denote a standard which is partially supported
and some the latest standard which is (almost) fully supported. On a Unix-alike configure will
try to identify a compiler and flags for each of the standards: this relies heavily on the reported
values of __cplusplus.
The webpage https://en.cppreference.com/w/cpp/compiler_support gives some infor-
mation on which compilers are known to support recent C++ features.
C++ standards have deprecated and later removed features. Be aware that some current com-
pilers still accept removed features in C++17 mode, such as std::unary_function (deprecated
in C++11, removed in C++17).
Different versions of R have used different default C++ standards, so for maximal portability
a package should specify the standard it requires. In order to specify C++14 code in a package
with a Makevars file (or Makevars.win or Makevars.ucrt on Windows) should include the line
CXX_STD = CXX14
Compilation and linking will then be done with the C++14 compiler (if any). Analogously for
other standards (details below). On the other hand, specifying C++1149 when the code is valid
under C++14 or C++17 reduces future portability.
Packages without a src/Makevars or src/Makefile file may specify a C++ standard for code
in the src directory by including something like ‘C++14’ in the ‘SystemRequirements’ field of
the DESCRIPTION file, e.g.
SystemRequirements: C++14

47
Some changes are linked from https://isocpp.org/std/standing-documents/
sd-6-sg10-feature-test-recommendations: there were also additional deprecations.
48
Values 201103L, 201402L, 201703L and 202002L are most commonly used for C++11, C++14, C++17 and C++20
respectively, but some compilers set 1L. For C++23 all that can currently be assumed is a value greater than
that for C++20: for example g++ 12 uses 202100L and clang++ (LLVM 15, Apple 14) uses 202101L.
49
Often historically used to mean ‘not C++98’
Chapter 1: Creating R packages 35

If a package does have a src/Makevars[.win] file then also setting the make variable
‘CXX_STD’ there is recommended, as it allows R CMD SHLIB to work correctly in the package’s
src directory.
A requirement of C++17 or later should always be declared in the ‘SystemRequirements’
field (as well as in src/Makevars or src/Makefile) so this is shown on the package’s summary
pages on CRAN or similar. This is also good practice for a requirement of C++14. Note that
support of C++14 or C++17 is only available from R 3.4.0, so if the package has an R version
requirement it needs to take that into account.
Essentially complete C++14 support is available from GCC 5, LLVM clang 3.4 and currently-
used versions of Apple clang.
Code needing C++14 features can check for their presence via ‘SD-6 feature tests’50 . Such a
check could be
#include <memory> // header where this is defined
#if defined(__cpp_lib_make_unique) && (__cpp_lib_make_unique >= 201304)
using std::make_unique;
#else
// your emulation
#endif
ec RHEL 8 (8.x, 9.x available. full support 2024-05 + 8 more years) ec RHEL 9 (11.x
available, full support 2027-05 + 8 more years) C++17 (as from R 3.4.0), C++20 (as from R 4.0.0)
and C++23 (as from R 4.3.0) can be specified in an analogous way (replacing 14 by 17, 20 or 23)
but compiler/OS support is platform-dependent. Some C++17 and C++20 support is available
with the default builds of R on macOS and Windows as from R 4.0.0. Much of g++’s support for
C++17 needs version 7 or later: that is more recent than some still-current Linux distributions
but often packages for later compilers are available: for RHEL/Centos 7 look for ‘devtoolset’.
Note that C++17 or later ‘support’ does not mean complete support: use feature tests as
well as resources such as https://en.cppreference.com/w/cpp/compiler_support, https://
gcc.gnu.org/projects/cxx-status.html and https://clang.llvm.org/cxx_status.html
to see if the features you want to use are widely implemented.
Attempts to specify an unknown C++ standard are silently ignored: recent versions of R throw
an error for C++98 and for known standards for which no compiler+flags has been detected.
If a package using C++ has a configure script it is essential that the script selects the correct
C++ compiler and standard, via something like
CXX17=`"${R_HOME}/bin/R" CMD config CXX17`
if test -z "$CXX17"; then
AC_MSG_ERROR([No C++17 compiler is available])
fi
CXX17STD=`"${R_HOME}/bin/R" CMD config CXX17STD`
CXX="${CXX17} ${CXX17STD}"
CXXFLAGS=`"${R_HOME}/bin/R" CMD config CXX17FLAGS`
## for an configure.ac file
AC_LANG(C++)
if C++17 was specified, but using
CXX=`"${R_HOME}/bin/R" CMD config CXX`
CXXFLAGS=`"${R_HOME}/bin/R" CMD config CXXFLAGS`
## for an configure.ac file
50
See https://isocpp.org/std/standing-documents/sd-6-sg10-feature-test-recommendations or
https://en.cppreference.com/w/cpp/experimental/feature_test. It seems a reasonable assumption that
any compiler promising some C++14 conformance will provide these—e.g. g++ 4.9.x did but 4.8.5 did not.
Chapter 1: Creating R packages 36

AC_LANG(C++)
if no standard was specified.
If you want to compile C++ code in a subdirectory, make sure you pass down the macros to
specify the appropriate compiler, e.g. in src/Makevars
sublibs:
@(cd libs && $(MAKE) \
CXX="$(CXX17) $(CXX17STD)" CXXFLAGS="$(CXX17FLAGS) $(CXX17PICFLAGS)")
The discussion above is about the standard R ways of compiling C++: it will not apply to
packages using src/Makefile or building in a subdirectory that do not set the C++ standard.
And compilers’ default C++ standards varies widely and gets changed frequently by vendors – for
example Apple clang up to at least 15 defaults to C++98, LLVM clang 14–15 to C++14, LLVM
clang 16–18 to C++17 and g++ 11–13 to C++17.
For a package with a src/Makefile (or a Windows analogue), a non-default C++ compiler
can be selected by including something like
CXX14 = `"${R_HOME}/bin/R" CMD config CXX14`
CXX14STD = `"${R_HOME}/bin/R" CMD config CXX14STD`
CXX = ${CXX14} ${CXX14STD}
CXXFLAGS = `"${R_HOME}/bin/R" CMD config CXX14FLAGS`
CXXPICFLAGS = `"${R_HOME}/bin/R" CMD config CXX14PICFLAGS`
SHLIB_LD = "${R_HOME}/bin/R" CMD config SHLIB_CXX14LD`
SHLIB_LDFLAGS = "${R_HOME}/bin/R" CMD config SHLIB_CXX14LDFLAGS`
and ensuring these values are used in relevant compilations, after checking they are non-empty.
A common use of src/Makefile is to compile an executable, when likely something like (for
example for C++14)
CXX14 = `"${R_HOME}/bin/R" CMD config CXX14`
CXX14STD = `"${R_HOME}/bin/R" CMD config CXX14STD`
CXX = ${CXX14} ${CXX14STD}
CXXFLAGS = `"${R_HOME}/bin/R" CMD config CXX14FLAGS`
suffices. On Unix (and on Windows from R 4.3.0) this can be simplified to
CXX = ${CXX14} ${CXX14STD}
CXXFLAGS = ${CXX14FLAGS}
On a Unix-alike C++ compilation defaulted to C++11 from R 3.6.0, to C++14 from R 4.1.0
and to C++17 from R 4.3.0. However, only ‘if available’, so platforms using very old OSes might
have used the previous default. Even older versions of R defaulted to the compiler’s default,
almost certainly C++98 for compilers of comparable vintage.
On Windows the default was changed from C++98 to C++11 in R 3.6.2, to C++14 in R 4.2.3
and to C++17 in R 4.3.0.
The C++11 standard could be specified as from R 3.1.0 and C++14 or C++17 as from R 3.4.0,
for C++20 from R 4.0.0 and for C++23 from R 4.3.0 (although they may not be supported by the
compilers in use). C++11 support became mandatory in R 4.0.0 and C++17 support in R 4.4.0.
The .so/.dll in a package may need to be linked by the C++ compiler if it or any library it
links to contains compiled C++ code. Dynamic linking usually brings in the C++ runtime library
(commonly libstdc++ but can be, for example, libc++) but static linking (as used for external
libraries on Windows and macOS) will not. R CMD INSTALL will link with the C++ compiler if
there are any top-level C++ files in src, but not if these are all in subdirectories. The simplest
way to force linking by the C++ compiler is to include an empty C++ file in src..
Chapter 1: Creating R packages 37

1.2.5 C standards
C has had standards C89/C90, C99, C11, C17 (also known as C18), and C23 is in final draft and
expected to be published in early 2024. C11 was a minor change to C99 which introduced some
new features and made others optional, and C17 is a ‘bug-fix’ update to C11. On the other hand,
C23 makes extensive changes, including making bool, true and false reserved words, finally
disallowing K&R-style function declarations and clarifying the formerly deprecated meaning of
function declarations with an empty parameter list to mean zero parameters. (There are many
other additions: see for example https://en.cppreference.com/w/c/23.)
The configure script in recent versions of R aims to choose a C compiler which supports
C11: as the default in recent versions of gcc, LLVM clang and Apple clang is C17, that is
what is likely to be chosen. On the other hand, until R 4.3.0 the makefiles for the Windows
build specified C99. They now use the compiler default which for the recommended compiler is
C17.
Packages may want to either avoid or embrace the changes in C23, and can do so via specifying
‘USE_Cnn’ for 17, 23, 90 or 99 in the ‘SystemRequirements’ field of their DESCRIPTION file
of a package depending on ‘R (>= 4.3.0)’. Those using a configure script should set the
corresponding compiler and flags, for example using
CC=`"${R_HOME}/bin/R" CMD config CC23`
CFLAGS=`"${R_HOME}/bin/R" CMD config C23FLAGS`
CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
LDFLAGS=`"${R_HOME}/bin/R" CMD config LDFLAGS`
The (claimed) C standard in use can be checked by the macro __STDC_VERSION__. This is
undefined in C89/C90 and should have values 199901L, 201112L and 201710L for C99, C11 and
C17. As C23 is not yet published there is as yet no definitive value: compilers are currently using
202000L. C23 has macros similar to C++ ‘feature tests’ for many of its changes, for example
__STDC_VERSION_LIMITS_H__.
However, note the ‘claimed’ as no compiler had 100% conformance, and it is better to use
configure to test for the feature you want to use than to condition on the value of __STDC_
VERSION__. In particular, C11 alignment functionality such as _Alignas and aligned_alloc is
not implemented on Windows.
End users can specify a standard by something like R CMD INSTALL --use-C17. This overrides
the ‘SystemRequirements’ field, but not for any configure file.

1.2.6 Using cmake

Packages often wish to include the sources of other software and compile that for inclusion in their
.so or .dll, which is normally done by including (or unpacking) the sources in a subdirectory
of src, as considered above.
Further issues arise when the external software uses another build system such as cmake,
principally to ensure that all the settings for compilers, include and load paths etc are made.
This section has already mentioned the need to set at least some of
CC CFLAGS CXX CXXFLAGS CPPFLAGS LDFLAGS
CFLAGS and CXXFLAGS will need to include CPICFLAGS and CXXPICFLAGS respectively unless (as
below) cmake is asked to generate PIC code.
Setting these (and more) as environment variables controls the behaviour of cmake
(https://cmake.org/cmake/help/latest/manual/cmake-env-variables.7.html#
manual:cmake-env-variables(7)), but it may be desirable to translate these into native
settings such as
CMAKE_C_COMPILER
CMAKE_C_FLAGS
Chapter 1: Creating R packages 38

CMAKE_CXX_COMPILER
CMAKE_CXX_FLAGS
CMAKE_INCLUDE_PATH
CMAKE_LIBRARY_PATH
CMAKE_SHARED_LINKER_FLAGS_INIT
CMAKE_OSX_DEPLOYMENT_TARGET
and it is often necessary to ensure a static library of PIC code is built by
-DBUILD_SHARED_LIBS:bool=OFF
-DCMAKE_POSITION_INDEPENDENT_CODE:bool=ON
If R is to be detected or used, this must be the build being used for package installation –
"${R_HOME}"/bin/R.
To fix ideas, consider a package with sources for a library myLib under src/libs. Two
approaches have been used. It is often most convenient to build the external software in a
directory other than its sources (particularly during development when the build directory can
be removed between builds rather than attempting to clean the sources) – this is illustrated in
the first approach.
1. Use the package’s configure script to create a static library src/build/libmyLib.a.
This can then be treated in the same way as external software, for example having in
src/Makevars
PKG_CPPFLAGS = -Ilibs/include
PKG_LIBS = build/libmyLib.a
(-Lbuild -lmyLib could also be used but this explicit specification avoids any confusion
with dynamic libraries of the same name.)
The configure script will need to contain something like (for C code)
: ${R_HOME=`R RHOME`}
if test -z "${R_HOME}"; then
echo "could not determine R_HOME"
exit 1
fi
CC=`"${R_HOME}/bin/R" CMD config CC`
CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
LDFLAGS=`"${R_HOME}/bin/R" CMD config LDFLAGS`

cd src
mkdir build && cd build
cmake ../libs \
-DCMAKE_BUILD_TYPE=Release \
-DBUILD_SHARED_LIBS:bool=OFF \
-DCMAKE_POSITION_INDEPENDENT_CODE:bool=ON
${MAKE}
2. Use src/Makevars (or src/Makevars.win or Makevars.ucrt) to build within the subdi-
rectory. This could be something like (for C code)
PKG_CPPFLAGS = -Ilibs/include
PKG_LIBS = libs/libmyLib.a

$(SHLIB): mylibs

mylibs:
Chapter 1: Creating R packages 39

(cd libs; \
CC="$(CC)" CFLAGS="$(CFLAGS)" \
CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)" \
cmake . \
-DCMAKE_BUILD_TYPE=Release \
-DBUILD_SHARED_LIBS:bool=OFF \
-DCMAKE_POSITION_INDEPENDENT_CODE:bool=ON; \
$(MAKE))

the compiler and other settings having been set as Make variables by an R makefile included
by INSTALL before src/Makevars.
A complication is that on macOS cmake (where installed) is commonly not on the path but
at /Applications/CMake.app/Contents/bin/cmake. One way to work around this is for the
package’s configure script to include
if test -z "$CMAKE"; then CMAKE="`which cmake`"; fi
if test -z "$CMAKE"; then CMAKE=/Applications/CMake.app/Contents/bin/cmake; fi
if test -f "$CMAKE"; then echo "no 'cmake' command found"; exit 1; fi
and for the second approach to substitute CMAKE into src//Makevars.

1.3 Checking and building packages

Before using these tools, please check that your package can be installed. R CMD check will inter
alia do this, but you may get more detailed error messages doing the install directly.
If your package specifies an encoding in its DESCRIPTION file, you should run these tools in a
locale which makes use of that encoding: they may not work at all or may work incorrectly in
other locales (although UTF-8 locales will most likely work).
Note: R CMD check and R CMD build run R processes with --vanilla in which
none of the user’s startup files are read. If you need R_LIBS set (to find packages
in a non-standard library) you can set it in the environment: also you can use
the check and build environment files (as specified by the environment variables
R_CHECK_ENVIRON and R_BUILD_ENVIRON; if unset, files51 ~/.R/check.Renviron
and ~/.R/build.Renviron are used) to set environment variables when using these
utilities.
Note to Windows users: R CMD build may make use of the Windows toolset (see the
“R Installation and Administration” manual) if present and in your path, and it is
required for packages which need it to install (including those with configure.win,
cleanup.win, configure.ucrt or cleanup.ucrt scripts or a src directory) and
e.g. need vignettes built.
You may need to set the environment variable TMPDIR to point to a suitable writable
directory with a path not containing spaces – use forward slashes for the separators.
Also, the directory needs to be on a case-honouring file system (some network-
mounted file systems are not).

1.3.1 Checking packages

Using R CMD check, the R package checker, one can test whether source R packages work cor-
rectly. It can be run on one or more directories, or compressed package tar archives with
extension .tar.gz, .tgz, .tar.bz2 or .tar.xz.
51
On systems which use sub-architectures, architecture-specific versions such as ~/.R/check.Renviron.x64 take
precedence.
Chapter 1: Creating R packages 40

It is strongly recommended that the final checks are run on a tar archive prepared by R CMD
build.
This runs a series of checks, including
1. The package is installed. This will warn about missing cross-references and duplicate aliases
in help files.
2. The file names are checked to be valid across file systems and supported operating system
platforms.
3. The files and directories are checked for sufficient permissions (Unix-alikes only).
4. The files are checked for binary executables, using a suitable version of file if available52 .
(There may be rare false positives.)
5. The DESCRIPTION file is checked for completeness, and some of its entries for correctness.
Unless installation tests are skipped, checking is aborted if the package dependencies cannot
be resolved at run time. (You may need to set R_LIBS in the environment if dependent
packages are in a separate library tree.) One check is that the package name is not that of
a standard package, nor one of the defunct standard packages (‘ctest’, ‘eda’, ‘lqs’, ‘mle’,
‘modreg’, ‘mva’, ‘nls’, ‘stepfun’ and ‘ts’). Another check is that all packages mentioned
in library or requires or from which the NAMESPACE file imports or are called via :: or
::: are listed (in ‘Depends’, ‘Imports’, ‘Suggests’): this is not an exhaustive check of the
actual imports.
6. Available index information (in particular, for demos and vignettes) is checked for com-
pleteness.
7. The package subdirectories are checked for suitable file names and for not being empty. The
checks on file names are controlled by the option --check-subdirs=value. This defaults to
‘default’, which runs the checks only if checking a tarball: the default can be overridden
by specifying the value as ‘yes’ or ‘no’. Further, the check on the src directory is only
run if the package does not contain a configure script (which corresponds to the value
‘yes-maybe’) and there is no src/Makefile or src/Makefile.in.
To allow a configure script to generate suitable files, files ending in ‘.in’ will be allowed
in the R directory.
A warning is given for directory names that look like R package check directories – many
packages have been submitted to CRAN containing these.
8. The R files are checked for syntax errors. Bytes which are non-ASCII are reported as
warnings, but these should be regarded as errors unless it is known that the package will
always be used in the same locale.
9. It is checked that the package can be loaded, first with the usual default packages and then
only with package base already loaded. It is checked that the namespace can be loaded
in an empty session with only the base namespace loaded. (Namespaces and packages can
be loaded very early in the session, before the default packages are available, so packages
should work then.)
10. The R files are checked for correct calls to library.dynam. Package startup functions
are checked for correct argument lists and (incorrect) calls to functions which modify the
search path or inappropriately generate messages. The R code is checked for possible prob-
lems using codetools (https://CRAN.R-project.org/package=codetools). In addition,
it is checked whether S3 methods have all the arguments of the corresponding generic, and
whether the final argument of replacement functions is called ‘value’. All foreign function
calls (.C, .Fortran, .Call and .External calls) are tested to see if they have a PACKAGE
52
A suitable file.exe is part of the Windows toolset: it checks for gfile if a suitable file is not found: the
latter is available in the OpenCSW collection for Solaris at https://www.opencsw.org/. The source repository
is http://ftp.astron.com/pub/file/.
Chapter 1: Creating R packages 41

argument, and if not, whether the appropriate DLL might be deduced from the namespace
of the package. Any other calls are reported. (The check is generous, and users may want to
supplement this by examining the output of tools::checkFF("mypkg", verbose=TRUE),
especially if the intention were to always use a PACKAGE argument)
11. The Rd files are checked for correct syntax and metadata, including the presence of the
mandatory fields (\name, \alias, \title and \description). The Rd name and title are
checked for being non-empty, and there is a check for missing cross-references (links).
12. A check is made for missing documentation entries, such as undocumented user-level objects
in the package.
13. Documentation for functions, data sets, and S4 classes is checked for consistency with the
corresponding code.
14. It is checked whether all function arguments given in \usage sections of Rd files are docu-
mented in the corresponding \arguments section.
15. The data directory is checked for non-ASCII characters and for the use of reasonable levels
of compression.
16. C, C++ and Fortran source and header files53 are tested for portable (LF-only) line endings.
If there is a Makefile or Makefile.in or Makevars or Makevars.in file under the src
directory, it is checked for portable line endings and the correct use of ‘$(BLAS_LIBS)’ and
‘$(LAPACK_LIBS)’
Compiled code is checked for symbols corresponding to functions which might terminate
R or write to stdout/stderr instead of the console. Note that the latter might give false
positives in that the symbols might be pulled in with external libraries and could never
be called. Windows54 users should note that the Fortran and C++ runtime libraries are
examples of such external libraries.
17. Some checks are made of the contents of the inst/doc directory. These always include
checking for files that look like leftovers, and if suitable tools (such as qpdf) are available,
checking that the PDF documentation is of minimal size.
18. The examples provided by the package’s documentation are run. (see Chapter 2 [Writing
R documentation files], page 80, for information on using \examples to create executable
example code.) If there is a file tests/Examples/pkg-Ex.Rout.save, the output of running
the examples is compared to that file.
Of course, released packages should be able to run at least their own examples. Each
example is run in a ‘clean’ environment (so earlier examples cannot be assumed to have
been run), and with the variables T and F redefined to generate an error unless they are set
in the example: See Section “Logical vectors” in An Introduction to R.
19. If the package sources contain a tests directory then the tests specified in that direc-
tory are run. (Typically they will consist of a set of .R source files and target output
files .Rout.save.) Please note that the comparison will be done in the end user’s lo-
cale, so the target output files should be ASCII if at all possible. (The command line
option --test-dir=foo may be used to specify tests in a non-standard location. For ex-
ample, unusually slow tests could be placed in inst/slowTests and then R CMD check
--test-dir=inst/slowTests would be used to run them. Other names that have been
suggested are, for example, inst/testWithOracle for tests that require Oracle to be in-
stalled, inst/randomTests for tests which use random values and may occasionally fail by
chance, etc.)

53
An exception is made for subdirectories with names starting ‘win’ or ‘Win’.
54
on most other platforms such runtime libraries are dynamic, but static libraries are currently used on Windows
because the toolchain is not a standard part of the OS.
Chapter 1: Creating R packages 42

20. The R code in package vignettes (see Section 1.4 [Writing package vignettes], page 45) is
executed, and the vignettes re-made from their sources as a check of completeness of the
sources (unless there is a ‘BuildVignettes’ field in the package’s DESCRIPTION file with a
false value). If there is a target output file .Rout.save in the vignette source directory, the
output from running the code in that vignette is compared with the target output file and
any differences are reported (but not recorded in the log file). (If the vignette sources are
in the deprecated location inst/doc, do mark such target output files to not be installed
in .Rinstignore.)
If there is an error55 in executing the R code in vignette foo.ext, a log file foo.ext.log is
created in the check directory. The vignettes are re-made in a copy of the package sources
in the vign_test subdirectory of the check directory, so for further information on errors
look in directory pkgname/vign_test/vignettes. (It is only retained if there are errors or
if environment variable _R_CHECK_CLEAN_VIGN_TEST_ is set to a false value.)
21. The PDF version of the package’s manual is created (to check that the Rd files can be
converted successfully). This needs LATEX and suitable fonts and LATEX packages to be
installed. See Section “Making the manuals” in R Installation and Administration.
22. Optionally (including by R CMD check --as-cran) the HTML version of the manual is cre-
ated and checked for compliance with the HTML5 standard. This requires a recent version56
of ‘HTML Tidy’, either on the path or at a location specified by environment variable R_
TIDYCMD. Up-to-date versions can be installed from http://binaries.html-tidy.org/
.
All these tests are run with collation set to the C locale, and for the examples and tests with
environment variable LANGUAGE=en: this is to minimize differences between platforms.
Use R CMD check --help to obtain more information about the usage of the R package
checker. A subset of the checking steps can be selected by adding command-line options. It
also allows customization by setting environment variables _R_CHECK_*_ as described in Section
“Tools” in R Internals: a set of these customizations similar to those used by CRAN can be
selected by the option --as-cran (which works best if Internet access is available). Some Win-
dows users may need to set environment variable R_WIN_NO_JUNCTIONS to a non-empty value.
The test of cyclic declarations57 in DESCRIPTION files needs repositories (including CRAN) set:
do this in ~/.Rprofile, by e.g.
options(repos = c(CRAN="https://cran.r-project.org"))
One check customization which can be revealing is
_R_CHECK_CODETOOLS_PROFILE_="suppressLocalUnused=FALSE"
which reports unused local assignments. Not only does this point out computations which are
unnecessary because their results are unused, it also can uncover errors. (Two such are to intend
to update an object by assigning a value but mistype its name or assign in the wrong scope,
for example using <- where <<- was intended.) This can give false positives, most commonly
because of non-standard evaluation for formulae and because the intention is to return objects
in the environment of a function for later use.
Complete checking of a package which contains a file README.md needs a reasonably current
version of pandoc installed: see https://pandoc.org/installing.html.
You do need to ensure that the package is checked in a suitable locale if it contains non-ASCII
characters. Such packages are likely to fail some of the checks in a C locale, and R CMD check
55
or if option --use-valgrind is used or environment variable _R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_ is set
to a true value or if there are differences from a target output file
56
for the most comprehensive checking this should be 5.8.0 or later: any for which tidy --version does not
report a version number will be too old – this includes the 2006 version shipped with macOS.
57
For example, in early 2014 gdata (https://CRAN.R-project.org/package=gdata) declared ‘Imports: gtools’
and gtools (https://CRAN.R-project.org/package=gtools) declared ‘Imports: gdata’.
Chapter 1: Creating R packages 43

will warn if it spots the problem. You should be able to check any package in a UTF-8 locale
(if one is available). Beware that although a C locale is rarely used at a console, it may be the
default if logging in remotely or for batch jobs.
Often R CMD check will need to consult a CRAN repository to check details of uninstalled
packages. Normally this defaults to the CRAN main site, but a mirror can be specified by
setting environment variables R_CRAN_WEB and (rarely needed) R_CRAN_SRC to the URL of a
CRAN mirror.

1.3.2 Building package tarballs

Packages may be distributed in source form as “tarballs” (.tar.gz files) or in binary form.
The source form can be installed on all platforms with suitable tools and is the usual form for
Unix-like systems; the binary form is platform-specific, and is the more common distribution
form for the Windows and macOS platforms.
Using R CMD build, the R package builder, one can build R package tarballs from their sources
(for example, for subsequent release). It is recommended that packages are built for release by
the current release version of R or ‘r-patched’, to avoid inadvertently picking up new features
of a development version of R.
Prior to actually building the package in the standard gzipped tar file format, a few diagnostic
checks and cleanups are performed. In particular, it is tested whether object indices exist and
can be assumed to be up-to-date, and C, C++ and Fortran source files and relevant makefiles in
a src directory are tested and converted to LF line-endings if necessary.
Run-time checks whether the package works correctly should be performed using R CMD check
prior to invoking the final build procedure.
To exclude files from being put into the package, one can specify a list of exclude patterns in
file .Rbuildignore in the top-level source directory. These patterns should be Perl-like regular
expressions (see the help for regexp in R for the precise details), one per line, to be matched
case-insensitively against the file and directory names relative to the top-level package source
directory. In addition, directories from source control systems58 or from eclipse59 , directories
with names check, chm, or ending .Rcheck or Old or old and files GNUMakefile60 , Read-and-
delete-me or with base names starting with ‘.#’, or starting and ending with ‘#’, or ending
in ‘~’, ‘.bak’ or ‘.swp’, are excluded by default61 . In addition, same-package tarballs (from
previous builds) and their binary forms will be excluded from the top-level directory, as well as
those files in the R, demo and man directories which are flagged by R CMD check as having invalid
names.
Use R CMD build --help to obtain more information about the usage of the R package
builder.
Unless R CMD build is invoked with the --no-build-vignettes option (or the package’s
DESCRIPTION contains ‘BuildVignettes: no’ or similar), it will attempt to (re)build the vi-
gnettes (see Section 1.4 [Writing package vignettes], page 45) in the package. To do so it installs
the current package into a temporary library tree, but any dependent packages need to be
installed in an available library tree (see the Note: at the top of this section).
Similarly, if the .Rd documentation files contain any \Sexpr macros (see Section 2.12 [Dy-
namic pages], page 94), the package will be temporarily installed to execute them. Post-execution
binary copies of those pages containing build-time macros will be saved in build/partial.rdb.
58
called CVS or .svn or .arch-ids or .bzr or .git (but not files called .git) or .hg.
59
called .metadata.
60
which is an error: GNU make uses GNUmakefile.
61
see tools:::.hidden_file_exclusions and tools:::get_exclude_patterns() for further excluded files and
file patterns, respectively.
Chapter 1: Creating R packages 44

If there are any install-time or render-time macros, a .pdf version of the package manual will
be built and installed in the build subdirectory. (This allows CRAN or other repositories to
display the manual even if they are unable to install the package.) This can be suppressed by
the option --no-manual or if package’s DESCRIPTION contains ‘BuildManual: no’ or similar.
One of the checks that R CMD build runs is for empty source directories. These are in
most (but not all) cases unintentional, if they are intentional use the option --keep-empty-
dirs (or set the environment variable _R_BUILD_KEEP_EMPTY_DIRS_ to ‘TRUE’, or have a
‘BuildKeepEmpty’ field with a true value in the DESCRIPTION file).
The --resave-data option allows saved images (.rda and .RData files) in the data directory
to be optimized for size. It will also compress tabular files and convert .R files to saved images.
It can take values no, gzip (the default if this option is not supplied, which can be changed
by setting the environment variable _R_BUILD_RESAVE_DATA_) and best (equivalent to giving it
without a value), which chooses the most effective compression. Using best adds a dependence
on R (>= 2.10) to the DESCRIPTION file if bzip2 or xz compression is selected for any of the
files. If this is thought undesirable, --resave-data=gzip (which is the default if that option is
not supplied) will do what compression it can with gzip. A package can control how its data
is resaved by supplying a ‘BuildResaveData’ field (with one of the values given earlier in this
paragraph) in its DESCRIPTION file.
The --compact-vignettes option will run tools::compactPDF over the PDF files in
inst/doc (and its subdirectories) to losslessly compress them. This is not enabled by default
(it can be selected by environment variable _R_BUILD_COMPACT_VIGNETTES_) and needs qpdf
(https://qpdf.sourceforge.io/) to be available.
It can be useful to run R CMD check --check-subdirs=yes on the built tarball as a final
check on the contents.
Where a non-POSIX file system is in use which does not utilize execute permissions, some
care is needed with permissions. This applies on Windows and to e.g. FAT-formatted drives and
SMB-mounted file systems on other OSes. The ‘mode’ of the file recorded in the tarball will be
whatever file.info() returns. On Windows this will record only directories as having execute
permission and on other OSes it is likely that all files have reported ‘mode’ 0777. A particular
issue is packages being built on Windows which are intended to contain executable scripts such as
configure and cleanup: R CMD build ensures those two are recorded with execute permission.
Directory build of the package sources is reserved for use by R CMD build: it contains infor-
mation which may not easily be created when the package is installed, including index informa-
tion on the vignettes and, rarely, information on the help pages and perhaps a copy of the PDF
reference manual (see above).

1.3.3 Building binary packages

Binary packages are compressed copies of installed versions of packages. They contain compiled
shared libraries rather than C, C++ or Fortran source code, and the R functions are included
in their installed form. The format and filename are platform-specific; for example, a binary
package for Windows is usually supplied as a .zip file, and for the macOS platform the default
binary package file extension is .tgz.
The recommended method of building binary packages is to use
R CMD INSTALL --build pkg
where pkg is either the name of a source tarball (in the usual .tar.gz format) or the location of
the directory of the package source to be built. This operates by first installing the package and
then packing the installed binaries into the appropriate binary package file for the particular
platform.
By default, R CMD INSTALL --build will attempt to install the package into the default library
tree for the local installation of R. This has two implications:
Chapter 1: Creating R packages 45

• If the installation is successful, it will overwrite any existing installation of the same package.
• The default library tree must have write permission; if not, the package will not install and
the binary will not be created.
To prevent changes to the present working installation or to provide an install location with
write access, create a suitably located directory with write access and use the -l option to build
the package in the chosen location. The usage is then
R CMD INSTALL -l location --build pkg
where location is the chosen directory with write access. The package will be installed as a
subdirectory of location, and the package binary will be created in the current directory.
Other options for R CMD INSTALL can be found using R CMD INSTALL --help, and platform-
specific details for special cases are discussed in the platform-specific FAQs.
Finally, at least one web-based service is available for building binary packages from (checked)
source code: WinBuilder (see https://win-builder.R-project.org/) is able to build Win-
dows binaries. Note that this is intended for developers on other platforms who do not have
access to Windows but wish to provide binaries for the Windows platform.

1.4 Writing package vignettes

In addition to the help files in Rd format, R packages allow the inclusion of documents in
arbitrary other formats. The standard location for these is subdirectory inst/doc of a source
package, the contents will be copied to subdirectory doc when the package is installed. Pointers
from package help indices to the installed documents are automatically created. Documents
in inst/doc can be in arbitrary format, however we strongly recommend providing them in
PDF format, so users on almost all platforms can easily read them. To ensure that they can be
accessed from a browser (as an HTML index is provided), the file names should start with an
ASCII letter and be comprised entirely of ASCII letters or digits or hyphen or underscore.
A special case is package vignettes. Vignettes are documents in PDF or HTML format ob-
tained from plain-text literate source files from which R knows how to extract R code and create
output (in PDF/HTML or intermediate LATEX). Vignette engines do this work, using “tangle”
and “weave” functions respectively. Sweave, provided by the R distribution, is the default
engine. Other vignette engines besides Sweave are supported; see Section 1.4.2 [Non-Sweave
vignettes], page 48.
Package vignettes have their sources in subdirectory vignettes of the package sources. Note
that the location of the vignette sources only affects R CMD build and R CMD check: the tarball
built by R CMD build includes in inst/doc the components intended to be installed.
Sweave vignette sources are normally given the file extension .Rnw or .Rtex, but for historical
reasons extensions62 .Snw and .Stex are also recognized. Sweave allows the integration of LATEX
documents: see the Sweave help page in R and the Sweave vignette in package utils for details
on the source document format.
Package vignettes are tested by R CMD check by executing all R code chunks they contain
(except those marked for non-evaluation, e.g., with option eval=FALSE for Sweave). The R
working directory for all vignette tests in R CMD check is a copy of the vignette source directory.
Make sure all files needed to run the R code in the vignette (data sets, . . . ) are accessible
by either placing them in the inst/doc hierarchy of the source package or by using calls to
system.file(). All other files needed to re-make the vignettes (such as LATEX style files, BibTEX
input files and files for any figures not created by running the code in the vignette) must be in
the vignette source directory. R CMD check will check that vignette production has succeeded by
comparing modification times of output files in inst/doc with the source in vignettes.
62
and to avoid problems with case-insensitive file systems, lower-case versions of all these extensions.
Chapter 1: Creating R packages 46

R CMD build will automatically63 create the (PDF or HTML versions of the) vignettes in
inst/doc for distribution with the package sources. By including the vignette outputs in the
package sources it is not necessary that these can be re-built at install time, i.e., the package au-
thor can use private R packages, screen snapshots and LATEX extensions which are only available
on their machine.64
By default R CMD build will run Sweave on all Sweave vignette source files in vignettes. If
Makefile is found in the vignette source directory, then R CMD build will try to run make after
the Sweave runs, otherwise texi2pdf is run on each .tex file produced.
The first target in the Makefile should take care of both creation of PDF/HTML files and
cleaning up afterwards (including after Sweave), i.e., delete all files that shall not appear in the
final package archive. Note that if the make step runs R it needs to be careful to respect the
environment values of R_LIBS and R_HOME65 . Finally, if there is a Makefile and it has a ‘clean:’
target, make clean is run.
All the usual caveats about including a Makefile apply. It must be portable (no GNU
extensions), use LF line endings and must work correctly with a parallel make: too many authors
have written things like
## BAD EXAMPLE
all: pdf clean

pdf: ABC-intro.pdf ABC-details.pdf

%.pdf: %.tex
texi2dvi --pdf $*

clean:
rm *.tex ABC-details-*.pdf
which will start removing the source files whilst pdflatex is working.
Metadata lines can be placed in the source file, preferably in LATEX comments in the preamble.
One such is a \VignetteIndexEntry of the form
%\VignetteIndexEntry{Using Animal}
Others you may see are \VignettePackage (currently ignored), \VignetteDepends
(a comma-separated list of package names) and \VignetteKeyword (which replaced
\VignetteKeywords). These are processed at package installation time to create the saved
data frame Meta/vignette.rds. The \VignetteEngine statement is described in Section 1.4.2
[Non-Sweave vignettes], page 48. Vignette metadata can be extracted from a source file using
tools::vignetteInfo.
At install time an HTML index for all vignettes in the package is automatically cre-
ated from the \VignetteIndexEntry statements unless a file index.html exists in directory
inst/doc. This index is linked from the HTML help index for the package. If you do supply a
inst/doc/index.html file it should contain relative links only to files under the installed doc
directory, or perhaps (not really an index) to HTML help files or to the DESCRIPTION file, and
be valid HTML as confirmed via the W3C Markup Validation Service (https://validator.w3.
org) or Validator.nu (https://validator.nu/).

63
unless inhibited by using ‘BuildVignettes: no’ in the DESCRIPTION file.
64
provided the conditions of the package’s license are met: many, including CRAN, see the omission of source
components as incompatible with an Open Source license.
65
R_HOME/bin is prepended to the PATH so that references to R or Rscript in the Makefile do make use of the
currently running version of R.
Chapter 1: Creating R packages 47

Sweave/Stangle allows the document to specify the split=TRUE option to create a single R
file for each code chunk: this will not work for vignettes where it is assumed that each vignette
source generates a single file with the vignette extension replaced by .R.
Do watch that PDFs are not too large – one in a CRAN package was 72MB! This is usually
caused by the inclusion of overly detailed figures, which will not render well in PDF viewers.
Sometimes it is much better to generate fairly high resolution bitmap (PNG, JPEG) figures and
include those in the PDF document.
When R CMD build builds the vignettes, it copies these and the vignette sources from direc-
tory vignettes to inst/doc. To install any other files from the vignettes directory, include
a file vignettes/.install_extras which specifies these as Perl-like regular expressions on one
or more lines. (See the description of the .Rinstignore file for full details.)

1.4.1 Encodings and vignettes

Vignettes will in general include descriptive text, R input, R output and figures, LATEX in-
clude files and bibliographic references. As any of these may contain non-ASCII characters, the
handling of encodings can become very complicated.
The vignette source file should be written in ASCII or contain a declaration of the encoding
(see below). This applies even to comments within the source file, since vignette engines process
comments to look for options and metadata lines. When an engine’s weave and tangle functions
are called on the vignette source, it will be converted to the encoding of the current R session.
Stangle() will produce an R code file in the current locale’s encoding: for a non-ASCII
vignette what that is is recorded in a comment at the top of the file.
Sweave() will produce a .tex file in the current encoding, or in UTF-8 if that is declared.
Non-ASCII encodings need to be declared to LATEX via a line like
\usepackage[utf8]{inputenc}
(It is also possible to use the more recent ‘inputenx’ LATEX package.) For files where this line
is not needed (e.g. chapters included within the body of a larger document, or non-Sweave
vignettes), the encoding may be declared using a comment like
%\VignetteEncoding{UTF-8}
If the encoding is UTF-8, this can also be declared using the declaration
%\SweaveUTF8
If no declaration is given in the vignette, it will be assumed to be in the encoding declared for
the package. If there is no encoding declared in either place, then it is an error to use non-ASCII
characters in the vignette.
In any case, be aware that LATEX may require the ‘usepackage’ declaration.
Sweave() will also parse and evaluate the R code in each chunk. The R output will also
be in the current locale (or UTF-8 if so declared), and should be covered by the ‘inputenc’
declaration. One thing people often forget is that the R output may not be ASCII even for
ASCII R sources, for many possible reasons. One common one is the use of ‘fancy’ quotes: see
the R help on sQuote: note carefully that it is not portable to declare UTF-8 or CP1252 to
cover such quotes, as their encoding will depend on the locale used to run Sweave(): this can
be circumvented by setting options(useFancyQuotes="UTF-8") in the vignette.
The final issue is the encoding of figures – this applies only to PDF figures and not PNG
etc. The PDF figures will contain declarations for their encoding, but the Sweave option
pdf.encoding may need to be set appropriately: see the help for the pdf() graphics device.
As a real example of the complexities, consider the fortunes (https://CRAN.R-project.
org/package=fortunes) package version ‘1.4-0’. That package did not have a declared encod-
ing, and its vignette was in ASCII. However, the data it displays are read from a UTF-8 CSV
Chapter 1: Creating R packages 48

file and will be assumed to be in the current encoding, so fortunes.tex will be in UTF-8 in
any locale. Had read.table been told the data were UTF-8, fortunes.tex would have been
in the locale’s encoding.

1.4.2 Non-Sweave vignettes

Vignettes in formats other than Sweave are supported via “vignette engines”. For example knitr
(https://CRAN.R-project.org/package=knitr) version 1.1 or later can create .tex files from
a variation on Sweave format, and .html files from a variation on “markdown” format. These
engines replace the Sweave() function with other functions to convert vignette source files into
LATEX files for processing into .pdf, or directly into .pdf or .html files. The Stangle() function
is replaced with a function that extracts the R source from a vignette.
R recognizes non-Sweave vignettes using filename extensions specified by the engine. For
example, the knitr (https://CRAN.R-project.org/package=knitr) package supports the ex-
tension .Rmd (standing for “R markdown”). The user indicates the vignette engine within the
vignette source using a \VignetteEngine line, for example
%\VignetteEngine{knitr::knitr}
This specifies the name of a package and an engine to use in place of Sweave in processing the
vignette. As Sweave is the only engine supplied with the R distribution, the package providing
any other engine must be specified in the ‘VignetteBuilder’ field of the package DESCRIPTION
file, and also specified in the ‘Suggests’, ‘Imports’ or ‘Depends’ field (since its namespace must
be available to build or check your package). If more than one package is specified as a builder,
they will be searched in the order given there. The utils package is always implicitly appended
to the list of builder packages, but may be included earlier to change the search order.
Note that a package with non-Sweave vignettes should always have a ‘VignetteBuilder’
field in the DESCRIPTION file, since this is how R CMD check recognizes that there are vignettes
to be checked: packages listed there are required when the package is checked.
The vignette engine can produce .tex, .pdf, or .html files as output. If it produces .tex
files, R will call texi2pdf to convert them to .pdf for display to the user (unless there is a
Makefile in the vignettes directory).
Package writers who would like to supply vignette engines need to register those engines in
the package .onLoad function. For example, that function could make the call
tools::vignetteEngine("knitr", weave = vweave, tangle = vtangle,
pattern = "[.]Rmd$", package = "knitr")
(The actual registration in knitr (https://CRAN.R-project.org/package=knitr) is more com-
plicated, because it supports other input formats.) See the ?tools::vignetteEngine help topic
for details on engine registration.

1.5 Package namespaces

R has a namespace management system for code in packages. This system allows the package
writer to specify which variables in the package should be exported to make them available to
package users, and which variables should be imported from other packages.
The namespace for a package is specified by the NAMESPACE file in the top level package
directory. This file contains namespace directives describing the imports and exports of the
namespace. Additional directives register any shared objects to be loaded and any S3-style
methods that are provided. Note that although the file looks like R code (and often has R-
style comments) it is not processed as R code. Only very simple conditional processing of if
statements is implemented.
Packages are loaded and attached to the search path by calling library or require. Only the
exported variables are placed in the attached frame. Loading a package that imports variables
Chapter 1: Creating R packages 49

from other packages will cause these other packages to be loaded as well (unless they have already
been loaded), but they will not be placed on the search path by these implicit loads. Thus code
in the package can only depend on objects in its own namespace and its imports (including the
base namespace) being visible66 .
Namespaces are sealed once they are loaded. Sealing means that imports and exports cannot
be changed and that internal variable bindings cannot be changed. Sealing allows a simpler
implementation strategy for the namespace mechanism and allows code analysis and compila-
tion tools to accurately identify the definition corresponding to a global variable reference in a
function body.
The namespace controls the search strategy for variables used by functions in the package.
If not found locally, R searches the package namespace first, then the imports, then the base
namespace and then the normal search path (so the base namespace precedes the normal search
rather than being at the end of it).

1.5.1 Specifying imports and exports

Exports are specified using the export directive in the NAMESPACE file. A directive of the form
export(f, g)
specifies that the variables f and g are to be exported. (Note that variable names may be
quoted, and reserved words and non-standard names such as [<-.fractions must be.)
For packages with many variables to export it may be more convenient to specify the names
to export with a regular expression using exportPattern. The directive
exportPattern("^[^\\.]")
exports all variables that do not start with a period. However, such broad patterns are not
recommended for production code: it is better to list all exports or use narrowly-defined
groups. (This pattern applies to S4 classes.) Beware of patterns which include names start-
ing with a period: some of these are internal-only variables and should never be exported, e.g.
‘.__S3MethodsTable__.’ (and loading excludes known cases).
Packages implicitly import the base namespace. Variables exported from other packages
with namespaces need to be imported explicitly using the directives import and importFrom.
The import directive imports all exported variables from the specified package(s). Thus the
directives
import(foo, bar)
specifies that all exported variables in the packages foo and bar are to be imported. If only
some of the exported variables from a package are needed, then they can be imported using
importFrom. The directive
importFrom(foo, f, g)
specifies that the exported variables f and g of the package foo are to be imported. Using
importFrom selectively rather than import is good practice and recommended notably when
importing from packages with more than a dozen exports and especially from those written by
others (so what they export can change in future).
To import every symbol from a package but for a few exceptions, pass the except argument
to import. The directive
import(foo, except=c(bar, baz))
imports every symbol from foo except bar and baz. The value of except should evaluate to
something coercible to a character vector, after substituting each symbol for its corresponding
string.
66
Note that lazy-loaded datasets are not in the package’s namespace so need to be accessed via ::, e.g.
survival::survexp.us.
Chapter 1: Creating R packages 50

It is possible to export variables from a namespace which it has imported from other name-
spaces: this has to be done explicitly and not via exportPattern.
If a package only needs a few objects from another package it can use a fully qualified variable
reference in the code instead of a formal import. A fully-qualified reference to the function f in
package foo is of the form foo::f. This is slightly less efficient than a formal import and also
loses the advantage of recording all dependencies in the NAMESPACE file (but they still need to
be recorded in the DESCRIPTION file). Evaluating foo::f will cause package foo to be loaded,
but not attached, if it was not loaded already—this can be an advantage in delaying the loading
of a rarely used package. However, if foo is listed only in ‘Suggests’ or ‘Enhances’ this also
delays the check that it is installed: it is good practice to use such imports conditionally (e.g.
via requireNamespace("foo", quietly = TRUE)).
Using the foo::f form will be necessary when a package needs to use a function of the same
name from more than one namespace.
Using foo:::f instead of foo::f allows access to unexported objects. This is generally
not recommended, as the existence or semantics of unexported objects may be changed by the
package author in routine maintenance.

1.5.2 Registering S3 methods

The standard method for S3-style UseMethod dispatching might fail to locate methods defined
in a package that is imported but not attached to the search path. To ensure that these methods
are available the packages defining the methods should ensure that the generics are imported
and register the methods using S3method directives. If a package defines a function print.foo
intended to be used as a print method for class foo, then the directive
S3method(print, foo)
ensures that the method is registered and available for UseMethod dispatch, and the function
print.foo does not need to be exported. Since the generic print is defined in base it does not
need to be imported explicitly.
(Note that function and class names may be quoted, and reserved words and non-standard
names such as [<- and function must be.)
It is possible to specify a third argument to S3method, the function to be used as the method,
for example
S3method(print, check_so_symbols, .print.via.format)
when print.check_so_symbols is not needed.
As from R 3.6.0 one can also use S3method() directives to perform delayed registration.
With
if(getRversion() >= "3.6.0") {
S3method(pkg::gen, cls)
}
function gen.cls will get registered as an S3 method for class cls and generic gen from package
pkg only when the namespace of pkg is loaded. This can be employed to deal with situations
where the method is not “immediately” needed, and having to pre-load the namespace of pkg
(and all its strong dependencies) in order to perform immediate registration is considered too
onerous.

1.5.3 Load hooks

There are a number of hooks called as packages are loaded, attached, detached, and unloaded.
See help(".onLoad") for more details.
Chapter 1: Creating R packages 51

Since loading and attaching are distinct operations, separate hooks are provided for each.
These hook functions are called .onLoad and .onAttach. They both take arguments67 libname
and pkgname; they should be defined in the namespace but not exported.
Packages can use a .onDetach or .Last.lib function (provided the latter is exported from
the namespace) when detach is called on the package. It is called with a single argument, the
full path to the installed package. There is also a hook .onUnload which is called when the
namespace is unloaded (via a call to unloadNamespace, perhaps called by detach(unload =
TRUE)) with argument the full path to the installed package’s directory. Functions .onUnload
and .onDetach should be defined in the namespace and not exported, but .Last.lib does need
to be exported.
Packages are not likely to need .onAttach (except perhaps for a start-up banner); code to
set options and load shared objects should be placed in a .onLoad function, or use made of the
useDynLib directive described next.
User-level hooks are also available: see the help on function setHook.
These hooks are often used incorrectly. People forget to export .Last.lib. Compiled
code should be loaded in .onLoad (or via a useDynLb directive: see below) and unloaded in
.onUnload. Do remember that a package’s namespace can be loaded without the namespace
being attached (e.g. by pkgname::fun) and that a package can be detached and re-attached
whilst its namespace remains loaded.
It is good practice for these functions to be quiet. Any messages should use
packageStartupMessage so users (include check scripts) can suppress them if desired.

1.5.4 useDynLib
A NAMESPACE file can contain one or more useDynLib directives which allows shared objects that
need to be loaded.68 The directive
useDynLib(foo)
registers the shared object foo69 for loading with library.dynam. Loading of registered ob-
ject(s) occurs after the package code has been loaded and before running the load hook func-
tion. Packages that would only need a load hook function to load a shared object can use the
useDynLib directive instead.
The useDynLib directive also accepts the names of the native routines that are to be used in
R via the .C, .Call, .Fortran and .External interface functions. These are given as additional
arguments to the directive, for example,
useDynLib(foo, myRoutine, myOtherRoutine)
By specifying these names in the useDynLib directive, the native symbols are resolved when
the package is loaded and R variables identifying these symbols are added to the package’s
namespace with these names. These can be used in the .C, .Call, .Fortran and .External
calls in place of the name of the routine and the PACKAGE argument. For instance, we can call
the routine myRoutine from R with the code
.Call(myRoutine, x, y)
rather than
.Call("myRoutine", x, y, PACKAGE = "foo")
There are at least two benefits to this approach. Firstly, the symbol lookup is done just
once for each symbol rather than each time the routine is invoked. Secondly, this removes any
67
they will be called with two unnamed arguments, in that order.
68
NB: this will only be read in all versions of R if the package contains R code in a R directory.
69
Note that this is the basename of the shared object, and the appropriate extension (.so or .dll) will be
added.
Chapter 1: Creating R packages 52

ambiguity in resolving symbols that might be present in more than one DLL. However, this
approach is nowadays deprecated in favour of supplying registration information (see below).
In some circumstances, there will already be an R variable in the package with the same name
as a native symbol. For example, we may have an R function in the package named myRoutine.
In this case, it is necessary to map the native symbol to a different R variable name. This can
be done in the useDynLib directive by using named arguments. For instance, to map the native
symbol name myRoutine to the R variable myRoutine_sym, we would use
useDynLib(foo, myRoutine_sym = myRoutine, myOtherRoutine)
We could then call that routine from R using the command
.Call(myRoutine_sym, x, y)
Symbols without explicit names are assigned to the R variable with that name.
In some cases, it may be preferable not to create R variables in the package’s namespace
that identify the native routines. It may be too costly to compute these for many routines
when the package is loaded if many of these routines are not likely to be used. In this case,
one can still perform the symbol resolution correctly using the DLL, but do this each time the
routine is called. Given a reference to the DLL as an R variable, say dll, we can call the routine
myRoutine using the expression
.Call(dll$myRoutine, x, y)
The $ operator resolves the routine with the given name in the DLL using a call to
getNativeSymbol. This is the same computation as above where we resolve the symbol when the
package is loaded. The only difference is that this is done each time in the case of dll$myRoutine.
In order to use this dynamic approach (e.g., dll$myRoutine), one needs the reference to the
DLL as an R variable in the package. The DLL can be assigned to a variable by using the
variable = dllName format used above for mapping symbols to R variables. For example, if
we wanted to assign the DLL reference for the DLL foo in the example above to the variable
myDLL, we would use the following directive in the NAMESPACE file:
myDLL = useDynLib(foo, myRoutine_sym = myRoutine, myOtherRoutine)
Then, the R variable myDLL is in the package’s namespace and available for calls such as
myDLL$dynRoutine to access routines that are not explicitly resolved at load time.
If the package has registration information (see Section 5.4 [Registering native routines],
page 126), then we can use that directly rather than specifying the list of symbols again in
the useDynLib directive in the NAMESPACE file. Each routine in the registration information
is specified by giving a name by which the routine is to be specified along with the address
of the routine and any information about the number and type of the parameters. Using the
.registration argument of useDynLib, we can instruct the namespace mechanism to create R
variables for these symbols. For example, suppose we have the following registration information
for a DLL named myDLL:
static R_NativePrimitiveArgType foo_t[] = {
REALSXP, INTSXP, STRSXP, LGLSXP
};

static const R_CMethodDef cMethods[] = {

{"foo", (DL_FUNC) &foo, 4, foo_t},
{"bar_sym", (DL_FUNC) &bar, 0},
{NULL, NULL, 0, NULL}
};

static const R_CallMethodDef callMethods[] = {

{"R_call_sym", (DL_FUNC) &R_call, 4},
Chapter 1: Creating R packages 53

{"R_version_sym", (DL_FUNC) &R_version, 0},

{NULL, NULL, 0}
};
Then, the directive in the NAMESPACE file
useDynLib(myDLL, .registration = TRUE)
causes the DLL to be loaded and also for the R variables foo, bar_sym, R_call_sym and R_
version_sym to be defined in the package’s namespace.
Note that the names for the R variables are taken from the entry in the registration informa-
tion and do not need to be the same as the name of the native routine. This allows the creator
of the registration information to map the native symbols to non-conflicting variable names in
R, e.g. R_version to R_version_sym for use in an R function such as
R_version <- function()
{
.Call(R_version_sym)
}
Using argument .fixes allows an automatic prefix to be added to the registered symbols,
which can be useful when working with an existing package. For example, package KernSmooth
(https://CRAN.R-project.org/package=KernSmooth) has
useDynLib(KernSmooth, .registration = TRUE, .fixes = "F_")
which makes the R variables corresponding to the Fortran symbols F_bkde and so on, and so
avoid clashes with R code in the namespace.
NB: Using these arguments for a package which does not register native symbols merely slows
down the package loading (although many CRAN packages have done so). Once symbols are
registered, check that the corresponding R variables are not accidentally exported by a pattern
in the NAMESPACE file.

1.5.5 An example
As an example consider two packages named foo and bar. The R code for package foo in file
foo.R is

x <- 1
f <- function(y) c(x,y)
foo <- function(x) .Call("foo", x, PACKAGE="foo")
print.foo <- function(x, ...) cat("<a foo>\n")

Some C code defines a C function compiled into DLL foo (with an appropriate extension). The
NAMESPACE file for this package is

useDynLib(foo)
export(f, foo)
S3method(print, foo)

The second package bar has code file bar.R


c <- function(...) sum(...)
g <- function(y) f(c(y, 7))
h <- function(y) y+9
Chapter 1: Creating R packages 54

and NAMESPACE file


import(foo)
export(g, h)

Calling library(bar) loads bar and attaches its exports to the search path. Package foo is also
loaded but not attached to the search path. A call to g produces
> g(6)
[1] 1 13
This is consistent with the definitions of c in the two settings: in bar the function c is defined
to be equivalent to sum, but in foo the variable c refers to the standard function c in base.

1.5.6 Namespaces with S4 classes and methods

Some additional steps are needed for packages which make use of formal (S4-style) classes and
methods (unless these are purely used internally). The package should have Depends: methods70
in its DESCRIPTION and import(methods) or importFrom(methods, ...) plus any classes and
methods which are to be exported need to be declared in the NAMESPACE file. For example, the
stats4 package has
export(mle) # exporting methods implicitly exports the generic
importFrom("stats", approx, optim, pchisq, predict, qchisq, qnorm, spline)
## For these, we define methods or (AIC, BIC, nobs) an implicit generic:
importFrom("stats", AIC, BIC, coef, confint, logLik, nobs, profile,
update, vcov)
exportClasses(mle, profile.mle, summary.mle)
## All methods for imported generics:
exportMethods(coef, confint, logLik, plot, profile, summary,
show, update, vcov)
## implicit generics which do not have any methods here
export(AIC, BIC, nobs)
All S4 classes to be used outside the package need to be listed in an exportClasses direc-
tive. Alternatively, they can be specified using exportClassPattern71 in the same style as
for exportPattern. To export methods for generics from other packages an exportMethods
directive can be used.
Note that exporting methods on a generic in the namespace will also export the generic, and
exporting a generic in the namespace will also export its methods. If the generic function is not
local to this package, either because it was imported as a generic function or because the non-
generic version has been made generic solely to add S4 methods to it (as for functions such as
coef in the example above), it can be declared via either or both of export or exportMethods,
but the latter is clearer (and is used in the stats4 example above). In particular, for primitive
functions there is no generic function, so export would export the primitive, which makes no
sense. On the other hand, if the generic is local to this package, it is more natural to export the
function itself using export(), and this must be done if an implicit generic is created without
setting any methods for it (as is the case for AIC in stats4).
A non-local generic function is only exported to ensure that calls to the function will dispatch
the methods from this package (and that is not done or required when the methods are for
70
Imports: methods may suffice, but package code is little exercised without the methods package on the search
path and may not be fully robust to this scenario.
71
This defaults to the same pattern as exportPattern: use something like exportClassPattern("^$") to
override this.
Chapter 1: Creating R packages 55

primitive functions). For this reason, you do not need to document such implicitly created
generic functions, and undoc in package tools will not report them.
If a package uses S4 classes and methods exported from another package, but does not
import the entire namespace of the other package72 , it needs to import the classes and methods
explicitly, with directives
importClassesFrom(package, ...)
importMethodsFrom(package, ...)
listing the classes and functions with methods respectively. Suppose we had two small packages
A and B with B using A. Then they could have NAMESPACE files

export(f1, ng1)
exportMethods("[")
exportClasses(c1)

and

importFrom(A, ng1)
importClassesFrom(A, c1)
importMethodsFrom(A, f1)
export(f4, f5)
exportMethods(f6, "[")
exportClasses(c1, c2)

respectively.
Note that importMethodsFrom will also import any generics defined in the namespace on
those methods.
It is important if you export S4 methods that the corresponding generics are available. You
may for example need to import coef from stats to make visible a function to be converted into
its implicit generic. But it is better practice to make use of the generics exported by stats4 as
this enables multiple packages to unambiguously set methods on those generics.

1.6 Writing portable packages

This section contains advice on writing packages to be used on multiple platforms or for distri-
bution (for example to be submitted to a package repository such as CRAN).
Portable packages should have simple file names: use only alphanumeric ASCII characters
and period (.), and avoid those names not allowed under Windows (see Section 1.1 [Package
structure], page 3).
Many of the graphics devices are platform-specific: even X11() (aka x11()) which although
emulated on Windows may not be available on a Unix-alike (and is not the preferred screen
device on OS X). It is rarely necessary for package code or examples to open a new device, but
if essential,73 use dev.new().
Use R CMD build to make the release .tar.gz file.
R CMD check provides a basic set of checks, but often further problems emerge when people
try to install and use packages submitted to CRAN – many of these involve compiled code. Here
are some further checks that you can do to make your package more portable.
72
if it does, there will be opaque warnings about replacing imports if the classes/methods are also imported.
73
People use dev.new() to open a device at a particular size: that is not portable but using dev.new(noRStudioGD
= TRUE) helps.
Chapter 1: Creating R packages 56

• If your package has a configure script, provide a configure.win or configure.ucrt script

to be used on Windows (an empty configure.win file if no actions are needed).
• If your package has a Makevars or Makefile file, make sure that you use only portable
make features. Such files should be LF-terminated74 (including the final line of the
file) and not make use of GNU extensions. (The POSIX specification is available
at https://pubs.opengroup.org/onlinepubs/9699919799/utilities/make.html; any-
thing not documented there should be regarded as an extension to be avoided. Further
advice can be found at https://www.gnu.org/software/autoconf/manual/autoconf.
html#Portable-Make. ) Commonly misused GNU extensions are conditional inclusions
(ifeq and the like), ${shell ...}, ${wildcard ...} and similar, and the use of +=75 and
:=. Also, the use of $< other than in implicit rules is a GNU extension, as is the $^ macro.
As is the use of .PHONY (some other makes ignore it). Unfortunately makefiles which use
GNU extensions often run on other platforms but do not have the intended results.
Note that the -C flag for make is not included in the POSIX specification and is not imple-
mented by some of the makes which have been used with R. However, it is more commonly
implemented (e.g. by FreeBSD make) than the GNU-specific --directory=.
You should not rely on built-in/default make rules, even when specified by POSIX, as some
makes do not have the POSIX ones and others have altered them.
The use of ${shell ...} can be avoided by using backticks, e.g.
PKG_CPPFLAGS = `gsl-config --cflags`
which works in all versions of make known76 to be used with R.
If you really must require GNU make, declare it in the DESCRIPTION file by
SystemRequirements: GNU make
and ensure that you use the value of environment variable MAKE (and not just make) in your
scripts. (On some platforms GNU make is available under a name such as gmake, and there
SystemRequirements is used to set MAKE.)
If you only need GNU make for parts of the package which are rarely needed (for example
to create bibliography files under vignettes), use a file called GNUmakefile rather than
Makefile as GNU make (only) will use the former.
macOS has used GNU make for many years (it previously used BSD make), but the version
has been frozen at 3.81 (from 2006).
Since the only viable make for Windows is GNU make, it is permissible to use GNU exten-
sions in files Makevars.win, Makevars.ucrt, Makefile.win or Makefile.ucrt.
• If you use src/Makevars to compile code in a subdirectory, ensure that you have followed
all the advice above. In particular
• Anticipate a parallel make. See Section 1.2.1 [Using Makevars], page 25.
• Pass macros down to the makefile in the subdirectory, including all the needed compiler
flags (including PIC and visibility flags). If they are used (even by a default rule) in
the subdirectory’s Makefile, this includes macros ‘AR’ and ‘RANLIB’. See Section 1.2.1.3
[Compiling in sub-directories], page 31, which has a C example. A C++ example:
pkg/libpkg.a:
(cd pkg && $(MAKE) -f make_pkg libpkg.a \
74
Solaris make did not accept CRLF-terminated Makefiles; Solaris warned about and some other makes ignore
incomplete final lines.
75
This was apparently introduced in SunOS 4, and is available elsewhere provided it is surrounded by spaces.
76
GNU make, BSD make and other variants of pmake in FreeBSD, NetBSD and formerly in macOS, and formerly
AT&T make as implemented on Solaris and ‘Distributed Make’ (dmake), part of Oracle Developer Studio and
available in other versions including from Apache OpenOffice.
Chapter 1: Creating R packages 57

CXX="$(CXX)" CXXFLAGS="$(CXXFLAGS) $(CXXPICFLAGS) $(C_VISIBILITY)" \

AR="$(AR)" RANLIB="$(RANLIB)")
• Ensure that cleanup will be performed by R CMD build, for example in a cleanup script
or a ‘clean’ target.
• If your package uses a src/Makefile file to compile code to be linked into R, ensure that
it uses exactly the same compiler and flag settings that R uses when compiling such code:
people often forget ‘PIC’ flags. If R CMD config is used, this needs something like (for C++)
RBIN = `"${R_HOME}/bin/R"`
CXX = `"${RBIN}" CMD config CXX`
CXXFLAGS = `"${RBIN}" CMD config CXXFLAGS` `"${RBIN}" CMD config CXXPICFLAGS`
• Names of source files including = (such as src/complex_Sig=gen.c) will confuse some make
programs and should be avoided.
• Bash extensions also need to be avoided in shell scripts, including expressions in Make-
files (which are passed to the shell for processing). Some R platforms use strict77 Bourne
shells: an earlier R toolset on Windows78 and some Unix-alike OSes use ash (https://en.
wikipedia.org/wiki/Almquist_shell, a ‘lightweight shell with few builtins) or derivatives
such as dash. Beware of assuming that all the POSIX command-line utilities are available,
especially on Windows where only a subset (which has changed by version of Rtools) is
provided for use with R. One particular issue is the use of echo, for which two behaviours
are allowed (https://pubs.opengroup.org/onlinepubs/9699919799/utilities/echo.
html) and both have occurred as defaults on R platforms: portable applications should
use neither -n (as the first argument) nor escape sequences. The recommended replace-
ment for echo -n is the command printf. Another common issue is the construction
export FOO=value
which is bash-specific (first set the variable then export it by name).
Using test -e (or [ -e ]) in shell scripts is not fully portable79 : -f is normally what is
intended. Flags -a and -o are nowadays declared obsolescent by POSIX and should not be
used.
Use of ‘brace expansion’, e.g.,
rm -f src/*.{o,so,d}
is not portable.
The -o flag for set in shell scripts is optional in POSIX and not supported on all the
platforms R is used on.
The variable ‘OSTYPE’ is shell-specific and its values are rather unpredictable and may
include a version such as ‘darwin19.0’: `uname` is often what is intended (with common
values ‘Darwin’, ‘Linux’ and ‘SunOS’).
On macOS which shell /bin/sh invokes is user- and platform-dependent: it might be bash
version 3.2, dash or zsh (for new accounts it is zsh, for accounts ported from Mojave or
earlier it is usually bash).
• R is not built by default as a shared library on non-Windows platforms (although it com-
monly is on macOS to support the GUI), so there need be not a file libR.so nor libR.dylib.
Users of cmake or rust have all too frequently assumed otherwise, so do ensure your package
is checked under a vanilla R build. See Section “Configuration options” in R Installation
and Administration.
77
For example, test options -a and -e are not portable, and not supported in the AT&T Bourne shell used on
Solaris 10/11, even though they are in the POSIX standard. Nor did Solaris support ‘$(cmd)’.
78
as from R 4.0.0 the default is bash.
79
it was not in the Bourne shell, and was not supported by Solaris 10.
Chapter 1: Creating R packages 58

• Make use of the abilities of your compilers to check the standards-conformance of your code.
For example, gcc, clang and gfortran80 can be used with options -Wall -pedantic to
alert you to potential problems. This is particularly important for C++, where g++ -Wall
-pedantic will alert you to the use of some of the GNU extensions which fail to compile
on most other C++ compilers. If R was not configured accordingly, one can achieve this via
personal Makevars files. See Section “Customizing package compilation” in R Installation
and Administration,
Portable C++ code needs to follow all of the 2011, 2014 and 2017 standards (including not
using deprecated/removed features) or to specify C+11/14/17/20/23 where available (which
is not the case on all R platforms). Currently C++20 support is patchy across R platforms.
If using Fortran with the GNU compiler, use the flags -std=f95 -Wall -pedantic which re-
ject most GNU extensions and features from later standards. (Although R only requires For-
tran 90, gfortran does not have a way to specify that standard.) Also consider -std=f2008
as some recent compilers have Fortran 2008 or even 2018 as the minimum supported stan-
dard.
As from macOS 11 (late 2020), its C compiler sets the flag -Werror=implicit-function-
declaration by default which forces stricter conformance to C99. This can be used on
other platforms with gcc or clang. If your package has a (autoconf-generated) configure
script, try installing it whilst using this flag, and read through the config.log file —
compilation warnings and errors can lead to features which are present not being detected.
(If possible do this on several platforms.)
• R CMD check performs some checks for non-portable compiler/linker flags in src/Makevars.
However, it cannot check the meaning of such flags, and some are commonly accepted but
with compiler-specific meanings. There are other non-portable flags which are not checked,
nor are src/Makefile files and makefiles in sub-directories. As a comment in the code says
It is hard to think of anything apart from -I* and -D* that is safe for general
use . . .
although -pthread is pretty close to portable. (Option -U is portable but little use on the
command line as it will only cancel built-in defines (not portable) and those defined earlier
on the command line (R does not use any).)
The GNU option -pipe used to be widely accepted by C/C++/Fortran compilers, but has
been removed in flang-new 18. In any case, it should not be used in distributed code as it
may lead to excessive memory use.
People have used configure to customize src/Makevars, including for specific compilers.
This is unsafe for several reasons. First, unintended compilers might meet the check—for
example, several compilers other than GCC identify themselves as ‘GCC’ whilst being only
partially conformant. Second, future versions of compilers may behave differently (including
updates to quite old series) so for example -Werror (and specializations) can make a package
non-installable under a future version. Third, using flags to suppress diagnostic messages
can hide important information for debugging on a platform not tested by the package
maintainer. (R CMD check can optionally report on unsafe flags which were used.)
Avoid the use of -march and especially -march=native. This allows the compiler to generate
code that will only run on a particular class of CPUs (that of the compiling machine for
‘native’). People assume this is a ‘minimum’ CPU specification, but that is not how it
is documented for gcc (it is accepted by clang but apparently it is undocumented what
precisely it does, and it can be accepted and may be ignored for other compilers). (For
personal use -mtune is safer, but still not portable enough to be used in a public package.)
80
https://fortranwiki.org/fortran/show/Modernizing+Old+Fortran may help explain some of the warnings
from gfortran -Wall -pedantic.
Chapter 1: Creating R packages 59

Not even gcc supports ‘native’ for all CPUs, and it can do surprising things if it finds a
CPU released later than its version.
• Do be very careful with passing arguments between R, C and Fortran code. In particular,
long in C will be 32-bit on some R platforms (including 64-bit Windows), but 64-bit on
most modern Unix and Linux platforms. It is rather unlikely that the use of long in C code
has been thought through: if you need a longer type than int you should use a configure
test for a C99/C++11 type such as int_fast64_t (and failing that, long long) and typedef
your own type, or use another suitable type (such as size_t, but beware that is unsigned
and ssize_t is not portable).
It is not safe to assume that long and pointer types are the same size, and they are not on
64-bit Windows. If you need to convert pointers to and from integers use the C99/C++11
integer types intptr_t and uintptr_t (in the headers <stdint.h> and <cstdint>: they
are not required to be implemented by the standards but are used in C code by R itself).
Note that integer in Fortran corresponds to int in C on all R platforms. There is no such
guarantee for Fortran logical, and recent gfortran maps it to int_least32_t on most
platforms.
• Under no circumstances should your compiled code ever call abort or exit81 : these ter-
minate the user’s R process, quite possibly losing all unsaved work. One usage that could
call abort is the assert macro in C or C++ functions, which should never be active in
production code. The normal way to ensure that is to define the macro NDEBUG, and R CMD
INSTALL does so as part of the compilation flags. Beware of including headers (including
from other packages) which could undefine it, now or in future versions. If you wish to use
assert during development. you can include -UNDEBUG in PKG_CPPFLAGS or #undef it in
your headers or code files. Note that your own src/Makefile or makefiles in sub-directories
may also need to define NDEBUG.
This applies not only to your own code but to any external software you compile in or link
to.
• Compiled code should not write to stdout or stderr and C++ and Fortran I/O should not
be used. As with the previous item such calls may come from external software and may
never be called, but package authors are often mistaken about that.
• Compiled code should not call the system random number generators such as rand, drand48
and random82 , but rather use the interfaces to R’s RNGs described in Section 6.3 [Random
numbers], page 167. In particular, if more than one package initializes a system RNG (e.g.
via srand), they will interfere with each other. This applies also to Fortran 90’s random_
number and random_seed, and Fortran 2018’s random_init. And to GNU Fortran’s rand,
irand and srand. Except for drand48, what PRNG these functions use is implementation-
dependent.
Nor should the C++11 random number library be used nor any other third-party random
number generators such as those in GSL.
• Use of sprintf and vsprintf is regarded as a potential security risk and warned about on
some platforms.83 R CMD check reports if any calls are found.
• Errors in memory allocation and reading/writing outside arrays are very common causes
of crashes (e.g., segfaults) on some machines. See Section 4.3 [Checking memory access],
page 109, for tools which can be used to look for this.

81
or where supported the variants _Exit and _exit.
82
This and srandom are in any case not portable. They are in POSIX but not in the C99 standard, and not
available on Windows.
83
including macOS as from version 13.
Chapter 1: Creating R packages 60

• Many platforms will allow unsatisfied entry points in compiled code, but will crash the
application (here R) if they are ever used. Some (notably Windows) will not. Looking at
the output of
nm -pg mypkg.so
and checking if any of the symbols marked U is unexpected is a good way to avoid this.
• Linkers have a lot of freedom in how to resolve entry points in dynamically-loaded code,
so the results may differ by platform. One area that has caused grief is packages including
copies of standard system software such as libz (especially those already linked into R).
In the case in point, entry point gzgets was sometimes resolved against the old version
compiled into the package, sometimes against the copy compiled into R and sometimes
against the system dynamic library. The only safe solution is to rename the entry points
in the copy in the package. We have even seen problems with entry point name myprintf,
which is a system entry point84 on some Linux systems.
A related issue is the naming of libraries built as part of the package installation. macOS
and Windows have case-insensitive file systems, so using
-L. -lLZ4
in PKG_LIBS will match liblz4. And -L. only appends to the list of searched locations,
and liblz4 might be found in an earlier-searched location (and has been). The only safe
way is to give an explicit path, for example
./libLZ4.a
• Conflicts between symbols in DLLs are handled in very platform-specific ways. Good ways
to avoid trouble are to make as many symbols as possible static (check with nm -pg), and
to use names which are clearly tied to your package (which also helps users if anything does
go wrong). Note that symbol names starting with R_ are regarded as part of R’s namespace
and should not be used in packages.
• It is good practice for DLLs to register their symbols (see Section 5.4 [Registering native
routines], page 126), restrict visibility (see Section 6.16 [Controlling visibility], page 186)
and not allow symbol search (see Section 5.4 [Registering native routines], page 126). It
should be possible for a DLL to have only one visible symbol, R_init_pkgname, on suitable
platforms85 , which would completely avoid symbol conflicts.
• It is not portable to call compiled code in R or other packages via .Internal, .C, .Fortran,
.Call or .External, since such interfaces are subject to change without notice and will
probably result in your code terminating the R process.
• Do not use (hard or symbolic) file links in your package sources. Where possible R CMD
build will replace them by copies.
• If you do not yourself have a Windows system, consider submitting your source package to
WinBuilder (https://win-builder.r-project.org/) before distribution. If you need to
check on an M1 Mac, there is a check service at https://mac.r-project.org/macbuilder/
submit.html.
• It is bad practice for package code to alter the search path using library, require or
attach and this often does not work as intended. For alternatives, see Section 1.1.3.1
[Suggested packages], page 12, and with().
• Examples can be run interactively via example as well as in batch mode when checking.
So they should behave appropriately in both scenarios, conditioning by interactive() the
parts which need an operator or observer. For instance, progress bars86 are only appropriate
in interactive use, as is displaying help pages or calling View() (see below).
84
in libselinux.
85
At least Linux and Windows, but not macOS.
86
except perhaps the simplest kind as used by download.file() in non-interactive use.
Chapter 1: Creating R packages 61

• Be careful with the order of entries in macros such as PKG_LIBS. Some linkers will re-order
the entries, and behaviour can differ between dynamic and static libraries. Generally -L
options should precede87 the libraries (typically specified by -l options) to be found from
those directories, and libraries are searched once in the order they are specified. Not all
linkers allow a space after -L .
• Care is needed with the use of LinkingTo. This puts one or more directories on the include
search path ahead of system headers but (prior to R 3.4.0) after those specified in the
CPPFLAGS macro of the R build (which normally includes -I/usr/local/include, but
most platforms ignore that and include it with the system headers).
Any confusion would be avoided by having LinkingTo headers in a directory named after
the package. In any case, name conflicts of headers and directories under package include
directories should be avoided, both between packages and between a package and system
and third-party software.
• The ar utility is often used in makefiles to make static libraries. Its modifier u is defined
by POSIX but is disabled in GNU ar on some Linux distributions which use ‘deterministic
mode’. The safest way to make a static library is to first remove any existing file of that
name then use $(AR) -cr and then $(RANLIB) if needed (which is system-dependent: on
most systems88 ar always maintains a symbol table). The POSIX standard says options
should be preceded by a hyphen (as in -cr), although most OSes accept them without.
Note that on some systems ar -cr must have at least one file specified.
The s modifier (to replace a separate call to ranlib) is required by X/OPEN but not
POSIX, so ar -crs is not portable.
For portability the AR and RANLIB macros should always be used – some builds require
wrappers such as gcc-ar or extra arguments to specify plugins.
• The strip utility is platform-specific (and CRAN prohibits removing debug symbols). For
example the options --strip-debug and --strip-unneeded of the GNU version are not
supported on macOS: the POSIX standard for strip does not mention any options, and
what calling it without options does is platform-dependent. Stripping a .so file could even
prevent it being dynamically loaded into R on an untested platform.
ld -S invokes strip --strip-debug for GNU ld (and similarly on macOS) but is not
portable: in particular on Solaris it did something completely different and took an argu-
ment.
• Some people have a need to set a locale. Locale names are not portable, and e.g.
‘fr_FR.utf8’ is commonly used on Linux but not accepted on macOS. ‘fr_FR.UTF-8’ is
more portable, being accepted on recent Linux, AIX, FreeBSD, macOS and Solaris (at
least). However, some Linux distributions micro-package, so locales defined by glibc (in-
cluding these examples) may not be installed.
• Avoid spaces in file names, not least as they can cause difficulties for external tools. An
example was a package with a knitr (https://CRAN.R-project.org/package=knitr) vi-
gnette that used spaces in plot names: this caused some older versions of pandoc to fail
with a baffling error message.
Non-ASCII filenames can also cause problems (particularly in non-UTF-8 locales).
• Take care in naming LATEX macros (also known as ‘commands’) in vignette sources: if these
are also defined in a future version of one of the LATEX packages used there will be a fatal
error. One instance in 2021 was package ‘hyperref’ newly defining ‘\C’, ‘\F’, ‘\G’, ‘\U’ and
‘\textapprox’. If you are confident that your definitions will be the only ones relevant you
can use ‘\renewcommand’ but it is better to use names clearly associated with your package.
87
Whereas the GNU linker reorders so -L options are processed first, the Solaris one did not.
88
some versions of macOS did not.
Chapter 1: Creating R packages 62

• Make sure that any version requirement for Java code is both declared in the
‘SystemRequirements’ field89 and tested at runtime (not least as the Java installation
when the package is installed might not be the same as when the package is run and will
not be for binary packages).
When specifying a minimum Java version please use the official version names, which are
(confusingly)
1.1 1.2 1.3 1.4 5.0 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
and as from 2018 a year.month scheme such as ‘18.9’ is also in use. Fortunately only the
integer values are likely to be relevant. If at all possible, use one of the LTS versions (8, 11,
17, 21 . . . ) as the minimum version. The preferred form of version specification is
SystemRequirements: Java (>= 11)
A suitable test for Java at least version 8 for packages using rJava (https://CRAN.
R-project.org/package=rJava) would be something like
.jinit()
jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.version")
if(substr(jv, 1L, 2L) == "1.") {
jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))
if(jvn < 1.8) stop("Java >= 8 is needed for this package but not available")
}
Java 9 changed the format of this string (which used to be something like ‘1.8.0_292-b10’);
Java 11 gave jv as ‘11+28’ whereas Java 11.0.11 gave ‘11.0.11+9’. (https://openjdk.
org:443/jeps/322 details the current scheme. Note that it is necessary to allow for pre-
releases like ‘11-ea+22’.)
Note too that the compiler used to produce a jar can impose a minimum Java version,
often resulting in an arcane message like
java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0
(Where https://en.wikipedia.org/wiki/Java_class_file maps class-file version num-
bers to Java versions.) Compile with something like javac -target 11 to ensure this is
avoided. Note this also applies to packages distributing (or even downloading) compiled
Java code produced by others, so their requirements need to be checked (they are often
not documented accurately) and accounted for. It should be possible to check the class-file
version via command-line utility javap, if necessary after extracting the .class files from
a .jar archive. For example,
jar xvf some.jar
javap -verbose path/to/some.class | grep major
Some packages have stated a requirement on a particular JDK, but a package should only
be requiring a JRE unless providing its own Java interface.
Java 8 is still in widespread use (and may remain so because of licence changes and support
on older OSes: OpenJDK has security support until March 2026). On the other hand,
newer platforms may only have support for recent versions of Java: for ‘arm64’ macOS the
first officially supported version was 17.
• A package with a hard-to-satisfy system requirement is by definition not portable, an-
noyingly so if this is not declared in the ‘SystemRequirements’ field. The most common
example is the use of pandoc, which is only available for a very limited range of platforms
(and has onerous requirements to install from source) and has capabilities90 that vary by
89
If a Java interpreter is required directly (not via rJava (https://CRAN.R-project.org/package=rJava)) this
must be declared and its presence tested like any other external command.
90
For example, the ability to handle ‘https://’ URLs.
Chapter 1: Creating R packages 63

build but are not documented. Several recent versions of pandoc for macOS did not work
on R’s then target of High Sierra (and this too was undocumented). Another example is
the Rust compilation system (cargo and rustc).
Usage of external commands should always be conditional on a test for presence (perhaps
using Sys.which), as well as declared in the ‘SystemRequirements’ field. A package should
pass its checks without warnings nor errors without the external command being present.
An external command can be a (possibly optional) requirement for an imported or suggested
package but needed for examples, tests or vignettes in the package itself. Such usages should
always be declared and conditional.
Interpreters for scripting languages such as Perl, Python and Ruby need to be declared as
system requirements and used conditionally: for example macOS 10.16 was announced not
to have them (but released as macOS 11 with them); later it was announced that macOS
12.3 does not have Python 2 and only a minimal install of Python 3 is included. Python 2
has passed end-of-life and been removed from many major distributions. Support for Rust
or Go cannot be assumed.
Command cmake is not commonly installed, and where it is, it might not
be on the path. In particular, the most common location on macOS is
/Applications/CMake.app/Contents/bin/cmake and that should be looked for
if cmake is not found on the path.
• Be sure to use portable encoding names: none of utf8, mac and macroman is portable. See
the help for file for more details.
• Do not invoke R by plain R, Rscript or (on Windows) Rterm in your examples, tests,
vignettes, makefiles or other scripts. As pointed out in several places earlier in this manual,
use something like
"$(R_HOME)/bin/Rscript"
"$(R_HOME)/bin$(R_ARCH_BIN)/Rterm"
with appropriate quotes (as, although not recommended, R_HOME can contain spaces).
• Do not use R_HOME in makefiles except when passing them to the shell. Specifically, do
not use R_HOME in the argument to include, as R_HOME can contain spaces. Quoting the
argument to include does not help. A portable and the recommended way to avoid the
problem of spaces in ${R_HOME} is using option -f of make. This is easy to do with recursive
invocation of make, which is also the only usual situation when R_HOME is needed in the
argument for include.
$(MAKE) -f "${R_HOME}/etc${R_ARCH}/Makeconf" -f Makefile.inner
• If distributing datasets involving date-times, consider if a time zone needs to be specified.
The most portable way to distribute date-times is as objects of class "POSIXct" and as
these record the time in UTC, the time represented is independent of the time zone: but
how it is printed may not be. Objects of class "POSIXlt" should have a "tzone" attribute.
Dates (e.g, birthdays) are conventionally considered independently of time zone.
• If at all possible avoid any Internet access during package installation. Installation and use
may well be on different machines/accounts and those allowed to install software may have
no Internet access, and being self-contained helps ensure long-term reproducibility.
Do be careful in what your tests (and examples) actually test. Bad practice seen in distributed
packages include:
• It is not reasonable to test the time taken by a command: you cannot know how fast or
how heavily loaded an R platform might be. At best you can test a ratio of times, and even
that is fraught with difficulties and not advisable: for example, the garbage collector may
trigger at unpredictable times following heuristics that may change without notice.
Chapter 1: Creating R packages 64

• Do not test the exact format of R messages (from R itself or from other packages): They
change, and they can be translated.
Packages have even tested the exact format of system error messages, which are platform-
dependent and perhaps locale-dependent. For example, in late 2021 libcurl changed its
warning/error messages, including when URLs are not found.
• Do not test for the absence of warnings (something users of testthat (https://CRAN.
R-project.org/package=testthat) are fond of). Future changes in either R or pack-
ages you make use of can create new warnings, and your tests should not make these into
errors. (Some deprecation notices may be intended to remain as warnings for a long time.)
• If you use functions such as View, remember that in testing there is no one to look at the
output. It is better to use something like one of
if(interactive()) View(obj) else print(head(obj))
if(interactive()) View(obj) else str(obj)
• Be careful when comparing file paths. There can be multiple paths to a single file, and
some of these can be very long character strings. If possible canonicalize paths before
comparisons, but study ?normalizePath to be aware of the pitfalls.
• Only test the accuracy of results if you have done a formal error analysis. Things such
as checking that probabilities numerically sum to one are silly: numerical tests should
always have a tolerance. That the tests on your platform achieve a particular tolerance says
little about other platforms. R is configured by default to make use of long doubles where
available, but they may not be available or be too slow for routine use. Most R platforms
use ‘ix86’ or ‘x86_64’ CPUs: these may use extended precision registers on some but not all
of their FPU instructions. Thus the achieved precision can depend on the compiler version
and optimization flags—our experience is that 32-bit builds tend to be less precise than
64-bit ones. But not all platforms use those CPUs, and not all91 which use them configure
them to allow the use of extended precision. In particular, current ARM CPUs do not
have extended precision nor long doubles, and clang currently has long double the same
as double on all ARM CPUs. On the other hand some CPUs have higher-precision modes
which may be used for long double, notably 64-bit PowerPC and Sparc.
If you must try to establish a tolerance empirically, configure and build R with --disable-
long-double and use appropriate compiler flags (such as -ffloat-store and -fexcess-
precision=standard for gcc, depending on the CPU type92 ) to mitigate the effects of
extended-precision calculations. The platform most often seen to give different numerical
results is ‘arm64’ macOS, so be sure to include that in any empirical determination.
Tests which involve random inputs or non-deterministic algorithms should normally set a
seed or be tested for many seeds.
• Tests should use options(warn = 1) as reporting
There were 22 warnings (use warnings() to see them)
is pointless, especially for automated checking systems.
• If your package uses dates/times, ensure that it works in all timezones, especially those
near boundaries (problems have most often be seen in ‘Europe/London’ (zero offset in
Winter) and ‘Pacific/Auckland’, near enough the International Date line) and with off-
sets not in whole hours (Adelaide, Chatham Islands, . . . ). More extreme examples are
‘Africa/Conakry’ (permanent UTC), ‘Asia/Calcutta’ (no DST, permanent half-hour off-
set) and ‘Pacific/Kiritimati’(no DST, more than 12 hours ahead of UTC).

91
Not doing so is the default on Windows, overridden for the R executables.
92
These are not needed for the default compiler settings on ‘x86_64’ but are likely to be needed on ‘ix86’.
Chapter 1: Creating R packages 65

1.6.1 PDF size

There are a several tools available to reduce the size of PDF files: often the size can be reduced
substantially with no or minimal loss in quality. Not only do large files take up space: they can
stress the PDF viewer and take many minutes to print (if they can be printed at all).
qpdf (https://qpdf.sourceforge.io/) can compress losslessly. It is fairly readily available
(e.g. it has binaries for Windows and packages in Debian/Ubuntu/Fedora, and is installed as
part of the CRAN macOS distribution of R). R CMD build has an option to run qpdf over PDF
files under inst/doc and replace them if at least 10Kb and 10% is saved. The full path to the
qpdf command can be supplied as environment variable R_QPDF (and is on the CRAN binary
of R for macOS). It seems MiKTeX does not use PDF object compression and so qpdf can
reduce considerably the sizes of files it outputs: MiKTeX’s defaults can be overridden by code
in the preamble of an Sweave or LATEX file — see how this is done for the R reference manual
at https://svn.r-project.org/R/trunk/doc/manual/refman.top.
Other tools can reduce the size of PDFs containing bitmap images at excessively high reso-
lution. These are often best re-generated (for example Sweave defaults to 300 ppi, and 100–150
is more appropriate for a package manual). These tools include Adobe Acrobat (not Reader),
Apple’s Preview93 and Ghostscript (which converts PDF to PDF by
ps2pdf options -dAutoRotatePages=/None -dPrinted=false in.pdf out.pdf
and suitable options might be
-dPDFSETTINGS=/ebook
-dPDFSETTINGS=/screen
See https://ghostscript.readthedocs.io/en/latest/VectorDevices.html for more such
and consider all the options for image downsampling). There have been examples in CRAN
packages for which current versions of Ghostscript produced much bigger reductions than ear-
lier ones (e.g. at the upgrades from 9.50 to 9.52, from 9.55 to 9.56 and then to 10.00.0).
We come across occasionally large PDF files containing excessively complicated figures using
PDF vector graphics: such figures are often best redesigned or failing that, output as PNG files.
Option --compact-vignettes to R CMD build defaults to value ‘qpdf’: use ‘both’ to
try harder to reduce the size, provided you have Ghostscript available (see the help for
tools::compactPDF).

1.6.2 Check timing

There are several ways to find out where time is being spent in the check process. Start by setting
the environment variable _R_CHECK_TIMINGS_ to ‘0’. This will report the total CPU times (not
Windows) and elapsed times for installation and running examples, tests and vignettes, under
each sub-architecture if appropriate. For tests and vignettes, it reports the time for each as well
as the total.
Setting _R_CHECK_TIMINGS_ to a positive value sets a threshold (in seconds elapsed time) for
reporting timings.
If you need to look in more detail at the timings for examples, use option --timings to R CMD
check (this is set by --as-cran). This adds a summary to the check output for all the examples
with CPU or elapsed time of more than 5 seconds. It produces a file mypkg.Rcheck/mypkg-
Ex.timings containing timings for each help file: it is a tab-delimited file which can be read
into R for further analysis.
Timings for the tests and vignette runs are given at the bottom of the corresponding log
file: note that log files for successful vignette runs are only retained if environment variable
_R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_ is set to a true value.
93
Select ‘Save as’, and select ‘Reduce file size’ from the ‘Quartz filter’ menu’: this can be accessed in other ways,
for example by Automator.
Chapter 1: Creating R packages 66

1.6.3 Encoding issues

The issues in this subsection have been much alleviated by the change in R 4.2.0 to running
the Windows port of R in a UTF-8 locale where available. However, Windows users might be
running an earlier version of R on an earlier version of Windows which does not support UTF-8
locales.
Care is needed if your package contains non-ASCII text, and in particular if it is intended to
be used in more than one locale. It is possible to mark the encoding used in the DESCRIPTION
file and in .Rd files, as discussed elsewhere in this manual.
First, consider carefully if you really need non-ASCII text. Some users of R will only be
able to view correctly text in their native language group (e.g. Western European, Eastern
European, Simplified Chinese) and ASCII.94 . Other characters may not be rendered at all,
rendered incorrectly, or cause your R code to give an error. For .Rd documentation, marking
the encoding and including ASCII transliterations is likely to do a reasonable job. The set of
characters which is commonly supported is wider than it used to be around 2000, but non-
Latin alphabets (Greek, Russian, Georgian, . . . ) are still often problematic and those with
double-width characters (Chinese, Japanese, Korean, emoji) often need specialist fonts to render
correctly.
Several CRAN packages have messages in their R code in French (and a few in German). A
better way to tackle this is to use the internationalization facilities discussed elsewhere in this
manual.
Function showNonASCIIfile in package tools can help in finding non-ASCII bytes in files.
There is a portable way to have arbitrary text in character strings (only) in your R code,
which is to supply them in Unicode as ‘\uxxxx’ escapes (or, rarely needed except for emojis,
‘\Uxxxxxxxx’ escapes). If there are any characters not in the current encoding the parser will
encode the character string as UTF-8 and mark it as such. This applies also to character strings
in datasets: they can be prepared using ‘\uxxxx’ escapes or encoded in UTF-8 in a UTF-8
locale, or even converted to UTF-8 via iconv(). If you do this, make sure you have ‘R (>=
2.10)’ (or later) in the ‘Depends’ field of the DESCRIPTION file.
R sessions running in non-UTF-8 locales will if possible re-encode such strings for display
(and this is done by RGui on older versions of Windows, for example). Suitable fonts will need
to be selected or made available95 both for the console/terminal and graphics devices such as
‘X11()’ and ‘windows()’. Using ‘postscript’ or ‘pdf’ will choose a default 8-bit encoding
depending on the language of the UTF-8 locale, and your users would need to be told how to
select the ‘encoding’ argument.
Note that the previous two paragraphs only apply to character strings in R code. Non-ASCII
characters are particularly prevalent in comments (in the R code of the package, in examples,
tests, vignettes and even in the NAMESPACE file) but should be avoided there. Most commonly
people use the Windows extensions to Latin-1 (often directional single and double quotes, ellipsis,
bullet and en and em dashes) which are not supported in strict Latin-1 locales nor in CJK locales
on Windows. A surprisingly common misuse is to use a right quote in ‘don't’ instead of the
correct apostrophe.
Datasets can include marked UTF-8 or Latin-1 character strings. As R is nowadays unlikely
to be run in a Latin-1 or Windows’ CP1252 locale, for performance reasons these should be
converted to UTF-8.
If you want to run R CMD check on a Unix-alike over a package that sets a package encoding
in its DESCRIPTION file and do not use a UTF-8 locale you may need to specify a suitable locale
via environment variable R_ENCODING_LOCALES. The default is equivalent to the value
94
except perhaps some special characters such as backslash and hash which may be taken over for currency
symbols.
95
Typically on a Unix-alike this is done by telling fontconfig where to find suitable fonts to select glyphs from.
Chapter 1: Creating R packages 67

"latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@euro"
(which is appropriate for a system based on glibc: macOS requires latin9=fr_FR.ISO8859-
15) except that if the current locale is UTF-8 then the package code is translated to UTF-8 for
syntax checking, so it is strongly recommended to check in a UTF-8 locale.

1.6.4 Portable C and C++ code

Writing portable C and C++ code is mainly a matter of observing the standards (C99, C++14
or where declared C++11/17/20) and testing that extensions (such as POSIX functions) are
supported. Do make maximal use of your compiler diagnostics — this typically means using
flags -Wall and -pedantic for both C and C++ and additionally -Werror=implicit-function-
declaration and -Wstrict-prototypes for C (on some platforms and compiler versions) these
are part of -Wall or -pedantic).
C++ standards: From version 3.6.0 (3.6.2 on Windows), R defaulted to C++11 where avail-
able96 ; from R 4.1.0 to C++14 and from R 4.3.0 to C++17 (where available). However, in earlier
versions the default standard was that of the compiler used, often C++98 or C++14, and the
default is likely to change in future. For maximal portability a package should either specify a
standard (see Section 1.2.4 [Using C++ code], page 34) or be tested under all of C++11, C++98,
C++14 and C++17. (Specifying C++14 or later will limit portability.)
Note that the ‘TR1’ C++ extensions are not part of any of these standards and the <tr1/name>
headers are not supplied by some of the compilers used for R, including on macOS. (Use the
C++11 versions instead.)
A common error is to assume recent versions of compilers or OSes. In production environ-
ments ‘long term support’ versions of OSes may be in use for many years,97 and their compilers
may not be updated during that time. For example, GCC 4.8 was still in use in 2022 and could
be (in RHEL 7) until 2028: that supports neither C++14 nor C++17.
The POSIX standards only require recently-defined functions to be declared if certain macros
are defined with large enough values, and on some compiler/OS combinations98 they are not
declared otherwise. So you may need to include something like one of
#define _XOPEN_SOURCE 600
or
#ifdef __GLIBC__
# define _POSIX_C_SOURCE 200809L
#endif
before any headers. (strdup, strncasecmp and strnlen are such functions – there were several
older platforms which did not have the POSIX 2008 function strnlen.)
However, some common errors are worth pointing out here. It can be helpful to look up
functions at https://cplusplus.com/reference/ or https://en.cppreference.com/w/ and
compare what is defined in the various standards.
More care is needed for functions such as mallinfo which are not specified by any of these
standards—hopefully the man page on your system will tell you so. Searching online for such
pages for various OSes (preferably at least Linux and macOS, and the FreeBSD manual pages at
https://man.freebsd.org/cgi/man.cgi allow you to select many OSes) should reveal useful
information but a configure script is likely to be needed to check availability and functionality.
96
which it is on all known platforms, and is required as from R 4.0.0
97
Ubuntu provides 5 years of support (but people were running 14.04 after 7 years) and RHEL provides 10 years
full support and up to 14 with extended support.
98
This is seen on Linux, Solaris and FreeBSD, although each has other ways to turn on all extensions, e.g.
defining _GNU_SOURCE, __EXTENSIONS__ or _BSD_SOURCE: the GCC compilers by default define _GNU_SOURCE
unless a strict standard such as -std=c99 is used. On macOS extensions are declared unless one of these
macros is given too small a value.
Chapter 1: Creating R packages 68

Both the compiler and OS (via system header files, which may differ by architecture even
for nominally the same OS) affect the compilability of C/C++ code. Compilers from the GCC,
LLVM (clang and flang) Intel and Oracle Developer Studio suites have been used with R, and
both LLVM clang and Oracle have more than one implementation of C++ headers and library.
The range of possibilities makes comprehensive empirical checking impossible, and regrettably
compilers are patchy at best on warning about non-standard code.
• Mathematical functions such as sqrt are defined in C++11 for floating-point arguments:
float, double, long double and possibly more. The standard specifies what happens with
an argument of integer type but this is not always implemented, resulting in a report of
‘overloading ambiguity’: this was commonly seen on Solaris, but for pow also seen on macOS
and other platforms using clang++.
A not-uncommonly-seen problem is to mistakenly call floor(x/y) or ceil(x/y) for int
arguments x and y. Since x/y does integer division, the result is of type int and ‘overloading
ambiguity’ may be reported. Some people have (pointlessly) called floor and ceil on
arguments of integer type, which may have an ‘overloading ambiguity’.
A surprising common misuse is things like pow(10, -3): this should be the constant 1e-
3. Note that there are constants such as M_SQRT2 defined via Rmath.h99 for sqrt(2.0),
frequently mis-coded as sqrt(2).
• Function fabs is defined only for floating-point types, except in C++11 and later which
have overloads for std::fabs in <cmath> for integer types. Function abs is defined in
C99’s <stdlib.h> for int and in C++’s <cstdlib> for integer types, overloaded in <cmath>
for floating-point types. C++11 has additional overloads for std::abs in <cmath> for integer
types. The effect of calling abs with a floating-point type is implementation-specific: it may
truncate to an integer. For clarity and to avoid compiler warnings, use abs for integer types
and fabs for double values, and when using C++ include <cmath> and use the std:: prefix.
• It is an error (and make little sense, although has been seen) to call macros/functions
isnan, isinf and isfinite for integer arguments: a few compilers give a compilation
error. Function finite is obsolete, and some compilers will warn about its use100 .
• The GNU C/C++ compilers support a large number of non-portable extensions. For exam-
ple, INFINITY (which is a float value in C99 and C++11), for which R provides the portable
double value R_PosInf (and R_NegInf for -INFINITY). And NAN101 is just one NaN float
value: for use with R, NA_REAL is often what is intended, but R_NaN is also available.
Some (but not all) extensions are listed at https://gcc.gnu.org/onlinedocs/
gcc/C-Extensions.html and https://gcc.gnu.org/onlinedocs/gcc/
C_002b_002b-Extensions.html.
Other GNU extensions which have bitten package writers are the use of non-portable char-
acters such as ‘$’ in identifiers and use of C++ headers under ext.
item Including C-style headers in C++ code is not portable. Including the legacy header102
math.h in C++ code may conflict with cmath which may be included by other headers. In
C++11, functions like sqrt and isnan are defined for double arguments in math.h and for
a range of types including double in cmath. Similar issues have been seen for stdlib.h and
cstdlib. Including the C++ header first used to be a sufficient workaround but for some
2016 compilers only one could be included.

99
often taken from the toolchain’s headers.
100
at the time of writing ‘arm64’ macOS both warned and did not supply a prototype in math.h which resulted
in a compilation error.
101
also part of C++11 and later.
102
which often is the same as the header included by the C compiler, but some compilers have wrappers for some
of the C headers.
Chapter 1: Creating R packages 69

• Be careful to include the headers which define the functions you use. Some compilers/OSes
include other system headers in their headers which are not required by the standards,
and so code may compile on such systems and not on others. (A prominent example is
the C++ header <random> which is indirectly included by <algorithm> by g++. Another
issue is the C header <time.h> which is included by other headers on Linux and Windows
but not macOS.) g++ 11 often needs explicit inclusion of the C++ headers <limits> (for
numeric_limits) or <exception> (for set_terminate and similar), whereas earlier ver-
sions included these in other headers. g++ 13 requires the explicit inclusion of <cstdint>
for types such as uint32_t which was previously included implicitly. (For more such, see
https://gcc.gnu.org/gcc-13/porting_to.html.)
Note that malloc, calloc, realloc and free are defined by C99 in the header stdlib.h
and (in the std:: namespace) by C++ header cstdlib. Some earlier implementations used
a header malloc.h, but that is not portable and does not exist on macOS.
This also applies to types such as ssize_t. The POSIX standards say that is declared in
headers unistd.h and sys/types.h, and the latter is often included indirectly by other
headers on some but not all systems.
Similarly for constants: for example SIZE_MAX is defined in stdint.h alongside size_t.
• Some headers are not portable: we have just mentioned malloc.h and often CRAN sub-
missions attempt to use endian.h. The latter is a glibc extension: some OSes have
machine/endian.h or sys/endian.h but some have neither.
• Use #include "my.h" not #include <my.h> for headers in your package. The second form
is intended for system headers and the search order for such headers is platform-dependent
(and may not include the current directory). For extra safety, name headers in a way that
cannot be confused with a system header so not, for example, types.h.
• For C++ code, be careful to specify namespaces where needed. Many functions are defined
by the standards to be in the std namespace, but g++ puts many such also in the C++ main
namespace. One way to do so is to use declarations such as
using std::floor;
but it is usually preferable to use explicit namespace prefixes in the code.
Examples seen in CRAN packages include
abs acos atan bind calloc ceil div exp fabs floor fmod free log malloc
memcpy memset pow printf qsort round sin sprintf sqrt strcmp strcpy
strerror strlen strncmp strtol tan trunc
This problem is less common than it used to be, but in 2019 LLVM clang did not have bind
in the main namespace. Also seen has been type size_t defined only in the std namespace.
NB: These functions are only guaranteed to be in the std namespace if the correct C++
header is included, e.g. <cmath> rather than <math.h>.
If you define functions in C++ which are inspired by later standards, put them in a namespace
and refer to them using the namespace. We have seen conflicts with std::make_unique
from C++14 and std::byte, std::data, std::sample and std::size from C++17.
• In C++ code
using namesapace std;
is not good practice, and has caused platform-dependent errors if included before headers,
especially system headers (which may be included by other headers). The best practice is
to use explicit std:: prefixes for all functions declared by the C++ standard to be in that
namespace.
• Some C++ compilers refuse to compile constructs such as
if(ptr > 0) { ....}
Chapter 1: Creating R packages 70

which compares a pointer to the integer 0. This could just use if(ptr) (pointer addresses
cannot be negative) but if needed pointers can be tested against nullptr (C++11) or NULL.
• Macros defined by the compiler/OS can cause problems. Identifiers starting with an under-
score followed by an upper-case letter or another underscore are reserved for system macros
and should not be used in portable code (including not as guards in C/C++ headers). Other
macros, typically upper-case, may be defined by the compiler or system headers and can
cause problems. Some of these can be avoided by defining _POSIX_C_SOURCE before in-
cluding any system headers, but it is better to only use all-upper-case names which have a
unique prefix such as the package name.
• typedefs in OS headers can conflict with those in the package: examples have included
ulong, index_t, single and thread. (Note that these may conflict with other uses as
identifiers, e.g. defining a C++ function called single.) The POSIX standard reserves (in
§2.2.2) all identifiers ending in _t.
• Some compilers do not allow a space between -D and the macro to be defined. Similarly for
-U.
• If you use OpenMP, check carefully that you have followed the advice in the subsection on
Section 1.2.1.1 [OpenMP support], page 28. In particular, any use of OpenMP in C/C++
code will need to use
#ifdef _OPENMP
# include <omp.h>
#endif
Any use of OpenMP functions, e.g. omp_set_num_threads, also needs to be conditioned.
To avoid incessant warnings such as
warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
uses of such pragmas should also be conditioned (or commented out if they are used in code
in a package not enabling OpenMP on any platform).
Do not hardcode -lgomp: not only is that specific to the GCC family of compilers, using
the correct linker flag often sets up the run-time path to the library.
• Package authors commonly assume things are part of C/C++ when they are not: the most
common example is POSIX103 function strdup. The most common C library on Linux,
glibc, will hide the declarations of such extensions unless a ‘feature-test macro’ is defined
before (almost) any system header is included. So for strdup you need
#define _POSIX_C_SOURCE 200809L
...
#include <string.h>
...
strdup call(s)
where the appropriate value can be found by man strdup on Linux. (Use of strncasecmp
is similar.)
However, modes of gcc with ‘GNU EXTENSIONS’ (which are the default, either
-std=gnu99 or -std=gnu11) declare enough macros to ensure that missing declarations
are rarely seen.
This applies also to constants such as M_PI and M_LN2, which are part of the X/Open
standard: to use these define _XOPEN_SOURCE before including any headers, or include the
R header Rmath.h.
• Using alloca portably is tricky: it is neither an ISO C/C++ nor a POSIX function. An
adequately portable preamble is
#ifdef __GNUC__
103
Although this is expected to be part of C23, full support of that is years away.
Chapter 1: Creating R packages 71

/* Includes GCC, clang and Intel compilers */

# undef alloca
# define alloca(x) __builtin_alloca((x))
#elif defined(__sun) || defined(_AIX)
/* this was necessary (and sufficient) for Solaris 10 and AIX 6: */
# include <alloca.h>
#endif
• Compiler writers feel free to implement features from later standards than the one speci-
fied, so for example they may implement or warn on C++14/17/20 features when C++11 is
specified. Portable code will not use such features – it can be hard to know what they are
but the most common warnings are
'register' storage class specifier is deprecated and incompatible with C++17

ISO C++11 does not allow conversion from string literal to 'char *'
(where conversion should be to const char *). Keyword register was not mentioned in
C++98, deprecated in C++11 and removed in C++17.
There are quite a lot of other C++98 features deprecated in C++11 and removed in C++17,
and LLVM clang 9 and later warn about them (and as from version 16 they have been
removed). Examples include bind1st/bind2nd (use std::bind or lambdas104 ) std::auto_
ptr (replaced by std::unique_ptr), std::mem_fun_ref and std::ptr_fun.
• Later versions of standards may add reserved words: for example bool, false and true
became keywords in C23 and are no longer available as variable names. As noted above,
C++17 uses byte, data, sample and size.
So avoid common words and keywords from other programming languages.
• Be careful about including C headers in C++ code. Issues include
• Use of the register storage class specifier (see the previous but one item).
• The C99 keyword restrict is not part of 105 any C++ standard and is rejected by some
C++ compilers.
• Inclusion by such headers of C-style headers such as math.h (see above).
The most portable way to interface to other software with a C API is to use C code (which
can normally be mixed with C++ code in a package).
• reinterpret_cast in C++ is not safe for pointers: for example the types may have dif-
ferent alignment requirements. Use memcpy to copy the contents to a fresh variable of the
destination type.
• Avoid platform-specific code if at all possible, but if you need to test for a platform ensure
that all platforms are covered. For example, __unix__ is not defined on all Unix-alikes, in
particular not on macOS. A reasonably portable way to condition code for a Unix-alike is
#if defined (__unix__) || (defined (__APPLE__) && defined (__MACH__))
#endif
but
#ifdef _WIN32
// Windows-specific code
#else
// Unix-alike code
#endif
104
https://stackoverflow.com/questions/32739018/a-replacement-for-stdbind2nd
105
it is allowed but ignored in system headers.
Chapter 1: Creating R packages 72

would be better. For a Unix-alike it is much better to use configure to test for the
functionality needed than make assumptions about OSes (and people all too frequently
forget R is used on platforms other than Linux, Windows and macOS — and some forget
macOS).
• Headers in subdirectories are often not portable. For C++, this includes bits/, tr1/ and
tr2/, none of which exist on macOS (and ext/ exists there but with different content from
g++-based platforms). Header bits/stdc++.h is both not portable and not recommended
for end-user code even on platforms which include it.
• Be careful if using malloc or calloc. First, their return value must always be checked to
see if the allocation succeeded – it is almost always easier to use R’s R_Calloc, which does
check. Second, the first argument is of type size_t and recent compilers are warning about
passing signed arguments (which could get promoted to ridiculously large values).
• For C code, consider using the flag -Wstrict-prototypes which is supported by gcc and
LLVM and Apple clang. This has found quite a number of errors where functions have
been declared without arguments and is likely to become the default in future compilers.
(It already is for LLVM clang in C23 mode.) Note that using f() for a function without
any parameters was deprecated in C99 and C11, but it expected to be non-deprecated in
C23. However, f(void) is supported by all standards and avoids any uncertainty.
LLVM clang has a separate warning -Wdeprecated-non-prototype which is enabled by
-Wstrict-prototypes. This warns on K&R-style usage, which will not be accepted in C23.
• Several C entry points are warned against in their man pages on most systems, often in
very strong terms such as ’Do not use these functions’. macOS has started to warn106 if
these are used for sprintf, vsprintf, gets, mktemp, tempmam and tmpnam. It is highly
recommended that you use safer alternatives (on any platform) but the warning can be
avoided by defining ‘_POSIX_C_SOURCE’ to for example ‘200809L’ before including the (C
or C++) header which defines them. (However, this may hide other extensions.)
• Compilers may interpret comments in source code, so it is necessary to remove any intended
for a compiler to interpret. The main example has been comments for Visual Fortran (as
the Intel Fortran compiler has been known on Windows107 ) like
!DEC$ ATTRIBUTES DLLEXPORT,C,REFERENCE,ALIAS:'kdenestmlcvb' :: kdenestmlcvb
which are interpreted by Intel Fortran on all platforms (and are inappropriate for use with
R on Windows). gfortran has similar forms starting with !GCC$.
• The C++ new operator takes argument std::size_t size, which is unsigned. Using a
signed integer type such as int may lead to compiler warnings such as
warning: argument 1 value '18446744073709551615' exceeds maximum object
size 9223372036854775807 [-Walloc-size-larger-than=]
(especially if LTO is used). So don’t do that!

Some additional information for C++ is available at https://journal.r-project.org/

archive/2011-2/RJournal_2011-2_Plummer.pdf by Martyn Plummer.

1.6.4.1 Common symbols

Most OSes (including all those commonly used for R) have the concept of ‘tentative definitions’
where global C variables are defined without an initializer. Traditionally the linker resolves all
tentative definitions of the same variable in different object files to the same object, or to a

106
when using the macOS 13 SDK with a deployment target of macOS 13.
107
and at one time as DEC Fortran, hence the DEC.
Chapter 1: Creating R packages 73

non-tentative definition. However, gcc 10108 and LLVM clang 11109 changed their default so
that tentative definitions cannot be merged and the linker will give an error if the same variable
is defined in more than one object file. To avoid this, all but one of the C source files should
declare the variable extern — which means that any such variables included in header files need
to be declared extern. A commonly used idiom (including by R itself) is to define all global
variables as extern in a header, say globals.h (and nowhere else), and then in one (and one
only) source file use
#define extern
# include "globals.h"
#undef extern
A cleaner approach is not to have global variables at all, but to place in a single file common
variables (declared static) followed by all the functions which make use of them: this may
result in more efficient code.
The ‘modern’ behaviour can be seen110 by using compiler flag -fno-common as part of ‘CFLAGS’
in earlier versions of gcc and clang.
-fno-common is said to be particularly beneficial for ARM CPUs.
This is not pertinent to C++ which does not permit tentative definitions.

1.6.4.2 C++17 issues

R 4.3.0 and later default to C++17 when compiling C++, and that finally removed many C++98
features which were deprecated as long ago as C++11. Compiler/runtime authors have been slow
to remove these, but LLVM clang with its libc++ runtime library finally started to do so in
2023 – some others warn but some do not.
The principal offender is the ‘Boost’ collection of C++ headers and libraries. There are two
little-documented ways to work around aspects of its outdated code. One is to add
-D_HAS_AUTO_PTR_ETC=0
to PKG_CPPLAGS in src/Makevars, src/Makevars.win and src/Makevars.ucrt. This covers
the removal of
std::auto_ptr
std::unary_function
std::binary_function
std::random_shuffle
std::binder1st
std::binder2nd
with most issues seen with code that includes boost/functional.hpp, usually indirectly.
A rarer issue is the use of illegal values for enum types, usually negative ones such as
BOOST_MPL_AUX_STATIC_CAST(AUX_WRAPPER_VALUE_TYPE, (value - 1));
in boost/mpl/aux_/integral_wrapper.hpp. Adding
-Wno-error=enum-constexpr-conversion
to PKG_CXXFLAGS will allow this, but that flag is only accepted by recent versions of LLVM
clang (and will not be in future) so needs a configure test.
Pre=built versions of current clang/libc++ are usually available from https://github.
com/llvm/llvm-project/releases for a wide range of platforms (but the Windows builds
108
see https://gcc.gnu.org/gcc-10/porting_to.html.
109
See https://prereleases.llvm.org/11.0.0/rc2/tools/clang/docs/ReleaseNotes.html#
modified-compiler-flags.
110
In principle this could depend on the OS, but has been checked on Linux and macOS.
Chapter 1: Creating R packages 74

there are not compatible with Rtools and the macOS ones are unsigned). To select libc++ add
-stdlib=libc++ to CXX, for example by having
CXX="/path/to/clang/clang++ -std=gnu++17 -stdlib=libc++"
in ~/.R/Makevars.
Another build for Windows which may be sufficiently compatible with Rtools can be found
at https://github.com/mstorsjo/llvm-mingw: this uses libc++.

1.6.5 Portable Fortran code

For many years almost all known R platforms used gfortran as their Fortran compiler, but
now there are LLVM and ‘classic’ flang and the Intel compilers ifort111 and ifx are now
free-of-change.
There is still a lot of Fortran code in CRAN packages which predates Fortran 77. Modern
Fortran compilers are being written to target a minimum standard of Fortran 2018. and it is
desirable that Fortran code in packages complies with that standard. For gfortran this can be
checked by adding -std=f2018 to FFLAGS. The most commonly seen issues are
• The use of DFLOAT, which was superseded by DBLE in Fortran 77. Also, use of DCMPLX,
DCONJG, DIMAG and similar.
• The use of GNU Fortran extensions. Some are listed at https://gcc.gnu.org/
onlinedocs/gfortran/Extensions-implemented-in-GNU-Fortran.html. Others which
have caused problems include etime, getpid, isnan112 and sizeof.
One that frequently catches package writers is that it allows out-of-order declarations: in
standard-conformant Fortran variables must be declared (explicitly or implicitly) before use
in other declarations such as dimensions.
Unfortunately this flags extensions such as DOUBLE COMPLEX and COMPLEX*16. R has tested that
DOUBLE COMPLEX works and so is preferred to COMPLEX*16. (One can also use something like
COMPLEX(KIND=KIND(0.0D0)).)
GNU Fortran 10 and later give a compilation error for the previously widespread practice of
passing a Fortran array element where an array is expected, or a scalar instead of a length-one ar-
ray. See https://gcc.gnu.org/gcc-10/porting_to.html. As do the Intel Fortran compilers,
and they can be stricter.
The use of IMPLICIT NONE is highly recommended – Intel compilers with -warn will warn on
variables without an explicit type.
Common non-portable constructions include
• The use of Fortran types such as REAL(KIND=8) is very far from portable. According to the
standards this merely enumerates different supported types, so DOUBLE PRECISION might
be REAL(KIND=3) (and is on an actual compiler). Even if for a particular compiler the value
indicates the size in bytes, which values are supported is platform-specific — for example
gfortran supports values of 4 and 8 on all current platforms and 10 and 16 on a few (but
not for example on all ‘arm’ CPUs).
The same applies to INTEGER(KIND=4) and COMPLEX(KIND=16).
Many uses of integer and real variable in Fortran code in packages will interwork with C (for
example .Fortran is written in C), and R has checked that INTEGER and DOUBLE PRECISION
correspond to the C types int and double. To make this explicit, from Fortran 2003 one
can use the named constants c_int, c_double and c_double_complex from module iso_
c_binding.
111
discontinued in 2023.
112
There is a portable way to do this in Fortran 2003 (ieee_is_nan() in module ieee_arithmetic), but that
was not supported in the versions 4.x of GNU Fortran. A pretty robust alternative is to test if(my_var /=
my_var).
Chapter 1: Creating R packages 75

• The Intel compilers only recognize the extensions .f (fixed-form) and .f90 (free-form) and
not .f95. R CMD INSTALL works around this for packages without a src/Makefile.
• Use of extensions .F and .F90 to indicate source code to be preprocessed: the preprocessor
used is compiler-specific and may or may not be cpp.
• Fixed form Fortran (with extension .f) should only use 72 columns, and free-form at most
132 columns. This includes trailing comments. Over-long lines may be silently truncated
or give a warning. %% The Intel compilers warn.

1.6.6 Binary distribution

If you want to distribute a binary version of a package on Windows or macOS, there are further
checks you need to do to check it is portable: it is all too easy to depend on external software
on your own machine that other users will not have.
For Windows, check what other DLLs your package’s DLL depends on (‘imports’ from in the
DLL tools’ parlance). A convenient GUI-based tool to do so is ‘Dependency Walker’ (https://
www.dependencywalker.com/) for both 32-bit and 64-bit DLLs – note that this will report as
missing links to R’s own DLLs such as R.dll and Rblas.dll. The command-line tool objdump
in the appropriate toolchain will also reveal what DLLs are imported from. If you use a toolchain
other than one provided by the R developers or use your own makefiles, watch out in partic-
ular for dependencies on the toolchain’s runtime DLLs such as libgfortran, libstdc++ and
libgcc_s.
For macOS, using R CMD otool -L on the package’s shared object(s) in the libs direc-
tory will show what they depend on: watch for any dependencies in /usr/local/lib or
/usr/local/gfortran/lib, notably libgfortran.?.dylib and libquadmath.0.dylib. (For
ways to fix these, see Section “Building binary-packages” in R Installation and Administration.)
Many people (including the CRAN package repository) will not accept source packages con-
taining binary files as the latter are a security risk. If you want to distribute a source package
which needs external software on Windows or macOS, options include
• To arrange for installation of the package to download the additional software from a URL,
as e.g. package Cairo (https://CRAN.R-project.org/package=Cairo) used to.
• To negotiate with Tomas Kalibera to include Windows software in Rtools or with Simon
Urbanek to include macOS software in his ‘recipes’ system.
• (For CRAN.) To negotiate with Uwe Ligges to host the additional components on Win-
Builder, and write a configure.win file to install them.
Be aware that license requirements you may require you to supply the sources for the additional
components (and will if your package has a GPL-like license).

1.7 Diagnostic messages

Diagnostic messages can be made available for translation, so it is important to write them in
a consistent style. Using the tools described in the next section to extract all the messages can
give a useful overview of your consistency (or lack of it). Some guidelines follow.
• Messages are sentence fragments, and not viewed in isolation. So it is conventional not to
capitalize the first word and not to end with a period (or other punctuation).
• Try not to split up messages into small pieces. In C error messages use a single format
string containing all English words in the messages.
In R error messages do not construct a message with paste (such messages will not be
translated) but via multiple arguments to stop or warning, or via gettextf.
• Do not use colloquialisms such as “can’t” and “don’t”.
Chapter 1: Creating R packages 76

• Conventionally single quotation marks are used for quotations such as

'ord' must be a positive integer, at most the number of knots
and double quotation marks when referring to an R character string or a class, such as
'format' must be "normal" or "short" - using "normal"
Since ASCII does not contain directional quotation marks, it is best to use ‘'’ and let the
translator (including automatic translation) use directional quotations where available. The
range of quotation styles is immense: unfortunately we cannot reproduce them in a portable
texinfo document. But as a taster, some languages use ‘up’ and ‘down’ (comma) quotes
rather than left or right quotes, and some use guillemets (and some use what Adobe calls
‘guillemotleft’ to start and others use it to end).
In R messages it is also possible to use sQuote or dQuote as in
stop(gettextf("object must be of class %s or %s",
dQuote("manova"), dQuote("maov")),
domain = NA)
• Occasionally messages need to be singular or plural (and in other languages there may be
no such concept or several plural forms – Slovenian has four). So avoid constructions such
as was once used in library
if((length(nopkgs) > 0) && !missing(lib.loc)) {
if(length(nopkgs) > 1)
warning("libraries ",
paste(sQuote(nopkgs), collapse = ", "),
" contain no packages")
else
warning("library ", paste(sQuote(nopkgs)),
" contains no package")
}
and was replaced by
if((length(nopkgs) > 0) && !missing(lib.loc)) {
pkglist <- paste(sQuote(nopkgs), collapse = ", ")
msg <- sprintf(ngettext(length(nopkgs),
"library %s contains no packages",
"libraries %s contain no packages",
domain = "R-base"),
pkglist)
warning(msg, domain=NA)
}
Note that it is much better to have complete clauses as here, since in another language one
might need to say ‘There is no package in library %s’ or ‘There are no packages in libraries
%s’.

1.8 Internationalization
There are mechanisms to translate the R- and C-level error and warning messages. There are
only available if R is compiled with NLS support (which is requested by configure option
--enable-nls, the default).
The procedures make use of msgfmt and xgettext which are part of GNU gettext and this
will need to be installed: Windows users can find pre-compiled binaries at https://www.stats.
ox.ac.uk/pub/Rtools/goodies/gettext-tools.zip.
Chapter 1: Creating R packages 77

1.8.1 C-level messages

The process of enabling translations is
• In a header file that will be included in all the C (or C++ or Objective C/C++) files containing
messages that should be translated, declare
#include <R.h> /* to include Rconfig.h */

#ifdef ENABLE_NLS
#include <libintl.h>
#define _(String) dgettext ("pkg", String)
/* replace pkg as appropriate */
#else
#define _(String) (String)
#endif
• For each message that should be translated, wrap it in _(...), for example
error(_("'ord' must be a positive integer"));
If you want to use different messages for singular and plural forms, you need to add
#ifndef ENABLE_NLS
#define dngettext(pkg, String, StringP, N) (N == 1 ? String : StringP)
#endif
and mark strings by
dngettext("pkg", <singular string>, <plural string>, n)
• In the package’s src directory run
xgettext --keyword=_ -o pkg.pot *.c
The file src/pkg.pot is the template file, and conventionally this is shipped as po/pkg.pot.

1.8.2 R messages
Mechanisms are also available to support the automatic translation of R stop, warning and
message messages. They make use of message catalogs in the same way as C-level messages,
but using domain R-pkg rather than pkg. Translation of character strings inside stop, warning
and message calls is automatically enabled, as well as other messages enclosed in calls to gettext
or gettextf. (To suppress this, use argument domain=NA.)
Tools to prepare the R-pkg.pot file are provided in package tools: xgettext2pot will prepare
a file from all strings occurring inside gettext/gettextf, stop, warning and message calls.
Some of these are likely to be spurious and so the file is likely to need manual editing. xgettext
extracts the actual calls and so is more useful when tidying up error messages.
The R function ngettext provides an interface to the C function of the same name: see exam-
ple in the previous section. It is safest to use domain="R-pkg" explicitly in calls to ngettext,
and necessary for earlier versions of R unless they are calls directly from a function in the
package.

1.8.3 Preparing translations

Once the template files have been created, translations can be made. Conventional translations
have file extension .po and are placed in the po subdirectory of the package with a name that
is either ‘ll.po’ or ‘R-ll.po’ for translations of the C and R messages respectively to language
with code ‘ll’.
See Section “Localization of messages” in R Installation and Administration, for details of
language codes.
Chapter 1: Creating R packages 78

There is an R function, update_pkg_po in package tools, to automate much of the mainte-

nance of message translations. See its help for what it does in detail.
If this is called on a package with no existing translations, it creates the directory pkgdir/po,
creates a template file of R messages, pkgdir/po/R-pkg.pot, within it, creates the ‘en@quot’
translation and installs that. (The ‘en@quot’ pseudo-language interprets quotes in their direc-
tional forms in suitable (e.g. UTF-8) locales.)
If the package has C source files in its src directory that are marked for translation, use
touch pkgdir/po/pkg.pot
to create a dummy template file, then call update_pkg_po again (this can also be done before
it is called for the first time).
When translations to new languages are added in the pkgdir/po directory, running the same
command will check and then install the translations.
If the package sources are updated, the same command will update the template files, merge
the changes into the translation .po files and then installed the updated translations. You
will often see that merging marks translations as ‘fuzzy’ and this is reported in the coverage
statistics. As fuzzy translations are not used, this is an indication that the translation files need
human attention.
The merged translations are run through tools::checkPofile to check that C-style formats
are used correctly: if not the mismatches are reported and the broken translations are not
installed.
This function needs the GNU gettext-tools installed and on the path: see its help page.

1.9 CITATION files

An installed file named CITATION will be used by the citation() function. (It should be in the
inst subdirectory of the package sources.)
The CITATION file is parsed as R code (in the package’s declared encoding, or in ASCII if
none is declared). It will contain calls to function bibentry. Here is that for nlme (https://
CRAN.R-project.org/package=nlme):
## R package reference generated from DESCRIPTION metadata
citation(auto = meta)

## NLME book
bibentry(bibtype = "Book",
title = "Mixed-Effects Models in S and S-PLUS",
author = c(person(c("José", "C."), "Pinheiro"),
person(c("Douglas", "M."), "Bates")),
year = "2000", publisher = "Springer", address = "New York",
doi = "10.1007/b98882")
Note how the first call auto-generates citation information from object meta, a parsed ver-
sion of the DESCRIPTION file – it is tempting to hardcode such information, but it normally
then gets outdated. How the first entry would look like as a bibentry call can be seen from
print(citation("pkgname", auto = TRUE), style = "R") for any installed package. Auto-
generated information is returned by default if no CITATION file is present.
See ?bibentry for further details of the information which can be provided. In case a biben-
try contains LATEX markup (e.g., for accented characters or mathematical symbols), it may be
necessary to provide a text representation to be used for printing via the textVersion argument
to bibentry. E.g., earlier versions of nlme (https://CRAN.R-project.org/package=nlme) ad-
ditionally used something like
textVersion =
Chapter 1: Creating R packages 79

paste0("Jose Pinheiro, Douglas Bates, Saikat DebRoy, ",

"Deepayan Sarkar and the R Core Team (",
sub("-.*", "", meta$Date),
"). nlme: Linear and Nonlinear Mixed Effects Models. ",
sprintf("R package version %s", meta$Version), ".")
The CITATION file should itself produce no output when source-d.
It is desirable (and essential for CRAN) that the CITATION file does not contain calls to
functions such as packageDescription which assume the package is installed in a library tree
on the package search path.

1.10 Package types

The DESCRIPTION file has an optional field Type which if missing is assumed to be ‘Package’,
the sort of extension discussed so far in this chapter. Currently one other type is recognized;
there used also to be a ‘Translation’ type.

1.10.1 Frontend
This is a rather general mechanism, designed for adding new front-ends such as the former
gnomeGUI package (see the Archive area on CRAN). If a configure file is found in the top-
level directory of the package it is executed, and then if a Makefile is found (often generated by
configure), make is called. If R CMD INSTALL --clean is used make clean is called. No other
action is taken.
R CMD build can package up this type of extension, but R CMD check will check the type and
skip it.
Many packages of this type need write permission for the R installation directory.

1.11 Services
Several members of the R project have set up services to assist those writing R packages,
particularly those intended for public distribution.
win-builder.r-project.org (https://win-builder.r-project.org) offers the automated
preparation of (64-bit) Windows binaries from well-tested source packages.
R-Forge (R-Forge.r-project.org (https://R-Forge.r-project.org)) and RForge
(www.rforge.net (https://www.rforge.net)) are similar services with similar names. Both
provide source-code management through SVN, daily building and checking, mailing lists
and a repository that can be accessed via install.packages (they can be selected by
setRepositories and the GUI menus that use it). Package developers have the opportunity
to present their work on the basis of project websites or news announcements. Mailing lists,
forums or wikis provide useRs with convenient instruments for discussions and for exchanging
information between developers and/or interested useRs.
 80

2 Writing R documentation files

2.1 Rd format
R objects are documented in files written in “R documentation” (Rd) format, a simple markup
language much of which closely resembles (La)TEX, which can be processed into a variety of
formats, including LATEX, HTML and plain text. The translation is carried out by functions in
the tools package called by the script Rdconv in R_HOME/bin and by the installation scripts for
packages.
The R distribution contains more than 1400 such files which can be found in the
src/library/pkg/man directories of the R source tree, where pkg stands for one of the
standard packages which are included in the R distribution.
As an example, let us look at a simplified version of src/library/base/man/load.Rd which
documents the R function load.

% File src/library/base/man/load.Rd
\name{load}
\alias{load}
\title{Reload Saved Datasets}
\description{
Reload datasets written with the function \code{save}.
}
\usage{
load(file, envir = parent.frame(), verbose = FALSE)
}
\arguments{
\item{file}{a (readable binary-mode) \link{connection}
or a character string giving the name of the file to load
(when \link{tilde expansion} is done).}
\item{envir}{the environment where the data should be loaded.}
\item{verbose}{should item names be printed during loading?}
}
\value{
A character vector of the names of objects created, invisibly.
}
\seealso{
\code{\link{save}}.
}
\examples{
## save all data
save(list = ls(all.names = TRUE), file = "all.RData")

## restore the saved values to the current environment

load("all.RData")
}
\keyword{file}

An Rd file consists of three parts. The header gives basic information about the name of
the file, the topics documented, a title, a short textual description and R usage information for
the objects documented. The body gives further information (for example, on the function’s
arguments and return value, as in the above example). Finally, there is an optional footer with
keyword information. The header is mandatory.
Information is given within a series of sections with standard names (and user-defined sections
are also allowed). Unless otherwise specified1 these should occur only once in an Rd file (in any
1
e.g. \alias, \keyword and \note sections.
Chapter 2: Writing R documentation files 81

order), and the processing software will retain only the first occurrence of a standard section in
the file, with a warning.
See “Guidelines for Rd files” (https://developer.r-project.org/Rds.html) for guide-
lines for writing documentation in Rd format which should be useful for package writers. The
R generic function prompt is used to construct a bare-bones Rd file ready for manual editing.
Methods are defined for documenting functions (which fill in the proper function and argument
names) and data frames. There are also functions promptData, promptPackage, promptClass,
and promptMethods for other types of Rd file.
The general syntax of Rd files is summarized below. For a detailed technical discussion of
current Rd syntax, see “Parsing Rd files” (https://developer.r-project.org/parseRd.pdf).
Rd files consist of four types of text input. The most common is LATEX-like, with the backslash
used as a prefix on markup (e.g. \alias), and braces used to indicate arguments (e.g. {load}).
The least common type of text is ‘verbatim’ text, where no markup other than the comment
marker (%) is processed. There is also a rare variant of ‘verbatim’ text (used in \eqn, \deqn,
\figure, and \newcommand) where comment markers need not be escaped. The final type is
R-like, intended for R code, but allowing some embedded macros. Quoted strings within R-like
text are handled specially: regular character escapes such as \n may be entered as-is. Only
markup starting with \l (e.g. \link) or \v (e.g. \var) will be recognized within quoted strings.
The rarely used vertical tab \v must be entered as \\v.
Each macro defines the input type for its argument. For example, the file initially uses
LAT EX-like syntax, and this is also used in the \description section, but the \usage section
uses R-like syntax, and the \alias macro uses ‘verbatim’ syntax. Comments run from a percent
symbol % to the end of the line in all types of text except the rare ‘verbatim’ variant (as on the
first line of the load example).
Because backslashes, braces and percent symbols have special meaning, to enter them into
text sometimes requires escapes using a backslash. In general balanced braces do not need to be
escaped, but percent symbols always do, except in the ‘verbatim’ variant. For the complete list
of macros and rules for escapes, see “Parsing Rd files” (https://developer.r-project.org/
parseRd.pdf).

2.1.1 Documenting functions

The basic markup commands used for documenting R objects (in particular, functions) are given
in this subsection.
\name{name}
name typically2 is the basename of the Rd file containing the documentation. It is
the “name” of the Rd object represented by the file and has to be unique in a package.
To avoid problems with indexing the package manual, it may not contain ‘!’ ‘|’ nor
‘@’. (LATEX special characters are allowed, but may not be collated correctly in the
index.) There can only be one \name entry in a file, and it must not contain any
markup and should only contain printable ASCII characters. Entries in the package
manual will be in alphabetic3 order of the \name entries.
\alias{topic}
The \alias sections specify all “topics” the file documents. This information is
collected into index data bases for lookup by the on-line (plain text and HTML)
help systems. The topic can contain spaces, but (for historical reasons) leading and
2
There can be exceptions: for example Rd files are not allowed to start with a dot, and have to be uniquely
named on a case-insensitive file system.
3
in the current locale, and with special treatment for LATEX special characters and with any ‘pkgname-package’
topic moved to the top of the list.
Chapter 2: Writing R documentation files 82

trailing spaces will be stripped. Percent and left brace need to be escaped by a
backslash.
There may be several \alias entries. Quite often it is convenient to document
several R objects in one file. For example, file Normal.Rd documents the density,
distribution function, quantile function and generation of random variates for the
normal distribution, and hence starts with
\name{Normal}
\alias{Normal}
\alias{dnorm}
\alias{pnorm}
\alias{qnorm}
\alias{rnorm}
Also, it is often convenient to have several different ways to refer to an R object,
and an \alias does not need to be the name of an object.
Note that the \name is not necessarily a topic documented, and if so desired it needs
to have an explicit \alias entry (as in this example).
\title{Title}
Title information for the Rd file. This should be capitalized and not end in a period;
try to limit its length to at most 65 characters for widest compatibility.
Markup is supported in the text, but use of characters other than English text and
punctuation (e.g., ‘<’) may limit portability.
There must be one (and only one) \title section in a help file.
\description{...}
A short description of what the function(s) do(es) (one paragraph, a few lines only).
(If a description is too long and cannot easily be shortened, the file probably tries to
document too much at once.) This is mandatory except for package-overview files.
\usage{fun(arg1, arg2, ...)}
One or more lines showing the synopsis of the function(s) and variables documented
in the file. These are set in typewriter font. This is an R-like command.
The usage information specified should match the function definition exactly (such
that automatic checking for consistency between code and documentation is possi-
ble).
To indicate that a function can be used in several different ways, depending on the
named arguments specified, use section \details. E.g., abline.Rd contains
\details{
Typical usages are
\preformatted{abline(a, b, ...)
......
}
Use \method{generic}{class} to indicate the name of an S3 method for the generic
function generic for objects inheriting from class "class". In the printed versions,
this will come out as generic (reflecting the understanding that methods should not
be invoked directly but via method dispatch), but codoc() and other QC tools
always have access to the full name.
For example, print.ts.Rd contains
\usage{
\method{print}{ts}(x, calendar, \dots)
}
Chapter 2: Writing R documentation files 83

which will print as

Usage:

## S3 method for class 'ts':

print(x, calendar, ...)
Usage for replacement functions should be given in the style of dim(x) <- value
rather than explicitly indicating the name of the replacement function ("dim<-" in
the above). Similarly, one can use \method{generic}{class}(arglist) <- value
to indicate the usage of an S3 replacement method for the generic replacement
function "generic<-" for objects inheriting from class "class".
Usage for S3 methods for extracting or replacing parts of an object, S3 methods for
members of the Ops group, and S3 methods for user-defined (binary) infix opera-
tors (‘%xxx%’) follows the above rules, using the appropriate function names. E.g.,
Extract.factor.Rd contains
\usage{
\method{[}{factor}(x, \dots, drop = FALSE)
\method{[[}{factor}(x, \dots)
\method{[}{factor}(x, \dots) <- value
}
which will print as
Usage:

## S3 method for class 'factor':

x[..., drop = FALSE]
## S3 method for class 'factor':
x[[...]]
## S3 replacement method for class 'factor':
x[...] <- value
\S3method is accepted as an alternative to \method.
\arguments{...}
Description of the function’s arguments, using an entry of the form
\item{arg_i}{Description of arg_i.}
for each element of the argument list. (Note that there is no whitespace between
the three parts of the entry.) Arguments can also be described jointly by separating
their names with commas (and optional whitespace) in the \item label. There may
be optional text outside the \item entries, for example to give general information
about groups of parameters.
\details{...}
A detailed if possible precise description of the functionality provided, extending
the basic information in the \description slot.
\value{...}
Description of the function’s return value.
If a list with multiple values is returned, you can use entries of the form
\item{comp_i}{Description of comp_i.}
for each component of the list returned. There may be optional text outside the
\item entries (see for example the joint help for rle and inverse.rle, or the
sets of items in l10n_info). Note that \value is implicitly a \describe environ-
Chapter 2: Writing R documentation files 84

ment, so that environment should not be used for listing components, just individual
\item{}{} entries.4
\references{...}
A section with references to the literature. Use \url{} or \href{}{} for web
pointers, and \doi{} for DOIs (this needs R >= 3.3, see Section 2.13 [User-defined
macros], page 95, for more info).
\note{...}
Use this for a special note you want to have pointed out. Multiple \note sections
are allowed, but might be confusing to the end users.
For example, pie.Rd contains
\note{
Pie charts are a very bad way of displaying information.
The eye is good at judging linear measures and bad at
judging relative areas.
......
}
\author{...}
Information about the author(s) of the Rd file. Use \email{} without extra delim-
iters (such as ‘( )’ or ‘< >’) to specify email addresses, or \url{} or \href{}{} for
web pointers.
\seealso{...}
Pointers to related R objects, using \code{\link{...}} to refer to them (\code is
the correct markup for R object names, and \link produces hyperlinks in output
formats which support this. See Section 2.3 [Marking text], page 88, and Section 2.5
[Cross-references], page 90).
\examples{...}
Examples of how to use the function. Code in this section is set in typewriter font
without reformatting and is run by example() unless marked otherwise (see below).
Examples are not only useful for documentation purposes, but also provide test code
used for diagnostic checking of R code. By default, text inside \examples{} will
be displayed in the output of the help page and run by example() and by R CMD
check. You can use \dontrun{} for text that should only be shown, but not run,
and \dontshow{} for extra commands for testing that should not be shown to users,
but will be run by example(). (Previously this was called \testonly, and that is
still accepted.)
Text inside \dontrun{} is ‘verbatim’, but the other parts of the \examples section
are R-like text.
For example,
x <- runif(10) # Shown and run.
\dontrun{plot(x)} # Only shown.
\dontshow{log(x)} # Only run.
Thus, example code not included in \dontrun must be executable! In addition, it
should not use any system-specific features or require special facilities (such as In-
ternet access or write permission to specific directories). Text included in \dontrun
is indicated by comments in the processed help files: it need not be valid R code but
4
\describe can still be used for more general lists, including when \item labels need special markup such as
\var for metasyntactic variables, see Section 2.3 [Marking text], page 88.
Chapter 2: Writing R documentation files 85

the escapes must still be used for %, \ and unpaired braces as in other ‘verbatim’
text.
Example code must be capable of being run by example, which uses source. This
means that it should not access stdin, e.g. to scan() data from the example file.
Data needed for making the examples executable can be obtained by random number
generation (for example, x <- rnorm(100)), or by using standard data sets listed
by data() (see ?data for more info).
Finally, there is \donttest, used (at the beginning of a separate line) to mark
code that should be run by example() but not by R CMD check (by default:
the option --run-donttest can be used). This should be needed only occa-
sionally but can be used for code which might fail in circumstances that are
hard to test for, for example in some locales. (Use e.g. capabilities() or
nzchar(Sys.which("someprogram")) to test for features needed in the examples
wherever possible, and you can also use try() or tryCatch(). Use interactive()
to condition examples which need someone to interact with.) Note that code in-
cluded in \donttest must be correct R code, and any packages used should be
declared in the DESCRIPTION file. It is good practice to include a comment in the
\donttest section explaining why it is needed.
Output from code between comments
## IGNORE_RDIFF_BEGIN
## IGNORE_RDIFF_END
is ignored when comparing check output to reference output (a -Ex.Rout.save file).
This markup can also be used for scripts under tests.

\keyword{key}
There can be zero or more \keyword sections per file. Each \keyword section
should specify a single keyword, preferably one of the standard keywords as listed
in file KEYWORDS in the R documentation directory (default R_HOME/doc). Use e.g.
RShowDoc("KEYWORDS") to inspect the standard keywords from within R. There can
be more than one \keyword entry if the R object being documented falls into more
than one category, or none.
Do strongly consider using \concept (see Section 2.9 [Indices], page 93) instead of
\keyword if you are about to use more than very few non-standard keywords.
The special keyword ‘internal’ marks a page of internal topics (typically, objects
that are not part of the package’s API). If the help page for topic foo has keyword
‘internal’, then help(foo) gives this help page, but foo is excluded from several
topic indices, including the alphabetical list of topics in the HTML help system.
help.search() can search by keyword, including user-defined values: however the
‘Search Engine & Keywords’ HTML page accessed via help.start() provides single-
click access only to a pre-defined list of keywords.

2.1.2 Documenting data sets

The structure of Rd files which document R data sets is slightly different. Sections such as
\arguments and \value are not needed but the format and source of the data should be ex-
plained.
As an example, let us look at src/library/datasets/man/rivers.Rd which documents the
standard R data set rivers.
Chapter 2: Writing R documentation files 86


\name{rivers}
\docType{data}
\alias{rivers}
\title{Lengths of Major North American Rivers}
\description{
This data set gives the lengths (in miles) of 141 \dQuote{major}
rivers in North America, as compiled by the US Geological
Survey.
}
\usage{rivers}
\format{A vector containing 141 observations.}
\source{World Almanac and Book of Facts, 1975, page 406.}
\references{
McNeil, D. R. (1977) \emph{Interactive Data Analysis}.
New York: Wiley.
}
\keyword{datasets}

This uses the following additional markup commands.

\docType{...}
Indicates the “type” of the documentation object. Always ‘data’ for data sets, and
‘package’ for pkg-package.Rd overview files. Documentation for S4 methods and
classes uses ‘methods’ (from promptMethods()) and ‘class’ (from promptClass()).
\format{...}
A description of the format of the data set (as a vector, matrix, data frame, time
series, . . . ). For matrices and data frames this should give a description of each
column, preferably as a list or table. See Section 2.4 [Lists and tables], page 90, for
more information.
\source{...}
Details of the original source (a reference or URL, see Section 1.1.8 [Specifying
URLs], page 20). In addition, section \references could give secondary sources
and usages.
Note also that when documenting data set bar,
• The \usage entry is always bar or (for packages which do not use lazy-loading of data)
data(bar). (In particular, only document a single data object per Rd file.)
• The \keyword entry should always be ‘datasets’.
If bar is a data frame, documenting it as a data set can be initiated via prompt(bar).
Otherwise, the promptData function may be used.

2.1.3 Documenting S4 classes and methods

There are special ways to use the ‘?’ operator, namely ‘class?topic’ and ‘methods?topic’,
to access documentation for S4 classes and methods, respectively. This mechanism depends on
conventions for the topic names used in \alias entries. The topic names for S4 classes and
methods respectively are of the form
class-class
generic,signature_list-method
where signature list contains the names of the classes in the signature of the method (without
quotes) separated by ‘,’ (without whitespace), with ‘ANY’ used for arguments without an explicit
specification. E.g., ‘genericFunction-class’ is the topic name for documentation for the S4
class "genericFunction", and ‘coerce,ANY,NULL-method’ is the topic name for documentation
for the S4 method for coerce for signature c("ANY", "NULL").
Chapter 2: Writing R documentation files 87

Skeletons of documentation for S4 classes and methods can be generated by using the func-
tions promptClass() and promptMethods() from package methods. If it is necessary or desired
to provide an explicit function declaration (in a \usage section) for an S4 method (e.g., if it has
“surprising arguments” to be mentioned explicitly), one can use the special markup
\S4method{generic}{signature_list}(argument_list)
(e.g., ‘\S4method{coerce}{ANY,NULL}(from, to)’).
To make full use of the potential of the on-line documentation system, all user-visible S4
classes and methods in a package should at least have a suitable \alias entry in one of the
package’s Rd files. If a package has methods for a function defined originally somewhere else,
and does not change the underlying default method for the function, the package is responsible
for documenting the methods it creates, but not for the function itself or the default method.
An S4 replacement method is documented in the same way as an S3 one: see the description
of \method in Section 2.1.1 [Documenting functions], page 81.
See help("Documentation", package = "methods") for more information on using and cre-
ating on-line documentation for S4 classes and methods.

2.1.4 Documenting packages

Packages may have an overview help page with an \alias pkgname-package, e.g.
‘utils-package’ for the utils package, when package?pkgname will open that help page. If a
topic named pkgname does not exist in another Rd file, it is helpful to use this as an additional
\alias.
Skeletons of documentation for a package can be generated using the function
promptPackage(). If the final = TRUE argument is used, then the Rd file will be generated in
final form, containing the information that would be produced by library(help = pkgname).
Otherwise (the default) comments will be inserted giving suggestions for content.
Apart from the mandatory \name and \title and the pkgname-package alias, the only
requirement for the package overview page is that it include a \docType{package} statement.
All other content is optional. We suggest that it should be a short overview, to give a reader
unfamiliar with the package enough information to get started. More extensive documentation is
better placed into a package vignette (see Section 1.4 [Writing package vignettes], page 45) and
referenced from this page, or into individual man pages for the functions, datasets, or classes.

2.2 Sectioning
To begin a new paragraph or leave a blank line in an example, just insert an empty line (as in
(La)TEX). To break a line, use \cr.
In addition to the predefined sections (such as \description{}, \value{}, etc.), you can
“define” arbitrary ones by \section{section_title}{...}. For example
\section{Warning}{
You must not call this function unless ...
}
For consistency with the pre-assigned sections, the section name (the first argument to \section)
should be capitalized (but not all upper case) and not end in a period. Whitespace between the
first and second braced expressions is not allowed. Markup (e.g. \code) within the section title
may cause problems with the latex conversion (depending on the version of macro packages such
as ‘hyperref’) and so should be avoided.
The \subsection macro takes arguments in the same format as \section, but is used within
a section, so it may be used to nest subsections within sections or other subsections. There is
no predefined limit on the nesting level, but formatting is not designed for more than 3 levels
(i.e. subsections within subsections within sections).
Chapter 2: Writing R documentation files 88

Note that additional named sections are always inserted at a fixed position in the output
(before \note, \seealso and the examples), no matter where they appear in the input (but in
the same order amongst themselves as in the input).

2.3 Marking text

The following logical markup commands are available for emphasizing or quoting text.
\emph{text}
\strong{text}
Emphasize text using italic and bold font if possible; \strong is regarded as stronger
(more emphatic).
\bold{text}
Set text in bold font where possible.
\sQuote{text}
\dQuote{text}
Portably single or double quote text (without hard-wiring the characters used for
quotation marks).
Each of the above commands takes LATEX-like input, so other macros may be used within
text.
The following logical markup commands are available for indicating specific kinds of text.
Except as noted, these take ‘verbatim’ text input, and so other macros may not be used within
them. Some characters will need to be escaped (see Section 2.8 [Insertions], page 92).
\code{text}
Indicate text that is a literal example of a piece of an R program, e.g., a fragment of
R code or the name of an R object. Text is entered in R-like syntax, and displayed
using typewriter font where possible. Macros \var and \link are interpreted
within text.
\preformatted{text}
Indicate text that is a literal example of a piece of a program. Text is displayed
using typewriter font where possible. Formatting, e.g. line breaks, is preserved.
(Note that this includes a line break after the initial {, so typically text should start
on the same line as the command.)
Due to limitations in LATEX as of this writing, this macro may not be nested within
other markup macros other than \dQuote and \sQuote, as errors or bad formatting
may result.
\kbd{keyboard-characters}
Indicate keyboard input, using slanted typewriter font if possible, so users can
distinguish the characters they are supposed to type from computer output. Text
is entered ‘verbatim’.
\samp{text}
Indicate text that is a literal example of a sequence of characters, entered ‘verbatim’,
to be included within word-wrapped text. Displayed within single quotation marks
and using typewriter font where possible.
\verb{text}
Indicate text that is a literal example of a sequence of characters, entered ‘verbatim’.
No wrapping or reformatting will occur. Displayed using typewriter font where
possible.
Chapter 2: Writing R documentation files 89

\pkg{package_name}
Indicate the name of an R package. LATEX-like.
\file{file_name}
Indicate the name of a file. Text is LATEX-like, so backslash needs to be escaped.
Displayed using a distinct font where possible.
\email{email_address}
Indicate an electronic mail address. LATEX-like, will be rendered as a hyperlink in
HTML and PDF conversion. Displayed using typewriter font where possible.
\url{uniform_resource_locator}
Indicate a uniform resource locator (URL) for the World Wide Web. The argument
is handled as ‘verbatim’ text (with percent and braces escaped by backslash), and
rendered as a hyperlink in HTML and PDF conversion. Line feeds are removed, and
leading and trailing whitespace5 is removed. See Section 1.1.8 [Specifying URLs],
page 20.
Displayed using typewriter font where possible.
\href{uniform_resource_locator}{text}
Indicate a hyperlink to the World Wide Web. The first argument is handled as
‘verbatim’ text (with percent and braces escaped by backslash) and is used as the
URL in the hyperlink, with the second argument of LATEX-like text displayed to
the user. Line feeds are removed from the first argument, and leading and trailing
whitespace is removed.
Note that RFC3986-encoded URLs (e.g. using ‘%28VS.85%29’ in place of ‘(VS.85)’)
may not work correctly in versions of R before 3.1.3 and are best avoided—use
URLdecode() to decode them.
\var{metasyntactic_variable}
Indicate a metasyntactic variable. In most cases this will be rendered distinctly, e.g.
in italic (PDF/HTML) or wrapped in ‘<...>’ (text), but not in all6 . LATEX-like.
\env{environment_variable}
Indicate an environment variable. ‘Verbatim’. Displayed using typewriter font
where possible
\option{option}
Indicate a command-line option. ‘Verbatim’. Displayed using typewriter font
where possible.
\command{command_name}
Indicate the name of a command. LATEX-like, so \var is interpreted. Displayed
using typewriter font where possible.
\dfn{term}
Indicate the introductory or defining use of a term. LATEX-like.
\cite{reference}
Indicate a reference without a direct cross-reference via \link (see Section 2.5
[Cross-references], page 90), such as the name of a book. LATEX-like.
\acronym{acronym}
Indicate an acronym (an abbreviation written in all capital letters), such as GNU.
LATEX-like.
5
as defined by the R function trimws.
6
Currently it is rendered differently in HTML conversions, and in LATEX and text conversion outside ‘\usage’
and ‘\examples’ environments.
Chapter 2: Writing R documentation files 90

\abbr{abbr}
Indicates an abbreviation. LATEX-like.

2.4 Lists and tables

The \itemize and \enumerate commands take a single argument, within which there may be
one or more \item commands. The text following each \item is formatted as one or more para-
graphs, suitably indented and with the first paragraph marked with a bullet point (\itemize)
or a number (\enumerate).
Note that unlike argument lists, \item in these formats is followed by a space and the text
(not enclosed in braces). For example
\enumerate{
\item A database consists of one or more records, each with one or
more named fields.
\item Regular lines start with a non-whitespace character.
\item Records are separated by one or more empty lines.
}
\itemize and \enumerate commands may be nested.
The \describe command is similar to \itemize but allows initial labels to be specified.
Each \item takes two arguments, the label and the body of the item, in exactly the same way
as an argument or value \item. \describe commands are mapped to <DL> lists in HTML and
\description lists in LATEX.
Using these without any \items may cause problems with some conversions and makes little
sense.
The \tabular command takes two arguments. The first gives for each of the columns the
required alignment (‘l’ for left-justification, ‘r’ for right-justification or ‘c’ for centring.) The
second argument consists of an arbitrary number of lines separated by \cr, and with fields
separated by \tab. For example:
\tabular{rlll}{
[,1] \tab Ozone \tab numeric \tab Ozone (ppb)\cr
[,2] \tab Solar.R \tab numeric \tab Solar R (lang)\cr
[,3] \tab Wind \tab numeric \tab Wind (mph)\cr
[,4] \tab Temp \tab numeric \tab Temperature (degrees F)\cr
[,5] \tab Month \tab numeric \tab Month (1--12)\cr
[,6] \tab Day \tab numeric \tab Day of month (1--31)
}
There must be the same number of fields on each line as there are alignments in the first
argument, and they must be non-empty (but can contain only spaces). (There is no whitespace
between \tabular and the first argument, nor between the two arguments.)

2.5 Cross-references
The markup \link{foo} (usually in the combination \code{\link{foo}}) produces a hyperlink
to the help for foo. Here foo is a topic, that is the argument of \alias markup in another Rd
file (possibly in another package). Hyperlinks are supported in some of the formats to which Rd
files are converted, for example HTML and PDF, but ignored in others, e.g. the text format.
One main usage of \link is in the \seealso section of the help page, see Section 2.1 [Rd
format], page 80.
Note that whereas leading and trailing spaces are stripped when extracting a topic from a
\alias, they are not stripped when looking up the topic of a \link.
Chapter 2: Writing R documentation files 91

You can specify a link to a different topic than its name by \link[=dest]{name} which links
to topic dest with name name. This can be used to refer to the documentation for S3/4 classes,
for example \code{"\link[=abc-class]{abc}"} would be a way to refer to the documentation
of an S4 class "abc" defined in your package, and \code{"\link[=terms.object]{terms}"}
to the S3 "terms" class (in package stats). To make these easy to read in the source file,
\code{"\linkS4class{abc}"} expands to the form given above.
There are two other forms with an optional argument, specified as \link[pkg]{foo} and
\link[pkg:bar]{foo}, to link to topics foo and bar respectively in the package pkg. They
are currently only used in HTML help (and ignored for hyperlinks in LATEX conversions of help
pages). One should be careful about topics containing special characters (such as arithmetic
operators) as they may result in unresolvable links, and preferably use a safer alias in the same
help page.
Historically (before R version 4.1.0), links of the form \link[pkg]{foo} and
\link[pkg:bar]{foo} used to be interpreted as links to files foo.html and bar.html in
package pkg, respectively. For this reason, the HTML help system looks for file foo.html in
package pkg if it does not find topic foo, and then searches for the topic in other installed
packages. To test that links work both with both old and new systems, the pre-4.1.0 behaviour
can be restored by setting the environment variable _R_HELP_LINKS_TO_TOPICS_=false.
Packages referred to by these ‘other forms’ should be declared in the DESCRIPTION file, in
the ‘Depends’, ‘Imports’, ‘Suggests’ or ‘Enhances’ fields.

2.6 Mathematics
Mathematical formulae should be set beautifully for printed documentation and in
KaTeX/MathJax-enhanced HTML help (as from R 4.2.0) yet we still want something useful for
plain-text (and legacy HTML) help. To this end, the two commands \eqn{latex}{ascii} and
\deqn{latex}{ascii} are used. Whereas \eqn is used for “inline” formulae (corresponding to
TEX’s $...$), \deqn gives “displayed equations” (as in LATEX’s displaymath environment, or
TEX’s $$...$$). Both arguments are treated as ‘verbatim’ text.
Both commands can also be used as \eqn{latexascii} (only one argument) which then
is used for both latex and ascii. No whitespace is allowed between command and the first
argument, nor between the first and second arguments.
The following example is from Poisson.Rd:
\deqn{p(x) = \frac{\lambda^x e^{-\lambda}}{x!}}{%
p(x) = \lambda^x exp(-\lambda)/x!}
for \eqn{x = 0, 1, 2, \ldots}.
For the LATEX manual and in enhanced HTML help, this becomes

λx e−λ
p(x) =
x!
for x = 0, 1, 2, . . ..

In plain-text help we get


p(x) = lambda^x exp(-lambda)/x!

for x = 0, 1, 2, ....

In legacy HTML help, Greek letters (both cases) will be rendered if preceded by a backslash,
\dots and \ldots will be rendered as ellipses and \sqrt, \ge and \le as mathematical symbols.
Chapter 2: Writing R documentation files 92

Note that only basic LATEX can be used, there being no provision to specify LATEX style files,
but AMS extensions are supported as from R 4.2.2.

2.7 Figures
To include figures in help pages, use the \figure markup. There are three forms.
The two commonly used simple forms are \figure{filename} and
\figure{filename}{alternate text}. This will include a copy of the figure in ei-
ther HTML or LATEX output. In text output, the alternate text will be displayed instead.
(When the second argument is omitted, the filename will be used.) Both the filename and
the alternate text will be parsed verbatim, and should not include special characters that are
significant in HTML or LATEX.
The expert form is \figure{filename}{options: string}. (The word ‘options:’ must be
typed exactly as shown and followed by at least one space.) In this form, the string is copied
into the HTML img tag as attributes following the src attribute, or into the second argument
of the \Figure macro in LATEX, which by default is used as options to an \includegraphics
call. As it is unlikely that any single string would suffice for both display modes, the expert
form would normally be wrapped in conditionals. It is up to the author to make sure that legal
HTML/LATEX is used. For example, to include a logo in both HTML (using the simple form) and
LATEX (using the expert form), the following could be used:
\if{html}{\figure{Rlogo.svg}{options: width=100 alt="R logo"}}
\if{latex}{\figure{Rlogo.pdf}{options: width=0.5in}}
The files containing the figures should be stored in the directory man/figures. Files
with extensions .jpg, .jpeg, .pdf, .png and .svg from that directory will be copied to the
help/figures directory at install time. (Figures in PDF format will not display in most HTML
browsers, but might be the best choice in reference manuals.) Specify the filename relative to
man/figures in the \figure directive.

2.8 Insertions
Use \R for the R system itself. The \dots macro is a historical alternative to using literal ‘...’
for the dots in function argument lists; use \ldots for ellipsis dots in ordinary text.7 These
macros can be followed by {}, and should be unless followed by whitespace.
After an unescaped ‘%’, you can put your own comments regarding the help text. The rest
of the line (but not the newline at the end) will be completely disregarded. Therefore, you can
also use it to make part of the “help” invisible.
You can produce a backslash (‘\’) by escaping it by another backslash. (Note that \cr is
used for generating line breaks.)
The “comment” character ‘%’ and unpaired braces8 almost always need to be escaped by
‘\’, and ‘\\’ can be used for backslash and needs to be when there are two or more adjacent
backslashes. In R-like code quoted strings are handled slightly differently; see “Parsing Rd files”
(https://developer.r-project.org/parseRd.pdf) for details – in particular braces should
not be escaped in quoted strings.
All of ‘% { } \’ should be escaped in LATEX-like text.
Text which might need to be represented differently in different encodings should be marked
by \enc, e.g. \enc{Jöreskog}{Joreskog} (with no whitespace between the braces) where the
7
There is only a fine distinction between \dots and \ldots. It is technically incorrect to use \ldots in code
blocks and tools::checkRd will warn about this—on the other hand the current converters treat them the
same way in code blocks, and elsewhere apart from the small distinction between the two in LATEX.
8
See the examples section in the file Paren.Rd for an example.
Chapter 2: Writing R documentation files 93

first argument will be used where encodings are allowed and the second should be ASCII (and
is used for e.g. the text conversion in locales that cannot represent the encoded form). (This is
intended to be used for individual words, not whole sentences or paragraphs.)

2.9 Indices
The \alias command (see Section 2.1.1 [Documenting functions], page 81) is used to specify
the “topics” documented, which should include all R objects in a package such as functions and
variables, data sets, and S4 classes and methods (see Section 2.1.3 [Documenting S4 classes and
methods], page 86). The on-line help system searches the index data base consisting of all alias
topics.
In addition, it is possible to provide “concept index entries” using \concept, which can be
used for help.search() lookups. E.g., file cor.test.Rd in the standard package stats contains
\concept{Kendall correlation coefficient}
\concept{Pearson correlation coefficient}
\concept{Spearman correlation coefficient}
so that e.g. ??Spearman will succeed in finding the help page for the test for association between
paired samples using Spearman’s ρ.
(Note that help.search() only uses “sections” of documentation objects with no additional
markup.)
Each \concept entry should give a single index term (word or phrase), and not use any Rd
markup.
If you want to cross reference such items from other help files via \link, you need to use
\alias and not \concept.

2.10 Platform-specific documentation

Sometimes the documentation needs to differ by platform. Currently two OS-specific options
are available, ‘unix’ and ‘windows’, and lines in the help source file can be enclosed in
#ifdef OS
...
#endif
or
#ifndef OS
...
#endif
for OS-specific inclusion or exclusion. Such blocks should not be nested, and should be entirely
within a block (that, is between the opening and closing brace of a section or item), or at
top-level contain one or more complete sections.
If the differences between platforms are extensive or the R objects documented are only
relevant to one platform, platform-specific Rd files can be put in a unix or windows subdirectory.

2.11 Conditional text

Occasionally the best content for one output format is different from the best content for another.
For this situation, the \if{format}{text} or \ifelse{format}{text}{alternate} markup is
used. Here format is a comma separated list of formats in which the text should be rendered.
The alternate will be rendered if the format does not match. Both text and alternate may be
any sequence of text and markup.
Currently the following formats are recognized: example, html, latex and text. These select
output for the corresponding targets. (Note that example refers to extracted example code
Chapter 2: Writing R documentation files 94

rather than the displayed example in some other format.) Also accepted are TRUE (matching
all formats) and FALSE (matching no formats). These could be the output of the \Sexpr macro
(see Section 2.12 [Dynamic pages], page 94).
The \out{literal} macro would usually be used within the text part of
\if{format}{text}. It causes the renderer to output the literal text exactly, with
no attempt to escape special characters. For example, use the following to output the markup
necessary to display the Greek letter in LATEX or HTML, and the text string alpha in other
formats:
\ifelse{latex}{\out{$\alpha$}}{\ifelse{html}{\out{&alpha;}}{alpha}}

2.12 Dynamic pages

Two macros supporting dynamically generated man pages are \Sexpr and \RdOpts. These are
modelled after Sweave, and are intended to contain executable R expressions in the Rd file.
The main argument to \Sexpr must be valid R code that can be executed. It may also take
options in square brackets before the main argument. Depending on the options, the code may
be executed at package build time, package install time, or man page rendering time.
The options follow the same format as in Sweave, but different options are supported. Cur-
rently the allowed options and their defaults are:
• eval=TRUE Whether the R code should be evaluated.
• echo=FALSE Whether the R code should be echoed. If TRUE and
results=verbatim, a display will be given in a preformatted block. For exam-
ple, \Sexpr[echo=TRUE,results=verbatim]{ x <- 1 } will be displayed as
> x <- 1
• keep.source=TRUE Whether to keep the author’s formatting when displaying the code, or
throw it away and use a deparsed version.
• results=text How should the results be displayed? The possibilities are:
− results=text Apply as.character() to the result of the code, and insert it as a text
element.
− results=verbatim Print the results of the code just as if it was executed at the console,
and include the printed results verbatim. (Invisible results will not print.)
− results=rd The result is assumed to be a character vector containing markup to be
passed to parse_Rd(), with the result inserted in place. This could be used to insert
computed aliases, for instance. parse_Rd() is called first with fragment = FALSE to
allow a single Rd section macro to be inserted. If that fails, it is called again with
fragment = TRUE, the older behavior.
− results=hide Insert no output.
• strip.white=true Remove leading and trailing blank lines in verbatim output if
strip.white=true (or TRUE). With strip.white=all, remove all blank lines.
• stage=install Control when this macro is run. Possible values are
− stage=build The macro is run when building a source tarball.
− stage=install The macro is run when installing from source.
− stage=render The macro is run when displaying the help page.
Conditionals such as #ifdef (see Section 2.10 [Platform-specific sections], page 93) are
applied after the build macros but before the install macros. In some situations (e.g.
installing directly from a source directory without a tarball, or building a binary package)
the above description is not literally accurate, but authors can rely on the sequence being
build, #ifdef, install, render, with all stages executed.
Chapter 2: Writing R documentation files 95

Code is only run once in each stage, so a \Sexpr[results=rd] macro can output an \Sexpr
macro designed for a later stage, but not for the current one or any earlier stage.
• width, height, fig These options are currently allowed but ignored.
The \RdOpts macro is used to set new defaults for options to apply to following uses of
\Sexpr.
For more details, see the online document “Parsing Rd files” (https://developer.
r-project.org/parseRd.pdf).

2.13 User-defined macros

The \newcommand and \renewcommand macros allow new macros to be defined within an Rd
file. These are similar but not identical to the same-named LATEX macros.
They each take two arguments which are parsed verbatim. The first is the name of the
new macro including the initial backslash, and the second is the macro definition. As in
LATEX, \newcommand requires that the new macro not have been previously defined, whereas
\renewcommand allows existing macros (including all built-in ones) to be replaced. (This test
is disabled by default, but may be enabled by setting the environment variable _R_WARN_
DUPLICATE_RD_MACROS_ to a true value.)
Also as in LATEX, the new macro may be defined to take arguments, and numeric placeholders
such as #1 are used in the macro definition. However, unlike LATEX, the number of arguments
is determined automatically from the highest placeholder number seen in the macro definition.
For example, a macro definition containing #1 and #3 (but no other placeholders) will define
a three argument macro (whose second argument will be ignored). As in LATEX, at most 9
arguments may be defined. If the # character is followed by a non-digit it will have no special
significance. All arguments to user-defined macros will be parsed as verbatim text, and simple
text-substitution will be used to replace the place-holders, after which the replacement text will
be parsed.
A number of macros are defined in the file share/Rd/macros/system.Rd of the R source
or home directory, and these will normally be available in all .Rd files. For example, that file
contains the definition
\newcommand{\PR}{\Sexpr[results=rd]{tools:::Rd_expr_PR(#1)}}
which defines \PR to be a single argument macro; then code (typically used in the NEWS.Rd file)
like
\PR{1234}
will expand to
\Sexpr[results=rd]{tools:::Rd_expr_PR(1234)}
when parsed.
Some macros that might be of general use are:
\CRANpkg{pkg}
A package on CRAN
\sspace A single space (used after a period that does not end a sentence).
\doi{numbers}
A digital object identifier (DOI).
See the system.Rd file in share/Rd/macros for more details and macro definitions, includ-
ing macros \packageTitle, \packageDescription, \packageAuthor, \packageMaintainer,
\packageDESCRIPTION and \packageIndices.
Chapter 2: Writing R documentation files 96

Packages may also define their own common macros; these would be stored in an .Rd file
in man/macros in the package source and will be installed into help/macros when the package
is installed. A package may also use the macros from a different package by listing the other
package in the ‘RdMacros’ field in the DESCRIPTION file.

2.14 Encoding
Rd files are text files and so it is impossible to deduce the encoding they are written in unless
ASCII: files with 8-bit characters could be UTF-8, Latin-1, Latin-9, KOI8-R, EUC-JP, etc. So an
\encoding{} section must be used to specify the encoding if it is not ASCII. (The \encoding{}
section must be on a line by itself, and in particular one containing no non-ASCII characters.
The encoding declared in the DESCRIPTION file will be used if none is declared in the file.) The Rd
files are converted to UTF-8 before parsing and so the preferred encoding for the files themselves
is now UTF-8.
Wherever possible, avoid non-ASCII chars in Rd files, and even symbols such as ‘<’, ‘>’, ‘$’,
‘^’, ‘&’, ‘|’, ‘@’, ‘~’, and ‘*’ outside ‘verbatim’ environments (since they may disappear in fonts
designed to render text). (Function showNonASCIIfile in package tools can help in finding
non-ASCII bytes in the files.)
For convenience, encoding names ‘latin1’ and ‘latin2’ are always recognized: these and
‘UTF-8’ are likely to work fairly widely. However, this does not mean that all characters in
UTF-8 will be recognized, and the coverage of non-Latin characters9 is fairly low. Using LATEX
inputenx (see ?Rd2pdf in R) will give greater coverage of UTF-8.
The \enc command (see Section 2.8 [Insertions], page 92) can be used to provide transliter-
ations which will be used in conversions that do not support the declared encoding.
The LATEX conversion converts the file to UTF-8 from the declared encoding, and includes a
\inputencoding{utf8}
command, and this needs to be matched by a suitable invocation of the \usepackage{inputenc}
command. The R utility R CMD Rd2pdf looks at the converted code and includes the encodings
used: it might for example use
\usepackage[utf8]{inputenc}
(Use of utf8 as an encoding requires LATEX dated 2003/12/01 or later. Also, the use of Cyrillic
characters in ‘UTF-8’ appears to also need ‘\usepackage[T2A]{fontenc}’, and R CMD Rd2pdf
includes this conditionally on the file t2aenc.def being present and environment variable _R_
CYRILLIC_TEX_ being set.)
Note that this mechanism works best with Latin letters: the coverage of UTF-8 in LATEX is
quite low.

2.15 Processing documentation files

There are several commands to process Rd files from the system command line.
Using R CMD Rdconv one can convert R documentation format to other formats, or extract
the executable examples for run-time testing. The currently supported conversions are to plain
text, HTML and LATEX as well as extraction of the examples.
R CMD Rd2pdf generates PDF output from documentation in Rd files, which can be specified
either explicitly or by the path to a directory with the sources of a package. In the latter case, a
reference manual for all documented objects in the package is created, including the information
in the DESCRIPTION files.
9
R 2.9.0 added support for UTF-8 Cyrillic characters in LATEX, but on some OSes this will need Cyrillic support
added to LATEX, so environment variable _R_CYRILLIC_TEX_ may need to be set to a non-empty value to enable
this.
Chapter 2: Writing R documentation files 97

R CMD Sweave and R CMD Stangle process vignette-like documentation files (e.g. Sweave vi-
gnettes with extension ‘.Snw’ or ‘.Rnw’, or other non-Sweave vignettes). R CMD Stangle is used
to extract the R code fragments.
The exact usage and a detailed list of available options for all of these commands can be ob-
tained by running R CMD command --help, e.g., R CMD Rdconv --help. All available commands
can be listed using R --help (or Rcmd --help under Windows).
All of these work under Windows. You may need to have installed the the tools to build
packages from source as described in the “R Installation and Administration” manual, although
typically all that is needed is a LATEX installation.

2.16 Editing Rd files

It can be very helpful to prepare .Rd files using a editor which knows about their syntax and
will highlight commands, indent to show the structure and detect mis-matched braces, and so
on.
The system most commonly used for this is some version of Emacs (including XEmacs) with
the ESS package (https://ESS.R-project.org/: it is often is installed with Emacs but may
need to be loaded, or even installed, separately).
Another is the Eclipse IDE with the Stat-ET plugin (https://projects.eclipse.org/
projects/science.statet), and (on Windows only) Tinn-R (https://sourceforge.net/
projects/tinn-r/).
People have also used LATEX mode in a editor, as .Rd files are rather similar to LATEX files.
Some R front-ends provide editing support for .Rd files, for example RStudio (https://
posit.co/).
 98

3 Tidying and profiling R code

R code which is worth preserving in a package and perhaps making available for others to use
is worth documenting, tidying up and perhaps optimizing. The last two of these activities are
the subject of this chapter.

3.1 Tidying R code

R treats function code loaded from packages and code entered by users differently. By default
code entered by users has the source code stored internally, and when the function is listed, the
original source is reproduced. Loading code from a package (by default) discards the source
code, and the function listing is re-created from the parse tree of the function.
Normally keeping the source code is a good idea, and in particular it avoids comments being
removed from the source. However, we can make use of the ability to re-create a function
listing from its parse tree to produce a tidy version of the function, for example with consistent
indentation and spaces around operators. If the original source does not follow the standard
format this tidied version can be much easier to read.
We can subvert the keeping of source in two ways.
1. The option keep.source can be set to FALSE before the code is loaded into R.
2. The stored source code can be removed by calling the removeSource() function, for example
by
myfun <- removeSource(myfun)
In each case if we then list the function we will get the standard layout.
Suppose we have a file of functions myfuns.R that we want to tidy up. Create a file tidy.R
containing
source("myfuns.R", keep.source = FALSE)
dump(ls(all.names = TRUE), file = "new.myfuns.R")
and run R with this as the source file, for example by R --vanilla < tidy.R or by pasting into
an R session. Then the file new.myfuns.R will contain the functions in alphabetical order in the
standard layout. Warning: comments in your functions will be lost.
The standard format provides a good starting point for further tidying. Although the de-
parsing cannot do so, we recommend the consistent use of the preferred assignment operator ‘<-’
(rather than ‘=’) for assignment. Many package authors use a version of Emacs (on a Unix-alike
or Windows) to edit R code, using the ESS[S] mode of the ESS Emacs package. See Section “R
coding standards” in R Internals for style options within the ESS[S] mode recommended for the
source code of R itself.

3.2 Profiling R code for speed

It is possible to profile R code on Windows and most1 Unix-alike versions of R.
The command Rprof is used to control profiling, and its help page can be consulted for full
details. Profiling works by recording at fixed intervals2 (by default every 20 msecs) which line
in which R function is being used, and recording the results in a file (default Rprof.out in the
working directory). Then the function summaryRprof or the command-line utility R CMD Rprof
Rprof.out can be used to summarize the activity.
1
R has to be built to enable this, but the option --enable-R-profiling is the default.
2
For Unix-alikes by default these are intervals of CPU time, and for Windows of elapsed (‘wall-clock’) time.
As from R 4.4.0, elapsed time is optional on Unix-alikes
Chapter 3: Tidying and profiling R code 99

As an example, consider the following code (from Venables & Ripley, 2002, pp. 225–6).
library(MASS); library(boot)
storm.fm <- nls(Time ~ b*Viscosity/(Wt - c), stormer,
start = c(b=30.401, c=2.2183))
st <- cbind(stormer, fit=fitted(storm.fm))
storm.bf <- function(rs, i) {
st$Time <- st$fit + rs[i]
tmp <- nls(Time ~ (b * Viscosity)/(Wt - c), st,
start = coef(storm.fm))
tmp$m$getAllPars()
}
rs <- scale(resid(storm.fm), scale = FALSE) # remove the mean
Rprof("boot.out")
storm.boot <- boot(rs, storm.bf, R = 4999) # slow enough to profile
Rprof(NULL)
Having run this we can summarize the results by
R CMD Rprof boot.out

Each sample represents 0.02 seconds.

Total run time: 22.52 seconds.

Total seconds: time spent in function and callees.

Self seconds: time spent in function alone.

% total % self
total seconds self seconds name
100.0 25.22 0.2 0.04 "boot"
99.8 25.18 0.6 0.16 "statistic"
96.3 24.30 4.0 1.02 "nls"
33.9 8.56 2.2 0.56 "<Anonymous>"
32.4 8.18 1.4 0.36 "eval"
31.8 8.02 1.4 0.34 ".Call"
28.6 7.22 0.0 0.00 "eval.parent"
28.5 7.18 0.3 0.08 "model.frame"
28.1 7.10 3.5 0.88 "model.frame.default"
17.4 4.38 0.7 0.18 "sapply"
15.0 3.78 3.2 0.80 "nlsModel"
12.5 3.16 1.8 0.46 "lapply"
12.3 3.10 2.7 0.68 "assign"
...

% self % total
self seconds total seconds name
5.7 1.44 7.5 1.88 "inherits"
4.0 1.02 96.3 24.30 "nls"
3.6 0.92 3.6 0.92 "$"
3.5 0.88 28.1 7.10 "model.frame.default"
3.2 0.80 15.0 3.78 "nlsModel"
2.8 0.70 9.8 2.46 "qr.coef"
2.7 0.68 12.3 3.10 "assign"
2.5 0.64 2.5 0.64 ".Fortran"
2.5 0.62 7.1 1.80 "qr.default"
2.2 0.56 33.9 8.56 "<Anonymous>"
2.1 0.54 5.9 1.48 "unlist"
2.1 0.52 7.9 2.00 "FUN"
...
This often produces surprising results and can be used to identify bottlenecks or pieces of R
code that could benefit from being replaced by compiled code.
Two warnings: profiling does impose a small performance penalty, and the output files can
be very large if long runs are profiled at the default sampling interval.
Profiling short runs can sometimes give misleading results. R from time to time performs
garbage collection to reclaim unused memory, and this takes an appreciable amount of time
Chapter 3: Tidying and profiling R code 100

which profiling will charge to whichever function happens to provoke it. It may be useful to
compare profiling code immediately after a call to gc() with a profiling run without a preceding
call to gc.
More detailed analysis of the output can be achieved by the tools in the CRAN packages
proftools (https://CRAN.R-project.org/package=proftools) and profr (https://CRAN.
R-project.org/package=profr): in particular these allow call graphs to be studied.

3.3 Profiling R code for memory use

Measuring memory use in R code is useful either when the code takes more memory than is
conveniently available or when memory allocation and copying of objects is responsible for slow
code. There are three ways to profile memory use over time in R code. The second and third
require R to have been compiled with --enable-memory-profiling, which is not the default,
but is currently used for the macOS and Windows binary distributions. All can be misleading,
for different reasons.
In understanding the memory profiles it is useful to know a little more about R’s memory
allocation. Looking at the results of gc() shows a division of memory into Vcells used to store
the contents of vectors and Ncells used to store everything else, including all the administrative
overhead for vectors such as type and length information. In fact the vector contents are divided
into two pools. Memory for small vectors (by default 128 bytes or less) is obtained in large chunks
and then parcelled out by R; memory for larger vectors is obtained directly from the operating
system.
Some memory allocation is obvious in interpreted code, for example,
y <- x + 1
allocates memory for a new vector y. Other memory allocation is less obvious and occurs because
R is forced to make good on its promise of ‘call-by-value’ argument passing. When an argument
is passed to a function it is not immediately copied. Copying occurs (if necessary) only when
the argument is modified. This can lead to surprising memory use. For example, in the ‘survey’
package we have
print.svycoxph <- function (x, ...)
{
print(x$survey.design, varnames = FALSE, design.summaries = FALSE, ...)
x$call <- x$printcall
NextMethod()
}
It may not be obvious that the assignment to x$call will cause the entire object x to be copied.
This copying to preserve the call-by-value illusion is usually done by the internal C function
duplicate.
The main reason that memory-use profiling is difficult is garbage collection. Memory is
allocated at well-defined times in an R program, but is freed whenever the garbage collector
happens to run.

3.3.1 Memory statistics from Rprof

The sampling profiler Rprof described in the previous section can be given the option
memory.profiling=TRUE. It then writes out the total R memory allocation in small vectors,
large vectors, and cons cells or nodes at each sampling interval. It also writes out the number
of calls to the internal function duplicate, which is called to copy R objects. summaryRprof
provides summaries of this information. The main reason that this can be misleading is that
the memory use is attributed to the function running at the end of the sampling interval. A
second reason is that garbage collection can make the amount of memory in use decrease, so a
function appears to use little memory. Running under gctorture helps with both problems: it
Chapter 3: Tidying and profiling R code 101

slows down the code to effectively increase the sampling frequency and it makes each garbage
collection release a smaller amount of memory.

3.3.2 Tracking memory allocations

The second method of memory profiling uses a memory-allocation profiler, Rprofmem(), which
writes out a stack trace to an output file every time a large vector is allocated (with a user-
specified threshold for ‘large’) or a new page of memory is allocated for the R heap. Summary
functions for this output are still being designed.
Running the example from the previous section with
> Rprofmem("boot.memprof",threshold=1000)
> storm.boot <- boot(rs, storm.bf, R = 4999)
> Rprofmem(NULL)
shows that apart from some initial and final work in boot there are no vector allocations over
1000 bytes.

3.3.3 Tracing copies of an object

The third method of memory profiling involves tracing copies made of a specific (presumably
large) R object. Calling tracemem on an object marks it so that a message is printed to standard
output when the object is copied via duplicate or coercion to another type, or when a new
object of the same size is created in arithmetic operations. The main reason that this can be
misleading is that copying of subsets or components of an object is not tracked. It may be
helpful to use tracemem on these components.
In the example above we can run tracemem on the data frame st
> tracemem(st)
[1] "<0x9abd5e0>"
> storm.boot <- boot(rs, storm.bf, R = 4)
memtrace[0x9abd5e0->0x92a6d08]: statistic boot
memtrace[0x92a6d08->0x92a6d80]: $<-.data.frame $<- statistic boot
memtrace[0x92a6d80->0x92a6df8]: $<-.data.frame $<- statistic boot
memtrace[0x9abd5e0->0x9271318]: statistic boot
memtrace[0x9271318->0x9271390]: $<-.data.frame $<- statistic boot
memtrace[0x9271390->0x9271408]: $<-.data.frame $<- statistic boot
memtrace[0x9abd5e0->0x914f558]: statistic boot
memtrace[0x914f558->0x914f5f8]: $<-.data.frame $<- statistic boot
memtrace[0x914f5f8->0x914f670]: $<-.data.frame $<- statistic boot
memtrace[0x9abd5e0->0x972cbf0]: statistic boot
memtrace[0x972cbf0->0x972cc68]: $<-.data.frame $<- statistic boot
memtrace[0x972cc68->0x972cd08]: $<-.data.frame $<- statistic boot
memtrace[0x9abd5e0->0x98ead98]: statistic boot
memtrace[0x98ead98->0x98eae10]: $<-.data.frame $<- statistic boot
memtrace[0x98eae10->0x98eae88]: $<-.data.frame $<- statistic boot
The object is duplicated fifteen times, three times for each of the R+1 calls to storm.bf. This
is surprising, since none of the duplications happen inside nls. Stepping through storm.bf in
the debugger shows that all three happen in the line
st$Time <- st$fit + rs[i]
Data frames are slower than matrices and this is an example of why. Using
tracemem(st$Viscosity) does not reveal any additional copying.

3.4 Profiling compiled code

Profiling compiled code is highly system-specific, but this section contains some hints gleaned
from various R users. Some methods need to be different for a compiled executable and for
dynamic/shared libraries/objects as used by R packages.
This chapter is based on reports from users and the information may not be current.
Chapter 3: Tidying and profiling R code 102

3.4.1 Profiling on Linux

Options include using sprof for a shared object, and oprofile (see https://oprofile.
sourceforge.io/news/) and perf (see https://perf.wiki.kernel.org/index.php/
Tutorial) for any executable or shared object. These seem less widely supplied than they used
to be. There is also ‘Google Performance Tools’, also known as gperftools or google-perftools.
All of these work best when R and any packages have been built with debugging symbols.

3.4.1.1 perf
This seems the most widely distributed tool. Here is an example on x86_64 Linux using R 4.3.1
built with LTO.
At its simplest
perf record R -f tests/Examples/stats-Ex.R
perf report --sort=dso
perf report --sort=srcfile
rm perf.data*
The first report is
75.67% R
9.25% libc.so.6
4.87% [unknown]
3.75% libz.so.1.2.11
3.37% stats.so
1.17% libm.so.6
0.63% libtirpc.so.3.0.0
0.41% graphics.so
0.30% grDevices.so
0.20% libRblas.so
0.09% libpcre2-8.so.0.11.0
0.07% methods.so
...
which shows which shared libraries (DSOs) the time was spent in.
perf annotate can be used on an application built with GCC and -ggdb: it interleaves
disassembled and source code.

3.4.1.2 oprofile and operf

The oprofile project has two modes of operation. Since version 0.9.8 (August 2012), the
preferred mode is to use operf, so we discuss only that.
Let us look at the boot example from §3.2 on x86_64 Linux using R 4.3.1.
This can be run under operf and analysed by commands like
operf R -f boot.R
opreport
opreport -l /path/to/R_HOME/bin/exec/R
opreport -l /path/to/R_HOME/library/stats/src/stats.so
opannotate --source /path/to/R_HOME/bin/exec/R
The first line had to be done as root.
The first report shows in which library (etc) the time was spent:
CPU_CLK_UNHALT...|
samples| %|
------------------
Chapter 3: Tidying and profiling R code 103

278341 91.9947 R
18290 6.0450 libc.so.6
2277 0.7526 kallsyms
1426 0.4713 stats.so
739 0.2442 libRblas.so
554 0.1831 libz.so.1.2.11
373 0.1233 libm.so.6
352 0.1163 libtirpc.so.3.0.0
153 0.0506 ld-linux-x86-64.so.2
12 0.0040 methods.so
(kallsyms is the kernel.)
The rest of the output is voluminous, and only extracts are shown.
Most of the time within R is spent in
samples % image name symbol name
52955 19.0574 R bcEval.lto_priv.0
16484 5.9322 R Rf_allocVector3
14224 5.1189 R Rf_findVarInFrame3
12581 4.5276 R CONS_NR
8289 2.9830 R Rf_matchArgs_NR
8034 2.8913 R Rf_cons
7114 2.5602 R R_gc_internal.lto_priv.0
6552 2.3579 R Rf_eval
5969 2.1481 R VECTOR_ELT
5684 2.0456 R Rf_applyClosure
5497 1.9783 R findVarLocInFrame.part.0.lto_priv.0
4827 1.7371 R Rf_mkPROMISE
4609 1.6587 R Rf_install
4317 1.5536 R Rf_findFun3
4035 1.4521 R getvar.lto_priv.0
3491 1.2563 R SETCAR
3179 1.1441 R Rf_defineVar
2892 1.0408 R duplicate1.lto_priv.0
and in stats.so
samples % image name symbol name
285 24.4845 stats.so termsform
284 24.3986 stats.so numeric_deriv
213 18.2990 stats.so modelframe
114 9.7938 stats.so nls_iter
55 4.7251 stats.so ExtractVars
47 4.0378 stats.so EncodeVars
37 3.1787 stats.so getListElement
32 2.7491 stats.so TrimRepeats
25 2.1478 stats.so InstallVar
20 1.7182 stats.so MatchVar
20 1.7182 stats.so isZeroOne
15 1.2887 stats.so ConvInfoMsg.isra.0
The profiling data is by default stored in sub-directory oprofile_data of the current direc-
tory, which can be removed at the end of the session.
Chapter 3: Tidying and profiling R code 104

3.4.1.3 sprof
You can select shared objects to be profiled with sprof by setting the environment variable
LD_PROFILE. For example
% setenv LD_PROFILE /path/to/R_HOME/library/stats/libs/stats.so
% R -f boot.R
% sprof /path/to/R_HOME/library/stats/libs/stats.so \
/var/tmp/path/to/R_HOME/library/stats/libs/stats.so.profile

Flat profile:

Each sample counts as 0.01 seconds.

% cumulative self self total
time seconds seconds calls us/call us/call name
76.19 0.32 0.32 0 0.00 numeric_deriv
16.67 0.39 0.07 0 0.00 nls_iter
7.14 0.42 0.03 0 0.00 getListElement

... to clean up ...

rm /var/tmp/path/to/R_HOME/library/stats/libs/stats.so.profile
It is possible that root access will be needed to create the directories used for the profile data.

3.4.2 Profiling on macOS

Developers have recommended Instruments (part of Xcode, see https://help.apple.com/
instruments/mac/current/), This had a command-line version prior to macOS 12.

3.4.3 Profiling on Windows

Very Sleepy (https://github.com/VerySleepy/verysleepy) has been used. There were
problems with accessing the debug information, but the best results which included function
names were obtained by attaching the profiler to an existing Rterm process, either via GUI or
using /a: (PID obtained via Sys.getpid()).
 105

4 Debugging
This chapter covers the debugging of R extensions, starting with the ways to get useful error
information and moving on to how to deal with errors that crash R.

4.1 Browsing
Most of the R-level debugging facilities are based around the built-in browser. This can be
used directly by inserting a call to browser() into the code of a function (for example, using
fix(my_function) ). When code execution reaches that point in the function, control returns
to the R console with a special prompt. For example
> fix(summary.data.frame) ## insert browser() call after for() loop
> summary(women)
Called from: summary.data.frame(women)
Browse[1]> ls()
[1] "digits" "i" "lbs" "lw" "maxsum" "nm" "nr" "nv"
[9] "object" "sms" "z"
Browse[1]> maxsum
[1] 7
Browse[1]>
height weight
Min. :58.0 Min. :115.0
1st Qu.:61.5 1st Qu.:124.5
Median :65.0 Median :135.0
Mean :65.0 Mean :136.7
3rd Qu.:68.5 3rd Qu.:148.0
Max. :72.0 Max. :164.0
> rm(summary.data.frame)
At the browser prompt one can enter any R expression, so for example ls() lists the objects in
the current frame, and entering the name of an object will1 print it. The following commands
are also accepted
• n
Enter ‘step-through’ mode. In this mode, hitting return executes the next line of code
(more precisely one line and any continuation lines). Typing c will continue to the end of
the current context, e.g. to the end of the current loop or function.
• c
In normal mode, this quits the browser and continues execution, and just return works in
the same way. cont is a synonym.
• where
This prints the call stack. For example
> summary(women)
Called from: summary.data.frame(women)
Browse[1]> where
where 1: summary.data.frame(women)
where 2: summary(women)

Browse[1]>
1
With the exceptions of the commands listed below: an object of such a name can be printed via an explicit
call to print.
Chapter 4: Debugging 106

• Q
Quit both the browser and the current expression, and return to the top-level prompt.
Errors in code executed at the browser prompt will normally return control to the browser
prompt. Objects can be altered by assignment, and will keep their changed values when the
browser is exited. If really necessary, objects can be assigned to the workspace from the browser
prompt (by using <<- if the name is not already in scope).

4.2 Debugging R code

Suppose your R program gives an error message. The first thing to find out is what R was doing
at the time of the error, and the most useful tool is traceback(). We suggest that this is run
whenever the cause of the error is not immediately obvious. Errors are often reported to the R
mailing lists as being in some package when traceback() would show that the error was being
reported by some other package or base R. Here is an example from the regression suite.
> success <- c(13,12,11,14,14,11,13,11,12)
> failure <- c(0,0,0,0,0,0,0,2,2)
> resp <- cbind(success, failure)
> predictor <- c(0, 5^(0:7))
> glm(resp ~ 0+predictor, family = binomial(link="log"))
Error: no valid set of coefficients has been found: please supply starting values
> traceback()
3: stop("no valid set of coefficients has been found: please supply
starting values", call. = FALSE)
2: glm.fit(x = X, y = Y, weights = weights, start = start, etastart = etastart,
mustart = mustart, offset = offset, family = family, control = control,
intercept = attr(mt, "intercept") > 0)
1: glm(resp ~ 0 + predictor, family = binomial(link ="log"))
The calls to the active frames are given in reverse order (starting with the innermost). So we
see the error message comes from an explicit check in glm.fit. (traceback() shows you all the
lines of the function calls, which can be limited by setting option "deparse.max.lines".)
Sometimes the traceback will indicate that the error was detected inside compiled code, for
example (from ?nls)
Error in nls(y ~ a + b * x, start = list(a = 0.12345, b = 0.54321), trace = TRUE) :
step factor 0.000488281 reduced below 'minFactor' of 0.000976563
> traceback()
2: .Call(R_nls_iter, m, ctrl, trace)
1: nls(y ~ a + b * x, start = list(a = 0.12345, b = 0.54321), trace = TRUE)
This will be the case if the innermost call is to .C, .Fortran, .Call, .External or .Internal,
but as it is also possible for such code to evaluate R expressions, this need not be the innermost
call, as in
> traceback()
9: gm(a, b, x)
8: .Call(R_numeric_deriv, expr, theta, rho, dir)
7: numericDeriv(form[[3]], names(ind), env)
6: getRHS()
5: assign("rhs", getRHS(), envir = thisEnv)
4: assign("resid", .swts * (lhs - assign("rhs", getRHS(), envir = thisEnv)),
envir = thisEnv)
3: function (newPars)
{
setPars(newPars)
assign("resid", .swts * (lhs - assign("rhs", getRHS(), envir = thisEnv)),
envir = thisEnv)
assign("dev", sum(resid^2), envir = thisEnv)
assign("QR", qr(.swts * attr(rhs, "gradient")), envir = thisEnv)
return(QR$rank < min(dim(QR$qr)))
}(c(-0.00760232418963883, 1.00119632515036))
Chapter 4: Debugging 107

2: .Call(R_nls_iter, m, ctrl, trace)

1: nls(yeps ~ gm(a, b, x), start = list(a = 0.12345, b = 0.54321))
Occasionally traceback() does not help, and this can be the case if S4 method dispatch is
involved. Consider the following example
> xyd <- new("xyloc", x=runif(20), y=runif(20))
Error in as.environment(pkg) : no item called "package:S4nswv"
on the search list
Error in initialize(value, ...) : S language method selection got
an error when called from internal dispatch for function 'initialize'
> traceback()
2: initialize(value, ...)
1: new("xyloc", x = runif(20), y = runif(20))
which does not help much, as there is no call to as.environment in initialize (and the note
“called from internal dispatch” tells us so). In this case we searched the R sources for the quoted
call, which occurred in only one place, methods:::.asEnvironmentPackage. So now we knew
where the error was occurring. (This was an unusually opaque example.)
The error message
evaluation nested too deeply: infinite recursion / options(expressions=)?
can be hard to handle with the default value (5000). Unless you know that there actually is
deep recursion going on, it can help to set something like
options(expressions=500)
and re-run the example showing the error.
Sometimes there is warning that clearly is the precursor to some later error, but it is not
obvious where it is coming from. Setting options(warn = 2) (which turns warnings into errors)
can help here.
Once we have located the error, we have some choices. One way to proceed is to find out
more about what was happening at the time of the crash by looking a post-mortem dump. To
do so, set options(error=dump.frames) and run the code again. Then invoke debugger() and
explore the dump. Continuing our example:
> options(error = dump.frames)
> glm(resp ~ 0 + predictor, family = binomial(link ="log"))
Error: no valid set of coefficients has been found: please supply starting values
which is the same as before, but an object called last.dump has appeared in the workspace.
(Such objects can be large, so remove it when it is no longer needed.) We can examine this at
a later time by calling the function debugger.
> debugger()
Message: Error: no valid set of coefficients has been found: please supply starting values
Available environments had calls:
1: glm(resp ~ 0 + predictor, family = binomial(link = "log"))
2: glm.fit(x = X, y = Y, weights = weights, start = start, etastart = etastart, mus
3: stop("no valid set of coefficients has been found: please supply starting values
Enter an environment number, or 0 to exit Selection:
which gives the same sequence of calls as traceback, but in outer-first order and with only the
first line of the call, truncated to the current width. However, we can now examine in more
detail what was happening at the time of the error. Selecting an environment opens the browser
in that frame. So we select the function call which spawned the error message, and explore some
of the variables (and execute two function calls).
Enter an environment number, or 0 to exit Selection: 2
Browsing in the environment with call:
glm.fit(x = X, y = Y, weights = weights, start = start, etas
Called from: debugger.look(ind)
Browse[1]> ls()
Chapter 4: Debugging 108

[1] "aic" "boundary" "coefold" "control" "conv"

[6] "dev" "dev.resids" "devold" "EMPTY" "eta"
[11] "etastart" "family" "fit" "good" "intercept"
[16] "iter" "linkinv" "mu" "mu.eta" "mu.eta.val"
[21] "mustart" "n" "ngoodobs" "nobs" "nvars"
[26] "offset" "start" "valideta" "validmu" "variance"
[31] "varmu" "w" "weights" "x" "xnames"
[36] "y" "ynames" "z"
Browse[1]> eta
1 2 3 4 5
0.000000e+00 -2.235357e-06 -1.117679e-05 -5.588393e-05 -2.794197e-04
6 7 8 9
-1.397098e-03 -6.985492e-03 -3.492746e-02 -1.746373e-01
Browse[1]> valideta(eta)
[1] TRUE
Browse[1]> mu
1 2 3 4 5 6 7 8
1.0000000 0.9999978 0.9999888 0.9999441 0.9997206 0.9986039 0.9930389 0.9656755
9
0.8397616
Browse[1]> validmu(mu)
[1] FALSE
Browse[1]> c
Available environments had calls:
1: glm(resp ~ 0 + predictor, family = binomial(link = "log"))
2: glm.fit(x = X, y = Y, weights = weights, start = start, etastart = etastart
3: stop("no valid set of coefficients has been found: please supply starting v

Enter an environment number, or 0 to exit Selection: 0

> rm(last.dump)
Because last.dump can be looked at later or even in another R session, post-mortem debug-
ging is possible even for batch usage of R. We do need to arrange for the dump to be saved: this
can be done either using the command-line flag --save to save the workspace at the end of the
run, or via a setting such as
> options(error = quote({dump.frames(to.file=TRUE); q()}))
See the help on dump.frames for further options and a worked example.
An alternative error action is to use the function recover():
> options(error = recover)
> glm(resp ~ 0 + predictor, family = binomial(link = "log"))
Error: no valid set of coefficients has been found: please supply starting values

Enter a frame number, or 0 to exit

1: glm(resp ~ 0 + predictor, family = binomial(link = "log"))

2: glm.fit(x = X, y = Y, weights = weights, start = start, etastart = etastart

Selection:
which is very similar to dump.frames. However, we can examine the state of the program
directly, without dumping and re-loading the dump. As its help page says, recover can be
routinely used as the error action in place of dump.calls and dump.frames, since it behaves
like dump.frames in non-interactive use.
Post-mortem debugging is good for finding out exactly what went wrong, but not necessarily
why. An alternative approach is to take a closer look at what was happening just before the
error, and a good way to do that is to use debug. This inserts a call to the browser at the
beginning of the function, starting in step-through mode. So in our example we could use
> debug(glm.fit)
> glm(resp ~ 0 + predictor, family = binomial(link ="log"))
debugging in: glm.fit(x = X, y = Y, weights = weights, start = start, etastart = etastart,
mustart = mustart, offset = offset, family = family, control = control,
Chapter 4: Debugging 109

intercept = attr(mt, "intercept") > 0)

debug: {
## lists the whole function
Browse[1]>
debug: x <- as.matrix(x)
...
Browse[1]> start
[1] -2.235357e-06
debug: eta <- drop(x %*% start)
Browse[1]> eta
1 2 3 4 5
0.000000e+00 -2.235357e-06 -1.117679e-05 -5.588393e-05 -2.794197e-04
6 7 8 9
-1.397098e-03 -6.985492e-03 -3.492746e-02 -1.746373e-01
Browse[1]>
debug: mu <- linkinv(eta <- eta + offset)
Browse[1]> mu
1 2 3 4 5 6 7 8
1.0000000 0.9999978 0.9999888 0.9999441 0.9997206 0.9986039 0.9930389 0.9656755
9
0.8397616
(The prompt Browse[1]> indicates that this is the first level of browsing: it is possible to step
into another function that is itself being debugged or contains a call to browser().)
debug can be used for hidden functions and S3 methods by e.g.
debug(stats:::predict.Arima). (It cannot be used for S4 methods, but an alter-
native is given on the help page for debug.) Sometimes you want to debug a function defined
inside another function, e.g. the function arimafn defined inside arima. To do so, set debug on
the outer function (here arima) and step through it until the inner function has been defined.
Then call debug on the inner function (and use c to get out of step-through mode in the outer
function).
To remove debugging of a function, call undebug with the argument previously given to
debug; debugging otherwise lasts for the rest of the R session (or until the function is edited or
otherwise replaced).
trace can be used to temporarily insert debugging code into a function, for example to insert
a call to browser() just before the point of the error. To return to our running example
## first get a numbered listing of the expressions of the function
> page(as.list(body(glm.fit)), method="print")
> trace(glm.fit, browser, at=22)
Tracing function "glm.fit" in package "stats"
[1] "glm.fit"
> glm(resp ~ 0 + predictor, family = binomial(link ="log"))
Tracing glm.fit(x = X, y = Y, weights = weights, start = start,
etastart = etastart, .... step 22
Called from: eval(expr, envir, enclos)
Browse[1]> n
## and single-step from here.
> untrace(glm.fit)
For your own functions, it may be as easy to use fix to insert temporary code, but trace can help
with functions in a namespace (as can fixInNamespace). Alternatively, use trace(,edit=TRUE)
to insert code visually.

4.3 Checking memory access

Errors in memory allocation and reading/writing outside arrays are very common causes of
crashes (e.g., segfaults) on some machines. Often the crash appears long after the invalid memory
Chapter 4: Debugging 110

access: in particular damage to the structures which R itself has allocated may only become
apparent at the next garbage collection (or even at later garbage collections after objects have
been deleted).
Note that memory access errors may be seen with LAPACK, BLAS, OpenMP and Java-
using packages: some at least of these seem to be intentional, and some are related to passing
characters to Fortran.
Some of these tools can detect mismatched allocation and deallocation. C++ programmers
should note that memory allocated by new [] must be freed by delete [], other uses of new by
delete, and memory allocated by malloc, calloc and realloc by free. Some platforms will
tolerate mismatches (perhaps with memory leaks) but others will segfault.

4.3.1 Using gctorture

We can help to detect memory problems in R objects earlier by running garbage collection as
often as possible. This is achieved by gctorture(TRUE), which as described on its help page
Provokes garbage collection on (nearly) every memory allocation. Intended to ferret
out memory protection bugs. Also makes R run very slowly, unfortunately.
The reference to ‘memory protection’ is to missing C-level calls to PROTECT/UNPROTECT (see
Section 5.9.1 [Garbage Collection], page 141) which if missing allow R objects to be garbage-
collected when they are still in use. But it can also help with other memory-related errors.
Normally running under gctorture(TRUE) will just produce a crash earlier in the R program,
hopefully close to the actual cause. See the next section for how to decipher such crashes.
It is possible to run all the examples, tests and vignettes covered by R CMD check under
gctorture(TRUE) by using the option --use-gct.
The function gctorture2 provides more refined control over the GC torture process. Its
arguments step, wait and inhibit_release are documented on its help page. Environment
variables can also be used at the start of the R session to turn on GC torture: R_GCTORTURE cor-
responds to the step argument to gctorture2, R_GCTORTURE_WAIT to wait, and R_GCTORTURE_
INHIBIT_RELEASE to inhibit_release.
If R is configured with --enable-strict-barrier then a variety of tests for the integrity of
the write barrier are enabled. In addition tests to help detect protect issues are enabled:
• All GCs are full GCs.
• New nodes in small node pages are marked as NEWSXP on creation.
• After a GC all free nodes that are not of type NEWSXP are marked as type FREESXP and
their previous type is recorded.
• Most calls to accessor functions check their SEXP inputs and SEXP outputs and signal an
error if a FREESXP is found. The address of the node and the old type are included in the
error message.
R CMD check --use-gct can be set to use gctorture2(n) rather than gctorture(TRUE) by
setting environment variable _R_CHECK_GCT_N_ to a positive integer value to be used as n.
Used with a debugger and with gctorture or gctorture2 this mechanism can be helpful in
isolating memory protect problems.

4.3.2 Using valgrind

If you have access to Linux on a common CPU type or supported versions of FreeBSD or Solaris2
you can use valgrind (https://valgrind.org/, pronounced to rhyme with ‘tinned’) to check
for possible problems. To run some examples under valgrind use something like
R -d valgrind --vanilla < mypkg-Ex.R
2
The macOS support is for long-obsolete versions.
Chapter 4: Debugging 111

R -d "valgrind --tool=memcheck --leak-check=full" --vanilla < mypkg-Ex.R

where mypkg-Ex.R is a set of examples, e.g. the file created in mypkg.Rcheck by R CMD check.
Occasionally this reports memory reads of ‘uninitialised values’ that are the result of compiler
optimization, so can be worth checking under an unoptimized compile: for maximal information
use a build with debugging symbols. We know there will be some small memory leaks from
readline and R itself — these are memory areas that are in use right up to the end of the R
session. Expect this to run around 20x slower than without valgrind, and in some cases much
slower than that. Several versions of valgrind were not happy with some optimized BLAS
libraries that use CPU-specific instructions so you may need to build a version of R specifically
to use with valgrind.
On platforms where valgrind and its headers3 are installed you can build a version of R
with extra instrumentation to help valgrind detect errors in the use of memory allocated from
the R heap. The configure option is --with-valgrind-instrumentation=level, where level
is 0, 1 or 2. Level 0 is the default and does not add anything. Level 1 will detect some uses4 of
uninitialised memory and has little impact on speed (compared to level 0). Level 2 will detect
many other memory-use bugs5 but make R much slower when running under valgrind. Using
this in conjunction with gctorture can be even more effective (and even slower).
An example of valgrind output is
==12539== Invalid read of size 4
==12539== at 0x1CDF6CBE: csc_compTr (Mutils.c:273)
==12539== by 0x1CE07E1E: tsc_transpose (dtCMatrix.c:25)
==12539== by 0x80A67A7: do_dotcall (dotcode.c:858)
==12539== by 0x80CACE2: Rf_eval (eval.c:400)
==12539== by 0x80CB5AF: R_execClosure (eval.c:658)
==12539== by 0x80CB98E: R_execMethod (eval.c:760)
==12539== by 0x1B93DEFA: R_standardGeneric (methods_list_dispatch.c:624)
==12539== by 0x810262E: do_standardGeneric (objects.c:1012)
==12539== by 0x80CAD23: Rf_eval (eval.c:403)
==12539== by 0x80CB2F0: Rf_applyClosure (eval.c:573)
==12539== by 0x80CADCC: Rf_eval (eval.c:414)
==12539== by 0x80CAA03: Rf_eval (eval.c:362)
==12539== Address 0x1C0D2EA8 is 280 bytes inside a block of size 1996 alloc'd
==12539== at 0x1B9008D1: malloc (vg_replace_malloc.c:149)
==12539== by 0x80F1B34: GetNewPage (memory.c:610)
==12539== by 0x80F7515: Rf_allocVector (memory.c:1915)
...

This example is from an instrumented version of R, while tracking down a bug in the Matrix
(https://CRAN.R-project.org/package=Matrix) package in 2006. The first line indicates that
R has tried to read 4 bytes from a memory address that it does not have access to. This is fol-
lowed by a C stack trace showing where the error occurred. Next is a description of the memory
that was accessed. It is inside a block allocated by malloc, called from GetNewPage, that is,
in the internal R heap. Since this memory all belongs to R, valgrind would not (and did not)
detect the problem in an uninstrumented build of R. In this example the stack trace was enough
to isolate and fix the bug, which was in tsc_transpose, and in this example running under
gctorture() did not provide any additional information.
valgrind is good at spotting the use of uninitialized values: use option --track-
origins=yes to show where these originated from. What it cannot detect is the misuse of
arrays allocated on the stack: this includes C automatic variables and some6 Fortran arrays.

3
in some distributions packaged separately, for example as valgrind-devel.
4
Those in some numeric, logical, integer, raw, complex vectors and in memory allocated by R_alloc.
5
including using the data sections of R vectors after they are freed.
6
small fixed-size arrays by default in gfortran, for example.
Chapter 4: Debugging 112

It is possible to run all the examples, tests and vignettes covered by R CMD check under
valgrind by using the option --use-valgrind. If you do this you will need to select the
valgrind options some other way, for example by having a ~/.valgrindrc file containing
--leak-check=full
--track-origins=yes
or setting the environment variable VALGRIND_OPTS. As from R 4.2.0, --use-valgrind also uses
valgrind when re-building the vignettes.
This section has described the use of memtest, the default (and most useful) of valgrind’s
tools. There are others described in its documentation: helgrind can be useful for threaded
programs.

4.3.3 Using the Address Sanitizer

AddressSanitizer (‘ASan’) is a tool with similar aims to the memory checker in valgrind. It
is available with suitable builds7 of gcc and clang on common Linux and macOS platforms.
See https://clang.llvm.org/docs/UsersManual.html#controlling-code-generation,
https://clang.llvm.org/docs/AddressSanitizer.html and https://github.com/google/
sanitizers.
More thorough checks of C++ code are done if the C++ library has been ‘annotated’: at the
time of writing this applied to std::vector in libc++ for use with clang and gives rise to
‘container-overflow’8 reports.
It requires code to have been compiled and linked with -fsanitize=address and compiling
with -fno-omit-frame-pointer will give more legible reports. It has a runtime penalty of 2–3x,
extended compilation times and uses substantially more memory, often 1–2GB, at run time. On
64-bit platforms it reserves (but does not allocate) 16–20TB of virtual memory: restrictive shell
settings can cause problems. It can be helpful to increase the stack size, for example to 40MB.
By comparison with valgrind, ASan can detect misuse of stack and global variables but not
the use of uninitialized memory.
Recent versions return symbolic addresses for the location of the error provided llvm-
symbolizer9 is on the path: if it is available but not on the path or has been renamed10 ,
one can use an environment variable, e.g.
ASAN_SYMBOLIZER_PATH=/path/to/llvm-symbolizer
An alternative is to pipe the output through asan_symbolize.py11 and perhaps then (for com-
piled C++ code) c++filt. (On macOS, you may need to run dsymutil to get line-number
reports.)
The simplest way to make use of this is to build a version of R with something like
CC="gcc -std=gnu99 -fsanitize=address"
CFLAGS="-fno-omit-frame-pointer -g -O2 -Wall -pedantic -mtune=native"

7
currently on ‘x86_64’/‘ix86’ Linux and FreeBSD, with some support for Intel macOS but not with the
toolchain normally used with R. (There is a faster variant, HWASAN, for ‘aarch64’ only.) On some platforms
the runtime library, libasan, needs to be installed separately, and for checking C++ you may also need libubsan.
8
see https://llvm.org/devmtg/2014-04/PDFs/LightningTalks/EuroLLVM%202014%20--%20container%20overflow.
pdf.
9
part of the LLVM project and distributed in llvm RPMs and .debs on Linux. It is not currently shipped by
Apple.
10
as Ubuntu has been said to do.
11
installed on some Linux systems as asan_symbolize, and obtainable from https://github.com/
llvm/llvm-project/blob/main/compiler-rt/lib/asan/scripts/asan_symbolize.py: it makes use of llvm-
symbolizer if available.
Chapter 4: Debugging 113

which will ensure that the libasan run-time library is compiled into the R executable. However
this check can be enabled on a per-package basis by using a ~/.R/Makevars file like
CC = gcc -std=gnu99 -fsanitize=address -fno-omit-frame-pointer
CXX = g++ -fsanitize=address -fno-omit-frame-pointer
FC = gfortran -fsanitize=address
(Note that -fsanitize=address has to be part of the compiler specification to ensure it is used
for linking. These settings will not be honoured by packages which ignore ~/.R/Makevars.) It
will be necessary to build R with
MAIN_LDFLAGS = -fsanitize=address
to link the runtime libraries into the R executable if it was not specified as part of ‘CC’ when R
was built. (For some builds without OpenMP, -pthread is also required.)
For options available via the environment variable ASAN_OPTIONS see https://github.com/
google/sanitizers/wiki/AddressSanitizerFlags. With gcc additional control is available
via the --param flag: see its man page.
For more detailed information on an error, R can be run under a debugger with a breakpoint
set before the address sanitizer report is produced: for gdb or lldb you could use
break __asan_report_error
(See https://github.com/google/sanitizers/wiki/AddressSanitizerAndDebugger.)
More recent versions12 added the flag -fsanitize-address-use-after-scope: see
https://github.com/google/sanitizers/wiki/AddressSanitizerUseAfterScope.
One of the checks done by ASan is that malloc/free and in C++ new/delete and
new[]/delete[] are used consistently (rather than say free being used to dealloc memory
allocated by new[]). This matters on some systems but not all: unfortunately on some of those
where it does not matter, system libraries13 are not consistent. The check can be suppressed by
including ‘alloc_dealloc_mismatch=0’ in ASAN_OPTIONS.
ASan also checks system calls and sometimes reports can refer to problems in the system
software and not the package nor R. A couple of reports have been of ‘heap-use-after-free’ errors
in the X11 libraries called from Tcl/Tk.

4.3.3.1 Using the Leak Sanitizer

For x86_64 Linux there is a leak sanitizer, ‘LSan’: see https://github.com/google/
sanitizers/wiki/AddressSanitizerLeakSanitizer. This is available on recent versions of
gcc and clang, and where available is compiled in as part of ASan.
One way to invoke this from an ASan-enabled build is by the environment variable
ASAN_OPTIONS='detect_leaks=1'
However, this was made the default as from clang 3.5 and gcc 5.1.0.
When LSan is enabled, leaks give the process a failure error status (by default 23). For an
R package this means the R process, and as the parser retains some memory to the end of the
process, if R itself was built against ASan all runs will have a failure error status (which may
include running R as part of building R itself).
To disable this, allocation-mismatch checking and some strict C++ checking use
setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_odr_violation=0'
LSan also has a ‘stand-alone’ mode where it is compiled in using -fsanitize=leak and
avoids the run-time overhead of ASan.
12
including gcc 7.1 and clang 4.0.0: for gcc it is implied by -fsanitize=address.
13
for example, X11/GL libraries on Linux, seen when checking package rgl (https://CRAN.R-project.org/
package=rgl) and some others using it—a workaround is to set environment variable RGL_USE_NULL=true.
Chapter 4: Debugging 114

4.3.4 Using the Undefined Behaviour Sanitizer

‘Undefined behaviour’ is where the language standard does not require particular behaviour from
the compiler. Examples include division by zero (where for doubles R requires the ISO/IEC 60559
behaviour but C/C++ do not), use of zero-length arrays, shifts too far for signed types (e.g. int
x, y; y = x << 31;), out-of-range coercion, invalid C++ casts and mis-alignment. Not uncom-
mon examples of out-of-range coercion in R packages are attempts to coerce a NaN or infinity
to type int or NA_INTEGER to an unsigned type such as size_t. Also common is y[x - 1]
forgetting that x might be NA_INTEGER.
‘UBSanitizer’ is a tool for C/C++ source code selected by -fsanitize=undefined in suit-
able builds14 of clang and GCC. Its (main) runtime library is linked into each package’s
DLL, so it is less often needed to be included in MAIN_LDFLAGS. Platforms supported
by clang are listed at https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html#
supported-platforms: CRAN uses it for C/C++ with both GCC and clang on ‘x86_64’ Linux:
the two toolchains often highlight different things with more reports from clang than GCC.
This sanitizer can be combined with the Address Sanitizer by
-fsanitize=undefined,address (where both are supported).
Finer control of what is checked can be achieved by other options.
For clang see https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html#
ubsan-checks. The current set is (on a single line):
-fsanitize=alignment,bool,bounds,builtin,enum,float-cast-overflow,
float-divide-by-zero,function,implicit-unsigned-integer-truncation,
implicit-signed-integer-truncation,implicit-integer-sign-change,
integer-divide-by-zero,nonnull-attribute,null,object-size,
pointer-overflow,return,returns-nonnull-attribute,shift,
signed-integer-overflow,unreachable,unsigned-integer-overflow,
unsigned-shift-base,vla-bound,vptr
(plus the more specific versions shift-base and shift-exponent) a subset of which could be
combined with address, or use something like
-fsanitize=undefined -fno-sanitize=float-divide-by-zero
Options function, return and vptr apply only to C++: to use vptr its run-time library needs
to be linked into the main R executable by building the latter with something like
MAIN_LD="clang++ -fsanitize=undefined"
Option float-divide-by-zero is undesirable for use with R which allow such divisions as
part of IEC 60559 arithmetic, and in versions of clang since June 2019 it is no longer part of
-fsanitize=undefined.
For GCC see https://gcc.gnu.org/onlinedocs/gcc/Instrumentation-Options.
html (or the manual for your version of GCC, installed or via https://gcc.gnu.org/
onlinedocs/: look for ‘Program Instrumentation Options’) for the options supported by GCC:
10 supported
-fsanitize=alignment,bool,bounds,builtin,enum,integer-divide-by-zero,
nonnull-attribute,null,object-size,pointer-overflow,return,
returns-nonnull-attribute,shift,signed-integer-overflow,
unreachable,vla-bound,vptr
plus the more specific versions shift-base and shift-exponent and non-default options
bound-strict,float-cast-overflow,float-divide-by-zero
where float-divide-by-zero is not desirable for R uses and bounds-strict is an extension
of bounds.
14
On some platforms the runtime library, libubsan, needs to be installed separately.
Chapter 4: Debugging 115

Other useful flags include

-no-fsanitize-recover
which causes the first report to be fatal (it always is for the unreachable and return subop-
tions). For more detailed information on where the runtime error occurs, using
setenv UBSAN_OPTIONS 'print_stacktrace=1'
will include a traceback in the report. Beyond that, R can be run under a debugger with a
breakpoint set before the sanitizer report is produced: for gdb or lldb you could use
break __ubsan_handle_float_cast_overflow
break __ubsan_handle_float_cast_overflow_abort
or similar (there are handlers for each type of undefined behaviour).
There are also the compiler flags -fcatch-undefined-behavior and -ftrapv, said to be
more reliable in clang than gcc.
For more details on the topic see https://blog.regehr.org/archives/213 and https://
blog.llvm.org/2011/05/what-every-c-programmer-should-know.html (which has 3 parts).
It may or may not be possible to build R itself with -fsanitize=undefined: problems have
been seen with OpenMP-using code with gcc but there has been success with clang.

4.3.5 Other analyses with ‘clang’

Recent versions of clang on ‘x86_64’ Linux have ‘ThreadSanitizer’ (https://github.com/
google/sanitizers/wiki#threadsanitizer), a ‘data race detector for C/C++ programs’,
and ‘MemorySanitizer’ (https://clang.llvm.org/docs/MemorySanitizer.html, https://
github.com/google/sanitizers) for the detection of uninitialized memory. Both are based
on and provide similar functionality to tools in valgrind.
clang has a ‘Static Analyzer’ which can be run on the source files during compilation: see
https://clang-analyzer.llvm.org/.

4.3.6 Other analyses with ‘gcc’

GCC 10 introduced a new flag -fanalyzer which does static analysis during compilation, cur-
rently for C code. It is regarded as experimental and it may slow down computation considerably
when problems are found (and use many GB of resident memory). There is some overlap with
problems detected by the Undefined Behaviour sanitizer, but some issues are only reported by
this tool and as it is a static analysis, it does not rely on code paths being exercised.
See https://gcc.gnu.org/onlinedocs/gcc-10.1.0/gcc/Static-Analyzer-Options.
html (or the documentation for your version of gcc if later) and https://developers.redhat.
com/blog/2020/03/26/static-analysis-in-gcc-10

4.3.7 Using ‘Dr. Memory’

‘Dr. Memory’ from https://drmemory.org/ is a memory checker for (currently) Windows,
Linux and macOS with similar aims to valgrind. It works with unmodified executables15 and
detects memory access errors, uninitialized reads and memory leaks.

4.3.8 Fortran array bounds checking

Most of the Fortran compilers used with R allow code to be compiled with checking of array
bounds: for example gfortran has option -fbounds-check. This will give an error when the
upper or lower bound is exceeded, e.g.
At line 97 of file .../src/appl/dqrdc2.f
Fortran runtime error: Index '1' of dimension 1 of array 'x' above upper bound of 0
15
but works better if inlining and frame pointer optimizations are disabled.
Chapter 4: Debugging 116

One does need to be aware that lazy programmers often specify Fortran dimensions as 1
rather than * or a real bound and these will be reported (as may * dimensions)
It is easy to arrange to use this check on just the code in your package: add to ~/.R/Makevars
something like (for gfortran)
FFLAGS = -g -O2 -mtune=native -fbounds-check
when you run R CMD check.
This may report errors with the way that Fortran character variables are passed, particularly
when Fortran subroutines are called from C code and character lengths are not passed (see
Section 6.6.1 [Fortran character strings], page 171).

4.4 Debugging compiled code

Sooner or later programmers will be faced with the need to debug compiled code loaded into R.
This section is geared to platforms using gdb with code compiled by gcc, but similar things are
possible with other debuggers such as lldb (https://lldb.llvm.org/, used on macOS) and
Sun’s dbx: some debuggers have graphical front-ends available.
Consider first ‘crashes’, that is when R terminated unexpectedly with an illegal memory
access (a ‘segfault’ or ‘bus error’), illegal instruction or similar. Unix-alike versions of R use a
signal handler which aims to give some basic information. For example
*** caught segfault ***
address 0x20000028, cause 'memory not mapped'

Traceback:
1: .identC(class1[[1]], class2)
2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(classi,
where = where))
3: validObject(t(cu))
4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t(cu)),
validObject(t(tu)))

Possible actions:
1: abort (with core dump)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 3
Since the R process may be damaged, the only really safe options are the first or third. (Note
that a core dump is only produced where enabled: a common default in a shell is to limit its
size to 0, thereby disabling it.)
A fairly common cause of such crashes is a package which uses .C or .Fortran and writes
beyond (at either end) one of the arguments it is passed. There is a good way to detect this:
using options(CBoundsCheck = TRUE) (which can be selected via the environment variable R_
C_BOUNDS_CHECK=yes) changes the way .C and .Fortran work to check if the compiled code
writes in the 64 bytes at either end of an argument.
Another cause of a ‘crash’ is to overrun the C stack. R tries to track that in its own code,
but it may happen in third-party compiled code. For modern POSIX-compliant OSes R can
safely catch that and return to the top-level prompt, so one gets something like
> .C("aaa")
Error: segfault from C stack overflow
>
Chapter 4: Debugging 117

However, C stack overflows are fatal under Windows and normally defeat attempts at debugging
on that platform. Further, the size of the stack is set when R is compiled on Windows, whereas
on POSIX OSes it can be set in the shell from which R is launched.
If you have a crash which gives a core dump you can use something like
gdb /path/to/R/bin/exec/R core.12345
to examine the core dump. If core dumps are disabled or to catch errors that do not generate a
dump one can run R directly under a debugger by for example
$ R -d gdb --vanilla
...
gdb> run
at which point R will run normally, and hopefully the debugger will catch the error and return
to its prompt. This can also be used to catch infinite loops or interrupt very long-running code.
For a simple example
> for(i in 1:1e7) x <- rnorm(100)
[hit Ctrl-C]
Program received signal SIGINT, Interrupt.
0x00397682 in _int_free () from /lib/tls/libc.so.6
(gdb) where
#0 0x00397682 in _int_free () from /lib/tls/libc.so.6
#1 0x00397eba in free () from /lib/tls/libc.so.6
#2 0xb7cf2551 in R_gc_internal (size_needed=313)
at /users/ripley/R/svn/R-devel/src/main/memory.c:743
#3 0xb7cf3617 in Rf_allocVector (type=13, length=626)
at /users/ripley/R/svn/R-devel/src/main/memory.c:1906
#4 0xb7c3f6d3 in PutRNGstate ()
at /users/ripley/R/svn/R-devel/src/main/RNG.c:351
#5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9698f98,
rho=0x9698f28) at /users/ripley/R/svn/R-devel/src/main/random.c:183
...
In many cases it is possible to attach a debugger to a running process: this is helpful if an
alternative front-end is in use or to investigate a task that seems to be taking far too long. This
is done by something like
gdb -p pid
where pid is the id of the R executable or front-end process and can be found from within a
running R process by calling Sys.getpid() or from a process monitor. This stops the process
so its state can be examined: use continue to resume execution.
Some “tricks” worth knowing follow:

4.4.1 Finding entry points in dynamically loaded code

Under most compilation environments, compiled code dynamically loaded into R cannot have
breakpoints set within it until it is loaded. To use a symbolic debugger on such dynamically
loaded code under Unix-alikes use
• Call the debugger on the R executable, for example by R -d gdb.
• Start R.
• At the R prompt, use dyn.load or library to load your shared object.
• Send an interrupt signal. This will put you back to the debugger prompt.
• Set the breakpoints in your code.
• Continue execution of R by typing signal 0RET.
Chapter 4: Debugging 118

Under Windows signals may not be able to be used, and if so the procedure is more compli-
cated. See the rw-FAQ.

4.4.2 Inspecting R objects when debugging

The key to inspecting R objects from compiled code is the function PrintValue(SEXP s) which
uses the normal R printing mechanisms to print the R object pointed to by s, or the safer version
R_PV(SEXP s) which will only print ‘objects’.

One way to make use of PrintValue is to insert suitable calls into the code to be debugged.

Another way is to call R_PV from the symbolic debugger. (PrintValue is hidden as Rf_
PrintValue.) For example, from gdb we can use

(gdb) p R_PV(ab)

using the object ab from the convolution example, if we have placed a suitable breakpoint in
the convolution C code.

To examine an arbitrary R object we need to work a little harder. For example, let

R> DF <- data.frame(a = 1:3, b = 4:6)

By setting a breakpoint at do_get and typing get("DF") at the R prompt, one can find out the
address in memory of DF, for example

Value returned is $1 = (SEXPREC *) 0x40583e1c

(gdb) p *$1
$2 = {
sxpinfo = {type = 19, obj = 1, named = 1, gp = 0,
mark = 0, debug = 0, trace = 0, = 0},
attrib = 0x40583e80,
u = {
vecsxp = {
length = 2,
type = {c = 0x40634700 "0>X@D>X@0>X@", i = 0x40634700,
f = 0x40634700, z = 0x40634700, s = 0x40634700},
truelength = 1075851272,
},
primsxp = {offset = 2},
symsxp = {pname = 0x2, value = 0x40634700, internal = 0x40203008},
listsxp = {carval = 0x2, cdrval = 0x40634700, tagval = 0x40203008},
envsxp = {frame = 0x2, enclos = 0x40634700},
closxp = {formals = 0x2, body = 0x40634700, env = 0x40203008},
promsxp = {value = 0x2, expr = 0x40634700, env = 0x40203008}
}
}

(Debugger output reformatted for better legibility).

Using R_PV() one can “inspect” the values of the various elements of the SEXP, for example,
Chapter 4: Debugging 119

(gdb) p R_PV($1->attrib)
$names
[1] "a" "b"

$row.names
[1] "1" "2" "3"

$class
[1] "data.frame"

$3 = void
To find out where exactly the corresponding information is stored, one needs to go “deeper”:
(gdb) set $a = $1->attrib
(gdb) p $a->u.listsxp.tagval->u.symsxp.pname->u.vecsxp.type.c
$4 = 0x405d40e8 "names"
(gdb) p $a->u.listsxp.carval->u.vecsxp.type.s[1]->u.vecsxp.type.c
$5 = 0x40634378 "b"
(gdb) p $1->u.vecsxp.type.s[0]->u.vecsxp.type.i[0]
$6 = 1
(gdb) p $1->u.vecsxp.type.s[1]->u.vecsxp.type.i[1]
$7 = 5
Another alternative is the R_inspect function which shows the low-level structure of the ob-
jects recursively (addresses differ from the above as this example is created on another machine):
(gdb) p R_inspect($1)
@100954d18 19 VECSXP g0c2 [OBJ,NAM(2),ATT] (len=2, tl=0)
@100954d50 13 INTSXP g0c2 [NAM(2)] (len=3, tl=0) 1,2,3
@100954d88 13 INTSXP g0c2 [NAM(2)] (len=3, tl=0) 4,5,6
ATTRIB:
@102a70140 02 LISTSXP g0c0 []
TAG: @10083c478 01 SYMSXP g0c0 [MARK,NAM(2),gp=0x4000] "names"
@100954dc0 16 STRSXP g0c2 [NAM(2)] (len=2, tl=0)
@10099df28 09 CHARSXP g0c1 [MARK,gp=0x21] "a"
@10095e518 09 CHARSXP g0c1 [MARK,gp=0x21] "b"
TAG: @100859e60 01 SYMSXP g0c0 [MARK,NAM(2),gp=0x4000] "row.names"
@102a6f868 13 INTSXP g0c1 [NAM(2)] (len=2, tl=1) -2147483648,-3
TAG: @10083c948 01 SYMSXP g0c0 [MARK,gp=0x4000] "class"
@102a6f838 16 STRSXP g0c1 [NAM(2)] (len=1, tl=1)
@1008c6d48 09 CHARSXP g0c2 [MARK,gp=0x21,ATT] "data.frame"
In general the representation of each object follows the format:
@<address> <type-nr> <type-name> <gc-info> [<flags>] ...

For a more fine-grained control over the depth of the recursion and the output of vectors
R_inspect3 takes additional two character() parameters: maximum depth and the maximal
number of elements that will be printed for scalar vectors. The defaults in R_inspect are
currently -1 (no limit) and 5 respectively.

4.4.3 Debugging on macOS

To debug code in a package it is easiest to unpack it in a directory and install it with
R CMD INSTALL --dsym pkgname
Chapter 4: Debugging 120

as macOS does not store debugging symbols in the .so file. (It is not necessary to have R built
with debugging symbols, although compiling the package should be done including -g in CFLAGS
/ CXXFLAGS / FFLAGS / FCFLAGS as appropriate.)
Security measures may prevent running a CRAN binary distribution of R under lldb or at-
taching this as a debugger (https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#
I-cannot-attach-debugger-to-R), although both were possible on High Sierra and are again
from R 4.2.0. This can also affect locally compiled builds, where attaching to an interactive R
session under Big Sur or Monterey worked in 2022 after giving administrator permission via a
popup-up. (To debug in what Apple deems a non-interactive session, e.g. logged in remotely,
see man DevToolsSecurity.)
Debugging a local build of R on macOS can raise additional hurdles as environment vari-
ables such as DYLD_FALLBACK_LIBRARY_PATH are not usually passed through16 the lldb process,
resulting in messages like
R -d lldb
...
(lldb) run
Process 16828 launched: '/path/to/bin/exec/R' (x86_64)
dyld: Library not loaded: libR.dylib
Referenced from: /path/to/bin/exec/R
A quick workaround is to symlink the dylibs under R_HOME/lib to somewhere where they will
be found such as the current working directory. It would be possible to do as the distribution
does17 and use install_name_tool, but that would have to be done for all the dylibs including
those in packages.
It may be simplest to attach the debugger to a running process (see above). Specifically, run
R and when it is at the prompt just before a command that is to be debugged, at a terminal
ps -ef | grep exec/R
# identify the PID pid for the next command: it is the second item
lldb -p pid
(lldb) continue
and then return to the R console.
For non-interactive use, one may need lldb --batch.

4.5 Using Link-time Optimization

Where supported, link time optimization provides a comprehensive way to check the consistency
of calls between Fortran files or between C and Fortran. Use this via R CMD INSTALL --use-LTO
(but that does not apply if there is a src/Makefile file or a Windows analogue).
To set up support on a Unix-alike, see Section “Link-Time Optimization” in R Installation
and Administration. On Linux using GCC without building R with LTO support, it should
suffice to set
LTO_OPT = -flto
LTO_FC_OPT = -flto
AR = gcc-ar
NM = gcc-nm
in a personal (or site) Makevars file: See Section “Customizing package compilation” in R
Installation and Administration,
16
By default as a security measure: see man dyld.
17
See https://svn.r-project.org/R-dev-web/trunk/CRAN/QA/Simon/R-build/fixpathR:
‘@executable_path’ could be used rather than absolute paths.
Chapter 4: Debugging 121

For Windows, first edit file etc/${R_ARCH}/Makeconf to give LTO_OPT the value -flto or
do so in a personal/site Makevars file; see also file src/gnuwin32/README.compilation in the
sources.
For example:
boot.f:61: warning: type of 'ddot' does not match original declaration [-Wlto-type-mism
y(j,i)=ddot(p,x(j,1),n,b(1,j,i),1)
crq.f:1023: note: return value type mismatch
where the package author forgot to declare
double precision ddot
external ddot
in boot.f. That package had its own copy of ddot: to detect misuse of the one in R’s BLAS
library would have needed R configured with --enable-lto=check.
Further examples:
rkpk2.f:77:5: warning: type of 'dstup' does not match original declaration [-Wlto-type-
*info, wk)
rkpk1.f:2565:5: note: type mismatch in parameter 14
subroutine dstup (s, lds, nobs, nnull, qraux, jpvt, y, q, ldqr,
rkpk1.f:2565:5: note: 'dstup' was previously declared here
where the fourteenth argument dum was missing in the call.
reg.f:78:33: warning: type of 'dqrdc' does not match original declaration [-Wlto-type-m
call dqrdc (sr, nobs, nobs, nnull, wk, dum, dum, 0)
dstup.f:20: note: 'dqrdc' was previously declared here
call dqrdc (s, lds, nobs, nnull, qraux, jpvt, work, 1)
dqrdc is a LINPACK routine from R, jpvt is an integer array and work is a double precision
one so dum cannot match both. (If --enable-lto=check had been used the comparison would
have been with the definition in R.)
For Fortran files all in the package, most inconsistencies can be detected by concatenating
the Fortran files and compiling the result, sometimes with clearer diagnostics than provided by
LTO. For our last two examples this gives
all.f:2966:72:

*info, work1)
1
Warning: Missing actual argument for argument 'dum' at (1)
and
all.f:1663:72:

*ipvtwk), wk(ikwk), wk(iwork1), wk(iwork2), info)

1
Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to INTEGER(4)
On a Unix-alike for a package with a src/Makefile file, LTO can be enabled by including
suitable flags in that file, for example
LTO = $(LTO_OPT)
LTO_FC = $(LTO_FC_OPT)
and ensuring these are used for compilation, for example as part of CFLAGS, CXXFLAGS or FCFLAGS.
If R CMD SHLIB is used for compilation, add --use-LTO to its call.
Chapter 4: Debugging 122

On Windows for a package with a src/Makefile.ucrt or src/Makefile.win file which

includes ‘"${R_HOME}/etc${R_ARCH}/Makeconf"’, include
LTO = $(LTO_OPT)
or to always use LTO however R was built,
LTO = -flto
 123

5 System and foreign language interfaces

5.1 Operating system access

Access to operating system functions is via the R functions system and system2. The details
will differ by platform (see the on-line help), and about all that can safely be assumed is that
the first argument will be a string command that will be passed for execution (not necessarily
by a shell) and the second argument to system will be internal which if true will collect the
output of the command into an R character vector.
On POSIX-compliant OSes these commands pass a command-line to a shell: Windows is not
POSIX-compliant and there is a separate function shell to do so.
The function system.time is available for timing. Timing on child processes is only available
on Unix-alikes, and may not be reliable there.

5.2 Interface functions .C and .Fortran

These two functions provide an interface to compiled code that has been linked into R, either
at build time or via dyn.load (see Section 5.3 [dyn.load and dyn.unload], page 125). They are
primarily intended for compiled C and Fortran code respectively, but the .C function can be
used with other languages which can generate C interfaces, for example C++ (see Section 5.6
[Interfacing C++ code], page 135).
The first argument to each function is a character string specifying the symbol name as
known1 to C or Fortran, that is the function or subroutine name. (That the symbol is loaded
can be tested by, for example, is.loaded("cg"). Use the name you pass to .C or .Fortran
rather than the translated symbol name.)
There can be up to 65 further arguments giving R objects to be passed to compiled code.
Normally these are copied before being passed in, and copied again to an R list object when
the compiled code returns. If the arguments are given names, these are used as names for the
components in the returned list object (but not passed to the compiled code).
The following table gives the mapping between the modes of R atomic vectors and the types
of arguments to a C function or Fortran subroutine.
R storage mode C type Fortran type
logical int * INTEGER
integer int * INTEGER
double double * DOUBLE PRECISION
complex Rcomplex * DOUBLE COMPLEX
character char ** CHARACTER(255)
raw unsigned char * none
On all R platforms int and INTEGER are 32-bit. Code ported from S-PLUS (which uses long *
for logical and integer) will not work on all 64-bit platforms (although it may appear to work
on some, including Windows). Note also that if your compiled code is a mixture of C functions
and Fortran subprograms the argument types must match as given in the table above.
C type Rcomplex is a structure with double members r and i defined in the header file
R_ext/Complex.h.2 (On most platforms this is stored in a way compatible with the C99 double
complex type: however, it may not be possible to pass Rcomplex to a C99 function expecting
a double complex argument. Nor need it be compatible with a C++ complex type. Moreover,
the compatibility can depend on the optimization level set for the compiler.)
1
possibly after some platform-specific translation, e.g. adding leading or trailing underscores.
2
This is currently included by R.h but may not be in future, so it should be included by code needing the type.
Chapter 5: System and foreign language interfaces 124

Only a single character string of fixed length can be passed to or from Fortran (the length
is not passed), and the success of this is compiler-dependent: its use was formally deprecated
in 2019. Other R objects can be passed to .C, but it is much better to use one of the other
interfaces.
It is possible to pass numeric vectors of storage mode double to C as float * or to Fortran as
REAL by setting the attribute Csingle, most conveniently by using the R functions as.single,
single or mode. This is intended only to be used to aid interfacing existing C or Fortran code.
Logical values are sent as 0 (FALSE), 1 (TRUE) or INT_MIN = -2147483648 (NA, but only if
NAOK is true), and the compiled code should return one of these three values. (Non-zero values
other than INT_MIN are mapped to TRUE.) Note that the use of int * for Fortran logical is
not guaranteed to be portable (although people have gotten away with it for many years): it is
better to pass integers and convert to/from Fortran logical in a Fortran wrapper.
Unless formal argument NAOK is true, all the other arguments are checked for missing values
NA and for the IEEE special values NaN, Inf and -Inf, and the presence of any of these generates
an error. If it is true, these values are passed unchecked.
Argument PACKAGE confines the search for the symbol name to a specific shared object (or
use "base" for code compiled into R). Its use is highly desirable, as there is no way to avoid two
package writers using the same symbol name, and such name clashes are normally sufficient to
cause R to crash. (If it is not present and the call is from the body of a function defined in a
package namespace, the shared object loaded by the first (if any) useDynLib directive will be
used.)
Note that the compiled code should not return anything except through its arguments: C
functions should be of type void and Fortran subprograms should be subroutines.
To fix ideas, let us consider a very simple example which convolves two finite sequences.
(This is hard to do fast in interpreted R code, but easy in C code.) We could do this using .C
by
void convolve(double *a, int *na, double *b, int *nb, double *ab)
{
int nab = *na + *nb - 1;

for(int i = 0; i < nab; i++)

ab[i] = 0.0;
for(int i = 0; i < *na; i++)
for(int j = 0; j < *nb; j++)
ab[i + j] += a[i] * b[j];
}
called from R by
conv <- function(a, b)
.C("convolve",
as.double(a),
as.integer(length(a)),
as.double(b),
as.integer(length(b)),
ab = double(length(a) + length(b) - 1))$ab
Note that we take care to coerce all the arguments to the correct R storage mode before
calling .C; mistakes in matching the types can lead to wrong results or hard-to-catch errors.
Special care is needed in handling character vector arguments in C (or C++). On entry the
contents of the elements are duplicated and assigned to the elements of a char ** array, and on
exit the elements of the C array are copied to create new elements of a character vector. This
Chapter 5: System and foreign language interfaces 125

means that the contents of the character strings of the char ** array can be changed, including
to \0 to shorten the string, but the strings cannot be lengthened. It is possible3 to allocate a
new string via R_alloc and replace an entry in the char ** array by the new string. However,
when character vectors are used other than in a read-only way, the .Call interface is much to
be preferred.
Passing character strings to Fortran code needs even more care, is deprecated and should be
avoided where possible. Only the first element of the character vector is passed in, as a fixed-
length (255) character array. Up to 255 characters are passed back to a length-one character
vector. How well this works (or even if it works at all) depends on the C and Fortran compilers
on each platform (including on their options). Often what is being passed to Fortran is one of
a small set of possible values (a factor in R terms) which could alternatively be passed as an
integer code: similarly Fortran code that wants to generate diagnostic messages could pass an
integer code to a C or R wrapper which would convert it to a character string.
It is possible to pass some R objects other than atomic vectors via .C, but this is only
supported for historical compatibility: use the .Call or .External interfaces for such objects.
Any C/C++ code that includes Rinternals.h should be called via .Call or .External.
.Fortran is primarily intended for Fortran 77 code, and long precedes any support for ‘mod-
ern’ Fortran. Nowadays implementations of Fortran support the Fortran 2003 module iso_c_
binding, a better way to interface modern Fortran code to R is to use .C and write a C interface
using use iso_c_binding.

5.3 dyn.load and dyn.unload

Compiled code to be used with R is loaded as a shared object (Unix-alikes including macOS,
see Section 5.5 [Creating shared objects], page 134, for more information) or DLL (Windows).
The shared object/DLL is loaded by dyn.load and unloaded by dyn.unload. Unloading
is not normally necessary and is not safe in general, but it is needed to allow the DLL to be
re-built on some platforms, including Windows. Unloading a DLL and then re-loading a DLL
of the same name may not work: Solaris used the first version loaded. A DLL that registers C
finalizers, but fails to unregister them when unloaded, may cause R to crash after unloading.
The first argument to both functions is a character string giving the path to the object.
Programmers should not assume a specific file extension for the object/DLL (such as .so) but
use a construction like
file.path(path1, path2, paste0("mylib", .Platform$dynlib.ext))
for platform independence. On Unix-alike systems the path supplied to dyn.load can be an
absolute path, one relative to the current directory or, if it starts with ‘~’, relative to the user’s
home directory.
Loading is most often done automatically based on the useDynLib() declaration in the
NAMESPACE file, but may be done explicitly via a call to library.dynam. This has the form
library.dynam("libname", package, lib.loc)
where libname is the object/DLL name with the extension omitted. Note that the first argument,
chname, should not be package since this will not work if the package is installed under another
name.
Under some Unix-alike systems there is a choice of how the symbols are resolved when the
object is loaded, governed by the arguments local and now. Only use these if really neces-
sary: in particular using now=FALSE and then calling an unresolved symbol will terminate R
unceremoniously.
3
Note that this is then not checked for over-runs by option CBoundsCheck = TRUE.
Chapter 5: System and foreign language interfaces 126

R provides a way of executing some code automatically when a object/DLL is either loaded
or unloaded. This can be used, for example, to register native routines with R’s dynamic symbol
mechanism, initialize some data in the native code, or initialize a third party library. On loading
a DLL, R will look for a routine within that DLL named R_init_lib where lib is the name of
the DLL file with the extension removed. For example, in the command
library.dynam("mylib", package, lib.loc)
R looks for the symbol named R_init_mylib. Similarly, when unloading the object, R looks for
a routine named R_unload_lib, e.g., R_unload_mylib. In either case, if the routine is present,
R will invoke it and pass it a single argument describing the DLL. This is a value of type DllInfo
which is defined in the Rdynload.h file in the R_ext directory.
Note that there are some implicit restrictions on this mechanism as the basename of the DLL
needs to be both a valid file name and valid as part of a C entry point (e.g. it cannot contain ‘.’):
for portable code it is best to confine DLL names to be ASCII alphanumeric plus underscore. If
entry point R_init_lib is not found it is also looked for with ‘.’ replaced by ‘_’.
The following example shows templates for the initialization and unload routines for the
mylib DLL.

#include <R_ext/Rdynload.h>

void
R_init_mylib(DllInfo *info)
{
/* Register routines,
allocate resources. */
}

void
R_unload_mylib(DllInfo *info)
{
/* Release resources. */
}

If a shared object/DLL is loaded more than once the most recent version is used.4 More
generally, if the same symbol name appears in several shared objects, the most recently loaded
occurrence is used. The PACKAGE argument and registration (see the next section) provide good
ways to avoid any ambiguity in which occurrence is meant.
On Unix-alikes the paths used to resolve dynamically linked dependent libraries are fixed (for
security reasons) when the process is launched, so dyn.load will only look for such libraries in
the locations set by the R shell script (via etc/ldpaths) and in the OS-specific defaults.
Windows allows more control (and less security) over where dependent DLLs are looked for.
On all versions this includes the PATH environment variable, but with lowest priority: note that
it does not include the directory from which the DLL was loaded. It is possible to add a single
path with quite high priority via the DLLpath argument to dyn.load. This is (by default) used
by library.dynam to include the package’s libs/x64 directory in the DLL search path.

5.4 Registering native routines

By ‘native’ routine, we mean an entry point in compiled code.
4
Strictly this is OS-specific, but no exceptions have been seen for many years.
Chapter 5: System and foreign language interfaces 127

In calls to .C, .Call, .Fortran and .External, R must locate the specified native routine by
looking in the appropriate shared object/DLL. By default, R uses the operating-system-specific
dynamic loader to lookup the symbol in all5 loaded DLLs and the R executable or libraries it is
linked to. Alternatively, the author of the DLL can explicitly register routines with R and use
a single, platform-independent mechanism for finding the routines in the DLL. One can use this
registration mechanism to provide additional information about a routine, including the number
and type of the arguments, and also make it available to R programmers under a different name.
Registering routines has two main advantages: it provides a faster6 way to find the address
of the entry point via tables stored in the DLL at compilation time, and it provides a run-time
check that the entry point is called with the right number of arguments and, optionally, the
right argument types.
To register routines with R, one calls the C routine R_registerRoutines. This is typically
done when the DLL is first loaded within the initialization routine R_init_dll name described in
Section 5.3 [dyn.load and dyn.unload], page 125. R_registerRoutines takes 5 arguments. The
first is the DllInfo object passed by R to the initialization routine. This is where R stores the
information about the methods. The remaining 4 arguments are arrays describing the routines
for each of the 4 different interfaces: .C, .Call, .Fortran and .External. Each argument is a
NULL-terminated array of the element types given in the following table:
.C R_CMethodDef
.Call R_CallMethodDef
.Fortran R_FortranMethodDef
.External R_ExternalMethodDef
Currently, the R_ExternalMethodDef type is the same as R_CallMethodDef type and con-
tains fields for the name of the routine by which it can be accessed in R, a pointer to the actual
native symbol (i.e., the routine itself), and the number of arguments the routine expects to be
passed from R. For example, if we had a routine named myCall defined as
SEXP myCall(SEXP a, SEXP b, SEXP c);
we would describe this as
static const R_CallMethodDef callMethods[] = {
{"myCall", (DL_FUNC) &myCall, 3},
{NULL, NULL, 0}
};
along with any other routines for the .Call interface. For routines with a variable number of
arguments invoked via the .External interface, one specifies -1 for the number of arguments
which tells R not to check the actual number passed.
Routines for use with the .C and .Fortran interfaces are described with similar data struc-
tures, which have one optional additional field for describing the type of each argument. If
specified, this field should be an array with the SEXP types describing the expected type of
each argument of the routine. (Technically, the elements of the types array are of type R_
NativePrimitiveArgType which is just an unsigned integer.) The R types and corresponding
type identifiers are provided in the following table:
numeric REALSXP
integer INTSXP
logical LGLSXP
single SINGLESXP

5
For calls from within a namespace the search is confined to the DLL loaded for that package.
6
For unregistered entry points the OS’s dlsym routine is used to find addresses. Its performance varies consid-
erably by OS and even in the best case it will need to search a much larger symbol table than, say, the table
of .Call entry points.
Chapter 5: System and foreign language interfaces 128

character STRSXP
list VECSXP
Consider a C routine, myC, declared as
void myC(double *x, int *n, char **names, int *status);
We would register it as
static R_NativePrimitiveArgType myC_type[] = {
REALSXP, INTSXP, STRSXP, LGLSXP
};

static const R_CMethodDef cMethods[] = {

{"myC", (DL_FUNC) &myC, 4, myC_type},
{NULL, NULL, 0, NULL}
};
If registering types, check carefully that the number of types matches the number of argu-
ments: as the type array (here myC_type) is passed as a pointer in C, the registration mechanism
cannot check this for you.
Note that .Fortran entry points are mapped to lowercase, so registration should use lower-
case only.
Having created the arrays describing each routine, the last step is to actually register them
with R. We do this by calling R_registerRoutines. For example, if we have the descriptions
above for the routines accessed by the .C and .Call we would use the following code:
void
R_init_myLib(DllInfo *info)
{
R_registerRoutines(info, cMethods, callMethods, NULL, NULL);
}
This routine will be invoked when R loads the shared object/DLL named myLib. The last
two arguments in the call to R_registerRoutines are for the routines accessed by .Fortran
and .External interfaces. In our example, these are given as NULL since we have no routines of
these types.
When R unloads a shared object/DLL, its registrations are removed. There is no other
facility for unregistering a symbol.
Examples of registering routines can be found in the different packages in the R source tree
(e.g., stats and graphics). Also, there is a brief, high-level introduction in R News (volume 1/3,
September 2001, pages 20–23, https://www.r-project.org/doc/Rnews/Rnews_2001-3.pdf).
Once routines are registered, they can be referred to as R objects if this is arranged in the
useDynLib call in the package’s NAMESPACE file (see Section 1.5.4 [useDynLib], page 51). So for
example the stats package has
# Refer to all C/Fortran routines by their name prefixed by C_
useDynLib(stats, .registration = TRUE, .fixes = "C_")
in its NAMESPACE file, and then ansari.test’s default methods can contain
pansari <- function(q, m, n)
.C(C_pansari, as.integer(length(q)), p = as.double(q),
as.integer(m), as.integer(n))$p
This avoids the overhead of looking up an entry point each time it is used, and ensures that the
entry point in the package is the one used (without a PACKAGE = "pkg" argument).
R_init_ routines are often of the form
void attribute_visible R_init_mypkg(DllInfo *dll)
Chapter 5: System and foreign language interfaces 129

{
R_registerRoutines(dll, CEntries, CallEntries, FortEntries,
ExternalEntries);
R_useDynamicSymbols(dll, FALSE);
R_forceSymbols(dll, TRUE);
...
}
The R_useDynamicSymbols call says the DLL is not to be searched for entry points specified
by character strings so .C etc calls will only find registered symbols: the R_forceSymbols call
only allows .C etc calls which specify entry points by R objects such as C_pansari (and not
by character strings). Each provides some protection against accidentally finding your entry
points when people supply a character string without a package, and avoids slowing down such
searches. (For the visibility attribute see Section 6.16 [Controlling visibility], page 186.)
In more detail, if a package mypkg contains entry points reg and unreg and the first is
registered as a 0-argument .Call routine, we could use (from code in the package)
.Call("reg")
.Call("unreg")
Without or with registration, these will both work. If R_init_mypkg calls R_
useDynamicSymbols(dll, FALSE), only the first will work. If in addition to registration the
NAMESPACE file contains
useDynLib(mypkg, .registration = TRUE, .fixes = "C_")
then we can call .Call(C_reg). Finally, if R_init_mypkg also calls R_forceSymbols(dll,
TRUE), only .Call(C_reg) will work (and not .Call("reg")). This is usually what we want:
it ensures that all of our own .Call calls go directly to the intended code in our package and
that no one else accidentally finds our entry points. (Should someone need to call our code from
outside the package, for example for debugging, they can use .Call(mypkg:::C_reg).)

5.4.1 Speed considerations

Sometimes registering native routines or using a PACKAGE argument can make a large difference.
The results can depend quite markedly on the OS (and even if it is 32- or 64-bit), on the version
of R and what else is loaded into R at the time.
To fix ideas, first consider x86_64 OS 10.7 and R 2.15.2. A simple .Call function might be
foo <- function(x) .Call("foo", x)
with C code
#include <Rinternals.h>

SEXP foo(SEXP x)
{
return x;
}
If we compile with by R CMD SHLIB foo.c, load the code by dyn.load("foo.so") and run
foo(pi) it took around 22 microseconds (us). Specifying the DLL by
foo2 <- function(x) .Call("foo", x, PACKAGE = "foo")
reduced the time to 1.7 us.
Now consider making these functions part of a package whose NAMESPACE file uses
useDynlib(foo). This immediately reduces the running time as "foo" will be preferentially
looked for foo.dll. Without specifying PACKAGE it took about 5 us (it needs to fathom out
the appropriate DLL each time it is invoked but it does not need to search all DLLs), and with
the PACKAGE argument it is again about 1.7 us.
Chapter 5: System and foreign language interfaces 130

Next suppose the package has registered the native routine foo. Then foo() still has to find
the appropriate DLL but can get to the entry point in the DLL faster, in about 4.2 us. And
foo2() now takes about 1 us. If we register the symbols in the NAMESPACE file and use
foo3 <- function(x) .Call(C_foo, x)
then the address for the native routine is looked up just once when the package is loaded, and
foo3(pi) takes about 0.8 us.
Versions using .C() rather than .Call() took about 0.2 us longer.
These are all quite small differences, but C routines are not uncommonly invoked millions
of times for run times of a few microseconds each, and those doing such things may wish to be
aware of the differences.
On Linux and Solaris there is a smaller overhead in looking up symbols.
Symbol lookup on Windows used to be far slower, so R maintains a small cache. If the cache
is currently empty enough that the symbol can be stored in the cache then the performance
is similar to Linux and Solaris: if not it may be slower. R’s own code always uses registered
symbols and so these never contribute to the cache: however many other packages do rely on
symbol lookup.
In more recent versions of R all the standard packages register native symbols and do not
allow symbol search, so in a new session foo() can only look in foo.so and may be as fast
as foo2(). This will no longer apply when many contributed packages are loaded, and gen-
erally those last loaded are searched first. For example, consider R 3.3.2 on x86 64 Linux.
In an empty R session, both foo() and foo2() took about 0.75 us; however after pack-
ages igraph (https://CRAN.R-project.org/package=igraph) and spatstat (https://CRAN.
R-project.org/package=spatstat) had been loaded (which loaded another 12 DLLs), foo()
took 3.6 us but foo2() still took about 0.80 us. Using registration in a package reduced this
to 0.55 us and foo3() took 0.40 us, times which were unchanged when further packages were
loaded.

5.4.2 Example: converting a package to use registration

The splines package was converted to use symbol registration in 2001, but we can use it as an
example7 of what needs to be done for a small package.
• Find the relevant entry points. This is somewhat OS-specific, but something like the fol-
lowing should be possible at the OS command-line
nm -g /path/to/splines.so | grep " T "
0000000000002670 T _spline_basis
0000000000001ec0 T _spline_value
This indicates that there are two relevant entry points. (They may or may not have a
leading underscore, as here. Fortran entry points will have a trailing underscore.) Check
in the R code that they are called by the package and how: in this case they are used by
.Call.
Alternatively, examine the package’s R code for all .C, .Fortran, .Call and .External
calls.
• Construct the registration table. First write skeleton registration code, conventionally in
file src/init.c (or at the end of the only C source file in the package: if included in a C++
file the ‘R_init’ function would need to be declared extern "C"):

7
Because it is a standard package, one would need to rename it before attempting to reproduce the account
here.
Chapter 5: System and foreign language interfaces 131

#include <stdlib.h> // for NULL

#include <R_ext/Rdynload.h>

#define CALLDEF(name, n) {#name, (DL_FUNC) &name, n}

static const R_CallMethodDef R_CallDef[] = {

CALLDEF(spline_basis, ?),
CALLDEF(spline_value, ?),
{NULL, NULL, 0}
};

void R_init_splines(DllInfo *dll)

{
R_registerRoutines(dll, NULL, R_CallDef, NULL, NULL);
}
and then replace the ? in the skeleton with the actual numbers of arguments. You will
need to add declarations (also known as ‘prototypes’) of the functions unless appending to
the only C source file. Some packages will already have these in a header file, or you could
create one and include it in init.c, for example splines.h containing
#include <Rinternals.h> // for SEXP
extern SEXP spline_basis(SEXP knots, SEXP order, SEXP xvals, SEXP derivs);
extern SEXP spline_value(SEXP knots, SEXP coeff, SEXP order, SEXP x, SEXP deriv);

Tools are available to extract declarations, at least for C and C++ code: see the help file for
package_native_routine_registration_skeleton in package tools. Here we could have
used
cproto -I/path/to/R/include -e splines.c
For examples of registering other types of calls, see packages graphics and stats. In partic-
ular, when registering entry points for .Fortran one needs declarations as if called from C,
such as
#include <R_ext/RS.h>
void F77_NAME(supsmu)(int *n, double *x, double *y,
double *w, int *iper, double *span, double *alpha,
double *smo, double *sc, double *edf);
gfortran 8.4, 9.2 and later can help generate such prototypes with its flag -fc-prototypes-
external (although one will need to replace the hard-coded trailing underscore with the
F77_NAME macro).
One can get away with inaccurate argument lists in the declarations: it is easy to specify
the arguments for .Call (all SEXP) and .External (one SEXP) and as the arguments for .C
and .Fortran are all pointers, specifying them as void * suffices. (For most platforms one
can omit all the arguments, although link-time optimization will warn, as will compilers set
up to warn on strict prototypes – and C23 will require correct arguments.)
Using -fc-prototypes-external will give a prototype using int_least32_t *lgl for For-
tran LOGICAL LGL, but this is not portable and traditionally it has been assumed that the
C/C++ equivalent was int *lgl. If adding a declaration just to register a .Fortran call,
the most portable version is void *lgl.
• (Optional but highly recommended.) Restrict .Call etc to use the symbols you chose to
register by editing src/init.c to contain
Chapter 5: System and foreign language interfaces 132

void R_init_splines(DllInfo *dll)

{
R_registerRoutines(dll, NULL, R_CallDef, NULL, NULL);
R_useDynamicSymbols(dll, FALSE);
}
A skeleton for the steps so far can be made using package_native_routine_registration_
skeleton in package tools. This will optionally create declarations based on the usage in the R
code.
The remaining steps are optional but recommended.
• Edit the NAMESPACE file to create R objects for the registered symbols:
useDynLib(splines, .registration = TRUE, .fixes = "C_")
• Find all the relevant calls in the R code and edit them to use the R objects. This entailed
changing the lines
temp <- .Call("spline_basis", knots, ord, x, derivs, PACKAGE = "splines")
y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], deriv, PACKAGE = "splines")
y = .Call("spline_value", knots, coef(object), ord, x, deriv, PACKAGE = "splines")
to
temp <- .Call(C_spline_basis, knots, ord, x, derivs)
y[accept] <- .Call(C_spline_value, knots, coeff, ord, x[accept], deriv)
y = .Call(C_spline_value, knots, coef(object), ord, x, deriv)
Check that there is no exportPattern directive which unintentionally exports the newly
created R objects.
• Restrict .Call to use the R symbols by editing src/init.c to contain
void R_init_splines(DllInfo *dll)
{
R_registerRoutines(dll, NULL, R_CallDef, NULL, NULL);
R_useDynamicSymbols(dll, FALSE);
R_forceSymbols(dll, TRUE);
}
• Consider visibility. On some OSes we can hide entry points from the loader, which precludes
any possible name clashes and calling them accidentally (usually with incorrect arguments
and crashing the R process). If we repeat the first step we now see
nm -g /path/to/splines.so | grep " T "
0000000000002e00 T _R_init_splines
00000000000025e0 T _spline_basis
0000000000001e20 T _spline_value
If there were any entry points not intended to be used by the package we should try to
avoid exporting them, for example by making them static. Now that the two relevant
entry points are only accessed via the registration table, we can hide them. There are two
ways to do so on some Unix-alikes. We can hide individual entry points via
#include <R_ext/Visibility.h>

SEXP attribute_hidden
spline_basis(SEXP knots, SEXP order, SEXP xvals, SEXP derivs)
...

SEXP attribute_hidden
spline_value(SEXP knots, SEXP coeff, SEXP order, SEXP x, SEXP deriv)
...
Chapter 5: System and foreign language interfaces 133

Alternatively, we can change the default visibility for all C symbols by including
PKG_CFLAGS = $(C_VISIBILITY)
in src/Makevars, and then we need to allow registration by declaring R_init_splines to
be visible:
#include <R_ext/Visibility.h>

void attribute_visible
R_init_splines(DllInfo *dll)
...
See Section 6.16 [Controlling visibility], page 186, for more details, including using Fortran
code and ways to restrict visibility on Windows.
• We end up with a file src/init.c containing

#include <stdlib.h>
#include <R_ext/Rdynload.h>
#include <R_ext/Visibility.h> // optional

#include "splines.h"

#define CALLDEF(name, n) {#name, (DL_FUNC) &name, n}

static const R_CallMethodDef R_CallDef[] = {

CALLDEF(spline_basis, 4),
CALLDEF(spline_value, 5),
{NULL, NULL, 0}
};

void
attribute_visible // optional
R_init_splines(DllInfo *dll)
{
R_registerRoutines(dll, NULL, R_CallDef, NULL, NULL);
R_useDynamicSymbols(dll, FALSE);
R_forceSymbols(dll, TRUE);
}

5.4.3 Linking to native routines in other packages

In addition to registering C routines to be called by R, it can at times be useful for one package
to make some of its C routines available to be called by C code in another package. The interface
consists of two routines declared in header R_ext/Rdynload.h as
void R_RegisterCCallable(const char *package, const char *name,
DL_FUNC fptr);
DL_FUNC R_GetCCallable(const char *package, const char *name);
A package packA that wants to make a C routine myCfun available to C code in other packages
would include the call
R_RegisterCCallable("packA", "myCfun", myCfun);
in its initialization function R_init_packA. A package packB that wants to use this routine
would retrieve the function pointer with a call of the form
p_myCfun = R_GetCCallable("packA", "myCfun");
Chapter 5: System and foreign language interfaces 134

As the type DL_FUNC is only appropriate for functions with no arguments, other users will need
to cast to an appropriate type. For example
typedef SEXP (*na_omit_xts_func) (SEXP x);
...
na_omit_xts_func fun = (na_omit_xts_func) R_GetCCallable("xts", "na_omit_xts");
return fun(x);
The author of packB is responsible for ensuring that p_myCfun has an appropriate declaration.
In the future R may provide some automated tools to simplify exporting larger numbers of
routines.
A package that wishes to make use of header files in other packages needs to declare them
as a comma-separated list in the field ‘LinkingTo’ in the DESCRIPTION file. This then arranges
for the include directories in the installed linked-to packages to be added to the include paths
for C and C++ code.
It must specify8 ‘Imports’ or ‘Depends’ of those packages, for they have to be loaded9 prior
to this one (so the path to their compiled code has been registered).
CRAN examples of the use of this mechanism include coxme (https://CRAN.R-project.org/
package=coxme) linking to bdsmatrix (https://CRAN.R-project.org/package=bdsmatrix)
and xts (https://CRAN.R-project.org/package=xts) linking to zoo (https://CRAN.
R-project.org/package=zoo).
NB: this mechanism is fragile, as changes to the interface provided by packA have to be
recognised by packB. The consequences of not doing so have included serious corruption to the
memory pool of the R session. Either packB has to depend on the exact version of packA or
there needs to be a mechanism for packB to test at runtime the version of packA it is linked to
matches that it was compiled against.

5.5 Creating shared objects

Shared objects for loading into R can be created using R CMD SHLIB. This accepts as arguments
a list of files which must be object files (with extension .o) or sources for C, C++, Fortran,
Objective C or Objective C++ (with extensions .c, .cc or .cpp, .f (fixed-form Fortran), .f90
or .f95 (free-form), .m, and .mm or .M, respectively), or commands to be passed to the linker. See
R CMD SHLIB --help (or the R help for SHLIB) for usage information. Note that files intended
for the Fortran pre-processor with extension .F are not accepted.
If compiling the source files does not work “out of the box”, you can specify additional flags by
setting some of the variables PKG_CPPFLAGS (for the C/C++ preprocessor, mainly ‘-I’, ‘-D’ and
‘-U’ flags), PKG_CFLAGS, PKG_CXXFLAGS, PKG_FFLAGS, PKG_OBJCFLAGS, and PKG_OBJCXXFLAGS
(for the C, C++, Fortran, Objective C, and Objective C++ compilers, respectively) in the file
Makevars in the compilation directory (or, of course, create the object files directly from the
command line). Similarly, variable PKG_LIBS in Makevars can be used for additional ‘-l’ and ‘-L’
flags to be passed to the linker when building the shared object. (Supplying linker commands
as arguments to R CMD SHLIB will take precedence over PKG_LIBS in Makevars.)
It is possible to arrange to include compiled code from other languages by setting the macro
‘OBJECTS’ in file Makevars, together with suitable rules to make the objects.
Flags that are already set (for example in file etcR_ARCH/Makeconf) can be overridden by
the environment variable MAKEFLAGS (at least for systems using a POSIX-compliant make), as
in (Bourne shell syntax)
MAKEFLAGS="CFLAGS=-O3" R CMD SHLIB *.c
8
whether or not ‘LinkingTo’ is used.
9
so there needs to be a corresponding import or importFrom entry in the NAMESPACE file.
Chapter 5: System and foreign language interfaces 135

It is also possible to set such variables in personal Makevars files, which are read after the
local Makevars and the system makefiles or in a site-wide Makevars.site file. See Section
“Customizing package compilation” in R Installation and Administration,
Note that as R CMD SHLIB uses Make, it will not remake a shared object just because the flags
have changed, and if test.c and test.f both exist in the current directory
R CMD SHLIB test.f
will compile test.c!
If the src subdirectory of an add-on package contains source code with one of the extensions
listed above or a file Makevars but not a file Makefile, R CMD INSTALL creates a shared object
(for loading into R through useDynlib in the NAMESPACE, or in the .onLoad function of the
package) using the R CMD SHLIB mechanism. If file Makevars exists it is read first, then the
system makefile and then any personal Makevars files.
If the src subdirectory of package contains a file Makefile, this is used by R CMD
INSTALL in place of the R CMD SHLIB mechanism. make is called with makefiles R_HOME/etcR_
ARCH/Makeconf, src/Makefile and any personal Makevars files (in that order). The first
target found in src/Makefile is used.
It is better to make use of a Makevars file rather than a Makefile: the latter should be
needed only exceptionally.
Under Windows the same commands work, but Makevars.win will be used in preference
to Makevars, and only src/Makefile.win will be used by R CMD INSTALL with src/Makefile
being ignored. Since R 4.2.0, Makevars.ucrt will be used in preference to Makevars.win and
src/Makefile.ucrt will be used in preference to src/Makefile.win. For past experiences of
building DLLs with a variety of compilers, see file ‘README.packages’. Under Windows you
can supply an exports definitions file called dllname-win.def: otherwise all entry points in
objects (but not libraries) supplied to R CMD SHLIB will be exported from the DLL. An example
is stats-win.def for the stats package: a CRAN example in package fastICA (https://CRAN.
R-project.org/package=fastICA).
If you feel tempted to read the source code and subvert these mechanisms, please resist. Far
too much developer time has been wasted in chasing down errors caused by failures to follow
this documentation, and even more by package authors demanding explanations as to why their
packages no longer work. In particular, undocumented environment or make variables are not
for use by package writers and are subject to change without notice.

5.6 Interfacing C++ code

Suppose we have the following hypothetical C++ library, consisting of the two files X.h and
X.cpp, and implementing the two classes X and Y which we want to use in R.

// X.h

class X {
public: X (); ~X ();
};

class Y {
public: Y (); ~Y ();
};
Chapter 5: System and foreign language interfaces 136


// X.cpp

#include <R.h>
#include "X.h"

static Y y;

X::X() { REprintf("constructor X\n"); }

X::~X() { REprintf("destructor X\n"); }
Y::Y() { REprintf("constructor Y\n"); }
Y::~Y() { REprintf("destructor Y\n"); }

To use with R, the only thing we have to do is writing a wrapper function and ensuring that
the function is enclosed in

extern "C" {

For example,

// X_main.cpp:

#include "X.h"

extern "C" {

void X_main () {
X x;
}

} // extern "C"

Compiling and linking should be done with the C++ compiler-linker (rather than the C
compiler-linker or the linker itself); otherwise, the C++ initialization code (and hence the con-
structor of the static variable Y) are not called. On a properly configured system, one can simply
use

R CMD SHLIB X.cpp X_main.cpp

to create the shared object, typically X.so (the file name extension may be different on your
platform). Now starting R yields

R version 2.14.1 Patched (2012-01-16 r58124)

Copyright (C) 2012 The R Foundation for Statistical Computing
...
Type "q()" to quit R.
Chapter 5: System and foreign language interfaces 137

R> dyn.load(paste("X", .Platform$dynlib.ext, sep = ""))

constructor Y
R> .C("X_main")
constructor X
destructor X
list()
R> q()
Save workspace image? [y/n/c]: y
destructor Y
The R for Windows FAQ (rw-FAQ) contains details of how to compile this example under
Windows.
Earlier versions of this example used C++ iostreams: this is best avoided. There is no
guarantee that the output will appear in the R console, and indeed it will not on the R for
Windows console. Use R code or the C entry points (see Section 6.5 [Printing], page 169) for
all I/O if at all possible. Examples have been seen where merely loading a DLL that contained
calls to C++ I/O upset R’s own C I/O (for example by resetting buffers on open files).
Most R header files can be included within C++ programs but they should not be included
within an extern "C" block (as they include system headers10 ).

5.6.1 External C++ code

Quite a lot of external C++ software is header-only (e.g. most of the Boost ‘libraries’ in-
cluding all those supplied by package BH (https://CRAN.R-project.org/package=BH), and
most of Armadillo as supplied by package RcppArmadillo (https://CRAN.R-project.org/
package=RcppArmadillo)) and so is compiled when an R package which uses it is installed.
This causes few problems.
A small number of external libraries used in R packages have a C++ interface to a li-
brary of compiled code, e.g. packages sf (https://CRAN.R-project.org/package=sf) and rjags
(https://CRAN.R-project.org/package=rjags). This raises many more problems! The C++
interface uses name-mangling and the ABI11 may depend on the compiler, version and even C++
defines12 , so requires the package C++ code to be compiled in exactly the same way as the library
(and what that was is often undocumented).
Even fewer external libraries use C++ internally but present a C interface, such as rgeos
(https://CRAN.R-project.org/package=rgeos). These require the C++ runtime library to be
linked into the package’s shared object/DLL, and this is best done by including a dummy C++
file in the package sources.
There is a trend to link to the C++ interfaces offered by C software such as hdf5, pcre and
ImageMagick. Their C interfaces are much preferred for portability (and can be used from C++
code). Also, the C++ interfaces are often optional in the software build or packaged separately
and so users installing from package sources are less likely to already have them installed.

5.7 Fortran I/O

We have already warned against the use of C++ iostreams not least because output is not
guaranteed to appear on the R console, and this warning applies equally to Fortran output to
units * and 6. See Section 6.5.1 [Printing from Fortran], page 169, which describes workarounds.
In the past most Fortran compilers implemented I/O on top of the C I/O system and so the
two interworked successfully. This was true of g77, but it is less true of gfortran as used in gcc
10
Even including C system headers in such a block has caused compilation errors.
11
https://en.wikipedia.org/wiki/Application_binary_interface.
12
For example, ‘_GLIBCXX_USE_CXX11_ABI’ in g++ 5.1 and later: https://gcc.gnu.org/onlinedocs/libstdc++/
manual/using_dual_abi.html.
Chapter 5: System and foreign language interfaces 138

4 and later. In particular, any package that makes use of Fortran I/O will when compiled on
Windows interfere with C I/O: when the Fortran I/O support code is initialized (typically when
the package is loaded) the C stdout and stderr are switched to LF line endings. (Function
init in file src/modules/lapack/init_win.c shows how to mitigate this. In a package this
would look something like
#ifdef _WIN32
# include <fcntl.h>
#endif

void R_init_mypkgname(DllInfo *dll)

{
// Native symbol registration calls

#ifdef _WIN32
// gfortran I/O initialization sets these to _O_BINARY
setmode(1, _O_TEXT); /* stdout */
setmode(2, _O_TEXT); /* stderr */
#endif
}
in the file used for native symbol registration.)

5.8 Linking to other packages

It is not in general possible to link a DLL in package packA to a DLL provided by package
packB (for the security reasons mentioned in Section 5.3 [dyn.load and dyn.unload], page 125,
and also because some platforms distinguish between shared objects and dynamic libraries), but
it is on Windows.
Note that there can be tricky versioning issues here, as package packB could be re-installed af-
ter package packA — it is desirable that the API provided by package packB remains backwards-
compatible.
Shipping a static library in package packB for other packages to link to avoids most of the
difficulties.

5.8.1 Unix-alikes
It is possible to link a shared object in package packA to a library provided by package packB
under limited circumstances on a Unix-alike OS. There are severe portability issues, so this is
not recommended for a distributed package.
This is easiest if packB provides a static library packB/lib/libpackB.a. (Note using di-
rectory lib rather than libs is conventional, and architecture-specific sub-directories may be
needed and are assumed in the sample code below. The code in the static library will need to be
compiled with PIC flags on platforms where it matters.) Then as the code from package packB
is incorporated when package packA is installed, we only need to find the static library at install
time for package packA. The only issue is to find package packB, and for that we can ask R by
something like (long lines broken for display here)
PKGB_PATH=`echo 'library(packB);
cat(system.file("lib", package="packB", mustWork=TRUE))' \
| "${R_HOME}/bin/R" --vanilla --no-echo`
PKG_LIBS="$(PKGB_PATH)$(R_ARCH)/libpackB.a"
For a dynamic library packB/lib/libpackB.so (packB/lib/libpackB.dylib on macOS:
note that you cannot link to a shared object, .so, on that platform) we could use
PKGB_PATH=`echo 'library(packB);
Chapter 5: System and foreign language interfaces 139

cat(system.file("lib", package="packB", mustWork=TRUE))' \

| "${R_HOME}/bin/R" --vanilla --no-echo`
PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -lpackB
This will work for installation, but very likely not when package packB is loaded, as the path
to package packB’s lib directory is not in the ld.so13 search path. You can arrange to put it
there before R is launched by setting (on some platforms) LD_RUN_PATH or LD_LIBRARY_PATH
or adding to the ld.so cache (see man ldconfig). On platforms that support it, the path to
the directory containing the dynamic library can be hardcoded at install time (which assumes
that the location of package packB will not be changed nor the package updated to a changed
API). On systems with the gcc or clang and the GNU linker (e.g. Linux) and some others this
can be done by e.g.
PKGB_PATH=`echo 'library(packB);
cat(system.file("lib", package="packB", mustWork=TRUE)))' \
| "${R_HOME}/bin/R" --vanilla --no-echo`
PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)" -lpackB
Some other systems (e.g. Solaris with its native linker) use -Rdir rather than -rpath,dir (and
this is accepted by the compiler as well as the linker).
It may be possible to figure out what is required semi-automatically from the result of R CMD
libtool --config (look for ‘hardcode’).
Making headers provided by package packB available to the code to be compiled in package
packA can be done by the LinkingTo mechanism (see Section 5.4 [Registering native routines],
page 126).

5.8.2 Windows
Suppose package packA wants to make use of compiled code provided by packB in DLL
packB/libs/exB.dll, possibly the package’s DLL packB/libs/packB.dll. (This can be ex-
tended to linking to more than one package in a similar way.) There are three issues to be
addressed:
• Making headers provided by package packB available to the code to be compiled in package
packA.
This is done by the LinkingTo mechanism (see Section 5.4 [Registering native routines],
page 126).
• preparing packA.dll to link to packB/libs/exB.dll.
This needs an entry in Makevars.win or Makevars.ucrt of the form
PKG_LIBS= -L<something> -lexB
and one possibility is that <something> is the path to the installed pkgB/libs directory.
To find that we need to ask R where it is by something like
PKGB_PATH=`echo 'library(packB);
cat(system.file("libs", package="packB", mustWork=TRUE))' \
| rterm --vanilla --no-echo`
PKG_LIBS= -L"$(PKGB_PATH)$(R_ARCH)" -lexB
Another possibility is to use an import library, shipping with package packA an exports file
exB.def. Then Makevars.win (or Makevars.ucrt) could contain
PKG_LIBS= -L. -lexB

all: $(SHLIB) before

13
dyld on macOS, and DYLD_LIBRARY_PATHS below.
Chapter 5: System and foreign language interfaces 140

before: libexB.dll.a
libexB.dll.a: exB.def
and then installing package packA will make and use the import library for exB.dll. (One
way to prepare the exports file is to use pexports.exe.)
• loading packA.dll which depends on exB.dll.
If exB.dll was used by package packB (because it is in fact packB.dll or packB.dll
depends on it) and packB has been loaded before packA, then nothing more needs to be
done as exB.dll will already be loaded into the R executable. (This is the most common
scenario.)
More generally, we can use the DLLpath argument to library.dynam to ensure that exB.dll
is found, for example by setting
library.dynam("packA", pkg, lib,
DLLpath = system.file("libs", package="packB"))
Note that DLLpath can only set one path, and so for linking to two or more packages you
would need to resort to setting environment variable PATH.

5.9 Handling R objects in C

Using C code to speed up the execution of an R function is often very fruitful. Traditionally this
has been done via the .C function in R. However, if a user wants to write C code using internal
R data structures, then that can be done using the .Call and .External functions. The syntax
for the calling function in R in each case is similar to that of .C, but the two functions have
different C interfaces. Generally the .Call interface is simpler to use, but .External is a little
more general.
A call to .Call is very similar to .C, for example
.Call("convolve2", a, b)
The first argument should be a character string giving a C symbol name of code that has already
been loaded into R. Up to 65 R objects can passed as arguments. The C side of the interface is
#include <R.h>
#include <Rinternals.h>

SEXP convolve2(SEXP a, SEXP b)

...
A call to .External is almost identical
.External("convolveE", a, b)
but the C side of the interface is different, having only one argument
#include <R.h>
#include <Rinternals.h>

SEXP convolveE(SEXP args)

...
Here args is a LISTSXP, a Lisp-style pairlist from which the arguments can be extracted.
In each case the R objects are available for manipulation via a set of functions and macros
defined in the header file Rinternals.h or some S-compatibility macros14 See Section 5.10
[Interface functions .Call and .External], page 151, for details on .Call and .External.

14
That is, similar to those defined in S version 4 from the 1990s: these are not kept up to date and are not
recommended for new projects.
Chapter 5: System and foreign language interfaces 141

Before you decide to use .Call or .External, you should look at other alternatives. First,
consider working in interpreted R code; if this is fast enough, this is normally the best option.
You should also see if using .C is enough. If the task to be performed in C is simple enough
involving only atomic vectors and requiring no call to R, .C suffices. A great deal of useful
code was written using just .C before .Call and .External were available. These interfaces
allow much more control, but they also impose much greater responsibilities so need to be used
with care. Neither .Call nor .External copy their arguments: you should treat arguments you
receive through these interfaces as read-only.
To handle R objects from within C code we use the macros and functions that have been
used to implement the core parts of R. A public15 subset of these is defined in the header
file Rinternals.h in the directory R_INCLUDE_DIR (default R_HOME/include) that should be
available on any R installation.
A substantial amount of R, including the standard packages, is implemented using the func-
tions and macros described here, so the R source code provides a rich source of examples and
“how to do it”: do make use of the source code for inspirational examples.
It is necessary to know something about how R objects are handled in C code. All the R
objects you will deal with will be handled with the type SEXP 16 , which is a pointer to a structure
with typedef SEXPREC. Think of this structure as a variant type that can handle all the usual
types of R objects, that is vectors of various modes, functions, environments, language objects
and so on. The details are given later in this section and in Section “R Internal Structures” in
R Internals, but for most purposes the programmer does not need to know them. Think rather
of a model such as that used by Visual Basic, in which R objects are handed around in C code
(as they are in interpreted R code) as the variant type, and the appropriate part is extracted
for, for example, numerical calculations, only when it is needed. As in interpreted R code, much
use is made of coercion to force the variant object to the right type.

5.9.1 Handling the effects of garbage collection

We need to know a little about the way R handles memory allocation. The memory allocated for
R objects is not freed by the user; instead, the memory is from time to time garbage collected.
That is, some or all of the allocated memory not being used is freed or marked as re-usable.
The R object types are represented by a C structure defined by a typedef SEXPREC in
Rinternals.h. It contains several things among which are pointers to data blocks and to
other SEXPRECs. A SEXP is simply a pointer to a SEXPREC.
If you create an R object in your C code, you must tell R that you are using the object by
using the PROTECT macro on a pointer to the object. This tells R that the object is in use so it
is not destroyed during garbage collection. Notice that it is the object which is protected, not
the pointer variable. It is a common mistake to believe that if you invoked PROTECT(p) at some
point then p is protected from then on, but that is not true once a new object is assigned to p.
Protecting an R object automatically protects all the R objects pointed to in the correspond-
ing SEXPREC, for example all elements of a protected list are automatically protected.
The programmer is solely responsible for housekeeping the calls to PROTECT. There is a
corresponding macro UNPROTECT that takes as argument an int giving the number of objects
to unprotect when they are no longer needed. The protection mechanism is stack-based, so
UNPROTECT(n) unprotects the last n objects which were protected. The calls to PROTECT and
UNPROTECT must balance when the user’s code returns and should balance in all functions. R
will warn about "stack imbalance in .Call" (or .External) if the housekeeping is wrong.

15
see Chapter 6 [The R API], page 165: note that these are not all part of the API.
16
SEXP is an acronym for S imple EXP ression, common in LISP-like language syntaxes.
Chapter 5: System and foreign language interfaces 142

Here is a small example of creating an R numeric vector in C code:

#include <R.h>
#include <Rinternals.h>

SEXP ab;
....
ab = PROTECT(allocVector(REALSXP, 2));
REAL(ab)[0] = 123.45;
REAL(ab)[1] = 67.89;
UNPROTECT(1);
Now, the reader may ask how the R object could possibly get removed during those manipu-
lations, as it is just our C code that is running. As it happens, we can do without the protection
in this example, but in general we do not know (nor want to know) what is hiding behind the
R macros and functions we use, and any of them might cause memory to be allocated, hence
garbage collection and hence our object ab to be removed. It is usually wise to err on the side
of caution and assume that any of the R macros and functions might remove the object.
In some cases it is necessary to keep better track of whether protection is really needed. Be
particularly aware of situations where a large number of objects are generated. The pointer
protection stack has a fixed size (default 10,000) and can become full. It is not a good idea
then to just PROTECT everything in sight and UNPROTECT several thousand objects at the end. It
will almost invariably be possible to either assign the objects as part of another object (which
automatically protects them) or unprotect them immediately after use.
There is a less-used macro UNPROTECT_PTR(s) that unprotects the object pointed to by the
SEXP s, even if it is not the top item on the pointer protection stack. This macro was introduced
for use in the parser, where the code interfacing with the R heap is generated and the generator
cannot be configured to insert proper calls to PROTECT and UNPROTECT. However, UNPROTECT_PTR
is dangerous to use in combination with UNPROTECT when the same object has been protected
multiple times. It has been superseded by multi-set based functions R_PreserveInMSet and
R_ReleaseFromMSet, which protect objects in a multi-set created by R_NewPreciousMSet and
typically itself protected using PROTECT. These functions should not be needed outside parsers.

Sometimes an object is changed (for example duplicated, coerced or grown) yet the current
value needs to be protected. For these cases PROTECT_WITH_INDEX saves an index of the pro-
tection location that can be used to replace the protected value using REPROTECT. For example
(from the internal code for optim)
PROTECT_INDEX ipx;

....
PROTECT_WITH_INDEX(s = eval(OS->R_fcall, OS->R_env), &ipx);
REPROTECT(s = coerceVector(s, REALSXP), ipx);
Note that it is dangerous to mix UNPROTECT_PTR also with PROTECT_WITH_INDEX, as the
former changes the protection locations of objects that were protected after the one being un-
protected.
There is another way to avoid the effects of garbage collection: a call to R_PreserveObject
adds an object to an internal list of objects not to be collects, and a subsequent call to R_
ReleaseObject removes it from that list. This provides a way for objects which are not returned
as part of R objects to be protected across calls to compiled code: on the other hand it becomes
the user’s responsibility to release them when they are no longer needed (and this often requires
the use of a finalizer). It is less efficient than the normal protection mechanism, and should be
used sparingly.
Chapter 5: System and foreign language interfaces 143

For functions from packages as well as R to safely co-operate in protecting objects, certain
rules have to be followed:
• Pointer-protection balance. Calls to PROTECT and UNPROTECT should balance in each func-
tion. A function may only call UNPROTECT or REPROTECT on objects it has itself protected.
Note that the pointer protection stack balance is restored automatically on non-local trans-
fer of control (See Section 6.12 [Condition handling and cleanup code], page 183.), as if a
call to UNPROTECT was invoked with the right argument.
• Caller protection. It is the responsibility of the caller that all arguments passed to a function
are protected and will stay protected for the whole execution of the callee. Typically this
is achieved by PROTECT and UNPROTECT calls.
• Protecting return values. Any R objects returned from a function are unprotected (the callee
must maintain pointer-protection balance), and hence should be protected immediately by
the caller. To be safe against future code changes, assume that any R object returned from
any function may need protection. Note that even when conceptually returning an existing
protected object, that object may be duplicated.
• All functions/macros allocate. To be safe against future code changes, assume that any
function or macro may allocate and hence garbage collector may run and destroy unpro-
tected objects.
It is always safe and recommended to follow those rules. In fact, several R functions and
macros protect their own arguments and some functions do not allocate or do not allocate when
used in a certain way, but that is subject to change, so relying on that may be fragile. PROTECT
and PROTECT_WITH_INDEX can be safely called with unprotected arguments and UNPROTECT does
not allocate.

5.9.2 Allocating storage

For many purposes it is sufficient to allocate R objects and manipulate those. There are quite
a few allocXxx functions defined in Rinternals.h—you may want to explore them.
One that is commonly used is allocVector, the C-level equivalent of R-level vector() and its
wrappers such as integer() and character(). One distinction is that whereas the R functions
always initialize the elements of the vector, allocVector only does so for lists, expressions and
character vectors (the cases where the elements are themselves R objects).
If storage is required for C objects during the calculations this is best allocating by calling
R_alloc; see Section 6.1 [Memory allocation], page 165. All of these memory allocation routines
do their own error-checking, so the programmer may assume that they will raise an error and
not return if the memory cannot be allocated.

5.9.3 Details of R types

Users of the Rinternals.h macros will need to know how the R types are known internally. The
different R data types are represented in C by SEXPTYPE. Some of these are familiar from R
and some are internal data types. The usual R object modes are given in the table.
SEXPTYPE R equivalent
REALSXP numeric with storage mode double
INTSXP integer
CPLXSXP complex
LGLSXP logical
STRSXP character
VECSXP list (generic vector)
LISTSXP pairlist
DOTSXP a ‘...’ object
NILSXP NULL
Chapter 5: System and foreign language interfaces 144

SYMSXP name/symbol
CLOSXP function or function closure
ENVSXP environment
Among the important internal SEXPTYPEs are LANGSXP, CHARSXP, PROMSXP, etc. (N.B.: although
it is possible to return objects of internal types, it is unsafe to do so as assumptions are made
about how they are handled which may be violated at user-level evaluation.) More details are
given in Section “R Internal Structures” in R Internals.
Unless you are very sure about the type of the arguments, the code should check the data
types. Sometimes it may also be necessary to check data types of objects created by evaluating
an R expression in the C code. You can use functions like isReal, isInteger and isString
to do type checking. Other such functions declared in the header file Rinternals.h include
isNull, isSymbol, isLogical, isComplex, isExpression, and isEnvironment. All of these
take a SEXP as argument and return 1 or 0 to indicate TRUE or FALSE.
What happens if the SEXP is not of the correct type? Sometimes you have no other option
except to generate an error. You can use the function error for this. It is usually better to
coerce the object to the correct type. For example, if you find that an SEXP is of the type
INTEGER, but you need a REAL object, you can change the type by using
newSexp = PROTECT(coerceVector(oldSexp, REALSXP));
Protection is needed as a new object is created; the object formerly pointed to by the SEXP is
still protected but now unused.17
All the coercion functions do their own error-checking, and generate NAs with a warning or
stop with an error as appropriate.
Note that these coercion functions are not the same as calling as.numeric (and so on) in R
code, as they do not dispatch on the class of the object. Thus it is normally preferable to do
the coercion in the calling R code.
So far we have only seen how to create and coerce R objects from C code, and how to extract
the numeric data from numeric R vectors. These can suffice to take us a long way in interfacing
R objects to numerical algorithms, but we may need to know a little more to create useful return
objects.

5.9.4 Attributes
Many R objects have attributes: some of the most useful are classes and the dim and dimnames
that mark objects as matrices or arrays. It can also be helpful to work with the names attribute
of vectors.
To illustrate this, let us write code to take the outer product of two vectors (which outer
and %o% already do). As usual the R code is simple
out <- function(x, y)
{
storage.mode(x) <- storage.mode(y) <- "double"
.Call("out", x, y)
}
where we expect x and y to be numeric vectors (possibly integer), possibly with names. This
time we do the coercion in the calling R code.
C code to do the computations is

17
If no coercion was required, coerceVector would have passed the old object through unchanged.
Chapter 5: System and foreign language interfaces 145

#include <R.h>
#include <Rinternals.h>

SEXP out(SEXP x, SEXP y)

{
int nx = length(x), ny = length(y);
SEXP ans = PROTECT(allocMatrix(REALSXP, nx, ny));
double *rx = REAL(x), *ry = REAL(y), *rans = REAL(ans);
for(int i = 0; i < nx; i++) {
double tmp = rx[i];
for(int j = 0; j < ny; j++)
rans[i + nx*j] = tmp * ry[j];
}
UNPROTECT(1);
return ans;
}
Note the way REAL is used: as it is a function call it can be considerably faster to store the result
and index that.
However, we would like to set the dimnames of the result. We can use
#include <R.h>
#include <Rinternals.h>

SEXP out(SEXP x, SEXP y)

{
int nx = length(x), ny = length(y);
SEXP ans = PROTECT(allocMatrix(REALSXP, nx, ny));
double *rx = REAL(x), *ry = REAL(y), *rans = REAL(ans);

for(int i = 0; i < nx; i++) {

double tmp = rx[i];
for(int j = 0; j < ny; j++)
rans[i + nx*j] = tmp * ry[j];
}

SEXP dimnames = PROTECT(allocVector(VECSXP, 2));

SET_VECTOR_ELT(dimnames, 0, getAttrib(x, R_NamesSymbol));
SET_VECTOR_ELT(dimnames, 1, getAttrib(y, R_NamesSymbol));
setAttrib(ans, R_DimNamesSymbol, dimnames);

UNPROTECT(2);
return ans;
}
This example introduces several new features. The getAttrib and setAttrib functions get
and set individual attributes. Their second argument is a SEXP defining the name in the symbol
table of the attribute we want; these and many such symbols are defined in the header file
Rinternals.h.
There are shortcuts here too: the functions namesgets, dimgets and dimnamesgets are the
internal versions of the default methods of names<-, dim<- and dimnames<- (for vectors and
arrays), and there are functions such as GetColNames, GetRowNames, GetMatrixDimnames and
GetArrayDimnames.
Chapter 5: System and foreign language interfaces 146

What happens if we want to add an attribute that is not pre-defined? We need to add a
symbol for it via a call to install. Suppose for illustration we wanted to add an attribute
"version" with value 3.0. We could use
SEXP version;
version = PROTECT(allocVector(REALSXP, 1));
REAL(version)[0] = 3.0;
setAttrib(ans, install("version"), version);
UNPROTECT(1);
Using install when it is not needed is harmless and provides a simple way to retrieve the
symbol from the symbol table if it is already installed. However, the lookup takes a non-trivial
amount of time, so consider code such as
static SEXP VerSymbol = NULL;
...
if (VerSymbol == NULL) VerSymbol = install("version");
if it is to be done frequently.
This example can be simplified by another convenience function:
SEXP version = PROTECT(ScalarReal(3.0));
setAttrib(ans, install("version"), version);
UNPROTECT(1);

5.9.5 Classes
In R the class is just the attribute named "class" so it can be handled as such, but there is a
shortcut classgets. Suppose we want to give the return value in our example the class "mat".
We can use
#include <R.h>
#include <Rinternals.h>
....
SEXP ans, dim, dimnames, class;
....
class = PROTECT(allocVector(STRSXP, 1));
SET_STRING_ELT(class, 0, mkChar("mat"));
classgets(ans, class);
UNPROTECT(4);
return ans;
}
As the value is a character vector, we have to know how to create that from a C character array,
which we do using the function mkChar.

5.9.6 Handling lists

Some care is needed with lists, as R moved early on from using LISP-like lists (now called
“pairlists”) to S-like generic vectors. As a result, the appropriate test for an object of mode
list is isNewList, and we need allocVector(VECSXP, n) and not allocList(n).
List elements can be retrieved or set by direct access to the elements of the generic vector.
Suppose we have a list object
a <- list(f = 1, g = 2, h = 3)
Then we can access a$g as a[[2]] by
double g;
....
g = REAL(VECTOR_ELT(a, 1))[0];
Chapter 5: System and foreign language interfaces 147

This can rapidly become tedious, and the following function (based on one in package stats)
is very useful:

/* get the list element named str, or return NULL */

SEXP getListElement(SEXP list, const char *str)

{
SEXP elmt = R_NilValue, names = getAttrib(list, R_NamesSymbol);

for (int i = 0; i < length(list); i++)

if(strcmp(CHAR(STRING_ELT(names, i)), str) == 0) {
elmt = VECTOR_ELT(list, i);
break;
}
return elmt;
}

and enables us to say

double g;
g = REAL(getListElement(a, "g"))[0];

5.9.7 Handling character data

R character vectors are stored as STRSXPs, a vector type like VECSXP where every element is
of type CHARSXP. The CHARSXP elements of STRSXPs are accessed using STRING_ELT and SET_
STRING_ELT.

CHARSXPs are read-only objects and must never be modified. In particular, the C-style string
contained in a CHARSXP should be treated as read-only and for this reason the CHAR function used
to access the character data of a CHARSXP returns (const char *) (this also allows compilers to
issue warnings about improper use). Since CHARSXPs are immutable, the same CHARSXP can be
shared by any STRSXP needing an element representing the same string. R maintains a global
cache of CHARSXPs so that there is only ever one CHARSXP representing a given string in memory.

You can obtain a CHARSXP by calling mkChar and providing a NUL-terminated C-style string.
This function will return a pre-existing CHARSXP if one with a matching string already exists,
otherwise it will create a new one and add it to the cache before returning it to you. The variant
mkCharLen can be used to create a CHARSXP from part of a buffer and will ensure null-termination.

Note that R character strings are restricted to 2^31 - 1 bytes, and hence so should the input
to mkChar be (C allows longer strings on 64-bit platforms).

5.9.8 Finding and setting variables

It will be usual that all the R objects needed in our C computations are passed as arguments to
.Call or .External, but it is possible to find the values of R objects from within the C given
their names. The following code is the equivalent of get(name, envir = rho).
Chapter 5: System and foreign language interfaces 148

SEXP getvar(SEXP name, SEXP rho)

{
SEXP ans;

if(!isString(name) || length(name) != 1)
error("name is not a single string");
if(!isEnvironment(rho))
error("rho should be an environment");
ans = findVar(installChar(STRING_ELT(name, 0)), rho);
Rprintf("first value is %f\n", REAL(ans)[0]);
return R_NilValue;
}
The main work is done by findVar, but to use it we need to install name as a name in the
symbol table. As we wanted the value for internal use, we return NULL.
Similar functions with syntax
void defineVar(SEXP symbol, SEXP value, SEXP rho)
void setVar(SEXP symbol, SEXP value, SEXP rho)
can be used to assign values to R variables. defineVar creates a new binding or changes the value
of an existing binding in the specified environment frame; it is the analogue of assign(symbol,
value, envir = rho, inherits = FALSE), but unlike assign, defineVar does not make a copy
of the object value.18 setVar searches for an existing binding for symbol in rho or its enclosing
environments. If a binding is found, its value is changed to value. Otherwise, a new binding with
the specified value is created in the global environment. This corresponds to assign(symbol,
value, envir = rho, inherits = TRUE).
At times it may also be useful to create a new environment frame in C code. R_NewEnv is a
C version of the R function new.env:
SEXP R_NewEnv(SEXP enclos, int hash, int size)

5.9.9 Some convenience functions

Some operations are done so frequently that there are convenience functions to handle them.
(All these are provided via the header file Rinternals.h.)
Suppose we wanted to pass a single logical argument ignore_quotes: we could use
int ign = asLogical(ignore_quotes);
if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FALSE");
which will do any coercion needed (at least from a vector argument), and return NA_LOGICAL if
the value passed was NA or coercion failed. There are also asInteger, asReal and asComplex.
The function asChar returns a CHARSXP. All of these functions ignore any elements of an input
vector after the first.
To return a length-one real vector we can use
double x;

...
return ScalarReal(x);
and there are versions of this for all the atomic vector types (those for a length-one character
vector being ScalarString with argument a CHARSXP and mkString with argument const char
*).
18
You can assign a copy of the object in the environment frame rho using defineVar(symbol,
duplicate(value), rho)).
Chapter 5: System and foreign language interfaces 149

SEXP ScalarReal(double);
SEXP ScalarInteger(int);
SEXP ScalarLogical(int)
SEXP ScalarRaw(Rbyte);
SEXP ScalarComplex(Rcomplex);
SEXP ScalarString(SEXP);
SEXP mkString(const char *);
Some of the isXXXX functions differ from their apparent R-level counterparts: for example
isVector is true for any atomic vector type (isVectorAtomic) and for lists and expressions
(isVectorList) (with no check on attributes). isMatrix is a test of a length-2 "dim" attribute.

Rboolean isVector(SEXP);
Rboolean isVectorAtomic(SEXP);
Rboolean isVectorList(SEXP);
Rboolean isMatrix(SEXP);
Rboolean isPairList(SEXP);
Rboolean isPrimitive(SEXP);
Rboolean isTs(SEXP);
Rboolean isNumeric(SEXP);
Rboolean isArray(SEXP);
Rboolean isFactor(SEXP);
Rboolean isObject(SEXP);
Rboolean isFunction(SEXP);
Rboolean isLanguage(SEXP);
Rboolean isNewList(SEXP);
Rboolean isList(SEXP);
Rboolean isOrdered(SEXP);
Rboolean isUnordered(SEXP);
There are a series of small macros/functions to help construct pairlists and language objects
(whose internal structures just differ by SEXPTYPE). Function CONS(u, v) is the basic building
block: it constructs a pairlist from u followed by v (which is a pairlist or R_NilValue). LCONS is
a variant that constructs a language object. Functions list1 to list6 construct a pairlist from
one to six items, and lang1 to lang6 do the same for a language object (a function to call plus
zero to five arguments). Functions elt and lastElt find the i-th element and the last element
of a pairlist, and nthcdr returns a pointer to the n-th position in the pairlist (whose CAR is the
n-th item).
Functions str2type and type2str map R length-one character strings to and from SEXPTYPE
numbers, and type2char maps numbers to C character strings.

5.9.9.1 Semi-internal convenience functions

There is quite a collection of functions that may be used in your C code if you are willing to
adapt to rare “API” changes. These typically contain “workhorses” of their R counterparts.
Functions any_duplicated and any_duplicated3 are fast versions of R’s
any(duplicated(.)).
Function R_compute_identical corresponds to R’s identical function.

5.9.10 Named objects and copying

[The NAMED mechanism has been replaced by reference counting.]
When assignments are done in R such as
x <- 1:10
Chapter 5: System and foreign language interfaces 150

y <- x
the named object is not necessarily copied, so after those two assignments y and x are bound to
the same SEXPREC (the structure a SEXP points to). This means that any code which alters one of
them has to make a copy before modifying the copy if the usual R semantics are to apply. Note
that whereas .C and .Fortran do copy their arguments (unless the dangerous dup = FALSE is
used), .Call and .External do not. So duplicate is commonly called on arguments to .Call
before modifying them.
However, at least some of this copying is unneeded. In the first assignment shown, x <- 1:10,
R first creates an object with value 1:10 and then assigns it to x but if x is modified no copy is
necessary as the temporary object with value 1:10 cannot be referred to again. R distinguishes
between named and unnamed objects via a field in a SEXPREC that can be accessed via the
macros NAMED and SET_NAMED. This can take values

0 The object is not bound to any symbol

1 The object has been bound to exactly one symbol
>= 2 The object has potentially been bound to two or more symbols, and one should
act as if another variable is currently bound to this value. The maximal value is
NAMEDMAX.

Note the past tenses: R does not do currently do full reference counting and there may currently
be fewer bindings.
It is safe to modify the value of any SEXP for which NAMED(foo) is zero, and if NAMED(foo) is
two or more, the value should be duplicated (via a call to duplicate) before any modification.
Note that it is the responsibility of the author of the code making the modification to do the
duplication, even if it is x whose value is being modified after y <- x.
The case NAMED(foo) == 1 allows some optimization, but it can be ignored (and duplication
done whenever NAMED(foo) > 0). (This optimization is not currently usable in user code.) It is
intended for use within replacement functions. Suppose we used
x <- 1:10
foo(x) <- 3
which is computed as
x <- 1:10
x <- "foo<-"(x, 3)
Then inside "foo<-" the object pointing to the current value of x will have NAMED(foo) as one,
and it would be safe to modify it as the only symbol bound to it is x and that will be rebound
immediately. (Provided the remaining code in "foo<-" make no reference to x, and no one is
going to attempt a direct call such as y <- "foo<-"(x).)
This mechanism was replaced in R 4.0.0. To support future changes, package code should
use the macros MAYBE_REFERENCED, MAYBE_SHARED, and MARK_NOT_MUTABLE. These currently
correspond to

MAYBE_REFERENCED(x)
NAMED(x) > 0
MAYBE_SHARED(x)
NAMED(x) > 1
MARK_NOT_MUTABLE(x)
SET_NAMED(x, NAMEDMAX)
Chapter 5: System and foreign language interfaces 151

5.10 Interface functions .Call and .External

In this section we consider the details of the R/C interfaces.

These two interfaces have almost the same functionality. .Call is based on the interface of
the same name in S version 4, and .External is based on R’s .Internal. .External is more
complex but allows a variable number of arguments.

5.10.1 Calling .Call

Let us convert our finite convolution example to use .Call. The calling function in R is

conv <- function(a, b) .Call("convolve2", a, b)

which could hardly be simpler, but as we shall see all the type coercion is transferred to the C
code, which is

#include <R.h>
#include <Rinternals.h>

SEXP convolve2(SEXP a, SEXP b)

{
int na, nb, nab;
double *xa, *xb, *xab;
SEXP ab;

a = PROTECT(coerceVector(a, REALSXP));
b = PROTECT(coerceVector(b, REALSXP));
na = length(a); nb = length(b); nab = na + nb - 1;
ab = PROTECT(allocVector(REALSXP, nab));
xa = REAL(a); xb = REAL(b); xab = REAL(ab);
for(int i = 0; i < nab; i++) xab[i] = 0.0;
for(int i = 0; i < na; i++)
for(int j = 0; j < nb; j++) xab[i + j] += xa[i] * xb[j];
UNPROTECT(3);
return ab;
}

5.10.2 Calling .External

We can use the same example to illustrate .External. The R code changes only by replacing
.Call by .External

conv <- function(a, b) .External("convolveE", a, b)

but the main change is how the arguments are passed to the C code, this time as a single SEXP.
The only change to the C code is how we handle the arguments.
Chapter 5: System and foreign language interfaces 152

#include <R.h>
#include <Rinternals.h>

SEXP convolveE(SEXP args)

{
int i, j, na, nb, nab;
double *xa, *xb, *xab;
SEXP a, b, ab;

a = PROTECT(coerceVector(CADR(args), REALSXP));
b = PROTECT(coerceVector(CADDR(args), REALSXP));
...
}
Once again we do not need to protect the arguments, as in the R side of the interface they are
objects that are already in use. The macros
first = CADR(args);
second = CADDR(args);
third = CADDDR(args);
fourth = CAD4R(args);
fifth = CAD5R(args);
provide convenient ways to access the first four arguments. More generally we can use the CDR
and CAR macros as in
args = CDR(args); a = CAR(args);
args = CDR(args); b = CAR(args);
which clearly allows us to extract an unlimited number of arguments (whereas .Call has a limit,
albeit at 65 not a small one).
More usefully, the .External interface provides an easy way to handle calls with a variable
number of arguments, as length(args) will give the number of arguments supplied (of which
the first is ignored). We may need to know the names (‘tags’) given to the actual arguments,
which we can by using the TAG macro and using something like the following example, that
prints the names and the first value of its arguments if they are vector types.
SEXP showArgs(SEXP args)
{
args = CDR(args); /* skip 'name' */
for(int i = 0; args != R_NilValue; i++, args = CDR(args)) {
const char *name =
isNull(TAG(args)) ? "" : CHAR(PRINTNAME(TAG(args)));
SEXP el = CAR(args);
if (length(el) == 0) {
Rprintf("[%d] '%s' R type, length 0\n", i+1, name);
continue;
}
switch(TYPEOF(el)) {
case REALSXP:
Rprintf("[%d] '%s' %f\n", i+1, name, REAL(el)[0]);
break;
case LGLSXP:
case INTSXP:
Rprintf("[%d] '%s' %d\n", i+1, name, INTEGER(el)[0]);
break;
Chapter 5: System and foreign language interfaces 153

case CPLXSXP:
{
Rcomplex cpl = COMPLEX(el)[0];
Rprintf("[%d] '%s' %f + %fi\n", i+1, name, cpl.r, cpl.i);
}
break;
case STRSXP:
Rprintf("[%d] '%s' %s\n", i+1, name,
CHAR(STRING_ELT(el, 0)));
break;
default:
Rprintf("[%d] '%s' R type\n", i+1, name);
}
}
return R_NilValue;
}
This can be called by the wrapper function
showArgs <- function(...) invisible(.External("showArgs", ...))
Note that this style of programming is convenient but not necessary, as an alternative style is
showArgs1 <- function(...) invisible(.Call("showArgs1", list(...)))
The (very similar) C code is in the scripts.
Additional functions for accessing pairlist components are CAAR, CDAR, CDDR, and CDDDR.
These components can be modified with SETCAR, SETCDR, SETCADR, SETCADDR, SETCADDDR, and
SETCAD4R.

5.10.3 Missing and special values

One piece of error-checking the .C call does (unless NAOK is true) is to check for missing (NA)
and IEEE special values (Inf, -Inf and NaN) and give an error if any are found. With the .Call
interface these will be passed to our code. In this example the special values are no problem,
as IEC 60559 arithmetic will handle them correctly. In the current implementation this is also
true of NA as it is a type of NaN, but it is unwise to rely on such details. Thus we will re-write
the code to handle NAs using macros defined in R_ext/Arith.h included by R.h.
The code changes are the same in any of the versions of convolve2 or convolveE:
...
for(int i = 0; i < na; i++)
for(int j = 0; j < nb; j++)
if(ISNA(xa[i]) || ISNA(xb[j]) || ISNA(xab[i + j]))
xab[i + j] = NA_REAL;
else
xab[i + j] += xa[i] * xb[j];
...
Note that the ISNA macro, and the similar macros ISNAN (which checks for NaN or NA) and
R_FINITE (which is false for NA and all the special values), only apply to numeric values of type
double. Missingness of integers, logicals and character strings can be tested by equality to the
constants NA_INTEGER, NA_LOGICAL and NA_STRING. These and NA_REAL can be used to set
elements of R vectors to NA.
The constants R_NaN, R_PosInf and R_NegInf can be used to set doubles to the special
values.
Chapter 5: System and foreign language interfaces 154

5.11 Evaluating R expressions from C

The main function we will use is
SEXP eval(SEXP expr, SEXP rho);
the equivalent of the interpreted R code eval(expr, envir = rho) (so rho must be an environ-
ment), although we can also make use of findVar, defineVar and findFun (which restricts the
search to functions).
To see how this might be applied, here is a simplified internal version of lapply for expres-
sions, used as
a <- list(a = 1:5, b = rnorm(10), test = runif(100))
.Call("lapply", a, quote(sum(x)), new.env())
with C code
SEXP lapply(SEXP list, SEXP expr, SEXP rho)
{
int n = length(list);
SEXP ans;

if(!isNewList(list)) error("'list' must be a list");

if(!isEnvironment(rho)) error("'rho' should be an environment");
ans = PROTECT(allocVector(VECSXP, n));
for(int i = 0; i < n; i++) {
defineVar(install("x"), VECTOR_ELT(list, i), rho);
SET_VECTOR_ELT(ans, i, eval(expr, rho));
}
setAttrib(ans, R_NamesSymbol, getAttrib(list, R_NamesSymbol));
UNPROTECT(1);
return ans;
}
It would be closer to lapply if we could pass in a function rather than an expression. One
way to do this is via interpreted R code as in the next example, but it is possible (if somewhat
obscure) to do this in C code. The following is based on the code in src/main/optimize.c.
SEXP lapply2(SEXP list, SEXP fn, SEXP rho)
{
int n = length(list);
SEXP R_fcall, ans;

if(!isNewList(list)) error("'list' must be a list");

if(!isFunction(fn)) error("'fn' must be a function");
if(!isEnvironment(rho)) error("'rho' should be an environment");
R_fcall = PROTECT(lang2(fn, R_NilValue));
ans = PROTECT(allocVector(VECSXP, n));
for(int i = 0; i < n; i++) {
SETCADR(R_fcall, VECTOR_ELT(list, i));
SET_VECTOR_ELT(ans, i, eval(R_fcall, rho));
}
setAttrib(ans, R_NamesSymbol, getAttrib(list, R_NamesSymbol));
UNPROTECT(2);
return ans;
}
used by
.Call("lapply2", a, sum, new.env())
Chapter 5: System and foreign language interfaces 155

Function lang2 creates an executable pairlist of two elements, but this will only be clear to
those with a knowledge of a LISP-like language.

As a more comprehensive example of constructing an R call in C code and evaluating, consider

the following fragment of printAttributes in src/main/print.c.

/* Need to construct a call to

print(CAR(a), digits=digits)
based on the R_print structure, then eval(call, env).
See do_docall for the template for this sort of thing.
*/
SEXP s, t;
t = s = PROTECT(allocList(3));
SET_TYPEOF(s, LANGSXP);
SETCAR(t, install("print")); t = CDR(t);
SETCAR(t, CAR(a)); t = CDR(t);
SETCAR(t, ScalarInteger(digits));
SET_TAG(t, install("digits"));
eval(s, env);
UNPROTECT(1);

At this point CAR(a) is the R object to be printed, the current attribute. There are three steps:
the call is constructed as a pairlist of length 3, the list is filled in, and the expression represented
by the pairlist is evaluated.

A pairlist is quite distinct from a generic vector list, the only user-visible form of list in R. A
pairlist is a linked list (with CDR(t) computing the next entry), with items (accessed by CAR(t))
and names or tags (set by SET_TAG). In this call there are to be three items, a symbol (pointing
to the function to be called) and two argument values, the first unnamed and the second named.
Setting the type to LANGSXP makes this a call which can be evaluated.

Customarily, the evaluation environment is passed from the calling R code (see rho above). In
special cases it is possible that the C code may need to obtain the current evaluation environment
which can be done via R_GetCurrentEnv() function.

5.11.1 Zero-finding
In this section we re-work the example of Becker, Chambers & Wilks (1988, pp.~205–10) on
finding a zero of a univariate function. The R code and an example are

zero <- function(f, guesses, tol = 1e-7) {

f.check <- function(x) {
x <- f(x)
if(!is.numeric(x)) stop("Need a numeric result")
as.double(x)
}
.Call("zero", body(f.check), as.double(guesses), as.double(tol),
new.env())
}

cube1 <- function(x) (x^2 + 1) * (x - 1.5)

zero(cube1, c(0, 5))

where this time we do the coercion and error-checking in the R code. The C code is
Chapter 5: System and foreign language interfaces 156

SEXP mkans(double x)
{
// no need for PROTECT() here, as REAL(.) does not allocate:
SEXP ans = allocVector(REALSXP, 1);
REAL(ans)[0] = x;
return ans;
}

double feval(double x, SEXP f, SEXP rho)

{
// a version with (too) much PROTECT()ion .. "better safe than sorry"
SEXP symbol, value;
PROTECT(symbol = install("x"));
PROTECT(value = mkans(x));
defineVar(symbol, value, rho);
UNPROTECT(2);
return(REAL(eval(f, rho))[0]);
}

SEXP zero(SEXP f, SEXP guesses, SEXP stol, SEXP rho)

{
double x0 = REAL(guesses)[0], x1 = REAL(guesses)[1],
tol = REAL(stol)[0];
double f0, f1, fc, xc;

if(tol <= 0.0) error("non-positive tol value");

f0 = feval(x0, f, rho); f1 = feval(x1, f, rho);
if(f0 == 0.0) return mkans(x0);
if(f1 == 0.0) return mkans(x1);
if(f0*f1 > 0.0) error("x[0] and x[1] have the same sign");

for(;;) {
xc = 0.5*(x0+x1);
if(fabs(x0-x1) < tol) return mkans(xc);
fc = feval(xc, f, rho);
if(fc == 0) return mkans(xc);
if(f0*fc > 0.0) {
x0 = xc; f0 = fc;
} else {
x1 = xc; f1 = fc;
}
}
}

5.11.2 Calculating numerical derivatives

We will use a longer example (by Saikat DebRoy) to illustrate the use of evaluation and
.External. This calculates numerical derivatives, something that could be done as effectively
in interpreted R code but may be needed as part of a larger C calculation.

An interpreted R version and an example are

Chapter 5: System and foreign language interfaces 157

numeric.deriv <- function(expr, theta, rho=sys.frame(sys.parent()))

{
eps <- sqrt(.Machine$double.eps)
ans <- eval(substitute(expr), rho)
grad <- matrix(, length(ans), length(theta),
dimnames=list(NULL, theta))
for (i in seq_along(theta)) {
old <- get(theta[i], envir=rho)
delta <- eps * max(1, abs(old))
assign(theta[i], old+delta, envir=rho)
ans1 <- eval(substitute(expr), rho)
assign(theta[i], old, envir=rho)
grad[, i] <- (ans1 - ans)/delta
}
attr(ans, "gradient") <- grad
ans
}
omega <- 1:5; x <- 1; y <- 2
numeric.deriv(sin(omega*x*y), c("x", "y"))
where expr is an expression, theta a character vector of variable names and rho the environment
to be used.
For the compiled version the call from R will be
.External("numeric_deriv", expr, theta, rho)
with example usage
.External("numeric_deriv", quote(sin(omega*x*y)),
c("x", "y"), .GlobalEnv)
Note the need to quote the expression to stop it being evaluated in the caller.
Here is the complete C code which we will explain section by section.
#include <R.h>
#include <Rinternals.h>
#include <float.h> /* for DBL_EPSILON */

SEXP numeric_deriv(SEXP args)

{
SEXP theta, expr, rho, ans, ans1, gradient, par, dimnames;
double tt, xx, delta, eps = sqrt(DBL_EPSILON), *rgr, *rans;
int i, start;

expr = CADR(args);
if(!isString(theta = CADDR(args)))
error("theta should be of type character");
if(!isEnvironment(rho = CADDDR(args)))
error("rho should be an environment");

ans = PROTECT(coerceVector(eval(expr, rho), REALSXP));

gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(theta)));
rgr = REAL(gradient); rans = REAL(ans);
Chapter 5: System and foreign language interfaces 158

for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(ans)) {

par = PROTECT(findVar(installChar(STRING_ELT(theta, i)), rho));
tt = REAL(par)[0];
xx = fabs(tt);
delta = (xx < 1) ? eps : xx*eps;
REAL(par)[0] += delta;
ans1 = PROTECT(coerceVector(eval(expr, rho), REALSXP));
for(int j = 0; j < LENGTH(ans); j++)
rgr[j + start] = (REAL(ans1)[j] - rans[j])/delta;
REAL(par)[0] = tt;
UNPROTECT(2); /* par, ans1 */
}

dimnames = PROTECT(allocVector(VECSXP, 2));

SET_VECTOR_ELT(dimnames, 1, theta);
dimnamesgets(gradient, dimnames);
setAttrib(ans, install("gradient"), gradient);
UNPROTECT(3); /* ans gradient dimnames */
return ans;
}
The code to handle the arguments is
expr = CADR(args);
if(!isString(theta = CADDR(args)))
error("theta should be of type character");
if(!isEnvironment(rho = CADDDR(args)))
error("rho should be an environment");
Note that we check for correct types of theta and rho but do not check the type of expr. That
is because eval can handle many types of R objects other than EXPRSXP. There is no useful
coercion we can do, so we stop with an error message if the arguments are not of the correct
mode.
The first step in the code is to evaluate the expression in the environment rho, by
ans = PROTECT(coerceVector(eval(expr, rho), REALSXP));
We then allocate space for the calculated derivative by
gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(theta)));
The first argument to allocMatrix gives the SEXPTYPE of the matrix: here we want it to be
REALSXP. The other two arguments are the numbers of rows and columns. (Note that LENGTH
is intended to be used for vectors: length is more generally applicable.)
for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(ans)) {
par = PROTECT(findVar(installChar(STRING_ELT(theta, i)), rho));
Here, we are entering a for loop. We loop through each of the variables. In the for loop, we
first create a symbol corresponding to the i-th element of the STRSXP theta. Here, STRING_
ELT(theta, i) accesses the i-th element of the STRSXP theta. Macro CHAR() extracts the
actual character representation19 of it: it returns a pointer. We then install the name and use
findVar to find its value.

19
see Section 5.15 [Character encoding issues], page 163, for why this might not be what is required.
Chapter 5: System and foreign language interfaces 159

tt = REAL(par)[0];
xx = fabs(tt);
delta = (xx < 1) ? eps : xx*eps;
REAL(par)[0] += delta;
ans1 = PROTECT(coerceVector(eval(expr, rho), REALSXP));

We first extract the real value of the parameter, then calculate delta, the increment to be
used for approximating the numerical derivative. Then we change the value stored in par (in
environment rho) by delta and evaluate expr in environment rho again. Because we are directly
dealing with original R memory locations here, R does the evaluation for the changed parameter
value.

for(int j = 0; j < LENGTH(ans); j++)

rgr[j + start] = (REAL(ans1)[j] - rans[j])/delta;
REAL(par)[0] = tt;
UNPROTECT(2);
}

Now, we compute the i-th column of the gradient matrix. Note how it is accessed: R stores
matrices by column (like Fortran).

dimnames = PROTECT(allocVector(VECSXP, 2));

SET_VECTOR_ELT(dimnames, 1, theta);
dimnamesgets(gradient, dimnames);
setAttrib(ans, install("gradient"), gradient);
UNPROTECT(3);
return ans;
}

First we add column names to the gradient matrix. This is done by allocating a list (a VECSXP)
whose first element, the row names, is NULL (the default) and the second element, the col-
umn names, is set as theta. This list is then assigned as the attribute having the symbol
R_DimNamesSymbol. Finally we set the gradient matrix as the gradient attribute of ans, unpro-
tect the remaining protected locations and return the answer ans.

5.12 Parsing R code from C

Suppose an R extension want to accept an R expression from the user and evaluate it. The
previous section covered evaluation, but the expression will be entered as text and needs to be
parsed first. A small part of R’s parse interface is declared in header file R_ext/Parse.h20 .

An example of the usage can be found in the (example) Windows package windlgs included
in the R source tree. The essential part is

20
This is only guaranteed to show the current interface: it is liable to change.
Chapter 5: System and foreign language interfaces 160

#include <R.h>
#include <Rinternals.h>
#include <R_ext/Parse.h>

SEXP menu_ttest3()
{
char cmd[256];
SEXP cmdSexp, cmdexpr, ans = R_NilValue;
ParseStatus status;
...
if(done == 1) {
cmdSexp = PROTECT(allocVector(STRSXP, 1));
SET_STRING_ELT(cmdSexp, 0, mkChar(cmd));
cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilValue));
if (status != PARSE_OK) {
UNPROTECT(2);
error("invalid call %s", cmd);
}
/* Loop is needed here as EXPSEXP will be of length > 1 */
for(int i = 0; i < length(cmdexpr); i++)
ans = eval(VECTOR_ELT(cmdexpr, i), R_GlobalEnv);
UNPROTECT(2);
}
return ans;
}
Note that a single line of text may give rise to more than one R expression.
R_ParseVector is essentially the code used to implement parse(text=) at R level. The first
argument is a character vector (corresponding to text) and the second the maximal number
of expressions to parse (corresponding to n). The third argument is a pointer to a variable of
an enumeration type, and it is normal (as parse does) to regard all values other than PARSE_
OK as an error. Other values which might be returned are PARSE_INCOMPLETE (an incomplete
expression was found) and PARSE_ERROR (a syntax error), in both cases the value returned being
R_NilValue. The fourth argument is a length one character vector to be used as a filename in
error messages, a srcfile object or the R NULL object (as in the example above). If a srcfile
object was used, a srcref attribute would be attached to the result, containing a list of srcref
objects of the same length as the expression, to allow it to be echoed with its original formatting.

5.12.1 Accessing source references

The source references added by the parser are recorded by R’s evaluator as it evaluates code.
Two functions make these available to debuggers running C code:
SEXP R_GetCurrentSrcref(int skip);
This function checks R_Srcref and the current evaluation stack for entries that contain
source reference information. The skip argument tells how many source references to skip
before returning the SEXP of the srcref object, counting from the top of the stack. If skip <
0, abs(skip) locations are counted up from the bottom of the stack. If too few or no source
references are found, NULL is returned.
SEXP R_GetSrcFilename(SEXP srcref);
This function extracts the filename from the source reference for display, returning a length
1 character vector containing the filename. If no name is found, "" is returned.
Chapter 5: System and foreign language interfaces 161

5.13 External pointers and weak references

The SEXPTYPEs EXTPTRSXP and WEAKREFSXP can be encountered at R level, but are created in
C code.
External pointer SEXPs are intended to handle references to C structures such as ‘handles’, and
are used for this purpose in package RODBC (https://CRAN.R-project.org/package=RODBC)
for example. They are unusual in their copying semantics in that when an R object is copied,
the external pointer object is not duplicated. (For this reason external pointers should only be
used as part of an object with normal semantics, for example an attribute or an element of a
list.)
An external pointer is created by
SEXP R_MakeExternalPtr(void *p, SEXP tag, SEXP prot);
where p is the pointer (and hence this cannot portably be a function pointer), and tag and prot
are references to ordinary R objects which will remain in existence (be protected from garbage
collection) for the lifetime of the external pointer object. A useful convention is to use the tag
field for some form of type identification and the prot field for protecting the memory that the
external pointer represents, if that memory is allocated from the R heap. Both tag and prot
can be R_NilValue, and often are.
An alternative way to create an external pointer from a function pointer is
typedef void * (*R_DL_FUNC)();
SEXP R_MakeExternalPtrFn(R_DL_FUNC p, SEXP tag, SEXP prot);
The elements of an external pointer can be accessed and set via
void *R_ExternalPtrAddr(SEXP s);
DL_FUNC R_ExternalPtrAddrFn(SEXP s);
SEXP R_ExternalPtrTag(SEXP s);
SEXP R_ExternalPtrProtected(SEXP s);
void R_ClearExternalPtr(SEXP s);
void R_SetExternalPtrAddr(SEXP s, void *p);
void R_SetExternalPtrTag(SEXP s, SEXP tag);
void R_SetExternalPtrProtected(SEXP s, SEXP p);
Clearing a pointer sets its value to the C NULL pointer.
An external pointer object can have a finalizer, a piece of code to be run when the object is
garbage collected. This can be R code or C code, and the various interfaces are, respectively.
void R_RegisterFinalizer(SEXP s, SEXP fun);
void R_RegisterFinalizerEx(SEXP s, SEXP fun, Rboolean onexit);

typedef void (*R_CFinalizer_t)(SEXP);

void R_RegisterCFinalizer(SEXP s, R_CFinalizer_t fun);
void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean onexit);
The R function indicated by fun should be a function of a single argument, the object to be
finalized. R does not perform a garbage collection when shutting down, and the onexit argument
of the extended forms can be used to ask that the finalizer be run during a normal shutdown of
the R session. It is suggested that it is good practice to clear the pointer on finalization.
The only R level function for interacting with external pointers is reg.finalizer which can
be used to set a finalizer.
It is probably not a good idea to allow an external pointer to be saved and then reloaded,
but if this happens the pointer will be set to the C NULL pointer.
Finalizers can be run at many places in the code base and much of it, including the R
interpreter, is not re-entrant. So great care is needed in choosing the code to be run in a
Chapter 5: System and foreign language interfaces 162

finalizer. Finalizers are marked to be run at garbage collection but only run at a somewhat safe
point thereafter.
Weak references are used to allow the programmer to maintain information on entities without
preventing the garbage collection of the entities once they become unreachable.
A weak reference contains a key and a value. The value is reachable is if it either reachable
directly or via weak references with reachable keys. Once a value is determined to be unreachable
during garbage collection, the key and value are set to R_NilValue and the finalizer will be run
later in the garbage collection.
Weak reference objects are created by one of
SEXP R_MakeWeakRef(SEXP key, SEXP val, SEXP fin, Rboolean onexit);
SEXP R_MakeWeakRefC(SEXP key, SEXP val, R_CFinalizer_t fin,
Rboolean onexit);
where the R or C finalizer are specified in exactly the same way as for an external pointer object
(whose finalization interface is implemented via weak references).
The parts can be accessed via
SEXP R_WeakRefKey(SEXP w);
SEXP R_WeakRefValue(SEXP w);
void R_RunWeakRefFinalizer(SEXP w);
A toy example of the use of weak references can be found at https://homepage.stat.uiowa.
edu/~luke/R/references/weakfinex.html, but that is used to add finalizers to external point-
ers which can now be done more directly. At the time of writing no CRAN or Bioconductor
package uses weak references.

5.13.1 An example
Package RODBC (https://CRAN.R-project.org/package=RODBC) uses external pointers to
maintain its channels, connections to databases. There can be several connections open at once,
and the status information for each is stored in a C structure (pointed to by thisHandle in the
code extract below) that is returned via an external pointer as part of the RODBC ‘channel’
(as the "handle_ptr" attribute). The external pointer is created by
SEXP ans, ptr;
ans = PROTECT(allocVector(INTSXP, 1));
ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_NilValue);
PROTECT(ptr);
R_RegisterCFinalizerEx(ptr, chanFinalizer, TRUE);
...
/* return the channel no */
INTEGER(ans)[0] = nChannels;
/* and the connection string as an attribute */
setAttrib(ans, install("connection.string"), constr);
setAttrib(ans, install("handle_ptr"), ptr);
UNPROTECT(3);
return ans;
Note the symbol given to identify the usage of the external pointer, and the use of the finalizer.
Since the final argument when registering the finalizer is TRUE, the finalizer will be run at the
end of the R session (unless it crashes). This is used to close and clean up the connection to the
database. The finalizer code is simply
static void chanFinalizer(SEXP ptr)
{
if(!R_ExternalPtrAddr(ptr)) return;
Chapter 5: System and foreign language interfaces 163

inRODBCClose(R_ExternalPtrAddr(ptr));
R_ClearExternalPtr(ptr); /* not really needed */
}
Clearing the pointer and checking for a NULL pointer avoids any possibility of attempting to
close an already-closed channel.
R’s connections provide another example of using external pointers, in that case purely to
be able to use a finalizer to close and destroy the connection if it is no longer is use.

5.14 Vector accessor functions

The vector accessors like REAL, INTEGER, LOGICAL, RAW, COMPLEX, and VECTOR_ELT are func-
tions when used in R extensions. (For efficiency they may be macros or inline functions when
used in the R source code, apart from SET_STRING_ELT and SET_VECTOR_ELT which are always
functions.)
The accessor functions check that they are being used on an appropriate type of SEXP.
Formerly it was possible for packages to obtain internal versions of some accessors by defin-
ing ‘USE_RINTERNALS’ before including Rinternals.h. This is no longer the case. Defining
‘USE_RINTERNALS’ now has no effect.

5.15 Character encoding issues

CHARSXPs can be marked as coming from a known encoding (Latin-1 or UTF-8). This is mainly
intended for human-readable output, and most packages can just treat such CHARSXPs as a
whole. However, if they need to be interpreted as characters or output at C level then it would
normally be correct to ensure that they are converted to the encoding of the current locale: this
can be done by accessing the data in the CHARSXP by translateChar rather than by CHAR. If
re-encoding is needed this allocates memory with R_alloc which thus persists to the end of the
.Call/.External call unless vmaxset is used (see Section 6.1.1 [Transient storage allocation],
page 165).
There is a similar function translateCharUTF8 which converts to UTF-8: this has the ad-
vantage that a faithful translation is almost always possible (whereas only a few languages can
be represented in the encoding of the current locale unless that is UTF-8).
Both translateChar and translateCharUTF8 will translate any input, using escapes such
as ‘<A9>’ and ‘<U+0093>’ to represent untranslatable parts of the input.
There is a public interface to the encoding marked on CHARSXPs via
typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE_ANY} cetype_t;
cetype_t getCharCE(SEXP);
SEXP mkCharCE(const char *, cetype_t);
Only CE_UTF8 and CE_LATIN1 are marked on CHARSXPs (and so Rf_getCharCE will only return
one of the first three), and these should only be used on non-ASCII strings. Value CE_BYTES is
used to make CHARSXPs which should be regarded as a set of bytes and not translated. Value
CE_SYMBOL is used internally to indicate Adobe Symbol encoding. Value CE_ANY is used to
indicate a character string that will not need re-encoding – this is used for character strings
known to be in ASCII, and can also be used as an input parameter where the intention is that
the string is treated as a series of bytes. (See the comments under mkChar about the length of
input allowed.)
Function
const char *reEnc(const char *x, cetype_t ce_in, cetype_t ce_out,
int subst);
Chapter 5: System and foreign language interfaces 164

can be used to re-encode character strings: like translateChar it returns a string allocated by
R_alloc. This can translate from CE_SYMBOL to CE_UTF8, but not conversely. Argument subst
controls what to do with untranslatable characters or invalid input: this is done byte-by-byte
with 1 indicates to output hex of the form <a0>, and 2 to replace by ., with any other value
causing the byte to produce no output.
There is also
SEXP mkCharLenCE(const char *, size_t, cetype_t);
to create marked character strings of a given length.
 165

6 The R API: entry points for C code

There are a large number of entry points in the R executable/DLL that can be called from C
code (and some that can be called from Fortran code). Only those documented here are stable
enough that they will only be changed with considerable notice.
The recommended procedure to use these is to include the header file R.h in your C code by
#include <R.h>
This will include several other header files from the directory R_INCLUDE_DIR/R_ext, and there
are other header files there that can be included too, but many of the features they contain
should be regarded as undocumented and unstable.
Most of these header files, including all those included by R.h, can be used from C++ code.
Note: Because R re-maps many of its external names to avoid clashes with system
or user code, it is essential to include the appropriate header files when using these
entry points.
This remapping can cause problems1 , and can be eliminated by defining R_NO_REMAP (be-
fore including any R headers) and prepending ‘Rf_’ to all the function names used from
Rinternals.h and R_ext/Error.h. These problems can usually be avoided by including other
headers (such as system headers and those for external software used by the package) before
any R headers. (Headers from other packages may include R headers directly or via inclusion
from further packages, and may define R_NO_REMAP with or without including Rinternals.h.)
We can classify the entry points as
API Entry points which are documented in this manual and declared in an installed
header file. These can be used in distributed packages and will only be changed
after deprecation.
public Entry points declared in an installed header file that are exported on all R platforms
but are not documented and subject to change without notice.
private Entry points that are used when building R and exported on all R platforms but
are not declared in the installed header files. Do not use these in distributed code.
hidden Entry points that are where possible (Windows and some modern Unix-alike com-
pilers/loaders when using R as a shared library) not exported.

6.1 Memory allocation

There are two types of memory allocation available to the C programmer, one in which R
manages the clean-up and the other in which user has full control (and responsibility).
These functions are declared in header R_ext/RS.h which is included by R.h.

6.1.1 Transient storage allocation

Here R will reclaim the memory at the end of the call to .C, .Call or .External. Use
char *R_alloc(size_t n, int size)
which allocates n units of size bytes each. A typical usage (from package stats) is
x = (int *) R_alloc(nrows(merge)+2, sizeof(int));
(size_t is defined in stddef.h which the header defining R_alloc includes.)
1
Known problems have been defining LENGTH, error, length, vector and warning: whether these matter
depends on the OS and toolchain, with many problem reports involving clang++. As from LLVM clang
13.0.0, the remapping of match breaks the subsequent inclusion of omp.h.
Chapter 6: The R API: entry points for C code 166

There is a similar call, S_alloc (named for compatibility with older versions of S) which
zeroes the memory allocated,
char *S_alloc(long n, int size)
and
char *S_realloc(char *p, long new, long old, int size)
which (for new > old) changes the allocation size from old to new units, and zeroes the additional
units. NB: these calls are best avoided as long is insufficient for large memory allocations on
64-bit Windows (where it is limited to 2^31-1 bytes).
This memory is taken from the heap, and released at the end of the .C, .Call or .External
call. Users can also manage it, by noting the current position with a call to vmaxget and
subsequently clearing memory allocated by a call to vmaxset. An example might be
void *vmax = vmaxget()
// a loop involving the use of R_alloc at each iteration
vmaxset(vmax)
This is only recommended for experts.
Note that this memory will be freed on error or user interrupt (if allowed: see Section 6.13
[Allowing interrupts], page 184).
The memory returned is only guaranteed to be aligned as required for double pointers: take
precautions if casting to a pointer which needs more. There is also
long double *R_allocLD(size_t n)
which is guaranteed to have the 16-byte alignment needed for long double pointers on some
platforms.
These functions should only be used in code called by .C etc, never from front-ends. They
are not thread-safe.

6.1.2 User-controlled memory

The other form of memory allocation is an interface to malloc, the interface providing R error
signaling. This memory lasts until freed by the user and is additional to the memory allocated
for the R workspace.
The interface macros are
type* R_Calloc(size_t n, type)
type* R_Realloc(any *p, size_t n, type)
void R_Free(any *p)
providing analogues of calloc, realloc and free. If there is an error during allocation it is
handled by R, so if these return the memory has been successfully allocated or freed. R_Free
will set the pointer p to NULL. (Some but not all versions of S did so.)
Users should arrange to R_Free this memory when no longer needed, including on error or
user interrupt. This can often be done most conveniently from an on.exit action in the calling
R function – see pwilcox for an example.
Do not assume that memory allocated by R_Calloc/R_Realloc comes from the same pool
as used by malloc:2 in particular do not use free or strdup with it.
Memory obtained by these macros should be aligned in the same way as malloc, that is
‘suitably aligned for any kind of variable’.

2
That was not the case on Windows prior to R 4.2.0.
Chapter 6: The R API: entry points for C code 167

Historically the macros Calloc, Free and Realloc were used, and these remain available
unless STRICT_R_HEADERS was defined prior to the inclusion of the header.
char * CallocCharBuf(size_t n)
void * Memcpy(q, p, n)
void * Memzero(p, n)
CallocCharBuf(n) is shorthand for R_Calloc(n+1, char) to allow for the nul termina-
tor. Memcpy and Memzero take n items from array p and copy them to array q or zero them
respectively.

6.2 Error signaling

The basic error signaling routines are the equivalents of stop and warning in R code, and use
the same interface.
void error(const char * format, ...);
void warning(const char * format, ...);
void errorcall(SEXP call, const char * format, ...);
void warningcall(SEXP call, const char * format, ...);
void warningcall_immediate(SEXP call, const char * format, ...);
These have the same call sequences as calls to printf, but in the simplest case can be called
with a single character string argument giving the error message. (Don’t do this if the string
contains ‘%’ or might otherwise be interpreted as a format.)
These are defined in header R_ext/Error.h included by R.h.

6.2.1 Error signaling from Fortran

There are two interface function provided to call error and warning from Fortran code, in each
case with a simple character string argument. They are defined as
subroutine rexit(message)
subroutine rwarn(message)
Messages of more than 255 characters are truncated, with a warning.

6.3 Random number generation

The interface to R’s internal random number generation routines is
double unif_rand();
double norm_rand();
double exp_rand();
double R_unif_index(double);
giving one uniform, normal or exponential pseudo-random variate. However, before these are
used, the user must call
GetRNGstate();
and after all the required variates have been generated, call
PutRNGstate();
These essentially read in (or create) .Random.seed and write it out after use.
These are defined in header R_ext/Random.h.
The random number generator is private to R; there is no way to select the kind of RNG nor
set the seed except by evaluating calls to the R functions.
The C code behind R’s rxxx functions can be accessed by including the header file Rmath.h;
See Section 6.7.1 [Distribution functions], page 174. Those calls should also be preceded and
followed by calls to GetRNGstate and PutRNGstate.
Chapter 6: The R API: entry points for C code 168

6.3.1 Random-number generation from Fortran

It was explained earlier that Fortran random-number generators should not be used in R pack-
ages, not least as packages cannot safely initialize them. Rather a package should call R’s built
in generators: one way to do so is to use C wrappers like

#include <R_ext/RS.h>
#include <R_ext/Random.h>

void F77_SUB(getRNGseed)(void) {
GetRNGstate();
}
void F77_SUB(putRNGseed)(void) {
PutRNGstate();
}
double F77_SUB(unifRand)(void) {
return(unif_rand());
}

called from Fortran code like

...
double precision X
call getRNGseed()
X = unifRand()
...
call putRNGseed()

Alternatively one could use Fortran 2003’s iso_c_binding module by something like (fixed-
form Fortran 90 code):

module rngfuncs
use iso_c_binding
interface
double precision
* function unifRand() bind(C, name = "unif_rand")
end function unifRand

subroutine getRNGseed() bind(C, name = "GetRNGstate")

end subroutine getRNGseed

subroutine putRNGseed() bind(C, name = "PutRNGstate")

end subroutine putRNGseed
end interface
end module

subroutine testit
use rngfuncs
double precision X
call getRNGseed()
X = unifRand()
print *, X
call putRNGSeed()
end
Chapter 6: The R API: entry points for C code 169

6.4 Missing and IEEE special values

A set of functions is provided to test for NA, Inf, -Inf and NaN. These functions are accessed
via macros:
ISNA(x) True for R’s NA only
ISNAN(x) True for R’s NA and IEEE NaN
R_FINITE(x) False for Inf, -Inf, NA, NaN
and via function R_IsNaN which is true for NaN but not NA.
Do use R_FINITE rather than isfinite or finite; the latter is often mendacious and
isfinite is only available on a some platforms, on which R_FINITE is a macro expanding
to isfinite.
Currently in C code ISNAN is a macro calling isnan. (Since this gives problems on some C++
systems, if the R headers is called from C++ code a function call is used.)
You can check for Inf or -Inf by testing equality to R_PosInf or R_NegInf, and set (but
not test) an NA as NA_REAL.
All of the above apply to double variables only. For integer variables there is a variable
accessed by the macro NA_INTEGER which can used to set or test for missingness.
These are defined in header R_ext/Arith.h included by R.h.

6.5 Printing
The most useful function for printing from a C routine compiled into R is Rprintf. This is used
in exactly the same way as printf, but is guaranteed to write to R’s output (which might be
a GUI console rather than a file, and can be re-directed by sink). It is wise to write complete
lines (including the "\n") before returning to R. It is defined in R_ext/Print.h.
The function REprintf is similar but writes on the error stream (stderr) which may or may
not be different from the standard output stream.
Functions Rvprintf and REvprintf are analogues using the vprintf interface. Because
that is a C993 interface, they are only defined by R_ext/Print.h in C++ code if the macro
R_USE_C99_IN_CXX is defined before it is included or (as from R 4.0.0) a C++11 compiler is
used.
Another circumstance when it may be important to use these functions is when using parallel
computation on a cluster of computational nodes, as their output will be re-directed/logged
appropriately.

6.5.1 Printing from Fortran

On many systems Fortran write and print statements can be used, but the output may not
interleave well with that of C, and may be invisible on GUI interfaces. They are not portable
and best avoided.
Some subroutines are provided to ease the output of information from Fortran code.
subroutine dblepr(label, nchar, data, ndata)
subroutine realpr(label, nchar, data, ndata)
subroutine intpr (label, nchar, data, ndata)
and from R 4.0.0,
subroutine labelpr(label, nchar)
subroutine dblepr1(label, nchar, var)
subroutine realpr1(label, nchar, var)
subroutine intpr1 (label, nchar, var)
3
also part of C++11.
Chapter 6: The R API: entry points for C code 170

Here label is a character label of up to 255 characters, nchar is its length (which can be -1
if the whole label is to be used), data is an array of length at least ndata of the appropriate
type (double precision, real and integer respectively) and var is a (scalar) variable. These
routines print the label on one line and then print data or var as if it were an R vector on
subsequent line(s). Note that some compilers will give an error or warning unless data is an
array: others will accept a scalar when ndata has value one or zero. NB: There is no check on
the type of data or var, so using real (including a real constant) instead of double precision
will give incorrect answers.
intpr works with zero ndata so can be used to print a label in earlier versions of R.

6.6 Calling C from Fortran and vice versa

Naming conventions for symbols generated by Fortran differ by platform: it is not safe to assume
that Fortran names appear to C with a trailing underscore. To help cover up the platform-specific
differences there is a set of macros4 that should be used.
F77_SUB(name)
to define a function in C to be called from Fortran
F77_NAME(name)
to declare a Fortran routine in C before use
F77_CALL(name)
to call a Fortran routine from C
F77_COMDECL(name)
to declare a Fortran common block in C
F77_COM(name)
to access a Fortran common block from C
On most current platforms these are all the same, but it is unwise to rely on this. Note that
names containing underscores were not legal in Fortran 77, and are not portably handled by the
above macros. (Also, all Fortran names for use by R are lower case, but this is not enforced by
the macros.)
For example, suppose we want to call R’s normal random numbers from Fortran. We need a
C wrapper along the lines of
#include <R.h>

void F77_SUB(rndstart)(void) { GetRNGstate(); }

void F77_SUB(rndend)(void) { PutRNGstate(); }
double F77_SUB(normrnd)(void) { return norm_rand(); }
to be called from Fortran as in
subroutine testit()
double precision normrnd, x
call rndstart()
x = normrnd()
call dblepr("X was", 5, x, 1)
call rndend()
end
Note that this is not guaranteed to be portable, for the return conventions might not be com-
patible between the C and Fortran compilers used. (Passing values via arguments is safer.)
4
The ‘F77_’ in the names is historical and dates back to usage in S.
Chapter 6: The R API: entry points for C code 171

The standard packages, for example stats, are a rich source of further examples.
Where supported, link time optimization provides a reliable way to check the consistency of
calls to C from Fortran or vice versa. See Section 4.5 [Using Link-time Optimization], page 120.
One place where this occurs is the registration of .Fortran calls in C code (see Section 5.4
[Registering native routines], page 126). For example
init.c:10:13: warning: type of 'vsom_' does not match original
declaration [-Wlto-type-mismatch]
extern void F77_NAME(vsom)(void *, void *, void *, void *,
void *, void *, void *, void *, void *);
vsom.f90:20:33: note: type mismatch in parameter 9
subroutine vsom(neurons,dt,dtrows,dtcols,xdim,ydim,alpha,train)
vsom.f90:20:33: note: 'vsom' was previously declared here
shows that a subroutine has been registered with 9 arguments (as that is what the .Fortran
call used) but only has 8.

6.6.1 Fortran character strings

Passing character strings from C to Fortran or vice versa is not portable, but can be done
with care. The internal representations are different: a character array in C (or C++) is NUL-
terminated so its length can be computed by strlen. Fortran character arrays are typically
stored as an array of bytes and a length. This matters when passing strings from C to Fortran
or vice versa: in many cases one has been able to get away with passing the string but not the
length. However, in 2019 this changed for gfortran, starting with version 9 but backported to
versions 7 and 8. Several months later, gfortran 9.2 introduced an option
-ftail-call-workaround
and made it the current default but said it might be withdrawn in future.
Suppose we want a function to report a message from Fortran to R’s console (one could
use labelpr, or intpr with dummy data, but this might be the basis of a custom reporting
function). Suppose the equivalent in Fortran would be
subroutine rmsg(msg)
character*(*) msg
print *.msg
end
in file rmsg.f. Using gfortran 9.2 and later we can extract the C view by
gfortran -c -fc-prototypes-external rmsg.f
which gives
void rmsg_ (char *msg, size_t msg_len);
(where size_t applies to version 8 and later). We could re-write that portably in C as
#ifndef USE_FC_LEN_T
# define USE_FC_LEN_T
#endif
#include <Rconfig.h> // included by R.h, so define USE_FC_LEN_T early

void F77_NAME(rmsg)(char *msg, FC_LEN_T msg_len)

{
char cmsg[msg_len+1];
strncpy(cmsg, msg, msg_len);
cmsg[msg_len] = '\0'; // nul-terminate the string, to be sure
// do something with 'cmsg'
}
Chapter 6: The R API: entry points for C code 172

in code depending on R(>= 3.6.2). For earlier versions of R we could just assume that msg is
NUL-terminated (not guaranteed, but people have been getting away with it for many years),
so the complete C side might be
#ifndef USE_FC_LEN_T
# define USE_FC_LEN_T
#endif
#include <Rconfig.h>

#ifdef FC_LEN_T
void F77_NAME(rmsg)(char *msg, FC_LEN_T msg_len)
{
char cmsg[msg_len+1];
strncpy(cmsg, msg, msg_len);
cmsg[msg_len] = '\0';
// do something with 'cmsg'
}
#else
void F77_NAME(rmsg)(char *msg)
{
// do something with 'msg'
}
#endif
(USE_FC_LEN_T is the default as from R 4.3.0.)
An alternative is to use Fortran 2003 features to set up the Fortran routine to pass a C-
compatible character string. We could use something like
module cfuncs
use iso_c_binding, only: c_char, c_null_char
interface
subroutine cmsg(msg) bind(C, name = 'cmsg')
use iso_c_binding, only: c_char
character(kind = c_char):: msg(*)
end subroutine cmsg
end interface
end module

subroutine rmsg(msg)
use cfuncs
character(*) msg
call cmsg(msg//c_null_char) ! need to concatenate a nul terminator
end subroutine rmsg
where the C side is simply
void cmsg(const char *msg)
{
// do something with nul-terminated string 'msg'
}
If you use bind to a C function as here, the only way to check that the bound definition is correct
is to compile the package with LTO (which requires compatible C and Fortran compilers, usually
gcc and gfortran).
Passing a variable-length string from C to Fortran is trickier, but https://www.intel.
com/content/www/us/en/docs/fortran-compiler/developer-guide-reference/2023-0/
Chapter 6: The R API: entry points for C code 173

bind-c.html provides a recipe. However, all the uses in BLAS and LAPACK are of a single
character, and for these we can write a wrapper in Fortran along the lines of
subroutine c_dgemm(transa, transb, m, n, k, alpha,
+ a, lda, b, ldb, beta, c, ldc)
+ bind(C, name = 'Cdgemm')
use iso_c_binding, only : c_char, c_int, c_double
character(c_char), intent(in) :: transa, transb
integer(c_int), intent(in) :: m, n, k, lda, ldb, ldc
real(c_double), intent(in) :: alpha, beta, a(lda, *), b(ldb, *)
real(c_double), intent(out) :: c(ldc, *)
call dgemm(transa, transb, m, n, k, alpha,
+ a, lda, b, ldb, beta, c, ldc)
end subroutine c_dgemm
which is then called from C with declaration
void
Cdgemm(const char *transa, const char *transb, const int *m,
const int *n, const int *k, const double *alpha,
const double *a, const int *lda, const double *b, const int *ldb,
const double *beta, double *c, const int *ldc);
Alternatively, do as R does as from version 3.6.2 and pass the character length(s) from C to
Fortran. A portable way to do this is
// before any R headers, or define in PKG_CPPFLAGS
#ifndef USE_FC_LEN_T
# define USE_FC_LEN_T
#endif
#include <Rconfig.h>
#include <R_ext/BLAS.h>
#ifndef FCONE
# define FCONE
#endif
...
F77_CALL(dgemm)("N", "T", &nrx, &ncy, &ncx, &one, x,
&nrx, y, &nry, &zero, z, &nrx FCONE FCONE);
(Note there is no comma before or between the FCONE invocations.) It is strongly recommended
that packages which call from C/C++ BLAS/LAPACK routines with character arguments adopt
this approach: packages not using will fail to install as from R 4.3.0.

6.6.2 Fortran LOGICAL

Passing Fortran LOGICAL variables to/from C/C++ is potentially compiler-dependent. Fortran
compilers have long used a 32-bit integer type so it is pretty portable to use int * on the C/C++
side. However, recent versions of gfortran via the option -fc-prototypes-external say the
C equivalent is int_least32_t *: ‘Link-Time Optimization’ will report int * as a mismatch.
It is possible to use iso_c_binding in Fortran 2003 to map LOGICAL variables to the C99
type _Bool, but it is usually simpler to pass integers to and fro.

6.6.3 Passing functions

A number of packages call C functions passed as arguments to Fortran code along the lines of
c subroutine fcn(m,n,x,fvec,iflag)
c integer m,n,iflag
c double precision x(n),fvec(m)
Chapter 6: The R API: entry points for C code 174

...
subroutine lmdif(fcn, ...
where the C declaration and call are
void fcn_lmdif(int *m, int *n, double *par, double *fvec, int *iflag);

void F77_NAME(lmdif)(void (*fcn_lmdif)(int *m, int *n, double *par,

double *fvec, int *iflag), ...

F77_CALL(lmdif)(&fcn_lmdif, ...
This works on most platforms but depends on the C and Fortran compilers agreeing on calling
conventions: this have been seen to fail. The most portable solution seems to be to convert the
Fortran code to C, perhaps using f2c.

6.7 Numerical analysis subroutines

R contains a large number of mathematical functions for its own use, for example numerical
linear algebra computations and special functions.
The header files R_ext/BLAS.h, R_ext/Lapack.h and R_ext/Linpack.h contains declara-
tions of the BLAS, LAPACK and LINPACK linear algebra functions included in R. These are
expressed as calls to Fortran subroutines, and they will also be usable from users’ Fortran code.
Although not part of the official API, this set of subroutines is unlikely to change (but might be
supplemented).
The header file Rmath.h lists many other functions that are available and documented in the
following subsections. Many of these are C interfaces to the code behind R functions, so the R
function documentation may give further details.

6.7.1 Distribution functions

The routines used to calculate densities, cumulative distribution functions and quantile functions
for the standard statistical distributions are available as entry points.
The arguments for the entry points follow the pattern of those for the normal distribution:
double dnorm(double x, double mu, double sigma, int give_log);
double pnorm(double x, double mu, double sigma, int lower_tail,
int give_log);
double qnorm(double p, double mu, double sigma, int lower_tail,
int log_p);
double rnorm(double mu, double sigma);
That is, the first argument gives the position for the density and CDF and probability for the
quantile function, followed by the distribution’s parameters. Argument lower tail should be
TRUE (or 1) for normal use, but can be FALSE (or 0) if the probability of the upper tail is desired
or specified.
Finally, give log should be non-zero if the result is required on log scale, and log p should
be non-zero if p has been specified on log scale.
Note that you directly get the cumulative (or “integrated”) hazard function, H(t) = − log(1−
F (t)), by using
- pdist(t, ..., /*lower_tail = */ FALSE, /* give_log = */ TRUE)
or shorter (and more cryptic) - pdist(t, ..., 0, 1).
The random-variate generation routine rnorm returns one normal variate. See Section 6.3
[Random numbers], page 167, for the protocol in using the random-variate routines.
Chapter 6: The R API: entry points for C code 175

Note that these argument sequences are (apart from the names and that rnorm has no n)
mainly the same as the corresponding R functions of the same name, so the documentation of the
R functions can be used. Note that the exponential and gamma distributions are parametrized
by scale rather than rate.
For reference, the following table gives the basic name (to be prefixed by ‘d’, ‘p’, ‘q’ or ‘r’
apart from the exceptions noted) and distribution-specific arguments for the complete set of
distributions.
beta beta a, b
non-central beta nbeta a, b, ncp
binomial binom n, p
Cauchy cauchy location, scale
chi-squared chisq df
non-central chi-squared nchisq df, ncp
exponential exp scale (and not rate)
F f n1, n2
non-central F nf n1, n2, ncp
gamma gamma shape, scale
geometric geom p
hypergeometric hyper NR, NB, n
logistic logis location, scale
lognormal lnorm logmean, logsd
negative binomial nbinom size, prob
normal norm mu, sigma
Poisson pois lambda
Student’s t t n
non-central t nt df, delta
Studentized range tukey (*) rr, cc, df
uniform unif a, b
Weibull weibull shape, scale
Wilcoxon rank sum wilcox m, n
Wilcoxon signed rank signrank n
Entries marked with an asterisk only have ‘p’ and ‘q’ functions available, and none of the non-
central distributions have ‘r’ functions.
(If remapping is suppressed, the Normal distribution names are Rf_dnorm4, Rf_pnorm5 and
Rf_qnorm5.)
Additionally, a multivariate RNG for the multinomial distribution is
void rmultinom(int n, double* prob, int K, int* rN)
where K = length(prob), π := prob[], K
P
j=1 πj = 1 and rN must point to a length-K integer
vector n1 n2 . . . nPK where each entry nj =rN[j] is “filled” by a random binomial from Bin(n; πj ),
constrained to K j=1 nj = n.
After calls to dwilcox, pwilcox or qwilcox the function wilcox_free() should be called,
and similarly signrank_free() for the signed rank functions. Since wilcox_free() and
signrank_free() were only added to Rmath.h in R 4.2.0, their use requires something like
#include "Rmath.h"
#include "Rversion.h"

#if R_VERSION < R_Version(4, 2, 0)

extern void wilcox_free(void);
extern void signrank_free(void);
#endif
Chapter 6: The R API: entry points for C code 176

For the negative binomial distribution (‘nbinom’), in addition to the (size, prob)
parametrization, the alternative (size, mu) parametrization is provided as well by functions
‘[dpqr]nbinom_mu()’, see ?NegBinomial in R.
Functions dpois_raw(x, *) and dbinom_raw(x, *) are versions of the Poisson and binomial
probability mass functions which work continuously in x, whereas dbinom(x,*) and dpois(x,*)
only return non zero values for integer x.
double dbinom_raw(double x, double n, double p, double q, int give_log)
double dpois_raw (double x, double lambda, int give_log)
Note that dbinom_raw() returns both p and q = 1 − p which may be advantageous when one
of them is close to 1.

6.7.2 Mathematical functions

double gammafn (double x) [Function]
double lgammafn (double x) [Function]
double digamma (double x) [Function]
double trigamma (double x) [Function]
double tetragamma (double x) [Function]
double pentagamma (double x) [Function]
double psigamma (double x, double deriv) [Function]
void dpsifn (double x, int n, int kode, int m, double* ans, [Function]
int* nz, int* ierr)
The Gamma function, the natural logarithm of its absolute value and first four deriva-
tives and the n-th derivative of Psi, the digamma function, which is the derivative of
lgammafn. In other words, digamma(x) is the same as psigamma(x,0), trigamma(x) ==
psigamma(x,1), etc. The underlying workhorse, dpsifn(), is useful, e.g., when several
derivatives of log Γ =lgammafn are desired. It computes and returns in ans[] the length-m se-
quence (−1)k+1 /Γ(k+1)∗ψ (k) (x) for k = n . . . n+m−1, where ψ (k) (x) is the k-th derivative of
ψ(x), i.e., psigamma(x,k). For more details, see the comments in src/nmath/polygamma.c.
double beta (double a, double b) [Function]
double lbeta (double a, double b) [Function]
The (complete) Beta function and its natural logarithm.
double choose (double n, double k) [Function]
double lchoose (double n, double k) [Function]
The number of combinations of k items chosen from n and the natural logarithm of its
absolute value, generalized to arbitrary real n. k is rounded to the nearest integer (with a
warning if needed).
double bessel_i (double x, double nu, double expo) [Function]
double bessel_j (double x, double nu) [Function]
double bessel_k (double x, double nu, double expo) [Function]
double bessel_y (double x, double nu) [Function]
Bessel functions of types I, J, K and Y with index nu. For bessel_i and bessel_k there
is the option to return exp(-x) I(x; nu) or exp(x) K(x; nu) if expo is 2. (Use expo == 1 for
unscaled values.)

6.7.3 Numerical Utilities

There are a few other numerical utility functions available as entry points.
double R_pow (double x, double y) [Function]
double R_pow_di (double x, int i) [Function]
Chapter 6: The R API: entry points for C code 177

double pow1p (double x, double y) [Function]

R_pow(x, y) and R_pow_di(x, i) compute x^y and x^i, respectively using R_FINITE checks
and returning the proper result (the same as R) for the cases where x, y or i are 0 or missing
or infinite or NaN.
pow1p(x, y) computes (1 + x)^y, accurately even for small x, i.e., |x|  1.

double log1p (double x) [Function]

Computes log(1 + x) (log 1 plus x ), accurately even for small x, i.e., |x|  1.
This should be provided by your platform, in which case it is not included in Rmath.h, but is
(probably) in math.h which Rmath.h includes (except under C++, so it may not be declared
for C++98).

double log1pmx (double x) [Function]

Computes log(1 + x) - x (log 1 plus x minus x), accurately even for small x, i.e., |x|  1.

double log1pexp (double x) [Function]

Computes log(1 + exp(x)) (log 1 plus exp), accurately, notably for large x, e.g., x > 720.

double log1mexp (double x) [Function]

Computes log(1 - exp(-x)) (log 1 minus exp), accurately, carefully for two regions of x,
optimally cutting off at log 2 (= 0.693147..), using ((-x) > -M_LN2 ? log(-expm1(-x)) :
log1p(-exp(-x))).

double expm1 (double x) [Function]

Computes exp(x) - 1 (exp x minus 1 ), accurately even for small x, i.e., |x|  1.
This should be provided by your platform, in which case it is not included in Rmath.h, but is
(probably) in math.h which Rmath.h includes (except under C++, so it may not be declared
for C++98).

double lgamma1p (double x) [Function]

Computes log(gamma(x + 1)) (log(gamma(1 plus x))), accurately even for small x, i.e., 0 <
x < 0.5.

double cospi (double x) [Function]

Computes cos(pi * x) (where pi is 3.14159...), accurately, notably for half integer x.
This might be provided by your platform5 , in which case it is not included in Rmath.h, but is
in math.h which Rmath.h includes. (Ensure that neither math.h nor cmath is included before
Rmath.h or define
#define __STDC_WANT_IEC_60559_FUNCS_EXT__ 1
before the first inclusion.)

double sinpi (double x) [Function]

Computes sin(pi * x) accurately, notably for (half) integer x.
This might be provided by your platform, in which case it is not included in Rmath.h, but is
in math.h which Rmath.h includes (but see the comments for cospi).

double Rtanpi (double x) [Function]

Computes tan(pi * x) accurately, notably for integer x, giving NaN for half integer x and
exactly +1 or -1 for (non half) quarter integers.

5
It is an optional C11 extension.
Chapter 6: The R API: entry points for C code 178

double tanpi (double x) [Function]

Computes tan(pi * x) accurately for integer x with possibly platform dependent behavior
for half (and quarter) integers. This might be provided by your platform, in which case it
is not included in Rmath.h, but is in math.h which Rmath.h includes (but see the comments
for cospi).

double logspace_add (double logx, double logy) [Function]

double logspace_sub (double logx, double logy) [Function]
double logspace_sum (const double* logx, int n) [Function]
Compute the log of a sum or difference from logs of terms, i.e., “x + y” as log (exp(logx) +
exp(logy)) and “x - y” as log (exp(logx) - exp(logy)), and “sum i x[i]” as log (sum[i
= 1:n exp(logx[i])] ) without causing unnecessary overflows or throwing away too much
accuracy.

int imax2 (int x, int y) [Function]

int imin2 (int x, int y) [Function]
double fmax2 (double x, double y) [Function]
double fmin2 (double x, double y) [Function]
Return the larger (max) or smaller (min) of two integer or double numbers, respectively. Note
that fmax2 and fmin2 differ from C99/C++11’s fmax and fmin when one of the arguments is
a NaN: these versions return NaN.

double sign (double x) [Function]

Compute the signum function, where sign(x) is 1, 0, or −1, when x is positive, 0, or negative,
respectively, and NaN if x is a NaN.

double fsign (double x, double y) [Function]

Performs “transfer of sign” and is defined as |x| ∗ sign(y).

double fprec (double x, double digits) [Function]

Returns the value of x rounded to digits decimal digits (after the decimal point).
This is the function used by R’s signif().

double fround (double x, double digits) [Function]

Returns the value of x rounded to digits significant decimal digits.
This is the function used by R’s round(). (Note that C99/C++11 provide a round function
but C++98 need not.)

double ftrunc (double x) [Function]

Returns the value of x truncated (to an integer value) towards zero.

6.7.4 Mathematical constants

R has a set of commonly used mathematical constants encompassing constants defined by POSIX
and usually found in headers math.h and cmath, as well as further ones that are used in statistical
computations. These are defined to (at least) 30 digits accuracy in Rmath.h. The following
definitions use ln(x) for the natural logarithm (log(x) in R).
Name Definition (ln = log) round(value, 7)
M_E e 2.7182818
M_LOG2E log2(e) 1.4426950
M_LOG10E log10(e) 0.4342945
M_LN2 ln(2) 0.6931472
M_LN10 ln(10) 2.3025851
M_PI π 3.1415927
Chapter 6: The R API: entry points for C code 179

M_PI_2 π/2 1.5707963

M_PI_4 π/4 0.7853982
M_1_PI 1/π 0.3183099
M_2_PI 2/π 0.6366198
M_2_SQRTPI 2/sqrt(π) 1.1283792
M_SQRT2 sqrt(2) 1.4142136
M_SQRT1_2 1/sqrt(2) 0.7071068
M_SQRT_3 sqrt(3) 1.7320508
M_SQRT_32 sqrt(32) 5.6568542
M_LOG10_2 log10(2) 0.3010300
M_2PI 2π 6.2831853
M_SQRT_PI sqrt(π) 1.7724539
M_1_SQRT_2PI 1/sqrt(2π) 0.3989423
M_SQRT_2dPI sqrt(2/π) 0.7978846
M_LN_SQRT_PI ln(sqrt(π)) 0.5723649
M_LN_SQRT_2PI ln(sqrt(2π)) 0.9189385
M_LN_SQRT_PId2 ln(sqrt(π/2)) 0.2257914
There are a set of constants (PI, DOUBLE_EPS) (and so on) defined (unless STRICT_R_HEADERS
is defined) in the included header R_ext/Constants.h, mainly for compatibility with S. All but
PI are deprecated and should be replaced by the C99/C++11 versions used in that file.
Further, the included header R_ext/Boolean.h has enumeration constants TRUE and FALSE
of type Rboolean in order to provide a way of using “logical” variables in C consistently. This
can conflict with other software: for example it conflicts with the headers in IJG’s jpeg-9 (but
not earlier versions).

6.8 Optimization
The C code underlying optim can be accessed directly. The user needs to supply a function to
compute the function to be minimized, of the type
typedef double optimfn(int n, double *par, void *ex);
where the first argument is the number of parameters in the second argument. The third
argument is a pointer passed down from the calling routine, normally used to carry auxiliary
information.
Some of the methods also require a gradient function
typedef void optimgr(int n, double *par, double *gr, void *ex);
which passes back the gradient in the gr argument. No function is provided for finite-differencing,
nor for approximating the Hessian at the result.
The interfaces (defined in header R_ext/Applic.h) are
• Nelder Mead:
void nmmin(int n, double *xin, double *x, double *Fmin, optimfn fn,
int *fail, double abstol, double intol, void *ex,
double alpha, double beta, double gamma, int trace,
int *fncount, int maxit);
• BFGS:
void vmmin(int n, double *x, double *Fmin,
optimfn fn, optimgr gr, int maxit, int trace,
int *mask, double abstol, double reltol, int nREPORT,
void *ex, int *fncount, int *grcount, int *fail);
Chapter 6: The R API: entry points for C code 180

• Conjugate gradients:
void cgmin(int n, double *xin, double *x, double *Fmin,
optimfn fn, optimgr gr, int *fail, double abstol,
double intol, void *ex, int type, int trace,
int *fncount, int *grcount, int maxit);
• Limited-memory BFGS with bounds:
void lbfgsb(int n, int lmm, double *x, double *lower,
double *upper, int *nbd, double *Fmin, optimfn fn,
optimgr gr, int *fail, void *ex, double factr,
double pgtol, int *fncount, int *grcount,
int maxit, char *msg, int trace, int nREPORT);
• Simulated annealing:
void samin(int n, double *x, double *Fmin, optimfn fn, int maxit,
int tmax, double temp, int trace, void *ex);
Many of the arguments are common to the various methods. n is the number of parameters, x
or xin is the starting parameters on entry and x the final parameters on exit, with final value
returned in Fmin. Most of the other parameters can be found from the help page for optim: see
the source code src/appl/lbfgsb.c for the values of nbd, which specifies which bounds are to
be used.

6.9 Integration
The C code underlying integrate can be accessed directly. The user needs to supply a vector-
izing C function to compute the function to be integrated, of the type
typedef void integr_fn(double *x, int n, void *ex);
where x[] is both input and output and has length n, i.e., a C function, say fn, of type integr_
fn must basically do for(i in 1:n) x[i] := f(x[i], ex). The vectorization requirement can
be used to speed up the integrand instead of calling it n times. Note that in the current
implementation built on QUADPACK, n will be either 15 or 21. The ex argument is a pointer
passed down from the calling routine, normally used to carry auxiliary information.
There are interfaces (defined in header R_ext/Applic.h) for integrals over finite and infinite
intervals (or “ranges” or “integration boundaries”).
• Finite:
void Rdqags(integr_fn f, void *ex, double *a, double *b,
double *epsabs, double *epsrel,
double *result, double *abserr, int *neval, int *ier,
int *limit, int *lenw, int *last,
int *iwork, double *work);
• Infinite:
void Rdqagi(integr_fn f, void *ex, double *bound, int *inf,
double *epsabs, double *epsrel,
double *result, double *abserr, int *neval, int *ier,
int *limit, int *lenw, int *last,
int *iwork, double *work);
Only the 3rd and 4th argument differ for the two integrators; for the finite range integral using
Rdqags, a and b are the integration interval bounds, whereas for an infinite range integral using
Rdqagi, bound is the finite bound of the integration (if the integral is not doubly-infinite) and
inf is a code indicating the kind of integration range,
inf = 1 corresponds to (bound, +Inf),
Chapter 6: The R API: entry points for C code 181

inf = -1 corresponds to (-Inf, bound),

inf = 2 corresponds to (-Inf, +Inf),
f and ex define the integrand function, see above; epsabs and epsrel specify the absolute
and relative accuracy requested, result, abserr and last are the output components value,
abs.err and subdivisions of the R function integrate, where neval gives the number of
integrand function evaluations, and the error code ier is translated to R’s integrate() $
message, look at that function definition. limit corresponds to integrate(..., subdivisions
= *). It seems you should always define the two work arrays and the length of the second one
as
lenw = 4 * limit;
iwork = (int *) R_alloc(limit, sizeof(int));
work = (double *) R_alloc(lenw, sizeof(double));
The comments in the source code in src/appl/integrate.c give more details, particularly
about reasons for failure (ier >= 1).

6.10 Utility functions

R has a fairly comprehensive set of sort routines which are made available to users’ C code. The
following is declared in header file Rinternals.h.

void R_orderVector (int* indx, int n, SEXP arglist, Rboolean [Function]

nalast, Rboolean decreasing)
void R_orderVector1 (int* indx, int n, SEXP x, Rboolean [Function]
nalast, Rboolean decreasing)
R_orderVector() corresponds to R’s order(..., na.last, decreasing). More specifi-
cally, indx <- order(x, y, na.last, decreasing) corresponds to R_orderVector(indx,
n, Rf_lang2(x, y), nalast, decreasing) and for three vectors, Rf_lang3(x,y,z) is used
as arglist.
Both R_orderVector and R_orderVector1 assume the vector indx to be allocated to length
≥ n. On return, indx[] contains a permutation of 0:(n-1), i.e., 0-based C indices (and not
1-based R indices, as R’s order()).
When ordering only one vector, R_orderVector1 is faster and corresponds (but is 0-based)
to R’s indx <- order(x, na.last, decreasing). It was added in R 3.3.0.

All other sort routines are declared in header file R_ext/Utils.h (included by R.h) and
include the following.

void R_isort (int* x, int n) [Function]

void R_rsort (double* x, int n) [Function]
void R_csort (Rcomplex* x, int n) [Function]
void rsort_with_index (double* x, int* index, int n) [Function]
The first three sort integer, real (double) and complex data respectively. (Complex numbers
are sorted by the real part first then the imaginary part.) NAs are sorted last.
rsort_with_index sorts on x, and applies the same permutation to index. NAs are sorted
last.

void revsort (double* x, int* index, int n) [Function]

Is similar to rsort_with_index but sorts into decreasing order, and NAs are not handled.

void iPsort (int* x, int n, int k) [Function]

void rPsort (double* x, int n, int k) [Function]
Chapter 6: The R API: entry points for C code 182

void cPsort (Rcomplex* x, int n, int k) [Function]

These all provide (very) partial sorting: they permute x so that x[k] is in the correct place
with smaller values to the left, larger ones to the right.

void R_qsort (double *v, size_t i, size_t j) [Function]

void R_qsort_I (double *v, int *I, int i, int j) [Function]
void R_qsort_int (int *iv, size_t i, size_t j) [Function]
void R_qsort_int_I (int *iv, int *I, int i, int j) [Function]
These routines sort v[i:j] or iv[i:j] (using 1-indexing, i.e., v[1] is the first element)
calling the quicksort algorithm as used by R’s sort(v, method = "quick") and documented
on the help page for the R function sort. The ..._I() versions also return the sort.index()
vector in I. Note that the ordering is not stable, so tied values may be permuted.
Note that NAs are not handled (explicitly) and you should use different sorting functions if
NAs can be present.

subroutine qsort4 (double precision v, integer indx, integer [Function]

ii, integer jj)
subroutine qsort3 (double precision v, integer ii, integer jj) [Function]
The Fortran interface routines for sorting double precision vectors are qsort3 and qsort4,
equivalent to R_qsort and R_qsort_I, respectively.

void R_max_col (double* matrix, int* nr, int* nc, int* maxes, [Function]
int* ties_meth)
Given the nr by nc matrix matrix in column-major (“Fortran”) order, R_max_col() returns
in maxes[i-1] the column number of the maximal element in the i-th row (the same as R’s
max.col() function). In the case of ties (multiple maxima), *ties_meth is an integer code
in 1:3 determining the method: 1 = “random”, 2 = “first” and 3 = “last”. See R’s help
page ?max.col.

int findInterval (double* xt, int n, double x, Rboolean [Function]

rightmost_closed, Rboolean all_inside, int ilo, int* mflag)
int findInterval2(double* xt, int n, double x, Rboolean [Function]
rightmost_closed, Rboolean all_inside, Rboolean left_open, int
ilo, int* mflag)
Given the ordered vector xt of length n, return the interval or index of x in xt[], typically
max(i; 1 ≤ i ≤ n & xt[i] ≤ x) where we use 1-indexing as in R and Fortran (but not C). If
rightmost closed is true, also returns n − 1 if x equals xt[n]. If all inside is not 0, the result
is coerced to lie in 1:(n-1) even when x is outside the xt[] range. On return, *mflag equals
−1 if x < xt[1], +1 if x >= xt[n], and 0 otherwise.
The algorithm is particularly fast when ilo is set to the last result of findInterval() and x
is a value of a sequence which is increasing or decreasing for subsequent calls.
findInterval2() is a generalization of findInterval(), with an extra Rboolean argument
left open. Setting left_open = TRUE basically replaces all left-closed right-open intervals [s
by left-open ones (s, see the help page of R function findInterval for details.
There is also an F77_CALL(interv)() version of findInterval() with the same arguments,
but all pointers.

A system-independent interface to produce the name of a temporary file is provided as

char * R_tmpnam (const char *prefix, const char *tmpdir) [Function]

char * R_tmpnam2 (const char *prefix, const char *tmpdir, [Function]
const char *fileext)
Chapter 6: The R API: entry points for C code 183

void R_free_tmpnam (char *name) [Function]

Return a pathname for a temporary file with name beginning with prefix and ending with
fileext in directory tmpdir. A NULL prefix or extension is replaced by "". Note that the
return value is dynamically allocated and should be freed using R_free_tmpnam when no
longer needed (unlike the system call tmpnam). Freeing the result using free is no longer
recommended.

There is also the internal function used to expand file names in several R functions, and
called directly by path.expand.

const char * R_ExpandFileName (const char *fn) [Function]

Expand a path name fn by replacing a leading tilde by the user’s home directory (if defined).
The precise meaning is platform-specific; it will usually be taken from the environment vari-
able HOME if this is defined.

For historical reasons there are Fortran interfaces to functions D1MACH and I1MACH. These
can be called from C code as e.g. F77_CALL(d1mach)(4). Note that these are emulations of the
original functions by Fox, Hall and Schryer on Netlib at https://netlib.org/slatec/src/ for
IEC 60559 arithmetic (required by R).

6.11 Re-encoding
R has its own C-level interface to the encoding conversion capabilities provided by iconv because
there are incompatibilities between the declarations in different implementations of iconv.
These are declared in header file R_ext/Riconv.h.

void * Riconv_open (const char *to, const char *from) [Function]

Set up a pointer to an encoding object to be used to convert between two encodings: ""
indicates the current locale.

size_t Riconv (void *cd, const char **inbuf, size_t [Function]

*inbytesleft, char **outbuf, size_t *outbytesleft)
Convert as much as possible of inbuf to outbuf. Initially the size_t variables indicate
the number of bytes available in the buffers, and they are updated (and the char pointers
are updated to point to the next free byte in the buffer). The return value is the number of
characters converted, or (size_t)-1 (beware: size_t is usually an unsigned type). It should
be safe to assume that an error condition sets errno to one of E2BIG (the output buffer is
full), EILSEQ (the input cannot be converted, and might be invalid in the encoding specified)
or EINVAL (the input does not end with a complete multi-byte character).

int Riconv_close (void * cd) [Function]

Free the resources of an encoding object.

6.12 Condition handling and cleanup code

Three functions are available for establishing condition handlers from within C code:
#include <Rinternals.h>

SEXP R_tryCatchError(SEXP (*fun)(void *data), void *data,

SEXP (*hndlr)(SEXP cond, void *hdata), void *hdata);

SEXP R_tryCatch(SEXP (*fun)(void *data), void *data,

SEXP,
SEXP (*hndlr)(SEXP cond, void *hdata), void *hdata,
Chapter 6: The R API: entry points for C code 184

void (*clean)(void *cdata), void *cdata);

SEXP R_withCallingErrorHandler(SEXP (*fun)(void *data), void *data,
SEXP (*hndlr)(SEXP cond, void *hdata), void *hdata)
R_tryCatchError establishes an exiting handler for conditions inheriting form class error.
R_tryCatch can be used to establish a handler for other conditions and to register a cleanup
action. The conditions to be handled are specified as a character vector (STRSXP). A NULL
pointer can be passed as fun or clean if condition handling or cleanup are not needed.
These are currently implemented using the R-level tryCatch mechanism so are subject to
some overhead.
R_withCallingErrorHandler establishes a calling handler for conditions inheriting form
class error. It establishes the handler without calling back into R and will therefore be more
efficient.
The function R_UnwindProtect can be used to ensure that a cleanup action takes place on
ordinary return as well as on a non-local transfer of control, which R implements as a longjmp.
SEXP R_UnwindProtect(SEXP (*fun)(void *data), void *data,
void (*clean)(void *data, Rboolean jump), void *cdata,
SEXP cont);
R_UnwindProtect can be used in two ways. The simper usage, suitable for use in C code,
passes NULL for the cont argument. R_UnwindProtect will call fun(data). If fun returns a
value, then R_UnwindProtect calls clean(cleandata, FALSE) before returning the value re-
turned by fun. If fun executes a non-local transfer of control, then clean(cleandata, TRUE)
is called, and the non-local transfer of control is resumed.
The second use pattern, suitable to support C++ stack unwinding, uses two additional func-
tions:
SEXP R_MakeUnwindCont();
NORET void R_ContinueUnwind(SEXP cont);
R_MakeUnwindCont allocates a continuation token cont to pass to R_UnwindProtect. This
token should be protected with PROTECT before calling R_UnwindProtect. When the clean
function is called with jump == TRUE, indicating that R is executing a non-local transfer of
control, it can throw a C++ exception to a C++ catch outside the C++ code to be unwound, and
then use the continuation token in the a call R_ContinueUnwind(cont) to resume the non-local
transfer of control within R.

6.13 Allowing interrupts

No part of R can be interrupted whilst running long computations in compiled code, so pro-
grammers should make provision for the code to be interrupted at suitable points by calling
from C
#include <R_ext/Utils.h>

void R_CheckUserInterrupt(void);
and from Fortran
subroutine rchkusr()
These check if the user has requested an interrupt, and if so branch to R’s error signaling
functions.
Note that it is possible that the code behind one of the entry points defined here if called
from your C or Fortran code could be interruptible or generate an error and so not return to
your code.
Chapter 6: The R API: entry points for C code 185

6.14 Platform and version information

The header files define USING_R, which can be used to test if the code is indeed being used with
R.
Header file Rconfig.h (included by R.h) is used to define platform-specific macros that are
mainly for use in other header files. The macro WORDS_BIGENDIAN is defined on big-endian6
systems (e.g. most OSes on Sparc and PowerPC hardware) and not on little-endian systems
(nowadays all the commoner R platforms). It can be useful when manipulating binary files.
NB: these macros apply only to the C compiler used to build R, not necessarily to another C or
C++ compiler.
Header file Rversion.h (not included by R.h) defines a macro R_VERSION giving the version
number encoded as an integer, plus a macro R_Version to do the encoding. This can be used to
test if the version of R is late enough, or to include back-compatibility features. For protection
against very old versions of R which did not have this macro, use a construction such as
#if defined(R_VERSION) && R_VERSION >= R_Version(3, 1, 0)
...
#endif
More detailed information is available in the macros R_MAJOR, R_MINOR, R_YEAR, R_MONTH and
R_DAY: see the header file Rversion.h for their format. Note that the minor version includes
the patchlevel (as in ‘2.2’).
Packages which use alloca need to ensure it is defined: as it is part of neither C nor POSIX
there is no standard way to do so. One can use
#include <Rconfig.h> // for HAVE_ALLOCA_H
#ifdef __GNUC__
// this covers gcc, clang, icc
# undef alloca
# define alloca(x) __builtin_alloca((x))
#elif defined(HAVE_ALLOCA_H)
// needed for native compilers on Solaris and AIX
# include <alloca.h>
#endif
(and this should be included before standard C headers such as stdlib.h, since on some plat-
forms these include malloc.h which may have a conflicting definition), which suffices for known
R platforms.

6.15 Inlining C functions

The C99 keyword inline should be recognized by all compilers nowadays used to build R.
Portable code which might be used with earlier versions of R can be written using the macro
R_INLINE (defined in file Rconfig.h included by R.h), as for example from package cluster
(https://CRAN.R-project.org/package=cluster)
#include <R.h>

static R_INLINE int ind_2(int l, int j)

{
...
}
Be aware that using inlining with functions in more than one compilation unit is almost im-
possible to do portably, see https://www.greenend.org.uk/rjk/tech/inline.html, so this
6
https://en.wikipedia.org/wiki/Endianness.
Chapter 6: The R API: entry points for C code 186

usage is for static functions as in the example. All the R configure code has checked is that
R_INLINE can be used in a single C file with the compiler used to build R. We recommend that
packages making extensive use of inlining include their own configure code.

6.16 Controlling visibility

Header R_ext/Visibility.h has some definitions for controlling the visibility of entry points.
These are only effective when ‘HAVE_VISIBILITY_ATTRIBUTE’ is defined – this is checked when
R is configured and recorded in header Rconfig.h (included by R_ext/Visibility.h). It is
often defined on modern Unix-alikes with a recent compiler7 , but not supported on macOS nor
Windows. Minimizing the visibility of symbols in a shared library will both speed up its loading
(unlikely to be significant) and reduce the possibility of linking to other entry points of the same
name.
C/C++ entry points prefixed by attribute_hidden will not be visible in the shared object.
There is no comparable mechanism for Fortran entry points, but there is a more comprehensive
scheme used by, for example package stats. Most compilers which allow control of visibility will
allow control of visibility for all symbols via a flag, and where known the flag is encapsulated
in the macros ‘C_VISIBILITY’, ‘CXX_VISIBILITY’8 and ‘F_VISIBILITY’ for C, C++ and Fortran
compilers.9 These are defined in etc/Makeconf and so available for normal compilation of
package code. For example, src/Makevars could include some of
PKG_CFLAGS=$(C_VISIBILITY)
PKG_CXXFLAGS=$(CXX_VISIBILITY)
PKG_FFLAGS=$(F_VISIBILITY)
This would end up with no visible entry points, which would be pointless. However, the
effect of the flags can be overridden by using the attribute_visible prefix. A shared object
which registers its entry points needs only for have one visible entry point, its initializer, so for
example package stats has
void attribute_visible R_init_stats(DllInfo *dll)
{
R_registerRoutines(dll, CEntries, CallEntries, FortEntries, NULL);
R_useDynamicSymbols(dll, FALSE);
...
}
Because the ‘C_VISIBILITY’ mechanism is only useful in conjunction with attribute_
visible, it is not enabled unless ‘HAVE_VISIBILITY_ATTRIBUTE’ is defined. The usual visibility
flag is -fvisibility=hidden: some compilers also support -fvisibility-inlines-hidden
which can be used by overriding ‘C_VISIBILITY’ and ‘CXX_VISIBILITY’ in config.site when
building R, or editing etc/Makeconf in the R installation.
Note that configure only checks that visibility attributes and flags are accepted, not that
they actually hide symbols.
The visibility mechanism is not available on Windows, but there is an equally effective way
to control which entry points are visible, by supplying a definitions file pkgnme/src/pkgname-
win.def: only entry points listed in that file will be visible. Again using stats as an example, it
has
LIBRARY stats.dll
EXPORTS
R_init_stats
7
It is defined by the Intel compilers, but also hides unsatisfied references and so cannot be used with R. It was
not supported by the AIX nor Solaris compilers.
8
This applies to the compiler for the default C++ dialect (currently C++11) and not necessarily to other dialects.
9
In some cases Fortran compilers accept the flag but do not actually hide their symbols.
Chapter 6: The R API: entry points for C code 187

6.17 Using these functions in your own C code

It is possible to build Mathlib, the R set of mathematical functions documented in Rmath.h, as a
standalone library libRmath under both Unix-alikes and Windows. (This includes the functions
documented in Section 6.7 [Numerical analysis subroutines], page 174, as from that header file.)
The library is not built automatically when R is installed, but can be built in the directory
src/nmath/standalone in the R sources: see the file README there. To use the code in your
own C program include
#define MATHLIB_STANDALONE
#include <Rmath.h>
and link against ‘-lRmath’ (and perhaps ‘-lm’). There is an example file test.c.
A little care is needed to use the random-number routines. You will need to supply the
uniform random number generator
double unif_rand(void)
or use the one supplied (and with a dynamic library or DLL you will have to use the one supplied,
which is the Marsaglia-multicarry with an entry points
set_seed(unsigned int, unsigned int)
to set its seeds and
get_seed(unsigned int *, unsigned int *)
to read the seeds).

6.18 Organization of header files

The header files which R installs are in directory R_INCLUDE_DIR (default R_HOME/include).
This currently includes
R.h includes many other files
Rinternals.h definitions for using R’s internal structures
Rdefines.h macros for an S-like interface to the above (no
longer maintained)
Rmath.h standalone math library
Rversion.h R version information
Rinterface.h for add-on front-ends (Unix-alikes only)
Rembedded.h for add-on front-ends
R_ext/Applic.h optimization and integration
R_ext/BLAS.h C definitions for BLAS routines
R_ext/Callbacks.h C (and R function) top-level task handlers
R_ext/GetX11Image.h X11Image interface used by package trkplot
R_ext/Lapack.h C definitions for some LAPACK routines
R_ext/Linpack.h C definitions for some LINPACK routines, not
all of which are included in R
R_ext/Parse.h a small part of R’s parse interface: not part of
the stable API.
R_ext/RStartup.h for add-on front-ends
R_ext/Rdynload.h needed to register compiled code in packages
R_ext/Riconv.h interface to iconv
R_ext/Visibility.h definitions controlling visibility
R_ext/eventloop.h for add-on front-ends and for packages that
need to share in the R event loops (not
Windows)
The following headers are included by R.h:
Chapter 6: The R API: entry points for C code 188

Rconfig.h configuration info that is made available

R_ext/Arith.h handling for NAs, NaNs, Inf/-Inf
R_ext/Boolean.h TRUE/FALSE type
R_ext/Complex.h C typedefs for R’s complex
R_ext/Constants.h constants
R_ext/Error.h error signaling
R_ext/Memory.h memory allocation
R_ext/Print.h Rprintf and variations.
R_ext/RS.h definitions common to R.h and the former S.h,
including F77_CALL etc.
R_ext/Random.h random number generation
R_ext/Utils.h sorting and other utilities
R_ext/libextern.h definitions for exports from R.dll on Windows.
The graphics systems are exposed in headers R_ext/GraphicsEngine.h, R_
ext/GraphicsDevice.h (which it includes) and R_ext/QuartzDevice.h. Facilities for defining
custom connection implementations are provided in R_ext/Connections.h, but make sure you
consult the file before use.
Let us re-iterate the advice to include system headers before the R header files, especially
Rinternals.h (included by Rdefines.h) and Rmath.h, which redefine names which may be used
in system headers (fewer if ‘R_NO_REMAP’ is defined before inclusion, or ‘R_NO_REMAP_RMATH’ for
Rmath.h).
 189

7 Generic functions and methods

R programmers will often want to add methods for existing generic functions, and may want to
add new generic functions or make existing functions generic. In this chapter we give guidelines
for doing so, with examples of the problems caused by not adhering to them.
This chapter only covers the ‘informal’ class system copied from S3, and not with the S4
(formal) methods of package methods.
First, a caveat: a function named gen.cl will be invoked by the generic gen for class cl, so
do not name functions in this style unless they are intended to be methods.
The key function for methods is NextMethod, which dispatches the next method. It is quite
typical for a method function to make a few changes to its arguments, dispatch to the next
method, receive the results and modify them a little. An example is
t.data.frame <- function(x)
{
x <- as.matrix(x)
NextMethod("t")
}
Note that the example above works because there is a next method, the default method, not
that a new method is selected when the class is changed.
Any method a programmer writes may be invoked from another method by NextMethod,
with the arguments appropriate to the previous method. Further, the programmer cannot predict
which method NextMethod will pick (it might be one not yet dreamt of), and the end user calling
the generic needs to be able to pass arguments to the next method. For this to work
A method must have all the arguments of the generic, including ... if the generic
does.
It is a grave misunderstanding to think that a method needs only to accept the arguments it
needs. The original S version of predict.lm did not have a ... argument, although predict
did. It soon became clear that predict.glm needed an argument dispersion to handle over-
dispersion. As predict.lm had neither a dispersion nor a ... argument, NextMethod could
no longer be used. (The legacy, two direct calls to predict.lm, lives on in predict.glm in R,
which is based on the workaround for S3 written by Venables & Ripley.)
Further, the user is entitled to use positional matching when calling the generic, and the
arguments to a method called by UseMethod are those of the call to the generic. Thus
A method must have arguments in exactly the same order as the generic.
To see the scale of this problem, consider the generic function scale, defined as
scale <- function (x, center = TRUE, scale = TRUE)
UseMethod("scale")
Suppose an unthinking package writer created methods such as
scale.foo <- function(x, scale = FALSE, ...) { }
Then for x of class "foo" the calls
scale(x, , TRUE)
scale(x, scale = TRUE)
would most likely do different things, to the justifiable consternation of the end user.
To add a further twist, which default is used when a user calls scale(x) in our example?
What if
scale.bar <- function(x, center, scale = TRUE) NextMethod("scale")
and x has class c("bar", "foo")? It is the default specified in the method that is used, but the
default specified in the generic may be the one the user sees. This leads to the recommendation:
Chapter 7: Generic functions and methods 190

If the generic specifies defaults, all methods should use the same defaults.
An easy way to follow these recommendations is to always keep generics simple, e.g.
scale <- function(x, ...) UseMethod("scale")
Only add parameters and defaults to the generic if they make sense in all possible methods
implementing it.

7.1 Adding new generics

When creating a new generic function, bear in mind that its argument list will be the maximal
set of arguments for methods, including those written elsewhere years later. So choosing a good
set of arguments may well be an important design issue, and there need to be good arguments
not to include a ... argument.
If a ... argument is supplied, some thought should be given to its position in the argument
sequence. Arguments which follow ... must be named in calls to the function, and they must
be named in full (partial matching is suppressed after ...). Formal arguments before ... can
be partially matched, and so may ‘swallow’ actual arguments intended for .... Although it is
commonplace to make the ... argument the last one, that is not always the right choice.
Sometimes package writers want to make generic a function in the base package, and request
a change in R. This may be justifiable, but making a function generic with the old definition as
the default method does have a small performance cost. It is never necessary, as a package can
take over a function in the base package and make it generic by something like
foo <- function(object, ...) UseMethod("foo")
foo.default <- function(object, ...) base::foo(object)
Earlier versions of this manual suggested assigning foo.default <- base::foo. This is not a
good idea, as it captures the base function at the time of installation and it might be changed
as R is patched or updated.
The same idea can be applied for functions in other packages.
 191

8 Linking GUIs and other front-ends to R

There are a number of ways to build front-ends to R: we take this to mean a GUI or other
application that has the ability to submit commands to R and perhaps to receive results back
(not necessarily in a text format). There are other routes besides those described here, for ex-
ample the package Rserve (https://CRAN.R-project.org/package=Rserve) (from CRAN, see
also https://www.rforge.net/Rserve/) and connections to Java in ‘JRI’ (part of the rJava
(https://CRAN.R-project.org/package=rJava) package on CRAN).
Note that the APIs described in this chapter are only intended to be used in an alternative
front-end: they are not part of the API made available for R packages and can be dangerous
to use in a conventional package (although packages may contain alternative front-ends). Con-
versely some of the functions from the API (such as R_alloc) should not be used in front-ends.

8.1 Embedding R under Unix-alikes

R can be built as a shared library1 if configured with --enable-R-shlib. This shared library
can be used to run R from alternative front-end programs. We will assume this has been done
for the rest of this section. Also, it can be built as a static library if configured with --enable-
R-static-lib, and that can be used in a very similar way (at least on Linux: on other platforms
one needs to ensure that all the symbols exported by libR.a are linked into the front-end).
The command-line R front-end, R_HOME/bin/exec/R, is one such example, and the former
GNOME (see package gnomeGUI on CRAN’s ‘Archive’ area) and macOS consoles are others.
The source for R_HOME/bin/exec/R is in file src/main/Rmain.c and is very simple
int Rf_initialize_R(int ac, char **av); /* in ../unix/system.c */
void Rf_mainloop(); /* in main.c */

extern int R_running_as_main_program; /* in ../unix/system.c */

int main(int ac, char **av)

{
R_running_as_main_program = 1;
Rf_initialize_R(ac, av);
Rf_mainloop(); /* does not return */
return 0;
}
indeed, misleadingly simple. Remember that R_HOME/bin/exec/R is run from a shell script
R_HOME/bin/R which sets up the environment for the executable, and this is used for
• Setting R_HOME and checking it is valid, as well as the path R_SHARE_DIR and R_DOC_DIR
to the installed share and doc directory trees. Also setting R_ARCH if needed.
• Setting LD_LIBRARY_PATH to include the directories used in linking R. This is recorded as
the default setting of R_LD_LIBRARY_PATH in the shell script R_HOME/etcR_ARCH/ldpaths.
• Processing some of the arguments, for example to run R under a debugger and to launch
alternative front-ends to provide GUIs.
The first two of these can be achieved for your front-end by running it via R CMD. So, for example
R CMD /usr/local/lib/R/bin/exec/R
R CMD exec/R
will both work in a standard R installation. (R CMD looks first for executables in R_HOME/bin.
These command-lines need modification if a sub-architecture is in use.) If you do not want to
1
In the parlance of macOS this is a dynamic library, and is the normal way to build R on that platform.
Chapter 8: Linking GUIs and other front-ends to R 192

run your front-end in this way, you need to ensure that R_HOME is set and LD_LIBRARY_PATH is
suitable. (The latter might well be, but modern Unix/Linux systems do not normally include
/usr/local/lib (/usr/local/lib64 on some architectures), and R does look there for system
components.)
The other senses in which this example is too simple are that all the internal defaults are used
and that control is handed over to the R main loop. There are a number of small examples2 in the
tests/Embedding directory. These make use of Rf_initEmbeddedR in src/main/Rembedded.c,
and essentially use
#include <Rembedded.h>

int main(int ac, char **av)

{
/* do some setup */
Rf_initEmbeddedR(argc, argv);
/* do some more setup */

/* submit some code to R, which is done interactively via

run_Rmainloop();

A possible substitute for a pseudo-console is

R_ReplDLLinit();
while(R_ReplDLLdo1() > 0) {
/* add user actions here if desired */
}

*/
Rf_endEmbeddedR(0);
/* final tidying up after R is shutdown */
return 0;
}
If you do not want to pass R arguments, you can fake an argv array, for example by
char *argv[]= {"REmbeddedPostgres", "--silent"};
Rf_initEmbeddedR(sizeof(argv)/sizeof(argv[0]), argv);
However, to make a GUI we usually do want to run run_Rmainloop after setting up various
parts of R to talk to our GUI, and arranging for our GUI callbacks to be called during the R
mainloop.
One issue to watch is that on some platforms Rf_initEmbeddedR and Rf_endEmbeddedR
change the settings of the FPU (e.g. to allow errors to be trapped and to make use of extended
precision registers).
The standard code sets up a session temporary directory in the usual way, unless R_TempDir
is set to a non-NULL value before Rf_initEmbeddedR is called. In that case the value is assumed
to contain an existing writable directory, and it is not cleaned up when R is shut down.
Rf_initEmbeddedR sets R to be in interactive mode: you can set R_Interactive (defined in
Rinterface.h) subsequently to change this.
Note that R expects to be run with the locale category ‘LC_NUMERIC’ set to its default value
of C, and so should not be embedded into an application which changes that.

2
but these are not part of the automated test procedures and so little tested.
Chapter 8: Linking GUIs and other front-ends to R 193

It is the user’s responsibility to attempt to initialize only once. To protect the R interpreter,
Rf_initialize_R will exit the process if re-initialization is attempted.

8.1.1 Compiling against the R library

Suitable flags to compile and link against the R (shared or static) library can be found by
R CMD config --cppflags
R CMD config --ldflags
(These apply only to an uninstalled copy or a standard install.)
If R is installed, pkg-config is available and neither sub-architectures nor a macOS frame-
work have been used, alternatives for a shared R library are
pkg-config --cflags libR
pkg-config --libs libR
and for a static R library
pkg-config --cflags libR
pkg-config --static --libs libR
(This may work for an installed OS framework if pkg-config is taught where to look for libR.pc:
it is installed inside the framework.)
However, a more comprehensive way is to set up a Makefile to compile the front-end.
Suppose file myfe.c is to be compiled to myfe. A suitable Makefile might be
## WARNING: does not work when ${R_HOME} contains spaces
include ${R_HOME}/etc${R_ARCH}/Makeconf
all: myfe

## The following is not needed, but avoids PIC flags.

myfe.o: myfe.c
$(CC) $(ALL_CPPFLAGS) $(CFLAGS) -c myfe.c -o $@

## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a static libR

myfe: myfe.o
$(MAIN_LINK) -o $@ myfe.o $(LIBR) $(LIBS)
invoked as
R CMD make
R CMD myfe
Even though not recommended, ${R_HOME} may contain spaces. In that case, it cannot be
passed as an argument to include in the makefile. Instead, one can instruct make using the
-f option to include Makeconf, for example via recursive invocation of make, see Section 1.6
[Writing portable packages], page 55.
all:
$(MAKE) -f "${R_HOME}/etc${R_ARCH}/Makeconf" -f Makefile.inner
Additional flags which $(MAIN_LINK) includes are, amongst others, those to select OpenMP
and --export-dynamic for the GNU linker on some platforms. In principle $(LIBS) is not
needed when using a shared R library as libR is linked against those libraries, but some platforms
need the executable also linked against them.

8.1.2 Setting R callbacks

For Unix-alikes there is a public header file Rinterface.h that makes it possible to change the
standard callbacks used by R in a documented way. This defines pointers (if R_INTERFACE_PTRS
is defined)
extern void (*ptr_R_Suicide)(const char *);
Chapter 8: Linking GUIs and other front-ends to R 194

extern void (*ptr_R_ShowMessage)(const char *);

extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);
extern void (*ptr_R_WriteConsole)(const char *, int);
extern void (*ptr_R_WriteConsoleEx)(const char *, int, int);
extern void (*ptr_R_ResetConsole)();
extern void (*ptr_R_FlushConsole)();
extern void (*ptr_R_ClearerrConsole)();
extern void (*ptr_R_Busy)(int);
extern void (*ptr_R_CleanUp)(SA_TYPE, int, int);
extern int (*ptr_R_ShowFiles)(int, const char **, const char **,
const char *, Rboolean, const char *);
extern int (*ptr_R_ChooseFile)(int, char *, int);
extern int (*ptr_R_EditFile)(const char *);
extern void (*ptr_R_loadhistory)(SEXP, SEXP, SEXP, SEXP);
extern void (*ptr_R_savehistory)(SEXP, SEXP, SEXP, SEXP);
extern void (*ptr_R_addhistory)(SEXP, SEXP, SEXP, SEXP);
extern int (*ptr_R_EditFiles)(int, const char **, const char **, const char *);
extern SEXP (*ptr_do_selectlist)(SEXP, SEXP, SEXP, SEXP);
extern SEXP (*ptr_do_dataentry)(SEXP, SEXP, SEXP, SEXP);
extern SEXP (*ptr_do_dataviewer)(SEXP, SEXP, SEXP, SEXP);
extern void (*ptr_R_ProcessEvents)();
which allow standard R callbacks to be redirected to your GUI. What these do is generally
documented in the file src/unix/system.txt.

void R_ShowMessage (char *message) [Function]

This should display the message, which may have multiple lines: it should be brought to the
user’s attention immediately.

void R_Busy (int which) [Function]

This function invokes actions (such as change of cursor) when R embarks on an extended
computation (which=1) and when such a state terminates (which=0).

int R_ReadConsole (const char *prompt, unsigned char *buf, int [Function]
buflen, int hist)
void R_WriteConsole (const char *buf, int buflen) [Function]
void R_WriteConsoleEx (const char *buf, int buflen, int otype) [Function]
void R_ResetConsole () [Function]
void R_FlushConsole () [Function]
void R_ClearerrConsole () [Function]
These functions interact with a console.
R_ReadConsole prints the given prompt at the console and then does a fgets(3)–like oper-
ation, transferring up to buflen characters into the buffer buf. The last two bytes should be
set to ‘"\n\0"’ to preserve sanity. If hist is non-zero, then the line should be added to any
command history which is being maintained. The return value is 0 is no input is available
and >0 otherwise.
R_WriteConsoleEx writes the given buffer to the console, otype specifies the output type
(regular output or warning/error). Call to R_WriteConsole(buf, buflen) is equivalent to
R_WriteConsoleEx(buf, buflen, 0). To ensure backward compatibility of the callbacks,
ptr_R_WriteConsoleEx is used only if ptr_R_WriteConsole is set to NULL. To ensure that
stdout() and stderr() connections point to the console, set the corresponding files to NULL
via
R_Outputfile = NULL;
Chapter 8: Linking GUIs and other front-ends to R 195

R_Consolefile = NULL;
R_ResetConsole is called when the system is reset after an error. R_FlushConsole is called
to flush any pending output to the system console. R_ClearerrConsole clears any errors
associated with reading from the console.

int R_ShowFiles (int nfile, const char **file, const char [Function]
**headers, const char *wtitle, Rboolean del, const char *pager)
This function is used to display the contents of files.

int R_ChooseFile (int new, char *buf, int len) [Function]

Choose a file and return its name in buf of length len. Return value is 0 for success, > 0
otherwise.

int R_EditFile (const char *buf) [Function]

Send a file to an editor window.

int R_EditFiles (int nfile, const char **file, const char [Function]
**title, const char *editor)
Send nfile files to an editor, with titles possibly to be used for the editor window(s).

SEXP R_loadhistory (SEXP, SEXP, SEXP, SEXP); [Function]

SEXP R_savehistory (SEXP, SEXP, SEXP, SEXP); [Function]
SEXP R_addhistory (SEXP, SEXP, SEXP, SEXP); [Function]
.Internal functions for loadhistory, savehistory and timestamp.
If the console has no history mechanism these can be as simple as
SEXP R_loadhistory (SEXP call, SEXP op, SEXP args, SEXP env)
{
errorcall(call, "loadhistory is not implemented");
return R_NilValue;
}
SEXP R_savehistory (SEXP call, SEXP op , SEXP args, SEXP env)
{
errorcall(call, "savehistory is not implemented");
return R_NilValue;
}
SEXP R_addhistory (SEXP call, SEXP op , SEXP args, SEXP env)
{
return R_NilValue;
}
The R_addhistory function should return silently if no history mechanism is present, as a
user may be calling timestamp purely to write the time stamp to the console.

void R_Suicide (const char *message) [Function]

This should abort R as rapidly as possible, displaying the message. A possible implementation
is
void R_Suicide (const char *message)
{
char pp[1024];
snprintf(pp, 1024, "Fatal error: %s\n", message);
R_ShowMessage(pp);
R_CleanUp(SA_SUICIDE, 2, 0);
}
Chapter 8: Linking GUIs and other front-ends to R 196

void R_CleanUp (SA_TYPE saveact, int status, int RunLast) [Function]

This function invokes any actions which occur at system termination. It needs to be quite
complex:
#include <Rinterface.h>
#include <Rembedded.h> /* for Rf_KillAllDevices */

void R_CleanUp (SA_TYPE saveact, int status, int RunLast)

{
if(saveact == SA_DEFAULT) saveact = SaveAction;
if(saveact == SA_SAVEASK) {
/* ask what to do and set saveact */
}
switch (saveact) {
case SA_SAVE:
if(runLast) R_dot_Last();
if(R_DirtyImage) R_SaveGlobalEnv();
/* save the console history in R_HistoryFile */
break;
case SA_NOSAVE:
if(runLast) R_dot_Last();
break;
case SA_SUICIDE:
default:
break;
}

R_RunExitFinalizers();
/* clean up after the editor e.g. CleanEd() */

R_CleanTempDir();

/* close all the graphics devices */

if(saveact != SA_SUICIDE) Rf_KillAllDevices();
fpu_setup(FALSE);

exit(status);
}

These callbacks should never be changed in a running R session (and hence cannot be called
from an extension package).

SEXP R_dataentry (SEXP, SEXP, SEXP, SEXP); [Function]

SEXP R_dataviewer (SEXP, SEXP, SEXP, SEXP); [Function]
SEXP R_selectlist (SEXP, SEXP, SEXP, SEXP); [Function]
.External functions for dataentry (and edit on matrices and data frames), View and
select.list. These can be changed if they are not currently in use.

8.1.3 Registering symbols

An application embedding R needs a different way of registering symbols because it is not a
dynamic library loaded by R as would be the case with a package. Therefore R reserves a
special DllInfo entry for the embedding application such that it can register symbols to be
Chapter 8: Linking GUIs and other front-ends to R 197

used with .C, .Call etc. This entry can be obtained by calling getEmbeddingDllInfo, so a
typical use is
DllInfo *info = R_getEmbeddingDllInfo();
R_registerRoutines(info, cMethods, callMethods, NULL, NULL);
The native routines defined by cMethods and callMethods should be present in the embed-
ding application. See Section 5.4 [Registering native routines], page 126, for details on registering
symbols in general.

8.1.4 Meshing event loops

One of the most difficult issues in interfacing R to a front-end is the handling of event loops, at
least if a single thread is used. R uses events and timers for
• Running X11 windows such as the graphics device and data editor, and interacting with
them (e.g., using locator()).
• Supporting Tcl/Tk events for the tcltk package (for at least the X11 version of Tk).
• Preparing input.
• Timing operations, for example for profiling R code and Sys.sleep().
• Interrupts, where permitted.
Specifically, the Unix-alike command-line version of R runs separate event loops for
• Preparing input at the console command-line, in file src/unix/sys-unix.c.
• Waiting for a response from a socket in the internal functions for direct socket access in file
src/modules/internet/Rsock.c and for the interface to libcurl.
• Mouse and window events when displaying the X11-based dataentry window, in file
src/modules/X11/dataentry.c. This is regarded as modal, and no other events are ser-
viced whilst it is active.
There is a protocol for adding event handlers to the first two types of event loops, using
types and functions declared in the header R_ext/eventloop.h and described in comments in
file src/unix/sys-std.c. It is possible to add (or remove) an input handler for events on a
particular file descriptor, or to set a polling interval (via R_wait_usec) and a function to be
called periodically via R_PolledEvents: the polling mechanism is used by the tcltk package.
It is not intended that these facilities are used by packages, but if they are needed exception-
ally, the package should ensure that it cleans up and removes its handlers when its namespace
is unloaded. Note that the header sys/select.h is needed3 : users should check this is available
and define HAVE_SYS_SELECT_H before including R_ext/eventloop.h. (It is often the case that
another header will include sys/select.h before eventloop.h is processed, but this should not
be relied on.)
An alternative front-end needs both to make provision for other R events whilst waiting for
input, and to ensure that it is not frozen out during events of the second type. The ability to
add a polled handler as R_timeout_handler is used by the tcltk package.

8.1.5 Threading issues

Embedded R is designed to be run in the main thread, and all the testing is done in that context.
There is a potential issue with the stack-checking mechanism where threads are involved. This
uses two variables declared in Rinterface.h (if CSTACK_DEFNS is defined) as
extern uintptr_t R_CStackLimit; /* C stack limit */
extern uintptr_t R_CStackStart; /* Initial stack address */
3
At least according to POSIX 2004 and later. Earlier standards prescribed sys/time.h: R_ext/eventloop.h
will include it if HAVE_SYS_TIME_H is defined.
Chapter 8: Linking GUIs and other front-ends to R 198

Note that uintptr_t is an optional C99 type for which a substitute is defined in R, so your code
needs to define HAVE_UINTPTR_T appropriately. To do so, test if the type is defined in C header
stdint.h or C++ header cstdint and if so include the header and define HAVE_UINTPTR_T before
including Rinterface.h. (For C code one can simply include Rconfig.h, possibly via R.h, and
for C++11 code Rinterface.h will include the header cstdint.)
These will be set4 when Rf_initialize_R is called, to values appropriate to the main thread.
Stack-checking can be disabled by setting R_CStackLimit = (uintptr_t)-1 immediately after
Rf_initialize_R is called, but it is better to if possible set appropriate values. (What these
are and how to determine them are OS-specific, and the stack size limit may differ for secondary
threads. If you have a choice of stack size, at least 10Mb is recommended.)
You may also want to consider how signals are handled: R sets signal handlers for sev-
eral signals, including SIGINT, SIGSEGV, SIGPIPE, SIGUSR1 and SIGUSR2, but these can all be
suppressed by setting the variable R_SignalHandlers (declared in Rinterface.h) to 0.
Note that these variables must not be changed by an R package: a package should not call
R internals which makes use of the stack-checking mechanism on a secondary thread.

8.2 Embedding R under Windows

All Windows interfaces to R call entry points in the DLL R.dll, directly or indirectly. Simpler
applications may find it easier to use the indirect route via (D)COM.

8.2.1 Using (D)COM

(D)COM is a standard Windows mechanism used for communication between Windows appli-
cations. One application (here R) is run as COM server which offers services to clients, here
the front-end calling application. The services are described in a ‘Type Library’ and are (more
or less) language-independent, so the calling application can be written in C or C++ or Visual
Basic or Perl or Python and so on. The ‘D’ in (D)COM refers to ‘distributed’, as the client and
server can be running on different machines.
The basic R distribution is not a (D)COM server, but two addons are currently available
that interface directly with R and provide a (D)COM server:
• There is a (D)COM server called StatConnector written by Thomas Baier available via
https://www.autstat.com/, which works with R packages to support transfer of data to
and from R and remote execution of R commands, as well as embedding of an R graphics
window.
Recent versions have usage restrictions.

8.2.2 Calling R.dll directly

The R DLL is mainly written in C and has _cdecl entry points. Calling it directly will be tricky
except from C code (or C++ with a little care).
There is a version of the Unix-alike interface calling
int Rf_initEmbeddedR(int ac, char **av);
void Rf_endEmbeddedR(int fatal);
which is an entry point in R.dll. Examples of its use (and a suitable Makefile.win) can be found
in the tests/Embedding directory of the sources. You may need to ensure that R_HOME/bin is
in your PATH so the R DLLs are found.
Examples of calling R.dll directly are provided in the directory src/gnuwin32/front-ends,
including a simple command-line front end rtest.c whose code is
#define Win32
4
at least on platforms where the values are available, that is having getrlimit and on Linux or having sysctl
supporting KERN_USRSTACK, including FreeBSD and macOS.
Chapter 8: Linking GUIs and other front-ends to R 199

#include <windows.h>
#include <stdio.h>
#include <Rversion.h>
#define LibExtern __declspec(dllimport) extern
#include <Rembedded.h>
#include <R_ext/RStartup.h>
/* for askok and askyesnocancel */
#include <graphapp.h>

/* for signal-handling code */

#include <psignal.h>

/* simple input, simple output */

/* This version blocks all events: a real one needs to call ProcessEvents
frequently. See rterm.c and ../system.c for one approach using
a separate thread for input.
*/
int myReadConsole(const char *prompt, unsigned char *buf, int len, int addtohistory)
{
fputs(prompt, stdout);
fflush(stdout);
if(fgets((char *)buf, len, stdin)) return 1; else return 0;
}

void myWriteConsole(const char *buf, int len)

{
printf("%s", buf);
}

void myCallBack(void)
{
/* called during i/o, eval, graphics in ProcessEvents */
}

void myBusy(int which)

{
/* set a busy cursor ... if which = 1, unset if which = 0 */
}

static void my_onintr(int sig) { UserBreak = 1; }

int main (int argc, char **argv)

{
structRstart rp;
Rstart Rp = &rp;
char Rversion[25], *RHome, *RUser;

sprintf(Rversion, "%s.%s", R_MAJOR, R_MINOR);

if(strcmp(getDLLVersion(), Rversion) != 0) {
fprintf(stderr, "Error: R.DLL version does not match\n");
exit(1);
}

R_setStartTime();
R_DefParamsEx(Rp, RSTART_VERSION);
if((RHome = get_R_HOME()) == NULL) {
fprintf(stderr, "R_HOME must be set in the environment or Registry\n");
exit(1);
}
Rp->rhome = RHome;
RUser = getRUser();
Rp->home = RUser;
Rp->CharacterMode = LinkDLL;
Rp->EmitEmbeddedUTF8 = FALSE;
Chapter 8: Linking GUIs and other front-ends to R 200

Rp->ReadConsole = myReadConsole;
Rp->WriteConsole = myWriteConsole;
Rp->CallBack = myCallBack;
Rp->ShowMessage = askok;
Rp->YesNoCancel = askyesnocancel;
Rp->Busy = myBusy;

Rp->R_Quiet = TRUE; /* Default is FALSE */

Rp->R_Interactive = FALSE; /* Default is TRUE */
Rp->RestoreAction = SA_RESTORE;
Rp->SaveAction = SA_NOSAVE;
R_SetParams(Rp);
freeRUser(RUser);
free_R_HOME(RHome);
R_set_command_line_arguments(argc, argv);

FlushConsoleInputBuffer(GetStdHandle(STD_INPUT_HANDLE));

signal(SIGBREAK, my_onintr);
GA_initapp(0, 0);
readconsolecfg();
setup_Rmainloop();
#ifdef SIMPLE_CASE
run_Rmainloop();
#else
R_ReplDLLinit();
while(R_ReplDLLdo1() > 0) {
/* add user actions here if desired */
}
/* only get here on EOF (not q()) */
#endif
Rf_endEmbeddedR(0);
return 0;
}
The ideas are
• Check that the front-end and the linked R.dll match – other front-ends may allow a looser
match.
• Find and set the R home directory and the user’s home directory. The former
may be available from the Windows Registry: it will be in HKEY_LOCAL_
MACHINE\Software\R-core\R\InstallPath from an administrative install and
HKEY_CURRENT_USER\Software\R-core\R\InstallPath otherwise, if selected during
installation (as it is by default).
• Define startup conditions and callbacks via the Rstart structure. R_DefParams sets the
defaults, and R_SetParams sets updated values. R_DefParamsEx takes an extra argument,
the version number of the Rstart structure provided (RSTART_VERSION refers to the current
version) and returns a non-zero status when that version is not supported by R.
• Record the command-line arguments used by R_set_command_line_arguments for use by
the R function commandArgs().
• Set up the signal handler and the basic user interface.
• Run the main R loop, possibly with our actions intermeshed.
• Arrange to clean up.
An underlying theme is the need to keep the GUI ‘alive’, and this has not been done in
this example. The R callback R_ProcessEvents needs to be called frequently to ensure that
Windows events in R windows are handled expeditiously. Conversely, R needs to allow the GUI
code (which is running in the same process) to update itself as needed – two ways are provided
to allow this:
Chapter 8: Linking GUIs and other front-ends to R 201

• R_ProcessEvents calls the callback registered by Rp->callback. A version of this is used

to run package Tcl/Tk for tcltk under Windows, for the code is
void R_ProcessEvents(void)
{
while (peekevent()) doevent(); /* Windows events for GraphApp */
if (UserBreak) { UserBreak = FALSE; onintr(); }
R_CallBackHook();
if(R_tcldo) R_tcldo();
}
• The mainloop can be split up to allow the calling application to take some action after each
line of input has been dealt with: see the alternative code below #ifdef SIMPLE_CASE.
It may be that no R GraphApp windows need to be considered, although these include
pagers, the windows() graphics device, the R data and script editors and various popups such
as choose.file() and select.list(). It would be possible to replace all of these, but it seems
easier to allow GraphApp to handle most of them.
It is possible to run R in a GUI in a single thread (as RGui.exe shows) but it will normally
be easier5 to use multiple threads.
Note that R’s own front ends use a stack size of 10Mb, whereas MinGW executables default
to 2Mb, and Visual C++ ones to 1Mb. The latter stack sizes are too small for a number of R
applications, so general-purpose front-ends should use a larger stack size.
Applications embedding R 4.2.0 and newer should use UCRT as the C runtime and opt in
for UTF-8 as the active code page in their manifest, as all frontends shipped with R do. This
will allow the embedded R to use UTF-8 as its native encoding on recent Windows systems.

8.2.3 Finding R HOME

Both applications which embed R and those which use a system call to invoke R (as
Rscript.exe, Rterm.exe or R.exe) need to be able to find the R bin directory. The sim-
plest way to do so is the ask the user to set an environment variable R_HOME and use that, but
naive users may be flummoxed as to how to do so or what value to use.
The R for Windows installers have for a long time allowed the value of R_HOME to be recorded
in the Windows Registry: this is optional but selected by default. Where it is recorded has
changed over the years to allow for multiple versions of R to be installed at once, and to allow
32- and 64-bit versions of R to be installed on the same machine. Only 64-bit versions are
supported since R 4.2.
The basic Registry location is Software\R-core\R. For an administrative install this is
under HKEY_LOCAL_MACHINE and on a 64-bit OS HKEY_LOCAL_MACHINE\Software\R-core\R is
by default redirected for a 32-bit application, so a 32-bit application will see the information for
the last 32-bit install, and a 64-bit application that for the last 64-bit install. For a personal
install, the information is under HKEY_CURRENT_USER\Software\R-core\R which is seen by both
32-bit and 64-bit applications and so records the last install of either architecture. To circumvent
this, with Intel builds there are locations Software\R-core\R32 and Software\R-core\R64
which always refer to one architecture.
When R is installed and recording is not disabled then two string values are written at that
location for keys InstallPath and Current Version, and these keys are removed when R is
uninstalled. To allow information about other installed versions to be retained, there is also
a key named something like 3.0.0 or 3.0.0 patched or 3.1.0 Pre-release with a value for
InstallPath.
5
An attempt to use only threads in the late 1990s failed to work correctly under Windows 95, the predominant
version of Windows at that time.
Chapter 8: Linking GUIs and other front-ends to R 202

So a comprehensive algorithm to search for R_HOME is something like

• Decide which of personal or administrative installs should have precedence. There are argu-
ments both ways: we find that with roaming profiles that HKEY_CURRENT_USER\Software
often gets reverted to an earlier version. Do the following for one or both of HKEY_CURRENT_
USER and HKEY_LOCAL_MACHINE.
• If the desired architecture is known, look in Software\R-core\R32 or Software\R-
core\R64, and if that does not exist or the architecture is immaterial, in Software\R-
core\R.
• If key InstallPath exists then this is R_HOME (recorded using backslashes). If it does
not, look for version-specific keys like 2.11.0 alpha, pick the latest (which is of itself a
complicated algorithm as 2.11.0 patched > 2.11.0 > 2.11.0 alpha > 2.8.1) and use its
value for InstallPath.
 203

Function and variable index

. \packageAuthor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
.C . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123 \packageDescription . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
.Call . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140, 151 \packageDESCRIPTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
.External . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140, 151 \packageIndices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
.Fortran . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123 \packageMaintainer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
.Last.lib . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 \packageTitle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
.onAttach . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50 \pkg . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
.onDetach . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 \preformatted . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
.onLoad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50 \R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
.onUnload . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 \RdOpts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
.Random.seed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167 \references . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
\renewcommand . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
\S3method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
\ \samp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
\abbr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90 \section . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
\acronym . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89 \seealso . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
\alias . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81 \Sexpr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
\arguments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83 \source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
\author . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84 \sQuote . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
\bold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88 \sspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
\cite . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
\strong . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
\code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
\tabular . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
\command . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
\title . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
\concept . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
\cr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87 \url . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
\CRANpkg{pkg} . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95 \usage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
\deqn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91 \value . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
\describe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90 \var . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
\description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82 \verb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
\details . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
\dfn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
\doi{numbers} . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
\dontrun . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
A
\dontshow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84 allocList . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
\dots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92 allocMatrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158
\dQuote . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88 allocVector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
\email . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89 any_duplicated . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
\emph . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88 any_duplicated3. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
\enc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92 asChar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
\enumerate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90 asComplex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
\env . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89 asInteger . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
\eqn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91 asLogical . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
\examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
asReal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
\figure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
AUTHORS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
\file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
\format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
\href . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
\if . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93 B
\ifelse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
\itemize . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90 bessel_i . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
\kbd . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88 bessel_j . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
\keyword . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85 bessel_k . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
\ldots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92 bessel_y . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
\link . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90 beta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
\linkS4class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90 BLAS_LIBS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
\method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82 browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
\name . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
\newcommand . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
\note . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
\option . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
\out . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Function and variable index 204

C F
CAAR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153 FALSE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
CAD4R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152 findFun . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
CAD5R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152 findInterval . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
CADDDR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152 findInterval2(double* . . . . . . . . . . . . . . . . . . . . . . . . . 182
CADDR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152 findVar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
CADR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152 FLIBS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Calloc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166 fmax2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
CallocCharBuf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167 fmin2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
CAR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152 fprec . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
CDAR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153 fpu_setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
Free . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166
CDDDR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
fround . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
CDDR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
fsign . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
CDR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
ftrunc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
cgmin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
choose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
CITATION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17, 78 G
classgets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
gammafn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
CleanEd . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
gctorture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
coerceVector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
GetArrayDimnames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
COMPLEX . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163 getAttrib . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
cons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149 getCharCE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
CONS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149 GetColNames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
COPYRIGHTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6, 17 GetMatrixDimnames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
cospi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177 GetRNGstate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
cPsort . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181 GetRowNames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145

D I
imax2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
dblepr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169 imin2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
dblepr1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169 import . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
debug . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108 importClassesFrom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
debugger . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107 importFrom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
defineVar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148 importMethodsFrom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
digamma . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176 install . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
dimgets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145 installChar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
dimnamesgets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145 INTEGER . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
dpsifn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176 integr_fn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
dump.frames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107 intpr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
duplicate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149 intpr1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
dyn.load . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125 iPsort . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
dyn.unload . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125 isArray . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
isComplex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
isEnvironment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
isExpression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
E isFactor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
elt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149 isFunction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
error . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167 isInteger . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
errorcall . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167 isLanguage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
eval . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154 isList . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
exp_rand . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167 isLogical . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
expm1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177 isMatrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
export . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 ISNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153, 169
exportClasses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54 ISNAN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153, 169
isNewList . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
exportClassPattern . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
isNull . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
exportMethods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
isNumeric . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
exportPattern . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49, 54
isObject . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
isOrdered . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
isPairList . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
isPrimitive . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
isReal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
Function and variable index 205

isString . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144 N
isSymbol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144 NA_REAL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
isTs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149 namesgets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
isUnordered . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149 NEWS.Rd . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
isVector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149 nmmin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
isVectorAtomic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149 norm_rand . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
isVectorList . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149 nrows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
nthcdr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149

L O
labelpr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169 OBJECTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26, 134
lang1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149 onintr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
lang2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149 optimfn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
lang3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149 optimgr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
lang4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
lang5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
lang6 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149 P
LAPACK_LIBS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 pentagamma . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
lastElt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149 PKG_CFLAGS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
lbeta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176 PKG_CPPFLAGS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
lbfgsb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180 PKG_CXXFLAGS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
lchoose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176 PKG_FCFLAGS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
lcons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149 PKG_FFLAGS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
LCONS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149 PKG_LIBS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
lgamma1p . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177 PKG_OBJCFLAGS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
lgammafn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176 PKG_OBJCXXFLAGS. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
library.dynam . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14, 125 pow1p . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
list1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149 PRINTNAME . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
list2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149 PrintValue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
prompt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
list3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
protect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
list4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
PROTECT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
list5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
PROTECT_WITH_INDEX . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
list6 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
psigamma . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
log1mexp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177 PutRNGstate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
log1p . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177
log1pexp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177
log1pmx . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177 Q
LOGICAL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163 qsort3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
logspace_add . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178 qsort4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
logspace_sub . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
logspace_sum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
R
R CMD build . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
M R CMD check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
R CMD config . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
M_E . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178 R CMD Rd2pdf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
M_PI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178 R CMD Rdconv . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
MARK_NOT_MUTABLE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150 R CMD SHLIB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
MAYBE_REFERENCED . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150 R CMD Stangle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
MAYBE_SHARED . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150 R CMD Sweave . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
Memcpy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167 R_addhistory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
Memzero . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167 R_alloc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
mkChar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147 R_allocLD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
mkCharCE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163 R_Busy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194
mkCharLen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147 R_Calloc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166
mkCharLenCE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164 R_CheckUserInterrupt . . . . . . . . . . . . . . . . . . . . . . . . . . 184
mkString . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148 R_ChooseFile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
R_CleanTempDir . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
R_CleanUp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
R_ClearerrConsole . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194
R_ClearExternalPtr . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
R_compute_identical . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
Function and variable index 206

R_ContinueUnwind . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184 R_ReleaseObject. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142

R_csort . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181 R_ReplDLLdo1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192
R_dataentry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196 R_ReplDLLinit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192
R_dataviewer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196 R_Reprotect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
R_DefParams . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200 R_ResetConsole . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194
R_DefParamsEx . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200 R_rsort . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
R_dot_Last . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196 R_RunExitFinalizers . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
R_EditFile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195 R_RunWeakRefFinalizer . . . . . . . . . . . . . . . . . . . . . . . . . 162
R_EditFiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195 R_SaveGlobalEnv. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
R_ExpandFileName . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183 R_savehistory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
R_ExternalPtrAddr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161 R_selectlist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
R_ExternalPtrAddrFn . . . . . . . . . . . . . . . . . . . . . . . . . . . 161 R_set_command_line_arguments . . . . . . . . . . . . . . . . . 198
R_ExternalPtrProtected. . . . . . . . . . . . . . . . . . . . . . . . 161 R_SetExternalPtrAddr . . . . . . . . . . . . . . . . . . . . . . . . . . 161
R_ExternalPtrTag . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161 R_SetExternalPtrProtected . . . . . . . . . . . . . . . . . . . . 161
R_FINITE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169 R_SetExternalPtrTag . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
R_FlushConsole . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194 R_SetParams . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
R_forceSymbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129 R_setStartTime . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
R_Free . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166 R_ShowFiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
R_free_tmpnam . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182 R_ShowMessage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194
R_GetCCallable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133 R_Srcref . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
R_GetCurrentEnv. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155 R_Suicide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
R_GetCurrentSrcref . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160 R_tmpnam . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
R_getEmbeddingDllInfo . . . . . . . . . . . . . . . . . . . . . . . . . 197 R_tmpnam2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
R_GetSrcFilename . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160 R_tryCatch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
R_INLINE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185 R_tryCatchError. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
R_IsNaN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169 R_unif_index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
R_isort . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181 R_UnwindProtect. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
R_LIBRARY_DIR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
R_useDynamicSymbols . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
R_loadhistory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
R_Version . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
R_MakeExternalPtr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
R_wait_usec . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
R_MakeExternalPtrFn . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
R_WeakRefKey . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
R_MakeUnwindCont . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
R_WeakRefValue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
R_MakeWeakRef . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
R_withCallingErrorHandler . . . . . . . . . . . . . . . . . . . . 184
R_MakeWeakRefC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
R_WriteConsole . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194
R_max_col . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
R_WriteConsoleEx . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194
R_NegInf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
RAW . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
R_NewEnv . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
rchkusr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
R_NewPreciousMSet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
R_orderVector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181 Rdqagi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
R_orderVector1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181 Rdqags . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
R_PACKAGE_DIR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21, 23 Realloc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166
R_PACKAGE_NAME . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21, 23 realpr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
R_ParseVector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160 realpr1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
R_PolledEvents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197 REAL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
R_PosInf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169 recover . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
R_pow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176 reEnc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
R_pow_di . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176 REprintf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
R_PreserveInMSet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142 REPROTECT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
R_PreserveObject . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142 REvprintf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
R_ProcessEvents. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201 revsort . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
R_ProtectWithIndex . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142 Rf_endEmbeddedR. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192
R_PV . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118 Rf_initEmbeddedR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192
R_qsort . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182 Rf_initialize_R. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
R_qsort_int . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182 Rf_KillAllDevices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
R_qsort_int_I . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182 Rf_mainloop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
R_qsort_I . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182 Riconv . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
R_ReadConsole . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194 Riconv_close . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
R_Realloc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166 Riconv_open . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
R_RegisterCCallable . . . . . . . . . . . . . . . . . . . . . . . . . . . 133 Rprintf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
R_RegisterCFinalizer . . . . . . . . . . . . . . . . . . . . . . . . . . 161 Rprof . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98, 100
R_RegisterCFinalizerEx. . . . . . . . . . . . . . . . . . . . . . . . 161 Rprofmem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
R_RegisterFinalizer . . . . . . . . . . . . . . . . . . . . . . . . . . . 161 rPsort . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
R_RegisterFinalizerEx . . . . . . . . . . . . . . . . . . . . . . . . . 161 rsort_with_index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
R_registerRoutines . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127 Rtanpi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177
R_ReleaseFromMSet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142 run_Rmainloop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192
Function and variable index 207

Rvprintf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169 T
TAG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
tanpi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
tetragamma . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
S trace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
S_alloc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165 traceback . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
S_realloc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165 tracemem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
translateChar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
S3method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
translateCharUTF8 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
SAFE_FFLAGS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
trigamma . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
samin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180 TRUE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
ScalarComplex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148 type2char . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
ScalarInteger . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148 type2str . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
ScalarLogical . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148 TYPEOF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
ScalarRaw . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
ScalarReal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
ScalarString . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148 U
SET_STRING_ELT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147 undebug . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
SET_TAG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155 unif_rand . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
SET_VECTOR_ELT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163 unprotect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
setAttrib . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145 unprotect_ptr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
SETCAD4R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153 UNPROTECT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
SETCADDDR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153 UNPROTECT_PTR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
SETCADDR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153 untracemem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
useDynLib . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
SETCADR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
SETCAR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
SETCDR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153 V
setup_Rmainloop. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
VECTOR_ELT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
setVar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
vmaxget . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
sign . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
vmaxset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
signrank_free . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175 vmmin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
sinpi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177
str2type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
STRING_ELT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147 W
summaryRprof . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100 warning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123 warningcall . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
system.time . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123 warningcall_immediate . . . . . . . . . . . . . . . . . . . . . . . . . 167
system2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123 wilcox_free . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
 208

Concept index

. F
.install extras file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 Figures in documentation . . . . . . . . . . . . . . . . . . . . . . . . . 92
.Rbuildignore file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 finalizer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
.Rinstignore file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 Finding variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147

A G
Allocating storage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143 Gamma function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
Attributes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144 Garbage collection. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
Generic functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189

B
Bessel functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
H
Beta function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176 handling character data . . . . . . . . . . . . . . . . . . . . . . . . . 147
Building binary packages . . . . . . . . . . . . . . . . . . . . . . . . . 44 Handling lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
Building source packages . . . . . . . . . . . . . . . . . . . . . . . . . 43 Handling R objects in C . . . . . . . . . . . . . . . . . . . . . . . . . 140

C I
C++ code, interfacing . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135 IEEE special values . . . . . . . . . . . . . . . . . . . . . . . . . 153, 169
Calling C from Fortran and vice versa . . . . . . . . . . . 170 INDEX file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Checking packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39 Indices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
citation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17, 78 Inspecting R objects when debugging . . . . . . . . . . . . 118
Classes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146 integration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
Cleanup code. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183 Interfaces to compiled code . . . . . . . . . . . . . . . . . 123, 151
cleanup file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 Interfacing C++ code . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
Condition handling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183 Interrupts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
conditionals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
configure file. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Copying objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149 L
CRAN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 LICENCE file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Creating packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 LICENSE file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Creating shared objects . . . . . . . . . . . . . . . . . . . . . . . . . 134 Lists and tables in documentation . . . . . . . . . . . . . . . . 90
Cross-references in documentation . . . . . . . . . . . . . . . . 90
cumulative hazard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
M
Marking text in documentation . . . . . . . . . . . . . . . . . . . 88
D Mathematics in documentation . . . . . . . . . . . . . . . . . . . 91
Debugging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116 Memory allocation from C . . . . . . . . . . . . . . . . . . . . . . . 165
DESCRIPTION file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 Memory use . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
Details of R types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143 Method functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
Distribution functions from C . . . . . . . . . . . . . . . . . . . 174 Missing values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153, 169
Documentation, writing . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Dynamic loading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
dynamic pages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94 N
namespaces. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
news . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
E Numerical analysis subroutines from C. . . . . . . . . . . 174
Editing Rd files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97 Numerical derivatives. . . . . . . . . . . . . . . . . . . . . . . . . . . . 156
encoding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
Error handling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
Error signaling from C . . . . . . . . . . . . . . . . . . . . . . . . . . 167 O
Error signaling from Fortran . . . . . . . . . . . . . . . . . . . . . 167 OpenMP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28, 185
Evaluating R expressions from C . . . . . . . . . . . . . . . . 154 Operating system access . . . . . . . . . . . . . . . . . . . . . . . . . 123
external pointer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161 optimization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
Concept index 209

P T
Package builder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 tarballs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Package structure. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 Tidying R code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
Package subdirectories . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Parsing R code from C . . . . . . . . . . . . . . . . . . . . . . . . . . 159
Platform-specific documentation . . . . . . . . . . . . . . . . . . 93 U
Polygamma functions. . . . . . . . . . . . . . . . . . . . . . . . . . . . 176 user-defined macros. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Printing from C . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
Printing from Fortran . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
Processing Rd format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96 V
Profiling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98, 100, 101
Version information from C . . . . . . . . . . . . . . . . . . . . . . 185
vignettes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
R Visibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
Random numbers in C . . . . . . . . . . . . . . . . . . . . . . 167, 174
Random numbers in Fortran . . . . . . . . . . . . . . . . . . . . . 170
Registering native routines . . . . . . . . . . . . . . . . . . . . . . 126 W
weak reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
S
Setting variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
Sort functions from C . . . . . . . . . . . . . . . . . . . . . . . . . . . 181 Z
Sweave . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45 Zero-finding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155