Radmin

R Installation and Administration
Version 3.5.1 (2018-07-02)
R Core Team
This manual is for R, version 3.5.1 (2018-07-02).
Copyright c 2001–2018 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
1 Obtaining R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.1 Getting and unpacking the sources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Getting patched and development versions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2.1 Using Subversion and rsync . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
2 Installing R under Unix-alikes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

2.1 Simple compilation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
2.2 Help options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
2.3 Making the manuals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
2.4 Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.5 Uninstallation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.6 Sub-architectures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.6.1 Multilib . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2.7 Other Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2.7.1 OpenMP Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
2.7.2 C++ Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
2.8 Testing an Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
3 Installing R under Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

3.1 Building from source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
3.1.1 Getting the tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
3.1.2 Getting the source files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
3.1.3 Building the core files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
3.1.4 Building the cairo devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
3.1.5 Using ICU for collation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
3.1.6 Support for libcurl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
3.1.7 Checking the build . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
3.1.8 Building the manuals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
3.1.9 Building the Inno Setup installer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
3.1.10 Building the MSI installer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
3.1.11 64-bit Windows builds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
3.2 Testing an Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
4 Installing R under macOS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

4.1 Running R under macOS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
4.2 Uninstalling under macOS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
4.3 Multiple versions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
5 Running R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
6 Add-on packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
6.1 Default packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
6.2 Managing libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
6.3 Installing packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
6.3.1 Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
6.3.2 macOS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
ii
6.3.3 Customizing package compilation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

6.3.4 Multiple sub-architectures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
6.3.5 Byte-compilation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
6.3.6 External software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
6.4 Updating packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
6.5 Removing packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
6.6 Setting up a package repository . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
6.7 Checking installed source packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
7 Internationalization and Localization . . . . . . . . . . . . . . . . . . . . . . . . 32

7.1 Locales . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
7.1.1 Locales under Unix-alikes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
7.1.2 Locales under Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
7.1.3 Locales under macOS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
7.2 Localization of messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
8 Choosing between 32- and 64-bit builds . . . . . . . . . . . . . . . . . . . . 35
9 The standalone Rmath library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

9.1 Unix-alikes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
9.2 Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Appendix A Essential and useful other

programs under a Unix-alike . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
A.1 Essential programs and libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
A.2 Useful libraries and programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
A.2.1 Tcl/Tk . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
A.2.2 Java support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
A.2.3 Other compiled languages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
A.3 Linear algebra. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
A.3.1 BLAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
A.3.1.1 ATLAS. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
A.3.1.2 Goto and OpenBLAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
A.3.1.3 Intel MKL. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
A.3.1.4 ACML . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
A.3.1.5 Shared BLAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
A.3.2 LAPACK . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
A.3.3 Caveats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Appendix B Configuration on a Unix-alike . . . . . . . . . . . . . . . . . . . 49

B.1 Configuration options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
B.2 Internationalization support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
B.3 Configuration variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
B.3.1 Setting paper size . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
B.3.2 Setting the browsers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
B.3.3 Compilation flags . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
B.3.4 Making manuals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
B.4 Setting the shell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
B.5 Using make . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
B.6 Using FORTRAN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
B.7 Compile and load flags . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
B.8 Maintainer mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
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Appendix C Platform notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

C.1 X11 issues. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
C.2 Linux . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
C.2.1 Clang . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
C.2.2 Intel compilers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
C.3 macOS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
C.3.1 Tcl/Tk headers and libraries. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
C.3.2 Java. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
C.3.3 Frameworks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
C.3.4 Building R.app . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
C.4 Solaris . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
C.4.1 64-bit builds. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
C.4.2 Using gcc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
C.5 AIX. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
C.6 FreeBSD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
C.7 OpenBSD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
C.8 Cygwin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
C.9 New platforms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Appendix D The Windows toolset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

D.1 LATEX . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
D.2 The Inno Setup installer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
D.3 The command line tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
D.4 The MinGW-w64 toolchain . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
D.5 Useful additional programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Function and variable index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Concept index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Environment variable index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76

1
1 Obtaining R
Sources, binaries and documentation for R can be obtained via CRAN, the “Comprehensive
R Archive Network” whose current members are listed at https://CRAN.R-project.org/
mirrors.html.
1.1 Getting and unpacking the sources

The simplest way is to download the most recent R-x.y.z.tar.gz file, and unpack it with
tar -xf R-x.y.z.tar.gz
on systems that have a suitable1 tar installed. On other systems you need to have the gzip
program installed, when you can use
gzip -dc R-x.y.z.tar.gz | tar -xf -
The pathname of the directory into which the sources are unpacked should not contain spaces,
as most make programs (and specifically GNU make) do not expect spaces.
If you want the build to be usable by a group of users, set umask before unpacking so that
the files will be readable by the target group (e.g., umask 022 to be usable by all users). Keep
this setting of umask whilst building and installing.
If you use a recent GNU version of tar and do this as a root account (which on Windows
includes accounts with administrator privileges) you may see many warnings about changing
ownership. In which case you can use
tar --no-same-owner -xf R-x.y.z.tar.gz
and perhaps also include the option --no-same-permissions. (These options can also be set
in the TAR_OPTIONS environment variable: if more than one option is included they should be
separated by spaces.)
1.2 Getting patched and development versions

A patched version of the current release, ‘r-patched’, and the current development version,
‘r-devel’, are available as daily tarballs and via access to the R Subversion repository. (For
the two weeks prior to the release of a minor (3.x.0) version, ‘r-patched’ tarballs may refer to
beta/release candidates of the upcoming release, the patched version of the current release being
available via Subversion.)
The tarballs are available from https: / / stat . ethz . ch / R / daily. Download
R-patched.tar.gz or R-devel.tar.gz (or the .tar.bz2 versions) and unpack as described in
the previous section. They are built in exactly the same way as distributions of R releases.
1.2.1 Using Subversion and rsync

Sources are also available via https://svn.R-project.org/R/, the R Subversion repository. If
you have a Subversion client (see https://subversion.apache.org/), you can check out and
update the current ‘r-devel’ from https://svn.r-project.org/R/trunk/ and the current
‘r-patched’ from ‘https://svn.r-project.org/R/branches/R-x-y-branch/’ (where x and y
are the major and minor number of the current released version of R). E.g., use
svn checkout https://svn.r-project.org/R/trunk/ path
to check out ‘r-devel’ into directory path (which will be created if necessary).
The alpha, beta and RC versions of an upcoming x.y.0 release are available from
‘https://svn.r-project.org/R/branches/R-x-y-branch/’ in the four-week period prior to
the release.
1
e.g. GNU tar version 1.15 or later, or that from the ‘libarchive’ (as used on macOS versions 10.6 and later)
or ‘Heirloom Toolchest’ distributions.
2
Note that ‘https:’ is required2 , and that the SSL certificate for the Subversion server of the
R project should be recognized as from a trusted source.
Note that retrieving the sources by e.g. wget -r or svn export from that URL will not work
(and will give a error early in the make process): the Subversion information is needed to build
R.
The Subversion repository does not contain the current sources for the recommended pack-
ages, which can be obtained by rsync or downloaded from CRAN. To use rsync to install the
appropriate sources for the recommended packages, run ./tools/rsync-recommended from the
top-level directory of the R sources.
If downloading manually from CRAN, do ensure that you have the correct versions of
the recommended packages: if the number in the file VERSION is ‘x.y.z’ you need to
download the contents of ‘https://CRAN.R-project.org/src/contrib/dir’, where dir is
‘x.y.z/Recommended’ for r-devel or x.y-patched/Recommended for r-patched, respectively, to
directory src/library/Recommended in the sources you have unpacked. After downloading
manually you need to execute tools/link-recommended from the top level of the sources to
make the requisite links in src/library/Recommended. A suitable incantation from the top
level of the R sources using wget might be (for the correct value of dir)
wget -r -l1 --no-parent -A\*.gz -nd -P src/library/Recommended \
https://CRAN.R-project.org/src/contrib/dir
./tools/link-recommended
2
for some Subversion clients ‘http:’ may appear to work, but requires continual redirection.
3
2 Installing R under Unix-alikes

R will configure and build under most common Unix and Unix-alike platforms including
‘cpu-*-linux-gnu’ for the ‘alpha’, ‘arm’, ‘hppa’, ‘ix86’, ‘m68k’, ‘mips’, ‘mipsel’, ‘powerpc’,
‘s390’, ‘sparc’, and ‘x86_64’ CPUs, ‘x86_64-apple-darwin’, ‘i386-sun-solaris’ and ‘sparc-
sun-solaris’ as well as perhaps (it is tested less frequently on these platforms) ‘i386-apple-
darwin’, ‘i386-*-freebsd’, ‘x86_64-*-freebsd’, ‘i386-*-netbsd’, ‘x86_64/*-openbsd’ and
‘powerpc-ibm-aix6*’
In addition, binary distributions are available for some common Linux distributions and for
macOS (formerly OS X and Mac OS). See the FAQ for current details. These are installed in
platform-specific ways, so for the rest of this chapter we consider only building from the sources.
Cross-building is not possible: installing R builds a minimal version of R and then runs many
R scripts to complete the build.
2.1 Simple compilation

First review the essential and useful tools and libraries in Appendix A [Essential and useful
other programs under a Unix-alike], page 39, and install those you want or need. Ensure that
the environment variable TMPDIR is either unset (and /tmp exists and can be written in and
scripts can be executed from) or points to the absolute path to a valid temporary directory (one
from which execution of scripts is allowed) which does not contain spaces.1
Choose a directory to install the R tree (R is not just a binary, but has additional data
sets, help files, font metrics etc). Let us call this place R HOME. Untar the source code. This
should create directories src, doc, and several more under a top-level directory: change to that
top-level directory (At this point North American readers should consult Section B.3.1 [Setting
paper size], page 50.) Issue the following commands:
./configure
make
(See Section B.5 [Using make], page 51, if your make is not called ‘make’.) Users of Debian-based
64-bit systems2 may need
./configure LIBnn=lib
make
Then check the built system works correctly by
make check
Failures are not necessarily problems as they might be caused by missing functionality, but
you should look carefully at any reported discrepancies. (Some non-fatal errors are expected in
locales that do not support Latin-1, in particular in true C locales and non-UTF-8 non-Western-
European locales.) A failure in tests/ok-errors.R may indicate inadequate resource limits
(see Chapter 5 [Running R], page 22).
More comprehensive testing can be done by
make check-devel
or
make check-all
see file tests/README and Section 2.8 [Testing a Unix-alike Installation], page 11, for the possibil-
ities of doing this in parallel. Note that these checks are only run completely if the recommended
packages are installed.
1
Most aspects will work with paths containing spaces, but external software used by R, e.g. texi2dvi version
4.8, may not.
2
which use lib rather than lib64 for their primary 64-bit library directories.
Chapter 2: Installing R under Unix-alikes 4
If the configure and make commands execute successfully, a shell-script front-end called R
will be created and copied to R_HOME/bin. You can link or copy this script to a place where
users can invoke it, for example to /usr/local/bin/R. You could also copy the man page R.1
to a place where your man reader finds it, such as /usr/local/man/man1. If you want to install
the complete R tree to, e.g., /usr/local/lib/R, see Section 2.4 [Installation], page 6. Note:
you do not need to install R: you can run it from where it was built.
You do not necessarily have to build R in the top-level source directory (say, TOP_SRCDIR).
To build in BUILDDIR, run
cd BUILDDIR
TOP_SRCDIR/configure
make
and so on, as described further below. This has the advantage of always keeping your source
tree clean and is particularly recommended when you work with a version of R from Subversion.
(You may need GNU make to allow this, and you will need no spaces in the path to the build
directory. It is unlikely to work if the source directory has previously been used for a build.)
Now rehash if necessary, type R, and read the R manuals and the R FAQ (files FAQ or
doc/manual/R-FAQ.html, or https: / / CRAN . R-project . org / doc / FAQ / R-FAQ . html which
always has the version for the latest release of R).
Note: if you already have R installed, check that where you installed R replaces or comes
earlier in your path than the previous installation. Some systems are set up to have /usr/bin
(the standard place for a system installation) ahead of /usr/local/bin (the default place for
installation of R) in their default path, and some do not have /usr/local/bin on the default
path.
2.2 Help options

By default HTML help pages are created when needed rather than being built at install time.
If you need to disable the server and want HTML help, there is the option to build HTML pages
when packages are installed (including those installed with R). This is enabled by the configure
option --enable-prebuilt-html. Whether R CMD INSTALL (and hence install.packages) pre-
builds HTML pages is determined by looking at the R installation and is reported by R CMD
INSTALL --help: it can be overridden by specifying one of the INSTALL options --html or
--no-html.
The server is disabled by setting the environment variable R_DISABLE_HTTPD to a non-
empty value, either before R is started or within the R session before HTML help (includ-
ing help.start) is used. It is also possible that system security measures will prevent the
server from being started, for example if the loopback interface has been disabled. See
?tools::startDynamicHelp for more details.
2.3 Making the manuals

There is a set of manuals that can be built from the sources,
‘fullrefman’
Printed versions of all the help pages for base and recommended packages (around
3500 pages).
‘refman’ Printed versions of the help pages for selected base packages (around 2000 pages)
‘R-FAQ’ R FAQ
‘R-intro’ “An Introduction to R”.
‘R-data’ “R Data Import/Export”.
‘R-admin’ “R Installation and Administration”, this manual.

‘R-exts’ “Writing R Extensions”.
‘R-lang’ “The R Language Definition”.
To make these (with ‘fullrefman’ rather than ‘refman’), use
make pdf to create PDF versions
make info to create info files (not ‘refman’ nor ‘fullrefman’).
You will not be able to build any of these unless you have texi2any version 5.1 or later
installed, and for PDF you must have texi2dvi and texinfo.tex installed (which are part
of the GNU texinfo distribution but are, especially texinfo.tex, often made part of the TEX
package in re-distributions). For historical reasons, the path to texi2any can be set by macro
‘MAKEINFO’ in config.site (makeinfo is nowadays a link to texi2any).
The PDF versions can be viewed using any recent PDF viewer: they have hyperlinks that
can be followed. The info files are suitable for reading online with Emacs or the standalone GNU
info program. The PDF versions will be created using the paper size selected at configuration
(default ISO a4): this can be overridden by setting R_PAPERSIZE on the make command line,
or setting R_PAPERSIZE in the environment and using make -e. (If re-making the manuals for a
different paper size, you should first delete the file doc/manual/version.texi. The usual value
for North America would be ‘letter’.)
There are some issues with making the PDF reference manual, fullrefman.pdf or
refman.pdf. The help files contain both ISO Latin1 characters (e.g. in text.Rd) and upright
quotes, neither of which are contained in the standard LATEX Computer Modern fonts. We
have provided four alternatives:
times (The default.) Using standard PostScript fonts, Times Roman, Helvetica and
Courier. This works well both for on-screen viewing and for printing. One dis-
advantage is that the Usage and Examples sections may come out rather wide:
this can be overcome by using in addition either of the options inconsolata (on
a Unix-alike only if found by configure) or beramono, which replace the Courier
monospaced font by Inconsolata or Bera Sans mono respectively. (You will need a
recent version of the appropriate LATEX package inconsolata3 or bera installed.)
Note that in most LATEX installations this will not actually use the standard fonts
for PDF, but rather embed the URW clones NimbusRom, NimbusSans and (for
Courier, if used) NimbusMon.
This needs LATEX packages times, helvetic and (if used) courier installed.
lm Using the Latin Modern fonts. These are not often installed as part of a TEX
distribution, but can obtained from https://www.ctan.org/tex-archive/fonts/
ps-type1/lm/ and mirrors. This uses fonts rather similar to Computer Modern,
but is not so good on-screen as times.
cm-super Using type-1 versions of the Computer Modern fonts by Vladimir Volovich. This is
a large installation, obtainable from https://www.ctan.org/tex-archive/fonts/
ps-type1/cm-super/ and its mirrors. These type-1 fonts have poor hinting and so
are nowhere near as readable on-screen as the other three options.
ae A package to use composites of Computer Modern fonts. This works well most of
the time, and its PDF is more readable on-screen than the previous two options.
There are three fonts for which it will need to use bitmapped fonts, tctt0900.600pk,
3
Instructions on how to install the latest version are at https: / / www . ctan . org / tex-archive / fonts /
inconsolata/.
tctt1000.600pk and tcrm1000.600pk. Unfortunately, if those files are not avail-

able, Acrobat Reader will substitute completely incorrect glyphs so you need to
examine the logs carefully.
The default can be overridden by setting the environment variable R_RD4PDF. (On Unix-
alikes, this will be picked up at install time and stored in etc/Renviron, but can still be
overridden when the manuals are built, using make -e.) The usual4 default value for R_RD4PDF
is ‘times,inconsolata,hyper’: omit ‘hyper’ if you do not want hyperlinks (e.g. for printing
the manual) or do not have LATEX package hyperref, and omit ‘inconsolata’ if you do not have
LATEX package inconsolata installed.
Further options, e.g for hyperref, can be included in a file Rd.cfg somewhere on your LATEX
search path. For example, if you prefer the text and not the page number in the table of contents
to be hyperlinked use
\ifthenelse{\boolean{Rd@use@hyper}}{\hypersetup{linktoc=section}}{}
or
\ifthenelse{\boolean{Rd@use@hyper}}{\hypersetup{linktoc=all}}{}
to hyperlink both text and page number.
Ebook versions of most of the manuals in one or both of .epub and .mobi formats can be
made by running in doc/manual one of
make ebooks
make epub
make mobi
This requires ebook-convert from Calibre (http://calibre-ebook.com/download), or from
most Linux distributions. If necessary the path to ebook-convert can be set as make macro
EBOOK to by editing doc/manual/Makefile (which contains a commented value suitable for
macOS).
2.4 Installation
To ensure that the installed tree is usable by the right group of users, set umask appropriately
(perhaps to ‘022’) before unpacking the sources and throughout the build process.
After
./configure
make
make check
(or, when building outside the source, TOP_SRCDIR/configure, etc) have been completed suc-
cessfully, you can install the complete R tree to your system by typing
make install
A parallel make can be used (but run make before make install). Those using GNU make 4.0
or later may want to use make -j n -O to avoid interleaving of output.
This will install to the following directories:
prefix/bin or bindir
the front-end shell script and other scripts and executables
prefix/man/man1 or mandir/man1
the man page
4
on a Unix-alike, ‘inconsolata’ is omitted if not found by configure.
prefix/LIBnn/R or libdir/R
all the rest (libraries, on-line help system, . . . ). Here LIBnn is usually ‘lib’, but may
be ‘lib64’ on some 64-bit Linux systems. This is known as the R home directory.
where prefix is determined during configuration (typically /usr/local) and can be set by run-
ning configure with the option --prefix, as in
./configure --prefix=/where/you/want/R/to/go
where the value should be an absolute path. This causes make install to install the R script
to /where/you/want/R/to/go/bin, and so on. The prefix of the installation directories can be
seen in the status message that is displayed at the end of configure. The installation may need
to be done by the owner of prefix, often a root account.
You can install into another directory tree by using
make prefix=/path/to/here install
at least with GNU or Solaris make (but not some older Unix makes).
More precise control is available at configure time via options: see configure --help for
details. (However, most of the ‘Fine tuning of the installation directories’ options are not used
by R.)
Configure options --bindir and --mandir are supported and govern where a copy of the R
script and the man page are installed.
The configure option --libdir controls where the main R files are installed: the default
is ‘eprefix/LIBnn’, where eprefix is the prefix used for installing architecture-dependent files,
defaults to prefix, and can be set via the configure option --exec-prefix.
Each of bindir, mandir and libdir can also be specified on the make install command
line (at least for GNU make).
The configure or make variables rdocdir and rsharedir can be used to install the system-
independent doc and share directories to somewhere other than libdir. The C header files
can be installed to the value of rincludedir: note that as the headers are not installed into a
subdirectory you probably want something like rincludedir=/usr/local/include/R-3.5.1.
If you want the R home to be something other than libdir/R, use rhome: for example
make install rhome=/usr/local/lib64/R-3.5.1
will use a version-specific R home on a non-Debian Linux 64-bit system.
If you have made R as a shared/static library you can install it in your system’s library
directory by
make prefix=/path/to/here install-libR
where prefix is optional, and libdir will give more precise control.5 However, you should not
install to a directory mentioned in LDPATHS (e.g. /usr/local/lib64) if you intend to work with
multiple versions of R, since that directory may be given precedence over the lib directory of
other R installations.
make install-strip
will install stripped executables, and on platforms where this is supported, stripped libraries in
directories lib and modules and in the standard packages.
Note that installing R into a directory whose path contains spaces is not supported, and
some aspects (such as installing source packages) will not work.
To install info and PDF versions of the manuals, use one or both of
make install-info
make install-pdf
5
This will be needed if more than one sub-architecture is to be installed.
Once again, it is optional to specify prefix, libdir or rhome (the PDF manuals are installed
under the R home directory). (make install-info needs Perl installed if there is no command
install-info on the system.)
More precise control is possible. For info, the setting used is that of infodir (default
prefix/info, set by configure option --infodir). The PDF files are installed into the R
doc tree, set by the make variable rdocdir.
A staged installation is possible, that it is installing R into a temporary directory in order to
move the installed tree to its final destination. In this case prefix (and so on) should reflect the
final destination, and DESTDIR should be used: see https://www.gnu.org/prep/standards/
html_node/DESTDIR.html.
You can optionally install the run-time tests that are part of make check-all by
make install-tests
which populates a tests directory in the installation.
2.5 Uninstallation
You can uninstall R by
make uninstall
optionally specifying prefix etc in the same way as specified for installation.
This will also uninstall any installed manuals. There are specific targets to uninstall info and
PDF manuals in file doc/manual/Makefile.
Target uninstall-tests will uninstall any installed tests, as well as removing the directory
tests containing the test results.
An installed shared/static libR can be uninstalled by
make prefix=/path/to/here uninstall-libR
2.6 Sub-architectures
Some platforms can support closely related builds of R which can share all but the executables
and dynamic objects. Examples include builds under Linux and Solaris for different CPUs or
32- and 64-bit builds.
R supports the idea of architecture-specific builds, specified by adding ‘r_arch=name’ to the
configure line. Here name can be anything non-empty, and is used to name subdirectories of
lib, etc, include and the package libs subdirectories. Example names from other software
are the use of sparcv9 on Sparc Solaris and 32 by gcc on ‘x86_64’ Linux.
If you have two or more such builds you can install them over each other (and for 32/64-bit
builds on one architecture, one build can be done without ‘r_arch’). The space savings can be
considerable: on ‘x86_64’ Linux a basic install (without debugging symbols) took 74Mb, and
adding a 32-bit build added 6Mb. If you have installed multiple builds you can select which
build to run by
R --arch=name
and just running ‘R’ will run the last build that was installed.
R CMD INSTALL will detect if more than one build is installed and try to install packages with
the appropriate library objects for each. This will not be done if the package has an executable
configure script or a src/Makefile file. In such cases you can install for extra builds by
R --arch=name CMD INSTALL --libs-only pkg1 pkg2 ...
If you want to mix sub-architectures compiled on different platforms (for example ‘x86_64’
Linux and ‘i686’ Linux), it is wise to use explicit names for each, and you may also need to set
libdir to ensure that they install into the same place.
When sub-architectures are used the version of Rscript in e.g. /usr/bin will be the last
installed, but architecture-specific versions will be available in e.g. /usr/lib64/R/bin/exec${R_
ARCH}. Normally all installed architectures will run on the platform so the architecture of
Rscript itself does not matter. The executable Rscript will run the R script, and at that time
the setting of the R_ARCH environment variable determines the architecture which is run.
When running post-install tests with sub-architectures, use
R --arch=name CMD make check[-devel|all]
to select a sub-architecture to check.
Sub-architectures are also used on Windows, but by selecting executables within the ap-
propriate bin directory, R_HOME/bin/i386 or R_HOME/bin/x64. For backwards compatibility
there are executables R_HOME/bin/R.exe and R_HOME/bin/Rscript.exe: these will run an exe-
cutable from one of the subdirectories, which one being taken first from the R_ARCH environment
variable, then from the --arch command-line option6 and finally from the installation default
(which is 32-bit for a combined 32/64 bit R installation).
2.6.1 Multilib
For some Linux distributions7 , there is an alternative mechanism for mixing 32-bit and 64-bit
libraries known as multilib. If the Linux distribution supports multilib, then parallel builds of
R may be installed in the sub-directories lib (32-bit) and lib64 (64-bit). The build to be run
may then be selected using the setarch command. For example, a 32-bit build may be run by
setarch i686 R
The setarch command is only operational if both 32-bit and 64-bit builds are installed. If
there is only one installation of R, then this will always be run regardless of the architecture
specified by the setarch command.
There can be problems with installing packages on the non-native architecture. It is a good
idea to run e.g. setarch i686 R for sessions in which packages are to be installed, even if that
is the only version of R installed (since this tells the package installation code the architecture
needed).
There is a potential problem with packages using Java, as the post-install for a ‘i686’ RPM
on ‘x86_64’ Linux reconfigures Java and will find the ‘x86_64’ Java. If you know where a 32-bit
Java is installed you may be able to run (as root)
export JAVA_HOME=<path to jre directory of 32-bit Java>
setarch i686 R CMD javareconf
to get a suitable setting.
When this mechanism is used, the version of Rscript in e.g. /usr/bin will be the last
installed, but an architecture-specific version will be available in e.g. /usr/lib64/R/bin. Nor-
mally all installed architectures will run on the platform so the architecture of Rscript does
not matter.
2.7 Other Options

There are many other installation options, most of which are listed by configure --help.
Almost all of those not listed elsewhere in this manual are either standard autoconf options
not relevant to R or intended for specialist uses by the R developers.
One that may be useful when working on R itself is the option --disable-byte-compiled-
packages, which ensures that the base and recommended packages are not byte-compiled. (Al-
ternatively the (make or environment) variable R_NO_BASE_COMPILE can be set to a non-empty
value for the duration of the build.)
6
with possible values ‘i386’, ‘x64’, ‘32’ and ‘64’.
7
mainly on RedHat and Fedora, whose layout is described here.
Option --with-internal-tzcode makes use of R’s own code and copy of the Olson data-
base for managing timezones. This will be preferred where there are issues with the system
implementation, usually involving times after 2037 or before 1916. An alternative time-zone
directory8 can be used, pointed to by environment variable TZDIR: this should contain files
such as Europe/London. On all tested OSes the system timezone was deduced correctly, but if
necessary it can be set as the value of environment variable TZ.
2.7.1 OpenMP Support

By default configure searches for suitable options9 for OpenMP support for the C, C++98,
FORTRAN 77 and Fortran compilers.
Only the C result is currently used for R itself, and only if MAIN_LD/DYLIB_LD were not
specified. This can be overridden by specifying
R_OPENMP_CFLAGS
Use for packages has similar restrictions (involving SHLIB_LD and similar: note that as FOR-
TRAN 77 code is normally linked by the C compiler, both need to support OpenMP) and can
be overridden by specifying some of
SHLIB_OPENMP_CFLAGS
SHLIB_OPENMP_CXXFLAGS
SHLIB_OPENMP_FCFLAGS
SHLIB_OPENMP_FFLAGS
Setting to an empty value will disable OpenMP for that compiler (and configuring with
--disable-openmp will disable all detection10 of OpenMP). The configure detection test is
to compile and link a standalone OpenMP program, which is not the same as compiling a
shared object and loading it into the C program of R’s executable. Note that overridden values
are not tested.
2.7.2 C++ Support

C++ is not used by R itself, but support is provided for installing packages with C++ code via
make macros defined in file etc/Makeconf (and with explanations in file config.site):
CXX
CXXFLAGS
CXXPICFLAGS
CXXSTD
CXX98
CXX98STD
CXX98FLAGS
CXX98PICFLAGS
CXX11
CXX11STD
CXX11FLAGS
CXX11PICFLAGS
CXX14
CXX14STD
8
How to prepare such a directory is described in file src/extra/tzone/Notes in the R sources.
9
for example, -fopenmp, -xopenmp or -qopenmp. This includes for clang and the Intel C compiler.
10
This does not necessarily disable use of OpenMP – the configure code allows for platforms where OpenMP
is used without a flag. For the flang compiler in late 2017, the Fortran runtime always used OpenMP.
CXX14FLAGS
CXX14PICFLAGS
CXX17
CXX17STD
CXX17FLAGS
CXX17PICFLAGS
The macros CXX etc are those used by default for C++ code. configure will attempt to set
the rest suitably, choosing for CXX11STD a suitable flag such as -std=c++11 for C++11 support.
Similarly, configure will if possible choose for CXX14STD a flag11 such as -std=c++14 for C++14
support and -std=c++1z for support for the forthcoming C++17 standard. The inferred values
can be overridden in file config.site or on the configure command line: user-supplied values
will be tested compiling some C++11/14/17 code.
R versions 3.1.0 to 3.3.3 used CXX1X rather than CXX11, and these forms are deprecated but
still accepted.
It may be12 that there is no suitable flag for C++11 support, in which case a different compiler
could be selected for CXX11 and its corresponding flags. Likewise, a different compiler can be
specified for C++14 support with CXX14 and for C++17 support with CXX17. Some compilers13
by default assume a later standard than C++98 whereas the latter is assumed by some packages.
So users of GCC 6 might like to specify
CXX=’g++ -std=gnu++98’
CXX11=g++
CXX11STD=’-std=c++11’
CXX14=g++
CXX14STD=’-std=c++14’
The -std flag is supported by the GCC, clang, Intel and Solaris compilers (the latter from
version 12.4). Currently accepted values are (plus some synonyms)
g++: c++98 gnu++98 c++11 gnu+11 c++14 gnu++14 c++1z gnu++1z
Intel: gnu+98 c++11 c++14 (from 16.0) c++17 (from 17.0)
Solaris: c++03 c++11 c++14 (from 12.5)
(Those for clang++ are not documented, but seem to be based on g++.) Versions 4.3.x to 4.8.x of
g++ accepted flag -std=c++0x with partial support14 for C++11: this is currently still accepted
as a deprecated synonym for -std=c++11. (At least for versions 4.8.x it has sufficient support
to be picked by configure.) Option -std=c++14 was introduced in version 5.x.
‘Standards’ for g++ starting with ‘gnu’ enable ‘GNU extensions’: what those are is hard to
track down.
For the use of C++11 and later in R packages see the ‘Writing R Extensions’ manual.
2.8 Testing an Installation

Full post-installation testing is possible only if the test files have been installed with
make install-tests
which populates a tests directory in the installation.
11
Currently this is a valid option for g++ 5 and later and 2016 versions of the Intel and Solaris compilers. For
earlier versions of g++ one could try -std=c++1y.
12
This is true for earlier versions of g++ such as 4.2.1, and also for commonly-used versions of the Solaris compiler
CC.
13
Currently only GCC 6 and later, but this has been mooted for others.
14
For when features were supported, see https://gcc.gnu.org/projects/cxx-status.html#cxx11.
If this has been done, two testing routes are available. The first is to move to the home
directory of the R installation (as given by R.home()) and run
cd tests
## followed by one of
../bin/R CMD make check
../bin/R CMD make check-devel
../bin/R CMD make check-all
and other useful targets are test-BasePackages and test-Recommended to run tests of the
standard and recommended packages (if installed) respectively.
This re-runs all the tests relevant to the installed R (including for example code in the package
vignettes), but not for example the ones checking the example code in the manuals nor making
the standalone Rmath library. This can occasionally be useful when the operating environment
has been changed, for example by OS updates or by substituting the BLAS (see Section A.3.1.5
[Shared BLAS], page 46).
Parallel checking of packages may be possible: set the environment variable TEST_MC_CORES
to the maximum number of processes to be run in parallel. This affects both checking the
package examples (part of make check) and package sources (part of make check-devel and
make check-recommended). It does require a make command which supports the make -j n
option: most do but on Solaris you need to select GNU make or dmake. Where parallel checking
of package sources is done, a log file pngname.log is left in the tests directory for inspection.
Alternatively, the installed R can be run, preferably with --vanilla. Then
Sys.setenv(LC_COLLATE = "C", LC_TIME = "C", LANGUAGE = "en")
tools::testInstalledBasic("both")
tools::testInstalledPackages(scope = "base")
tools::testInstalledPackages(scope = "recommended")
runs the basic tests and then all the tests on the standard and recommended packages. These
tests can be run from anywhere: the basic tests write their results in the tests folder of the R
home directory and run fewer tests than the first approach: in particular they do not test things
which need Internet access—that can be tested by
tools::testInstalledBasic("internet")
These tests work best if diff (in Rtools*.exe for Windows users) is in the path.
It is possible to test the installed packages (but not their package-specific tests) by
testInstalledPackages even if make install-tests was not run.
Note that the results may depend on the language set for times and messages: for maximal
similarity to reference results you may want to try setting (before starting the R session)
LANGUAGE=en
and use a UTF-8 or Latin-1 locale.
13
3 Installing R under Windows

The bin/windows directory of a CRAN site contains binaries for a base distribution and a large
number of add-on packages from CRAN to run on 32- or 64-bit Windows (Windows 7 and later
are tested; XP is known to fail some tests) on ‘ix86’ and ‘x86_64’ CPUs.
Your file system must allow long file names (as is likely except perhaps for some network-
mounted systems). If it doesn’t also support conversion to short name equivalents (a.k.a. DOS
8.3 names), then R must be installed in a path that does not contain spaces.
Installation is via the installer R-3.5.1-win.exe. Just double-click on the icon and follow
the instructions. When installing on a 64-bit version of Windows the options will include 32- or
64-bit versions of R (and the default is to install both). You can uninstall R from the Control
Panel.
Note that you will be asked to choose a language for installation, and that choice applies to
both installation and un-installation but not to running R itself.
See the R Windows FAQ (https://CRAN.R-project.org/bin/windows/base/rw-FAQ.
html) for more details on the binary installer.
3.1 Building from source

R can be built as either a 32-bit or 64-bit application on Windows: to build the 64-bit application
you need a 64-bit edition of Windows: such an OS can also be used to build 32-bit R.
The standard installer combines 32-bit and 64-bit builds into a single executable which can
then be installed into the same location and share all the files except the .exe and .dll files
and some configuration files in the etc directory.
Building is only tested in a 8-bit locale: using a multi-byte locale (as used for CJK languages)
is unsupported and may not work (the scripts do try to select a ‘C’ locale; Windows may not
honour this).
NB: The build process is currently being changed to require external binary distributions of
third-party software. Their location is set using macro EXT_LIBS with default setting $(LOCAL_
SOFT); the $(LOCAL SOFT) macro defaults to $(R_HOME)/extsoft. This directory can be
populated using make rsync-extsoft. The location can be overridden by setting EXT_LIBS to
a different path in src/gnuwin32/MkRules.local. A suitable collection of files can also be
obtained from https://CRAN.R-project.org/bin/windows/extsoft or https://www.stats.
ox.ac.uk/pub/Rtools/libs.html.
3.1.1 Getting the tools

If you want to build R from the sources, you will first need to collect, install and test an extensive
set of tools. See Appendix D [The Windows toolset], page 71, (and perhaps updates in https://
CRAN.R-project.org/bin/windows/Rtools/) for details.
The Rtools*.exe executable installer described in Appendix D [The Windows toolset],
page 71, also includes some source files in addition to the R source as noted below. You should
run it first, to obtain a working tar and other necessities. Choose a “Full installation”, and
install the extra files into your intended R source directory, e.g. C:/R. The directory name should
not contain spaces. We will call this directory R_HOME below.
3.1.2 Getting the source files

You need to collect the following sets of files:
• Get the R source code tarball R-3.5.1.tar.gz from CRAN. Open a command window (or
another shell) at directory R HOME, and run
tar -xf R-3.5.1.tar.gz
Chapter 3: Installing R under Windows 14
to create the source tree in R HOME. Beware: do use tar to extract the sources rather
than tools such as WinZip. If you are using an account with administrative privileges you
may get a lot of messages which can be suppressed by
tar --no-same-owner -xf R-3.5.1.tar.gz
or perhaps better, set the environment variable TAR_OPTIONS to the value
‘--no-same-owner --no-same-permissions’.
It is also possible to obtain the source code using Subversion; see Chapter 1 [Obtaining R],
page 1, for details.
• If you are not using a tarball you need to obtain copies of the recommended packages
from CRAN. Put the .tar.gz files in R_HOME/src/library/Recommended and run make
link-recommended. If you have an Internet connection, you can do this automatically by
running in R_HOME/src/gnuwin32
make rsync-recommended
• The binary distributions of external software. Download
https://www.stats.ox.ac.uk/pub/Rtools/goodies/multilib/local323.zip
(or a more recent version if appropriate), create an empty directory, say c:/R/extsoft,
and unpack it in that directory by e.g.
unzip local323.zip -d c:/R/extsoft
• Make a local copy of the configuration rules by
cd R_HOME/src/gnuwin32
cp MkRules.dist MkRules.local
and edit MkRules.local, uncommenting EXT_LIBS and setting it to the appropriate path
(in our example c:/R/extsoft).
Look through the file MkRules.local and make any other changes needed: in particular,
this is where a 64-bit build is selected and the locations are set of external software for ICU
collation and the cairo-based devices.
The following additional item is normally installed by Rtools*.exe. If instead you choose
to do a completely manual build you will also need
• The Tcl/Tk support files are contained in Rtools*.exe. Please make sure you install the
right version: there is a 32-bit version and a 64-bit version. They should be installed to
R_HOME, creating directory Tcl there.
3.1.3 Building the core files

Set the environment variable TMPDIR to the absolute path to a writable directory, with a path
specified with forward slashes and no spaces. (The default is /tmp, which may not be useful on
Windows.)
You may need to compile under a case-honouring file system: we found that a samba-mounted
file system (which maps all file names to lower case) did not work.
Open a command window at R_HOME/src/gnuwin32, then run
make all recommended vignettes
and sit back and wait while the basic compile takes place.
Notes:
• We have had reports that earlier versions of anti-virus software locking up the machine, but
not for several years. However, aggressive anti-virus checking such as the on-access scanning
of Sophos can slow the build down several-fold.
• You can run a parallel make by e.g.

make -j4 all
make -j4 recommended
make vignettes
but this is only likely to be worthwhile on a multi-core machine with ample memory, and
is not 100% reliable.
• It is possible (mainly for those working on R itself) to set the (make or environment) variable
R_NO_BASE_COMPILE to a non-empty value, which inhibits the byte-compilation of the base
and recommended packages.
3.1.4 Building the cairo devices

The devices based on cairographics (svg, cairo_pdf, cairo_ps and the type = "cairo" versions
of png, jpeg, tiff and bmp) are implemented in a separate DLL winCairo.dll which is loaded
when one of these devices is first used. It is not built by default, and needs to be built (after
make all) by make cairodevices.
To enable the building of these devices you need to install the static cairographics libraries
built by Simon Urbanek at https://www.rforge.net/Cairo/files/cairo-current-win.
tar.gz. Set the macro ‘CAIRO_HOME’ in MkRules.local. (Note that this tarball unpacks with
a top-level directory src/: ‘CAIRO_HOME’ needs to include that directory in its path.)
3.1.5 Using ICU for collation

It is recommended to build R to support ICU (International Components for Unicode, http://
site.icu-project.org/) for collation, as is commonly done on Unix-alikes.
Two settings are needed in MkRules.local,
# set to use ICU
# USE_ICU = YES
# path to parent of ICU headers
ICU_PATH = /path/to/ICU
The first should be uncommented and the second set to the top-level directory of a suitably
packaged binary build of ICU, for example that at https: / / www . stats . ox . ac . uk / pub /
Rtools/goodies/ICU_531.zip. Depending on the build, it may be necessary to edit the macro
ICU_LIBS.
Unlike on a Unix-alike, it is normally necessary to call icuSetCollate to set a locale before
ICU is actually used for collation, or set the environment variable R_ICU_LOCALE.
3.1.6 Support for libcurl

libcurl version 7.28.0 or later is used to support curlGetHeaders and the "libcurl" methods
of download.file and url.
A suitable distribution can be found via https://www.stats.ox.ac.uk/pub/Rtools/libs.
html and its unpacked location should be specified in file MkRules.local.
For secure use of e.g. ‘https://’ URLs Windows users may need to specify the path to
up-to-date CA root certificates: see ?download.file.
3.1.7 Checking the build

You can test a build by running
make check
The recommended packages can be checked by
make check-recommended
Other levels of checking are

make check-devel
for a more thorough check of the R functionality, and
make check-all
for both check-devel and check-recommended.
If a test fails, there will almost always be a .Rout.fail file in the directory being checked
(often tests/Examples or tests): examine the file to help pinpoint the problem.
Parallel checking of package sources (part of make check-devel and make
check-recommended) is possible: see the environment variable TEST_MC_CORES to the
maximum number of processes to be run in parallel.
3.1.8 Building the manuals

The PDF manuals require texinfo 5.1 or later, and can be made by
make manuals
If you want to make the info versions (not including the Reference Manual), use
cd ../../doc/manual
make -f Makefile.win info
(all assuming you have pdftex/pdflatex installed and in your path).
See the Section 2.3 [Making the manuals], page 4, section in the Unix-alike section for setting
options such as the paper size and the fonts used.
By default it is assumed that texinfo is not installed, and the manuals will not be built.
The comments in file MkRules.dist describe settings to build them. (Copy that file to
MkRules.local and edit it.) The texinfo 5.x package for use on Windows is available at
https://www.stats.ox.ac.uk/pub/Rtools/: you will also need to install Perl1
3.1.9 Building the Inno Setup installer

You need to have the files for a complete R build, including bitmap and Tcl/Tk support and
the manuals (which requires texinfo installed), as well as the recommended packages and Inno
Setup (see Section D.2 [The Inno Setup installer], page 72).
Once everything is set up
make distribution
make check-all
will make all the pieces and the installer and put them in the gnuwin32/cran subdirectory, then
check the build. This works by building all the parts in the sequence:
rbuild (the executables, the FAQ docs etc.)
rpackages (the base packages)
htmldocs (the HTML documentation)
cairodevices (the cairo-based graphics devices)
recommended (the recommended packages)
vignettes (the vignettes in base packages:
only needed if building from an svn checkout)
manuals (the PDF manuals)
rinstaller (the install program)
crandir (the CRAN distribution directory, only for 64-bit builds)
The parts can be made individually if a full build is not needed, but earlier parts must be
built before later ones. (The Makefile doesn’t enforce this dependency—some build targets
1
Suitable distributions include Strawberry Perl, http://strawberryperl.com/ and ActivePerl, https://www.
activestate.com/activeperl.
force a lot of computation even if all files are up to date.) The first four targets are the default
build if just make (or make all) is run.
Parallel make is not supported and likely to fail.
If you want to customize the installation by adding extra packages, replace make rinstaller
by something like
make rinstaller EXTRA_PKGS=’pkg1 pkg2 pkg3’
An alternative way to customize the installer starting with a binary distribution is to first
make an installation of R from the standard installer, then add packages and make other
customizations to that installation. Then (after having customized file MkRules, possibly via
MkRules.local, and having made R in the source tree) in src/gnuwin32/installer run
make myR IMAGEDIR=rootdir
where rootdir is the path to the root of the customized installation (in double quotes if it
contains spaces or backslashes).
Both methods create an executable with a standard name such as R-3.5.1-win.exe, so
please rename it to indicate that it is customized. If you intend to distribute a customized
installer please do check that license requirements are met – note that the installer will state
that the contents are distributed under GPL and this has a requirement for you to supply the
complete sources (including the R sources even if you started with a binary distribution of R, and
also the sources of any extra packages (including their external software) which are included).
The defaults for the startup parameters may also be customized. For example
make myR IMAGEDIR=rootdir MDISDI=1
will create an installer that defaults to installing R to run in SDI mode. See src/
gnuwin32/installer/Makefile for the names and values that can be set.
The standard CRAN distribution of a 32/64-bit installer is made by first building 32-bit R
(just
make 32-bit
is needed), and then (in a separate directory) building 64-bit R with the macro HOME32 set in file
MkRules.local to the top-level directory of the 32-bit build. Then the make rinstaller step
copies the files that differ between architectures from the 32-bit build as it builds the installer
image.
3.1.10 Building the MSI installer

It is also possible to build an installer for use with Microsoft Installer. This is intended for use
by sysadmins doing automated installs, and is not recommended for casual use.
It makes use of the Windows Installer XML (WiX) toolkit version 3.5 (or perhaps later,
untested) available from http://wixtoolset.org/. Once WiX is installed, set the path to its
home directory in MkRules.local.
You need to have the files for a complete R build, including bitmap and Tcl/Tk support
and the manuals, as well as the recommended packages. There is no option in the installer
to customize startup options, so edit etc/Rconsole and etc/Rprofile.site to set these as
required. Then
cd installer
make msi
which will result in a file with a name like R-3.5.1-win32.msi. This can be double-clicked to be
installed, but those who need it will know what to do with it (usually by running msiexec /i with
additional options). Properties that users might want to set from the msiexec command line
include ‘ALLUSERS’, ‘INSTALLDIR’ (something like c:\Program Files\R\R-3.5.1) and ‘RMENU’
(the path to the ‘R’ folder on the start menu) and ‘STARTDIR’ (the starting directory for R
shortcuts, defaulting to something like c:\Users\name\Documents\R).
The MSI installer can be built both from a 32-bit build of R (R-3.5.1-win32.msi) and from
a 64-bit build of R (R-3.5.1-win64.msi, optionally including 32-bit files by setting the macro
HOME32, when the name is R-3.5.1-win.msi). Unlike the main installer, a 64-bit MSI installer
can only be run on 64-bit Windows.
Thanks to David del Campo (Dept of Statistics, University of Oxford) for suggesting WiX
and building a prototype installer.
3.1.11 64-bit Windows builds

To build a 64-bit version of R you need a 64-bit toolchain: the only one discussed here is based
on the work of the MinGW-w64 project (http://sourceforge.net/projects/mingw-w64/,
but commercial compilers such as those from Intel and PGI could be used (and have been by R
redistributors).
Support for MinGW-w64 was developed in the R sources over the period 2008–10 and was
first released as part of R 2.11.0. The assistance of Yu Gong at a crucial step in porting R to
MinGW-w64 is gratefully acknowledged, as well as help from Kai Tietz, the lead developer of
the MinGW-w64 project.
Windows 64-bit is now completely integrated into the R and package build systems: a 64-bit
build is selected in file MkRules.local.
3.2 Testing an Installation

The Windows installer contains a set of test files used when building R.
The Rtools are not needed to run these tests. but more comprehensive analysis of errors
will be given if diff is in the path (and errorsAreFatal = FALSE is then not needed below).
Launch either Rgui or Rterm, preferably with --vanilla. Then run
Sys.setenv(LC_COLLATE = "C", LANGUAGE = "en")
library("tools")
testInstalledBasic("both")
testInstalledPackages(scope = "base", errorsAreFatal = FALSE)
testInstalledPackages(scope = "recommended", errorsAreFatal = FALSE)
runs the basic tests and then all the tests on the standard and recommended packages. These
tests can be run from anywhere: they write some of their results in the tests folder of the R
home directory (as given by R.home()), and hence may need to be run under the account used
to install R.
The results of example(md5sums) when testing tools will differ from the reference output as
some files are installed with Windows’ CRLF line endings.
19
4 Installing R under macOS

(‘macOS’ was known as ‘OS X’ from 2012–2016 and as ‘Mac OS X’ before that.)
The front page of a CRAN site has a link ‘Download R for OS X’. Click on that, then download
the file R-3.5.1.pkg and install it. This runs on macOS 10.11 and later (El Capitan, Sierra,
High Sierra, . . . ).
Installers for R-patched and R-devel are usually available from https://r.research.att.
com. (Some of these packages are unsigned: to install those Control/right/two-finger click, select
‘Open with’ and ‘Installer’.)
For some older versions of the OS you can in principle (it is little tested) install R from the
sources (see Section C.3 [macOS], page 59).
It is important that if you use a binary installer package that your OS is fully updated: look
at ‘Updates’ from the ‘App Store’ to be sure. (If using XQuartz, check that is current.)
To install, just double-click on the icon of the file you downloaded. At the ‘Installation Type’
stage, note the option to ‘Customize’. This currently shows four components: everyone will
need the ‘R Framework’ component: the remaining components are optional. (The ‘Tcl/Tk’
component is needed to use package tcltk. The ‘Texinfo’ component is only needed by those
installing source packages or R from its sources.)
This is an Apple Installer package. If you encounter any problem during the installation,
please check the Installer log by clicking on the “Window” menu and item “Installer Log”. The
full output (select “Show All Log”) is useful for tracking down problems. Note the the installer
is clever enough to try to upgrade the last-installed version of the application where you installed
it (which may not be where you want this time . . . ).
Various parts of the build require XQuartz to be installed: see https: / / xquartz .
macosforge.org/. These include the tcltk package and the X11 device: attempting to use
these without XQuartz will remind you. Also the cairographics-based devices (which are not
often used on macOS) such as png(type = "cairo").
If you update your macOS version, you should re-install R (and perhaps XQuartz): the
installer may tailor the installation to the current version of the OS.
For building R from source, see Section C.3 [macOS], page 59.
4.1 Running R under macOS

There are two ways to run R on macOS from a CRAN binary distribution.
There is a GUI console normally installed with the R icon in /Applications which you can
run by double-clicking (e.g. from Launchpad or Finder). (If you cannot find it there it was
possibly installed elsewhere so try searching for it in Spotlight.) This is usually referred to as
R.app to distinguish it from command-line R: its user manual is currently part of the macOS
FAQ at https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html and can be viewed
from R.app’s ‘Help’ menu.
You can run command-line R and Rscript from a Terminal1 so these can be typed as
commands like any other Unix-alike: see the next chapter of this manual. There are some small
differences which may surprise users of R on other platforms, notably the default location of
the personal library directory (under ~/Library/R, e.g. ~/Library/R/3.5/library), and that
warnings, messages and other output to stderr are highlighted in bold.
It has been reported that running R.app may fail if no preferences are stored, so if it fails
when launched for the very first time, try it again (the first attempt will store some preferences).
1
The installer as puts links to R and Rscript in /usr/local/bin. If these are missing, you can run directly
the copies in /Library/Frameworks/R.framework/Resources/.
Chapter 4: Installing R under macOS 20
Users of R.app need to be aware of the ‘App Nap’ feature (https://developer.apple.com/

library / mac / releasenotes / MacOSX / WhatsNewInOSX / Articles / MacOSX10_9 . html) which
can cause R tasks to appear to run very slowly when not producing output in the console. Here
are ways to avoid it:
• Ensure that the console is completely visible (or at least the activity indicator at the top
right corner is visible).
• In a Terminal, run
defaults write org.R-project.R NSAppSleepDisabled -bool YES
(see https: / / developer . apple . com / library / mac / releasenotes / MacOSX /
WhatsNewInOSX/Articles/MacOSX10_9.html).
Using the X11 device or the X11-based versions of View() and edit() for data frames and
matrices (the latter are the default for command-line R but not R.app) requires an X sub-system
to be installed: see Section C.3 [macOS], page 59. So do the tcltk package and some third-party
packages.
4.2 Uninstalling under macOS

R for macOS consists of two parts: the GUI (R.app) and the R framework. The un-installation
is as simple as removing those folders (e.g. by dragging them onto the Trash). The typical
installation will install the GUI into the /Applications/R.app folder and the R framework into
the /Library/Frameworks/R.framework folder. The links to R and Rscript in /usr/local/bin
should also be removed.
If you want to get rid of R more completely using a Terminal, simply run:
sudo rm -Rf /Library/Frameworks/R.framework /Applications/R.app \
/usr/local/bin/R /usr/local/bin/Rscript
The installation consists of up to four Apple packages:2 org.r-project.R.el-
capitan.fw.pkg, org.r-project.R.el-capitan.GUI.pkg, org.r-project.x86_
64.tcltk.x11 and org.r-project.x86_64.texinfo. You can use pkgutil --forget if you
want the Apple Installer to forget about the package without deleting its files (useful for the R
framework when installing multiple R versions in parallel), or after you have deleted the files.
Uninstalling the Tcl/Tk or Texinfo components (which are installed under /usr/local) is
not as simple. You can list the files they installed in a Terminal by
pkgutil --files org.r-project.x86_64.tcltk.x11
pkgutil --files org.r-project.x86_64.texinfo
These are paths relative to /, the root of the file system.
4.3 Multiple versions

The installer will remove any previous version3 of the R framework which it finds installed.
This can be avoided by using pkgutil --forget (see the previous section). However, note that
different versions are installed under /Library/Frameworks/R.framework/Versions as 3.4,
3.5 and so on, so it is not possible to have different ‘3.x.y’ versions installed for the same ‘x’.
A version of R can be run directly from the command-line as e.g.
/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R
2
The framework for R 3.3.x was named org.r-project.R.mavericks.fw.pkg: use pkgutil --pkgs | grep
org.r-project to check for earlier versions of R.
3
More precisely, of the Apple package of the same name: this means that installing a package for 3.3.x does
not remove an installation for 3.4.x or 3.5.x.
Chapter 4: Installing R under macOS 21
However, R.app will always run the ‘current’ version, that is the last installed version. A small
utility, Rswitch.app (available at https://r.research.att.com/ #other), can be used to
change the ‘current’ version. This is of limited use as R.app is compiled against a particular
version of R and will likely crash if switched to an earlier version. This may allow you to install
a development version of R (de-selecting R.app) and then switch back to the release version.
22
5 Running R
How to start R and what command-line options are available is discussed in Section “Invoking
R” in An Introduction to R.
You should ensure that the shell has set adequate resource limits: R expects a stack size
of at least 8MB and to be able to open at least 256 file descriptors. (Any modern OS should
have default limits at least as large as these, but apparently NetBSD may not. Use the shell
command ulimit (sh/bash) or limit (csh/tcsh) to check.)
R makes use of a number of environment variables, the default values of many of which are
set in file R_HOME/etc/Renviron (there are none set by default on Windows and hence no such
file). These are set at configure time, and you would not normally want to change them – a
possible exception is R_PAPERSIZE (see Section B.3.1 [Setting paper size], page 50). The paper
size will be deduced from the ‘LC_PAPER’ locale category if it exists and R_PAPERSIZE is unset,
and this will normally produce the right choice from ‘a4’ and ‘letter’ on modern Unix-alikes
(but can always be overridden by setting R_PAPERSIZE).
Various environment variables can be set to determine where R creates its per-session tem-
porary directory. The environment variables TMPDIR, TMP and TEMP are searched in turn and the
first one which is set and points to a writable area is used. If none do, the final default is /tmp
on Unix-alikes and the value of R_USER on Windows. The path should be an absolute path not
containing spaces (and it is best to avoid non-alphanumeric characters such as +).
Some Unix-alike systems are set up to remove files and directories periodically from /tmp,
for example by a cron job running tmpwatch. Set TMPDIR to another directory before starting
long-running jobs on such a system.
Note that TMPDIR will be used to execute configure scripts when installing packages, so if
/tmp has been mounted as ‘noexec’, TMPDIR needs to be set to a directory from which execution
is allowed.
23
6 Add-on packages
It is helpful to use the correct terminology. A package is loaded from a library by the function
library(). Thus a library is a directory containing installed packages; the main library is R_
HOME/library, but others can be used, for example by setting the environment variable R_LIBS
or using the R function .libPaths().
6.1 Default packages

The set of packages loaded on startup is by default
> getOption("defaultPackages")
[1] "datasets" "utils" "grDevices" "graphics" "stats" "methods"
(plus, of course, base) and this can be changed by setting the option in startup code (e.g. in
~/.Rprofile). It is initially set to the value of the environment variable R_DEFAULT_PACKAGES if
set (as a comma-separated list). Setting R_DEFAULT_PACKAGES=NULL ensures that only package
base is loaded.
Changing the set of default packages is normally used to reduce the set for speed when
scripting: in particular not using methods will reduce the start-up time by a factor of up to two.
But it can also be used to customize R, e.g. for class use. Rscript also checks the environment
variable R_SCRIPT_DEFAULT_PACKAGES; if set, this takes precedence over R_DEFAULT_PACKAGES.
6.2 Managing libraries

R packages are installed into libraries, which are directories in the file system containing a
subdirectory for each package installed there.
R comes with a single library, R_HOME/library which is the value of the R object ‘.Library’
containing the standard and recommended1 packages. Both sites and users can create others
and make use of them (or not) in an R session. At the lowest level ‘.libPaths()’ can be used
to add paths to the collection of libraries or to report the current collection.
R will automatically make use of a site-specific library R_HOME/site-library if this exists (it
does not in a vanilla R installation). This location can be overridden by setting2 ‘.Library.site’
in R_HOME/etc/Rprofile.site, or (not recommended) by setting the environment variable R_
LIBS_SITE. Like ‘.Library’, the site libraries are always included by ‘.libPaths()’.
Users can have one or more libraries, normally specified by the environment variable R_
LIBS_USER. This has a default value (to see it, use ‘Sys.getenv("R_LIBS_USER")’ within an R
session), but that is only used if the corresponding directory actually exists (which by default
it will not).
Both R_LIBS_USER and R_LIBS_SITE can specify multiple library paths, separated by colons
(semicolons on Windows).
6.3 Installing packages

Packages may be distributed in source form or compiled binary form. Installing source pack-
ages which contain C/C++/Fortran code requires that compilers and related tools be installed.
Binary packages are platform-specific and generally need no special tools to install, but see the
documentation for your platform for details.
Note that you may need to specify implicitly or explicitly the library to which the package
is to be installed. This is only an issue if you have more than one library, of course.
1
unless they were excluded in the build.
2
its binding is locked once the startup files have been read, so users cannot easily change it.
Chapter 6: Add-on packages 24
Ensure that the environment variable TMPDIR is either unset (and /tmp exists and can be writ-
ten in and executed from) or is the absolute path to a valid temporary directory, not containing
spaces.
For most users it suffices to call ‘install.packages(pkgname)’ or its GUI equivalent if
the intention is to install a CRAN package and internet access is available.3 On most systems
‘install.packages()’ will allow packages to be selected from a list box (typically with several
thousand items).
To install packages from source on a Unix-alike use in a terminal
R CMD INSTALL -l /path/to/library pkg1 pkg2 ...
The part ‘-l /path/to/library’ can be omitted, in which case the first library of a normal R
session is used (that shown by .libPaths()[1]).
There are a number of options available: use R CMD INSTALL --help to see the current list.
Alternatively, packages can be downloaded and installed from within R. First choose your
nearest CRAN mirror using chooseCRANmirror(). Then download and install packages pkg1
and pkg2 by
> install.packages(c("pkg1", "pkg2"))
The essential dependencies of the specified packages will also be fetched. Unless the library
is specified (argument lib) the first library in the library search path is used: if this is not
writable, R will ask the user (in an interactive session) if the default personal library should be
created, and if allowed to will install the packages there.
If you want to fetch a package and all those it depends on (in any way) that are not already
installed, use e.g.
> install.packages("Rcmdr", dependencies = TRUE)
install.packages can install a source package from a local .tar.gz file (or a URL to such
a file) by setting argument repos to NULL: this will be selected automatically if the name given
is a single .tar.gz file.
install.packages can look in several repositories, specified as a character vector by the
argument repos: these can include a CRAN mirror, Bioconductor, R-forge, rforge.net, local
archives, local files, . . . ). Function setRepositories() can select amongst those repositories
that the R installation is aware of.
Naive users sometimes forget that as well as installing a package, they have to use library
to make its functionality available.
6.3.1 Windows
What install.packages does by default is different on Unix-alikes (except macOS) and Win-
dows. On Unix-alikes it consults the list of available source packages on CRAN (or other repos-
itory/ies), downloads the latest version of the package sources, and installs them (via R CMD
INSTALL). On Windows it looks (by default) first at the list of binary versions of packages
available for your version of R and downloads the latest versions (if any). If no binary version
is available or the source version is newer, it will install the source versions of packages without
compiled C/C++/Fortran code, and offer to do so for those with, if make is available (and this
can be tuned by option "install.packages.compile.from.source").
On Windows install.packages can also install a binary package from a local zip file (or
the URL of such a file) by setting argument repos to NULL. Rgui.exe has a menu Packages
with a GUI interface to install.packages, update.packages and library.
Windows binary packages for R are distributed as a single binary containing either or both
architectures (32- and 64-bit).
3
If a proxy needs to be set, see ?download.file.
A few of the binary packages need other software to be installed on your system: see for exam-
ple https://CRAN.R-project.org/bin/windows/contrib/3.2/@ReadMe. Packages using Gtk+
(Cairo (https://CRAN.R-project.org/package=Cairo), RGtk2 (https://CRAN.R-project.
org/package=RGtk2), cairoDevice (https://CRAN.R-project.org/package=cairoDevice)
and those that depend on them) need the bin directory of a bundled distribution of Gtk2 from
http://ftp.gnome.org/pub/gnome/binaries/win32/gtk+ or http://ftp.gnome.org/pub/
gnome/binaries/win64/gtk+ in the path: it should work to have both 32- and 64-bit Gtk+
bin directories in the path on a 64-bit version of R.
R CMD INSTALL works in Windows to install source packages. No additional tools are needed if
the package does not contain compiled code, and install.packages(type="source") will work
for such packages (and for those with compiled code if the tools (see Appendix D [The Windows
toolset], page 71) are on the path, and the variables BINPREF and BINPREF64 are set properly;
see the discussion below). We have seen occasional permission problems after unpacking source
packages on some systems: these have been circumvented by setting the environment variable
R_INSTALL_TAR to ‘tar.exe’.
If you have only a source package that is known to work with current R and just want a
binary Windows build of it, you could make use of the building service offered at https://
win-builder.r-project.org/.
For almost all packages R CMD INSTALL will attempt to install both 32- and 64-bit builds of
a package if run from a 32/64-bit install of R. It will report success if the installation of the
architecture of the running R succeeded, whether or not the other architecture was successfully
installed. The exceptions are packages with a non-empty configure.win script or which make
use of src/Makefile.win. If configure.win does something appropriate to both architectures
use4 option --force-biarch: otherwise R CMD INSTALL --merge-multiarch can be applied to
a source tarball to merge separate 32- and 64-bit installs. (This can only be applied to a tarball,
and will only succeed if both installs succeed.)
If you have a package without compiled code and no Windows-specific help, you can zip
up an installation on another OS and install from that zip file on Windows. However, such a
package can be installed from the sources on Windows without any additional tools.
Packages with compiled code may need to have paths to the compilers set explicitly, and there
is provision to make use of a system-wide library of installed external software. The compiler
paths are set using the make variables BINPREF and (usually) BINPREF64. The library location
is set using make variable LOCAL_SOFT, to give an equivalent of /usr/local on a Unix-alike. All
of these can be set in src/gnuwin32/MkRules.local when R is built from sources (see the com-
ments in src/gnuwin32/MkRules.dist), or in file5 etc/i386/Makeconf or etc/x64/Makeconf
for an installed version of R. In the latter case only BINPREF is used, with the 64 bit path used
in etc/x64/Makeconf. The version used by CRAN can be installed as described in Section 3.1
[Building from source], page 13.
6.3.2 macOS
On macOS (formerly OS X) install.packages works as it does on other Unix-alike systems,
but there are additional types starting with mac.binary (available for the CRAN distribution but
not when compiling from source: mac.binary.el-capitan for a ‘El Capitan and later build with
"default" a synonym for the appropriate variant) which can be passed to install.packages in
order to download and install binary packages from a suitable repository. These binary package
files for macOS have the extension ‘.tgz’. The R.app GUI provides menus for installation of
either binary or source packages, from CRAN or local files.
4
for a small number of CRAN packages where this is known to be safe and is needed by the autobuilder this
is the default. Look at the source of tools:::.install_packages for the list. It can also be specified in the
package’s DESCRIPTION file.
5
or by adding it in a file such as etc/i386/Makevars.site, which does not exist by default.
On R builds using binary packages, the default is type both: this looks first at the list of
binary packages available for your version of R and installs the latest versions (if any). If no
binary version is available or the source version is newer, it will install the source versions of
packages without compiled C/C++/Fortran code and offer to do so for those with, if make is
available.
Note that most binary packages including compiled code are tied to a particular series (e.g.
R 3.5.x or 3.4.x) of R.
Installing source packages which do not contain compiled code should work with no additional
tools. For others you will need the ‘Command Line Tools’ for Xcode and compilers which match
those used to build R: see Section C.3 [macOS], page 59.
Package rJava (https://CRAN.R-project.org/package=rJava) and those which depend on
it need a Java runtime installed and several packages need X11 installed, including those using
Tk. See Section C.3 [macOS], page 59, and Section C.3.2 [Java (macOS)], page 62.
Tcl/Tk extensions BWidget and Tktable are part of the Tcl/Tk contained in the R installer.
These are required by a number of CRAN and Bioconductor packages.
A few of the binary packages need other software to be installed on your system. In particular
packages using Gtk+ (RGtk2 (https://CRAN.R-project.org/package=RGtk2), cairoDevice
(https://CRAN.R-project.org/package=cairoDevice) and those that depend on them) need
the GTK framework installed from https://r.research.att.com/libs/: the appropriate
version at the time of writing was https://r.research.att.com/libs/GTK_2.24.17-X11.pkg
The default compilers specified are shown in file /Library/Frameworks/R.framework/
Resources/etc/Makeconf. At the time of writing these setting assumed that the C, Fortran and
C++ compilers were on the path, and gfortan 6.1.0 (see Section C.3 [macOS], page 59). The set-
tings can be changed, either by editing that file or in a file such as ~/.R/Makevars (see the next
section). Entries which may need to be changed include ‘CC’, ‘CXX’, ‘FC’, ‘F77’, ‘FLIBS’ and the
corresponding flags, and perhaps ‘CXXCPP’, ‘DYLIB_LD’, ‘MAIN_LD’, ‘SHLIB_CXXLD’, ‘SHLIB_FCLD’
and ‘SHLIB_LD’, as well as the ‘CXX11’, ‘CXX14’ and ‘CXX17’ variants
So for example you could select a specific build of clang for both C and C++ with extensive
checking by having in ~/.R/Makevars
CC = /usr/local/clang4/bin/clang
CXX = /usr/local/clang4/bin/clang++
CFLAGS = -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion
CXXFLAGS = -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion
CXX11 = $CXX
CXX14 = $CXX
CXX17 = $CXX
CXX1X = $CXX
and the Sierra build of gfortran by
F77 = /usr/local/gfortran/bin/gfortran
FC = $F77
FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0
-L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
(line split for legibility here).
If using the C/C++ compilers from the Command Line Tools (which does not have OpenMP
support) one will need to include
SHLIB_OPENMP_CFLAGS =
SHLIB_OPENMP_CXXFLAGS =
to compile OpenMP-using packages.
Apple includes many Open Source libraries in macOS but increasingly without the corre-
sponding headers (not even in Xcode nor the Command Line Tools): they are often rather
old versions. If installing packages from source using them it is usually easiest to install a
statically-linked up-to-date copy of the Open Source package from its sources or from https://
r.research.att.com/libs. But sometimes it is desirable/necessary to use Apple’s dynamically
linked library, in which case appropriate headers could be extracted from the sources6 available
via https://opensource.apple.com.
6.3.3 Customizing package compilation

The R system and package-specific compilation flags can be overridden or added to by set-
ting the appropriate Make variables in the personal file HOME/.R/Makevars-R_PLATFORM (but
HOME/.R/Makevars.win or HOME/.R/Makevars.win64 on Windows), or if that does not exist,
HOME/.R/Makevars, where ‘R_PLATFORM’ is the platform for which R was built, as available in
the platform component of the R variable R.version. The path to an alternative personal file7
can be specified via the environment variable R_MAKEVARS_USER.
Package developers are encouraged to use this mechanism to enable a reasonable amount of
diagnostic messaging (“warnings”) when compiling, such as e.g. -Wall -pedantic for tools from
GCC, the Gnu Compiler Collection.
Note that this mechanism can also be used when it necessary to change the optimization
level for a particular package. For example
## for C code
CFLAGS=-g -O -mtune=native
## for C++ code
CXXFLAGS=-g -O -mtune=native
## for Fortran code
FFLAGS=-g -O -mtune=native
## for Fortran 9x code
FCFLAGS=-g -O -mtune=native
Another use is to override the settings in a binary installation of R. For example, to use a
different Fortran compiler on macOS
FC = $F77
(line split for legibility here).
There is also provision for a site-wide Makevars.site file under R_HOME/etc (in a sub-
architecture-specific directory if appropriate). This is read immediately after Makeconf, and the
path to an alternative file can be specified by environment variable R_MAKEVARS_SITE.
Note that these mechanisms do not work with packages which fail to pass settings down
to sub-makes, perhaps reading etc/Makeconf in makefiles in subdirectories. Fortunately such
packages are unusual.
6.3.4 Multiple sub-architectures

When installing packages from their sources, there are some extra considerations on installations
which use sub-architectures. These are commonly used on Windows but can in principle be used
on other platforms.
6
Note that capitalization and version may differ from the Open Source project.
7
using a path containing spaces is likely to cause problems
When a source package is installed by a build of R which supports multiple sub-architectures,

the normal installation process installs the packages for all sub-architectures. The exceptions
are
Unix-alikes
where there is an configure script, or a file src/Makefile.
Windows
where there is a non-empty configure.win script, or a file src/Makefile.win (with
some exceptions where the package is known to have an architecture-independent
configure.win, or if --force-biarch or field ‘Biarch’ in the DESCRIPTION file is
used to assert so).
In those cases only the current architecture is installed. Further sub-architectures can be in-
stalled by
R CMD INSTALL --libs-only pkg
using the path to R or R --arch to select the additional sub-architecture. There is also R CMD
INSTALL --merge-multiarch to build and merge the two architectures, starting with a source
tarball.
6.3.5 Byte-compilation
The base and recommended packages are byte-compiled by default. Other packages can be
byte-compiled on installation by using R CMD INSTALL with option --byte-compile or by
install.packages(type = "source", INSTALL_opts = "--byte-compile").
Not all contributed packages work correctly when byte-compiled. For most packages (espe-
cially those which make extensive use of compiled code) the speed-up is small. Unless a package
is used frequently the time spent in byte-compilation can outweigh the time saved in execution:
also byte-compilation can add substantially to the installed size of the package.
Byte-compilation can be controlled on a per-package basis by the ‘ByteCompile’ field in the
DESCRIPTION file.
6.3.6 External software

Some R packages contain compiled code which links to external software libraries. Unless the
external library is statically linked (which is done as much as possible for binary packages on
Windows and OS X), the libraries have to be found when the package is loaded and not just
when it is installed. How this should be done depends on the OS (and in some cases the version).
For Unix-alikes except macOS the primary mechanism is the ld.so cache controlled by
ldconfig: external dynamic libraries recorded in that cache will be found. Standard library
locations will be covered by the cache, and well-designed software will add its locations (as
for example openmpi does on Fedora). The secondary mechanism is to consult the environ-
ment variable LD_LIBRARY_PATH. Now the R script controls that variable, and sets it to the
concatenation of R_LD_LIBRARY_PATH, R_JAVA_LD_LIBRARY_PATH and the environment value of
LD_LIBRARY_PATH. The first two have defaults which are normally set when R is installed (but
can be overridden in the environment) so LD_LIBRARY_PATH is the best choice for a user to set.
On macOS the primary mechanism is to embed the absolute path to dependent dynamic
libraries into an object when it is compiled. Few R packages arrange to do so, but it can be
edited8 via install_name_tool — that only deals with direct dependencies and those would
also need to be compiled to include the absolute paths of their dependencies. If the choice of
absolute path is to be deferred to load time, how they are resolved is described in man dyld:
8
They need to have been created using -headerpad_max_install_names, which is the default for an R package.
the role of LD_LIBRARY_PATH is replaced on macOS by DYLD_LIBRARY_PATH and latterly DYLD_

FALLBACK_LIBRARY_PATH. Running R CMD otool -L on the package shared object will show
where (if anywhere) its dependencies are resolved. DYLD_FALLBACK_LIBRARY_PATH is preferred
(and it is that which is manipulated by the R script), but as from 10.11 (‘El Capitan’) the
default behaviour had been changed for security reasons to discard these environment variables
when invoking a shell script (and R is a shell script). That makes the only portable option to
set R_LD_LIBRARY_PATH in the environment, something like
export R_LD_LIBRARY_PATH="‘R RHOME‘/lib:/opt/local/lib"
The precise rules for where Windows looks for DLLs are complex and depend on the version
of Windows. But for present purposes the main solution is to put the directories containing
the DLLs the package links to (and any those DLLs link to) on the PATH. 64-bit versions of
Windows will ignore 32-bit DLLs from 64-bit R and vice versa.
The danger with any of the methods which involve setting environment variables is of in-
advertently masking a system library. This is less for DYLD_FALLBACK_LIBRARY_PATH and for
appending to PATH on Windows (as it should already contain the system library paths).
6.4 Updating packages

The command update.packages() is the simplest way to ensure that all the packages on your
system are up to date. It downloads the list of available packages and their current versions,
compares it with those installed and offers to fetch and install any that have later versions on
the repositories.
An alternative interface to keeping packages up-to-date is provided by the command
packageStatus(), which returns an object with information on all installed packages and pack-
ages available at multiple repositories. The print and summary methods give an overview of
installed and available packages, the upgrade method offers to fetch and install the latest ver-
sions of outdated packages.
One sometimes-useful additional piece of information that packageStatus() returns is the
status of a package, as "ok", "upgrade" or "unavailable" (in the currently selected reposito-
ries). For example
> inst <- packageStatus()$inst
> inst[inst$Status != "ok", c("Package", "Version", "Status")]
Package Version Status
Biobase Biobase 2.8.0 unavailable
RCurl RCurl 1.4-2 upgrade
Rgraphviz Rgraphviz 1.26.0 unavailable
rgdal rgdal 0.6-27 upgrade
6.5 Removing packages

Packages can be removed in a number of ways. From a command prompt they can be removed
by
R CMD REMOVE -l /path/to/library pkg1 pkg2 ...
From a running R process they can be removed by
> remove.packages(c("pkg1", "pkg2"),
lib = file.path("path", "to", "library"))
Finally, one can just remove the package directory from the library.
6.6 Setting up a package repository

Utilities such as install.packages can be pointed at any CRAN-style repository, and R users
may want to set up their own. The ‘base’ of a repository is a URL such as http: / / www .
stats.ox.ac.uk/pub/RWin: this must be an URL scheme that download.packages supports
(which also includes ‘https://’, ‘ftp://’ and ‘file://’). Under that base URL there should
be directory trees for one or more of the following types of package distributions:
• "source": located at src/contrib and containing .tar.gz files. Other forms of compres-
sion can be used, e.g. .tar.bz2 or .tar.xz files. Complete repositories contain the sources
corresponding to any binary packages, and in any case it is wise to have a src/contrib
area with a possibly empty PACKAGES file.
• "win.binary": located at bin/windows/contrib/x.y for R versions x.y.z and containing
.zip files for Windows.
• "mac.binary.el-capitan": located at bin/macosx/el-capitan/contrib/3.y for the
CRAN builds for ‘El Capitan (and later) for R versions 3.y.z, containing .tgz files.
Each terminal directory must also contain a PACKAGES file. This can be a concatenation of
the DESCRIPTION files of the packages separated by blank lines, but only a few of the fields
are needed. The simplest way to set up such a file is to use function write_PACKAGES in the
tools package, and its help explains which fields are needed. Optionally there can also be
PACKAGES.rds and PACKAGES.gz files, downloaded in preference to PACKAGES. (These files will
be smaller: PACKAGES.rds is used only from R 3.4.0. If you have a mis-configured server that
does not report correctly non-existent files you may need these files.)
To add your repository to the list offered by setRepositories(), see the help file for that
function.
Incomplete repositories are better specified via a contriburl argument than via being set
as a repository.
A repository can contain subdirectories, when the descriptions in the PACKAGES file of pack-
ages in subdirectories must include a line of the form
Path: path/to/subdirectory
—once again write_PACKAGES is the simplest way to set this up.
6.7 Checking installed source packages

It can be convenient to run R CMD check on an installed package, particularly on a platform
which uses sub-architectures. The outline of how to do this is, with the source package in
directory pkg (or a tarball filename):
R CMD INSTALL -l libdir pkg > pkg.log 2>&1
R CMD check -l libdir --install=check:pkg.log pkg
Where sub-architectures are in use the R CMD check line can be repeated with additional archi-
tectures by
R --arch arch CMD check -l libdir --extra-arch --install=check:pkg.log pkg
where --extra-arch selects only those checks which depend on the installed code and not those
which analyse the sources. (If multiple sub-architectures fail only because they need different
settings, e.g. environment variables, --no-multiarch may need to be added to the INSTALL
lines.) On Unix-alikes the architecture to run is selected by --arch: this can also be used on
Windows with R_HOME/bin/R.exe, but it is more usual to select the path to the Rcmd.exe of
the desired architecture.
So on Windows to install, check and package for distribution a source package from a tarball
which has been tested on another platform one might use
.../bin/i386/Rcmd INSTALL -l libdir tarball --build > pkg.log 2>&1
31
.../bin/i386/Rcmd check -l libdir --extra-arch --install=check:pkg.log pkg

.../bin/x64/Rcmd check -l libdir --extra-arch --install=check:pkg.log pkg
where one might want to run the second and third lines in a different shell with different settings
for environment variables and the path (to find external software, notably for Gtk+).
R CMD INSTALL can do a i386 install and then add the x64 DLL from a single command by
R CMD INSTALL --merge-multiarch -l libdir tarball
and --build can be added to zip up the installation.
32
7 Internationalization and Localization

Internationalization refers to the process of enabling support for many human languages, and
localization to adapting to a specific country and language.
Current builds of R support all the character sets that the underlying OS can handle. These
are interpreted according to the current locale, a sufficiently complicated topic to merit a
separate section. Note though that R has no built-in support for right-to-left languages and
bidirectional output, relying on the OS services. For example, how character vectors in UTF-8
containing both English digits and Hebrew characters are printed is OS-dependent (and perhaps
locale-dependent).
The other aspect of the internationalization is support for the translation of messages. This
is enabled in almost all builds of R.
7.1 Locales
A locale is a description of the local environment of the user, including the preferred language,
the encoding of characters, the currency used and its conventions, and so on. Aspects of the
locale are accessed by the R functions Sys.getlocale and Sys.localeconv.
The system of naming locales is OS-specific. There is quite wide agreement on schemes, but
not on the details of their implementation. A locale needs to specify
• A human language. These are generally specified by a lower-case two-character abbreviation
following ISO 639 (see e.g. https://en.wikipedia.org/wiki/ISO_639-1).
• A ‘territory’, used mainly to specify the currency. These are generally specified by an upper-
case two-character abbreviation following ISO 3166 (see e.g. https://en.wikipedia.org/
wiki/ISO_3166).
• A charset encoding, which determines both how a byte stream should be divided into charac-
ters, and which characters the subsequences of bytes represent. Sometimes the combination
of language and territory is used to specify the encoding, for example to distinguish between
traditional and simplified Chinese.
• Optionally, a modifier, for example to indicate that Austria is to be considered pre- or
post-Euro. The modifier is also used to indicate the script (@latin, @cyrillic for Serbian,
@iqtelif) or language dialect (e.g. @saaho, a dialect of Afar, and @bokmal and @nynorsk,
dialects of Norwegian regarded by some OSes as separate languages, no and nn).
R is principally concerned with the first (for translations) and third. Note that the charset
may be deducible from the language, as some OSes offer only one charset per language.
7.1.1 Locales under Unix-alikes

Modern Linux uses the XPG1 locale specifications which have the form ‘en_GB’, ‘en_GB.UTF-8’,
‘aa_ER.UTF-8@saaho’, ‘de_AT.iso885915@euro’, the components being in the order listed
above. (See man locale and locale -a for more details.) Similar schemes are used by most
Unix-alikes: some (including some distributions of Linux) use ‘.utf8’ rather than ‘.UTF-8’.
Note that whereas UTF-8 locales are nowadays almost universally used, locales such as
‘en_GB’ use 8-bit encodings for backwards compatibility.
7.1.2 Locales under Windows

Windows also uses locales, but specified in a rather less concise way. Most users will encounter
locales only via drop-down menus, but more information and lists can be found at https://
1
‘X/Open Portability Guide’, which has had several versions.
Chapter 7: Internationalization and Localization 33
msdn.microsoft.com/en-us/library/hzz3tw78(v=vs.80) (or if Microsoft moves it yet again,

search for ‘Windows language country strings’).
It offers only one encoding per language.
Some care is needed with Windows’ locale names. For example, chinese is Traditional
Chinese and not Simplified Chinese as used in most of the Chinese-speaking world.
7.1.3 Locales under macOS

macOS supports locales in its own particular way, but the R GUI tries to make this easier
for users. See https://developer.apple.com/library/content/documentation/MacOSX/
Conceptual/BPInternational/ for how users can set their locales. As with Windows, end users
will generally only see lists of languages/territories. Users of R in a terminal may need to set the
locale to something like ‘en_GB.UTF-8’ if it defaults to ‘C’ (as it sometimes does when logging
in remotely and for batch jobs: note whether Terminal sets the LANG environment variable is
an (advanced) preference, but does so by default).
Internally macOS uses a form similar to Linux: the main difference from other Unix-alikes is
that where a character set is not specified it is assumed to be UTF-8.
7.2 Localization of messages

The preferred language for messages is by default taken from the locale. This can be overridden
first by the setting of the environment variable LANGUAGE and then2 by the environment variables
LC_ALL, LC_MESSAGES and LANG. (The last three are normally used to set the locale and so should
not be needed, but the first is only used to select the language for messages.) The code tries
hard to map locales to languages, but on some systems (notably Windows) the locale names
needed for the environment variable LC_ALL do not all correspond to XPG language names and
so LANGUAGE may need to be set. (One example is ‘LC_ALL=es’ on Windows which sets the locale
to Estonian and the language to Spanish.)
It is usually possible to change the language once R is running via (not Windows)
Sys.setlocale("LC_MESSAGES", "new_locale"), or by setting an environment variable such
as LANGUAGE, provided 3 the language you are changing to can be output in the current character
set. But this is OS-specific, and has been known to stop working on an OS upgrade.
Messages are divided into domains, and translations may be available for some or all messages
in a domain. R makes use of the following domains.
• Domain R for the C-level error and warning messages from the R interpreter.
• Domain R-pkg for the R stop, warning and message messages in each package, including
R-base for the base package.
• Domain pkg for the C-level messages in each package.
• Domain RGui for the menus etc of the R for Windows GUI front-end.
Dividing up the messages in this way allows R to be extensible: as packages are loaded, their
message translation catalogues can be loaded too.
R can be built without support for translations, but it is enabled by default.
R-level and C-level domains are subtly different, for example in the way strings are canoni-
calized before being passed for translation.
Translations are looked for by domain according to the currently specified language, as specif-
ically as possible, so for example an Austrian (‘de_AT’) translation catalogue will be used in pref-
erence to a generic German one (‘de’) for an Austrian user. However, if a specific translation
2
On some systems setting LC_ALL or LC_MESSAGES to ‘C’ disables LANGUAGE.
3
If you try changing from French to Russian except in a UTF-8 locale, you will most likely find messages change
to English.
Chapter 7: Internationalization and Localization 34
catalogue exists but does not contain a translation, the less specific catalogues are consulted.
For example, R has catalogues for ‘en_GB’ that translate the Americanisms (e.g., ‘gray’) in the
standard messages into English.4 Two other examples: there are catalogues for ‘es’, which is
Spanish as written in Spain and these will by default also be used in Spanish-speaking Latin
American countries, and also for ‘pt_BR’, which are used for Brazilian locales but not for locales
specifying Portugal.
Translations in the right language but the wrong charset are made use of by on-the-fly re-
encoding. The LANGUAGE variable (only) can be a colon-separated list, for example ‘se:de’,
giving a set of languages in decreasing order of preference. One special value is ‘en@quot’, which
can be used in a UTF-8 locale to have American error messages with pairs of single quotes
translated to Unicode directional quotes.
If no suitable translation catalogue is found or a particular message is not translated in any
suitable catalogue, ‘English’5 is used.
See https://developer.r-project.org/Translations30.html for how to prepare and
install translation catalogues.
4
the language written in England: some people living in the USA appropriate this name for their language.
5
with Americanisms.
35
8 Choosing between 32- and 64-bit builds

Almost all current CPUs have both 32- and 64-bit sets of instructions. Most OSes running on
such CPUs offer the choice of building a 32-bit or a 64-bit version of R (and details are given
below under specific OSes). For most a 32-bit version is the default, but for some (e.g., ‘x86_64’
Linux and macOS ≥ 10.6) 64-bit is.
All current versions of R use 32-bit integers (this is enforced in the build) and ISO/IEC 605591
double-precision reals, and so compute to the same precision2 and with the same limits on the
sizes of numerical quantities. The principal difference is in the size of the pointers.
64-bit builds have both advantages and disadvantages:
• The total virtual memory space made available to a 32-bit process is limited by the pointer
size to 4GB, and on most OSes to 3GB (or even 2GB). The limits for 64-bit processes are
much larger (e.g. 8–128TB).
R allocates memory for large objects as needed, and removes any unused ones at garbage
collection. When the sizes of objects become an appreciable fraction of the address limit,
fragmentation of the address space becomes an issue and there may be no hole available
that is the size requested. This can cause more frequent garbage collection or the inability
to allocate large objects. As a guide, this will become an issue for 32-bit builds with objects
more than 10% of the size of the address space (around 300Mb) or when the total size of
objects in use is around one third (around 1Gb).
• Only 64-bit builds support ‘long vectors’, those with 231 or more elements (which needs at
least 16GB of storage for each numeric vector).
• Most 32-bit OSes by default limit file sizes to 2GB (and this may also apply to 32-bit builds
on 64-bit OSes). This can often be worked around: and configure selects suitable defines
if this is possible. (We have also largely worked around that limit on 32-bit Windows.)
64-bit builds have much larger limits.
• Because the pointers are larger, R’s basic structures are larger. This means that R objects
take more space and (usually) more time to manipulate. So 64-bit builds of R will, all
other things being equal, run slower than 32-bit builds. (On Sparc Solaris the difference
was 15-20%.)
• However, ‘other things’ may not be equal. In the specific case of ‘x86_64’ vs ‘ix86’, the
64-bit CPU has features (such as SSE2 instructions) which are guaranteed to be present
but are optional on the 32-bit CPU, and also has more general-purpose registers. This
means that on chips like a desktop Intel i7 the vanilla 64-bit version of R has been around
10% faster on both Linux and macOS. (Laptop CPUs are usually relatively slower in 64-bit
mode.)
So, for speed you may want to use a 32-bit build (especially on a laptop), but to handle large
datasets (and perhaps large files) a 64-bit build. You can often build both and install them
in the same place: See Section 2.6 [Sub-architectures], page 8. (This is done for the Windows
binary distributions.)
Even on 64-bit builds of R there are limits on the size of R objects (see
help("Memory-limits")), some of which stem from the use of 32-bit integers (espe-
cially in FORTRAN code). For example, the dimensions of an array are limited to
231 − 1.
1
also known as IEEE 754
2
at least when storing quantities: the on-FPU precision is allowed to vary
36
9 The standalone Rmath library

The routines supporting the distribution and special1 functions in R and a few others are declared
in C header file Rmath.h. These can be compiled into a standalone library for linking to other
applications. (Note that they are not a separate library when R is built, and the standalone
version differs in several ways.)
The makefiles and other sources needed are in directory src/nmath/standalone, so the
following instructions assume that is the current working directory (in the build directory tree
on a Unix-alike if that is separate from the sources).
Rmath.h contains ‘R_VERSION_STRING’, which is a character string containing the current R
version, for example "3.5.0".
There is full access to R’s handling of NaN, Inf and -Inf via special versions of the macros
and functions
ISNAN, R_FINITE, R_log, R_pow and R_pow_di
and (extern) constants R_PosInf, R_NegInf and NA_REAL.
There is no support for R’s notion of missing values, in particular not for NA_INTEGER nor
the distinction between NA and NaN for doubles.
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 shared library or DLL you may have to use the one supplied,
which is the Marsaglia-multicarry with an entry point
set_seed(unsigned int, unsigned int)
to set its seeds).
The facilities to change the normal random number generator are available through the
constant N01 kind. This takes values from the enumeration type
typedef enum {
BUGGY_KINDERMAN_RAMAGE,
AHRENS_DIETER,
BOX_MULLER,
USER_NORM,
INVERSION,
KINDERMAN_RAMAGE
} N01type;
(and ‘USER_NORM’ is not available).
9.1 Unix-alikes
If R has not already been made in the directory tree, configure must be run as described in
the main build instructions.
Then (in src/nmath/standalone)
make
will make standalone libraries libRmath.a and libRmath.so (libRmath.dylib on macOS):
‘make static’ and ‘make shared’ will create just one of them.
To use the routines in your own C or C++ programs, include
#define MATHLIB_STANDALONE
1
e.g. Bessel, beta and gamma functions
Chapter 9: The standalone Rmath library 37
#include <Rmath.h>
and link against ‘-lRmath’ (and ‘-lm’ if needed on your OS). The example file test.c does
nothing useful, but is provided to test the process (via make test). Note that you will probably
not be able to run it unless you add the directory containing libRmath.so to the LD_LIBRARY_
PATH environment variable (libRmath.dylib, DYLD_FALLBACK_LIBRARY_PATH on macOS).
The targets
make install
make uninstall
will (un)install the header Rmath.h and shared and static libraries (if built). Both prefix= and
DESTDIR are supported, together with more precise control as described for the main build.
‘make install’ installs a file for pkg-config to use by e.g.
$(CC) ‘pkg-config --cflags libRmath‘ -c test.c
$(CC) ‘pkg-config --libs libRmath‘ test.o -o test
On some systems ‘make install-strip’ will install a stripped shared library.
9.2 Windows
You need to set up2 almost all the tools to make R and then run (in a Unix-like shell)
(cd ../../gnuwin32; make MkRules)
(cd ../../include; make -f Makefile.win config.h Rconfig.h Rmath.h)
make -f Makefile.win
Alternatively, in a cmd.exe shell use
cd ../../include
make -f Makefile.win config.h Rconfig.h Rmath.h
cd ../nmath/standalone
make -f Makefile.win
This creates a static library libRmath.a and a DLL Rmath.dll. If you want an import
library libRmath.dll.a (you don’t need one), use
make -f Makefile.win shared implib
To use the routines in your own C or C++ programs using MinGW-w64, include
#include <Rmath.h>
and link against ‘-lRmath’. This will use the first found of libRmath.dll.a, libRmath.a and
Rmath.dll in that order, so the result depends on which files are present. You should be able
to force static or dynamic linking via
-Wl,-Bstatic -lRmath -Wl,Bdynamic
-Wl,-Bdynamic -lRmath
or by linking to explicit files (as in the ‘test’ target in Makefile.win: this makes two executa-
bles, test.exe which is dynamically linked, and test-static.exe, which is statically linked).
It is possible to link to Rmath.dll using other compilers, either directly or via an import
library: if you make a MinGW-w64 import library as above, you will create a file Rmath.def
which can be used (possibly after editing) to create an import library for other systems such as
Visual C++.
If you make use of dynamic linking you should use
#define RMATH_DLL
2
including copying MkRules.dist to MkRule.local and selecting the architecture.
38
#include <Rmath.h>
to ensure that the constants like NA_REAL are linked correctly. (Auto-import will probably work
with MinGW-w64, but it is better to be sure. This is likely to also work with VC++, Borland
and similar compilers.)
39
Appendix A Essential and useful other programs

under a Unix-alike
This appendix gives details of programs you will need to build R on Unix-like platforms, or
which will be used by R if found by configure.
Remember that some package management systems (such as RPM and Debian/Ubuntu’s)
make a distinction between the user version of a package and the development version. The
latter usually has the same name but with the extension ‘-devel’ or ‘-dev’: you need both
versions installed.
A.1 Essential programs and libraries

You need a means of compiling C and FORTRAN 90 (see Section B.6 [Using FORTRAN],
page 51). Your C compiler should be ISO/IEC 600591 , POSIX 1003.1 and C99-compliant.2 R
tries to choose suitable flags3 for the C compilers it knows about, but you may have to set CC or
CFLAGS suitably. For versions of gcc prior to 5.1 with glibc this means including -std=gnu994 .
(Note that options essential to run the compiler even for linking, such as those to set the
architecture, should be specified as part of CC rather than in CFLAGS.)
Unless you do not want to view graphs on-screen (or use macOS) you need ‘X11’ installed,
including its headers and client libraries. For recent Fedora/RedHat distributions it means (at
least) RPMs ‘libX11’, ‘libX11-devel’, ‘libXt’ and ‘libXt-devel’. On Debian/Ubuntu we
recommend the meta-package ‘xorg-dev’. If you really do not want these you will need to
explicitly configure R without X11, using --with-x=no.
The command-line editing (and command completion) depends on the GNU readline library
(including its headers): version 4.2 or later is needed for all the features to be enabled. Otherwise
you will need to configure with --with-readline=no (or equivalent).
A suitably comprehensive iconv function is essential. The R usage requires iconv to be
able to translate between "latin1" and "UTF-8", to recognize "" (as the current encoding) and
"ASCII", and to translate to and from the Unicode wide-character formats "UCS-[24][BL]E"
— this is true by default for glibc5 but not of most commercial Unixes. However, you can make
use of GNU libiconv (as used on macOS: see https://www.gnu.org/software/libiconv/).
The OS needs to have enough support6 for wide-character types: this is checked at configu-
ration. Some C99 functions7 are required and checked for at configuration. A small number of
POSIX functions8 are essential, and others9 will be used if available.
Installations of zlib (version 1.2.5 or later), libbz2 (version 1.0.6 or later: called bzip2-
libs/bzip2-devel or libbz2-1.0/libbz2-dev by some Linux distributions), liblzma10 version 5.0.3
or later are required.
1
also known as IEEE 754
2
Note that C11 compilers need not be C99-compliant: R requires support for double complex and variable-
length arrays which are optional in C11 but is mandatory in C99.
3
Examples are -std=gnu99, -std=c99 and -c99.
4
-std=c99 excludes POSIX functionality, but config.h will turn on all GNU extensions to include the POSIX
functionality for R itself: this does not apply to badly-written packages. The default mode for GCC 5.1 and
later is -std=gnu11, which currently includes the optional features R needs.
5
However, it is possible to break the default behaviour of glibc by re-specifying the gconv modules to be
loaded.
6
specifically, the C99 functionality of headers wchar.h and wctype.h, types wctans_t and mbstate_t and
functions mbrtowc, mbstowcs, wcrtomb, wcscoll, wcstombs, wctrans, wctype, and iswctype.
7
including expm1, hypot, log1p, nearbyint and va_copy.
8
including opendir, readdir, closedir, popen, stat, glob, access, getcwd and chdir system calls, select on
a Unix-alike, and either putenv or setenv.
9
such as realpath, symlink.
10
most often distributed as part of xz: possible names in Linux distributions include xz-devel/xz-libs and
liblzma-dev.
Appendix A: Essential and useful other programs under a Unix-alike 40
PCRE11 (version 8.32 or later, although versions 8.20–8.31 will be accepted with a deprecation
warning) is required (or just its library and headers if packaged separately). Only the ‘8-bit’
interface is used (and only that is built by default when installing from sources). PCRE must be
built with UTF-8 support (not the default, and checked by configure) and support for Unicode
properties is assumed by some R packages. JIT support (optionally available) is desirable for
the best performance: support for this and Unicode properties can be checked at run-time by
calling pcre_config(). If building PCRE for use with R a suitable configure command might
be
./configure --enable-utf --enable-unicode-properties --enable-jit --disable-cpp
The --enable-jit flag is supported for most common CPUs. (See also the comments for
Solaris.)
Library libcurl (version 7.22.0 or later12 ) is required, with at least 7.28.0 being desirable.
Information on libcurl is found from the curl-config script: if that is missing or needs to be
overridden13 there are macros to do so described in file config.site.
A tar program is needed to unpack the sources and packages (including the recommended
packages). A version14 that can automagically detect compressed archives is preferred for use
with untar(): the configure script looks for gtar and gnutar before tar – use environment
variable TAR to override this.
There need to be suitable versions of the tools grep and sed: the problems are usually with
old AT&T and BSD variants. configure will try to find suitable versions (including looking in
/usr/xpg4/bin which is used on some commercial Unixes).
You will not be able to build most of the manuals unless you have texi2any version 5.1 or
later installed, and if not most of the HTML manuals will be linked to a version on CRAN. To
make PDF versions of the manuals you will also need file texinfo.tex installed (which is part
of the GNU texinfo distribution but is often made part of the TEX package in re-distributions) as
well as texi2dvi.15 Further, the versions of texi2dvi and texinfo.tex need to be compatible:
we have seen problems with older TEX distributions.
If you want to build from the R Subversion repository then texi2any is highly recommended
as it is used to create files which are in the tarball but not stored in the Subversion repository.
The PDF documentation (including doc/NEWS.pdf) and building vignettes needs pdftex and
pdflatex. We require LATEX version 2005/12/01 or later (for UTF-8 support). Building PDF
package manuals (including the R reference manual) and vignettes is sensitive to the version of
the LATEX package hyperref and we recommend that the TEX distribution used is kept up-to-
date. A number of standard LATEX packages are required (including url and some of the font
packages such as times, helvetic, ec and cm-super) and others such as hyperref and inconsolata
are desirable (and without them you may need to change R’s defaults: see Section 2.3 [Making
the manuals], page 4). Note that package hyperref (currently) requires packages kvoptions,
ltxcmds and refcount. For distributions based on TeX Live the simplest approach may be to
install collections collection-latex, collection-fontsrecommended, collection-latexrecommended,
collection-fontsextra and collection-latexextra (assuming they are not installed by default): Fe-
dora uses names like texlive-collection-fontsextra and Debian/Ubuntu like texlive-fonts-extra.
11
sometimes known as PCRE1, and not PCRE2 which started at version 10.0.
12
but not a major version greater than 7 should there ever be one: the major version has been 7 since 2000.
13
for example to specify static linking with a build which has both shared and static libraries.
14
Such as GNU tar 1.15 or later, bsdtar (from https://github.com/libarchive/libarchive/, as used by
FreeBSD and OS X 10.6 and later) or tar from the Heirloom Toolchest (http://heirloom.sourceforge.
net/tools.html).
15
texi2dvi is normally a shell script. Some versions (including that from texinfo 5.2 and 6.0) need to be run
under bash rather than a Bourne shell, especially on Solaris. Some of the issues which have been observed
with broken versions of texi2dvi can be circumvented by setting the environment variable R_TEXI2DVICMD to
the value emulation.
The essential programs should be in your PATH at the time configure is run: this will capture
the full paths.
Those distributing binary versions of R may need to be aware of the licences of the external
libraries it is linked to (including ‘useful’ libraries from the next section). The liblzma library
is in the public domain and X11, libbzip2, libcurl and zlib have MIT-style licences. PCRE
has a BSD-style licence which requires distribution of the licence (included in R’s COPYRIGHTS
file) in binary distributions. GNU readline is licensed under GPL (which version(s) depending
on the readline version).
A.2 Useful libraries and programs

The ability to use translated messages makes use of gettext and most likely needs GNU gettext:
you do need this to work with new translations, but otherwise the version contained in the R
sources will be used if no suitable external gettext is found.
The ‘modern’ version of the X11(), jpeg(), png() and tiff() graphics devices uses the
cairo and (optionally) Pango libraries. Cairo version 1.2.0 or later is required. Pango needs
to be at least version 1.10, and 1.12 is the earliest version we have tested. (For Fedora users
we believe the pango-devel RPM and its dependencies suffice.) R checks for pkg-config, and
uses that to check first that the ‘pangocairo’ package is installed (and if not, ‘cairo’) and if
additional flags are needed for the ‘cairo-xlib’ package, then if suitable code can be compiled.
These tests will fail if pkg-config is not installed16 , and are likely to fail if cairo was built
statically (unusual). Most systems with Gtk+ 2.8 or later installed will have suitable libraries
For the best font experience with these devices you need suitable fonts installed: Linux users
will want the urw-fonts package. On platforms which have it available, the msttcorefonts
package17 provides TrueType versions of Monotype fonts such as Arial and Times New Ro-
man. Another useful set of fonts is the ‘liberation’ TrueType fonts available at https: / /
fedorahosted.org/liberation-fonts/,18 which cover the Latin, Greek and Cyrillic alphabets
plus a fair range of signs. These share metrics with Arial, Times New Roman and Courier
New, and contain fonts rather similar to the first two (https://en.wikipedia.org/wiki/
Liberation_fonts). Then there is the ‘Free UCS Outline Fonts’ project (https://www.gnu.
org/software/freefont/) which are OpenType/TrueType fonts based on the URW fonts but
with extended Unicode coverage. See the R help on X11 on selecting such fonts.
The bitmapped graphics devices jpeg(), png() and tiff() need the appropriate headers
and libraries installed: jpeg (version 6b or later, or libjpeg-turbo) or libpng (version 1.2.7
or later) and zlib or libtiff (any recent version – 3.9.[4567] and 4.0.[23] have been tested)
respectively. They also need support for either X11 or cairo (see above). Should support for
these devices not be required or broken system libraries need to be avoided there are configure
options --without-libpng, --without-jpeglib and --without-libtiff. For most system
installations the TIFF libraries will require JPEG libraries to be present and perhaps linked
explicitly, so --without-jpeglib may also disable the tiff() device. The tiff() devices only
require a basic build of libtiff (not even JPEG support is needed). Recent versions allow
several other libraries to be linked into libtiff such as lzma, jbig and jpeg12, and these may
need also to be present.
Option --with-system-tre is also available: it needs a recent version of TRE. (The current
sources are in the git repository at https://github.com/laurikari/tre/, but at the time of
writing the resulting build will not pass its checks.).
16
If necessary the path to pkg-config can be specified by setting PKGCONF in config.site, on the configure
command line or in the environment.
17
also known as ttf-mscorefonts-installer in the Debian/Ubuntu world: see also https://en.wikipedia.
org/wiki/Core_fonts_for_the_Web.
18
ttf-liberation in Debian/Ubuntu.
An implementation of XDR is required, and the R sources contain one which is likely to
suffice (although a system version may have higher performance). XDR is part of RPC and
historically has been part of libc on a Unix-alike. (In principle man xdr_string should tell you
which library is needed, but it often does not: on Solaris and others it is provided by libnsl.)
However some builds19 of glibc omit or hide it with the intention that the TI-RPC library be
used, in which case libtirpc (and its development version) needs to be installed, and its headers
need to be on the C include path or in /usr/include/tirpc.
Use of the X11 clipboard selection requires the Xmu headers and libraries. These are normally
part of an X11 installation (e.g. the Debian meta-package ‘xorg-dev’), but some distributions
have split this into smaller parts, so for example recent versions of Fedora require the ‘libXmu’
and ‘libXmu-devel’ RPMs.
Some systems (notably macOS and at least some FreeBSD systems) have inadequate support
for collation in multibyte locales. It is possible to replace the OS’s collation support by that
from ICU (International Components for Unicode, http://site.icu-project.org/), and this
provides much more precise control over collation on all systems. ICU is available as sources
and as binary distributions for (at least) most Linux distributions, Solaris, FreeBSD and AIX,
usually as libicu or icu4c. It will be used by default where available: should a very old or
broken version of ICU be found this can be suppressed by --without-ICU.
The bitmap and dev2bitmap devices and function embedFonts() use ghostscript (http://
www.ghostscript.com/). This should either be in your path when the command is run, or its
full path specified by the environment variable R_GSCMD at that time.
A.2.1 Tcl/Tk
The tcltk package needs Tcl/Tk ≥ 8.4 installed: the sources are available at https://www.tcl.
tk/. To specify the locations of the Tcl/Tk files you may need the configuration options
--with-tcltk
use Tcl/Tk, or specify its library directory
--with-tcl-config=TCL_CONFIG
specify location of tclConfig.sh
--with-tk-config=TK_CONFIG
specify location of tkConfig.sh
or use the configure variables TCLTK_LIBS and TCLTK_CPPFLAGS to specify the flags needed for
linking against the Tcl and Tk libraries and for finding the tcl.h and tk.h headers, respectively.
If you have both 32- and 64-bit versions of Tcl/Tk installed, specifying the paths to the correct
config files may be necessary to avoid confusion between them.
Versions of Tcl/Tk up to 8.5.19 and 8.6.4 have been tested (including most versions of 8.4.x,
but not recently).
Note that the tk.h header includes20 X11 headers, so you will need X11 and its development
files installed.
A.2.2 Java support

The build process looks for Java support on the host system, and if it finds it sets some settings
which are useful for Java-using packages (such as rJava (https: / / CRAN . R-project . org /
package=rJava) and JavaGD (https://CRAN.R-project.org/package=JavaGD)). This check
19
This is the default as from glibc 2.26 and has been announced for Fedora 28.
20
This is true even for the ‘Aqua’ version of Tk on macOS, but distributions of that include a copy of the X11
files needed.
can be suppressed by configure option --disable-java. Configure variable JAVA_HOME can be

set to point to a specific JRE/JDK, on the configure command line or in the environment.
Principal amongst these settings are some library paths to the Java libraries and JVM, which
are stored in environment variable R_JAVA_LD_LIBRARY_PATH in file R_HOME/etc/ldpaths (or a
sub-architecture-specific version). A typical setting for ‘x86_64’ Linux is
JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.71-1.b15.fc22.x86_64/jre
R_JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/lib/that/server
Unfortunately this depends on the exact version of the JRE/JDK installed, and so may need
updating if the Java installation is updated. This can be done by running R CMD javareconf
which updates settings in both R_HOME/etc/Makeconf and R_HOME/etc/ldpaths. See R CMD
javareconf --help for details: note that this needs to be done by the account owning the R
installation.
Another way of overriding those settings is to set the environment variable R_JAVA_LD_
LIBRARY_PATH (before R is started, hence not in ~/.Renviron), which suffices to run already-
installed Java-using packages. For example
R_JAVA_LD_LIBRARY_PATH=/usr/lib/jvm/java-1.8.0/jre/lib/amd64/server
It may be possible to avoid this by specifying an invariant link as the path when configuring.
For example, on that system any of
JAVA_HOME=/usr/lib/jvm/java
JAVA_HOME=/usr/lib/jvm/java-1.8.0
JAVA_HOME=/usr/lib/jvm/java-1.8.0/jre
worked.
A.2.3 Other compiled languages

Some add-on packages need a C++ compiler. This is specified by the configure variables CXX,
CXXFLAGS and similar. configure will normally find a suitable compiler. However, in many cases
this will be a C++98 compiler, and it is possible to specify an alternative compiler for use with
C++11 by the configure variables CXX11, CXX11STD, CXX11FLAGS and similar (see Section 2.7.2
[C++ Support], page 10). Again, configure will normally find a suitable value for CXX11STD if
the compiler given by CXX is capable of compiling C++11 code, but it is possible that a completely
different compiler will be needed.
Other packages need full Fortran 90 (or later) support. For source files with extension .f90
or .f95, the compiler defined by the macro FC is used by R CMD INSTALL. This is found when R
is configured and is often the same as F77: note that it is detected by the name of the command
without a test that it can actually compile Fortran 90 code. Set the configure variable FC to
override this if necessary: variables FCFLAGS, FCPICFLAGS, FCLIBS, SHLIB_FCLD and SHLIB_
FCLDFLAGS might also need to be set.
See file config.site in the R source for more details about these variables.
A.3 Linear algebra

A.3.1 BLAS
The linear algebra routines in R can make use of enhanced BLAS (Basic Linear Algebra Sub-
programs, http://www.netlib.org/blas/faq.html) routines. However, these have to be
explicitly requested at configure time: R provides an internal BLAS which is well-tested and will
be adequate for most uses of R.
You can specify a particular BLAS library via a value for the configuration option --with-
blas and not to use an external BLAS library by --without-blas (the default). If --with-blas
is given with no =, its value is taken from the environment variable BLAS_LIBS, set for example
in config.site. If neither the option nor the environment variable supply a value, a search is
made for a suitable BLAS. If the value is not obviously a linker command (starting with a dash
or giving the path to a library), it is prefixed by ‘-l’, so
--with-blas="foo"
is an instruction to link against ‘-lfoo’ to find an external BLAS (which needs to be found both
at link time and run time).
The configure code checks that the external BLAS is complete (it must include all double
precision and double complex routines, as well as LSAME), and appears to be usable. However,
an external BLAS has to be usable from a shared object (so must contain position-independent
code), and that is not checked.
Some enhanced BLASes are compiler-system-specific (sunperf on Solaris21 , libessl on IBM,
Accelerate on macOS). The correct incantation for these is often found via --with-blas with
no value on the appropriate platforms.
Some of the external BLASes are multi-threaded. One issue is that R profiling (which uses the
SIGPROF signal) may cause problems, and you may want to disable profiling if you use a multi-
threaded BLAS. Note that using a multi-threaded BLAS can result in taking more CPU time
and even more elapsed time (occasionally dramatically so) than using a similar single-threaded
BLAS. On a machine running other tasks, there can be contention for CPU caches that reduces
the effectiveness of the optimization of cache use by a BLAS implementation: some people warn
that this is especially problematic for hyperthreaded CPUs
Note that under Unix (but not under Windows) if R is compiled against a non-default
BLAS and --enable-BLAS-shlib is not used (it is the default on all platforms except AIX),
then all BLAS-using packages must also be. So if R is re-built to use an enhanced BLAS then
packages such as quantreg (https://CRAN.R-project.org/package=quantreg) will need to
be re-installed; they may be under other circumstances.
R relies on ISO/IEC 60559 compliance of an external BLAS. This can be broken if for
example the code assumes that terms with a zero factor are always zero and do not need to be
computed—whereas x*0 can be NaN. This is checked in the test suite.
External BLAS implementations often make less use of extended-precision floating-point reg-
isters (where available) and will almost certainly re-order computations. This can result in less
accuracy than using a reference BLAS, and may result in different solutions, e.g. different signs
in SVD and eigendecompositions.
Debian/Ubuntu systems provide a system-specific way to switch the BLAS in use.
Build R with -with-blas to select the OS version of the reference BLAS, and then use
update-alternatives to switch between the available BLAS libraries. See https://wiki.
debian.org/DebianScience/LinearAlgebraLibraries.
The URIs for several of these BLAS have been subject to frequent gratuitous changes, so you
will need to search for their current locations.
A.3.1.1 ATLAS
ATLAS (http://math-atlas.sourceforge.net/) is a “tuned” BLAS that runs on a wide
range of Unix-alike platforms. Unfortunately it is built by default as a static library that on
some platforms may not be able to be used with shared objects such as are used in R packages.
Be careful when using pre-built versions of ATLAS static libraries (they seem to work on ‘ix86’
platforms, but not always on ‘x86_64’ ones).
ATLAS contains replacements for a small number of LAPACK routines, but can be built to
merge these with LAPACK sources to include a full LAPACK library.
21
Using the Oracle Developer Studio cc and f95 compilers
Recent versions of ATLAS can be built as a single shared library, either libsatlas or
libtatlas (serial or threaded respectively): these may even contain a full LAPACK. Such
builds can be used by one of
--with-blas=satlas
--with-blas=tatlas
or, as on ‘x86_64’ Fedora where a path needs to be specified,
--with-blas="-L/usr/lib64/atlas -lsatlas"
--with-blas="-L/usr/lib64/atlas -ltatlas"
Distributed ATLAS libraries cannot be tuned to your machine and so are a compromise: for
example Fedora tunes ‘x86_64’ for CPUs with SSE3 extensions, and separate ‘atlas-sse2’ and
‘atlas-sse3’ ‘i686’ RPMs are available.22
Note that building R on Linux against distributed shared libraries may need ‘-devel’ or
‘-dev’ packages installed.
Linking against multiple static libraries requires one of
--with-blas="-lf77blas -latlas"
--with-blas="-lptf77blas -lpthread -latlas"
--with-blas="-L/path/to/ATLAS/libs -lf77blas -latlas"
--with-blas="-L/path/to/ATLAS/libs -lptf77blas -lpthread -latlas"
Consult its installation guide23 for how to build ATLAS as a shared library or as a static
library with position-independent code (on platforms where that matters).
According to the ATLAS FAQ24 the maximum number of threads used by multi-threaded
ATLAS is set at compile time. Also, the author advises against using multi-threaded ATLAS
on hyperthreaded CPUs without restricting affinities at compile-time to one virtual core per
physical CPU. (For the Fedora libraries the compile-time flag specifies 4 threads.)
A.3.1.2 Goto and OpenBLAS

Dr Kazushige Goto wrote a tuned BLAS for several processors and OSes, which was frozen in
mid-2010. The final version is known as GotoBLAS2, and was re-released under a much less
restrictive licence. OpenBLAS (http://www.openblas.net/) is a descendant project with
support for some later CPUs (e.g. Intel Sandy Bridge and Haswell).
These can be used by configuring R with something like
--with-blas="-lgoto2"
--with-blas="-lopenblas"
See see Section A.3.1.5 [Shared BLAS], page 46, for an alternative (and in many ways preferable)
way to use them.
Some platforms provide multiple builds of OpenBLAS: for example Fedora 26 has RPMs25
openblas
openblas-threads
openblas-openmp
providing shared libraries
libopenblas.so
libopenblasp.so
22
There were others for earlier versions of ATLAS, and are for non-Intel architectures. The only way to see
exactly which CPUs the distributed libraries have been tuned for is to read the atlas.spec file: at the time
of writing ‘HAMMER64SSE3’ and ‘Corei264AVX’ for ‘x86_64’ Fedora.
23
http://math-atlas.sourceforge.net/atlas_install/
24
http://math-atlas.sourceforge.net/faq.html#tnum
25
(and more, e.g. for 64-bit ints and static versions).
libopenblaso.so
respectively, each of which can be used as a shared BLAS. For the second and third the number of
threads is controlled by OPENBLAS_NUM_THREADS and OMP_NUM_THREADS (as usual for OpenMP)
respectively. There is also a Fedora RPM ‘openblas-Rblas’ to replace libRblas.so in their
distribution of R.
Note that building R on Linux against distributed libraries may need ‘-devel’ or ‘-dev’
packages installed.
For ‘ix86’ and ‘x86_64’ most distributed libraries contain several alternatives for different
CPU microarchitectures with the choice being made at run time.
A.3.1.3 Intel MKL

For Intel processors (and perhaps others) and some distributions of Linux, there is Intel’s Math
Kernel Library. You are strongly encouraged to read the MKL User’s Guide, which is installed
with the library, before attempting to link to MKL. This includes a ‘link line advisor’ which will
suggest appropriate incantations: its use is recommended. Or see https://software.intel.
com/en-us/articles/intel-mkl-link-line-advisor.
There are also versions of MKL for macOS and Windows, but at the time these were tried
they did not work with the default compilers used for R on those platforms.
The MKL interface has changed several times and may change again: the following examples
have been used with versions 10.3 to 2018.1, for GCC compilers on ‘x86_64’.
To use a sequential version of MKL we used
MKL_LIB_PATH=/path/to/intel_mkl/mkl/lib/intel64
export LD_LIBRARY_PATH=$MKL_LIB_PATH
MKL="-L${MKL_LIB_PATH} -lmkl_gf_lp64 -lmkl_core -lmkl_sequential"
./configure --with-blas="$MKL" --with-lapack
The option --with-lapack is used since MKL contains a tuned copy of LAPACK as well as
BLAS (see Section A.3.2 [LAPACK], page 47), although this can be omitted.
Threaded MKL may be used by replacing the line defining the variable MKL by
MKL="-L${MKL_LIB_PATH} -lmkl_gf_lp64 -lmkl_core \
-lmkl_gnu_thread -dl -lpthread"
The default number of threads will be chosen by the OpenMP software, but can be controlled
by setting OMP_NUM_THREADS or MKL_NUM_THREADS, and in recent versions seems to default to a
sensible value for sole use of the machine. (Parallel MKL has not always passed make check-all,
but did with MKL 2018.1.)
It has been reported that
--with-blas=’-mkl=parallel’ --with-lapack
worked with the Intel 2015.3 compilers on Centos 6.
A.3.1.4 ACML
The AMD Core Math Library (ACML) is now end-of-life, although downloads remained available
when checked in January 2018.
A.3.1.5 Shared BLAS

The BLAS library will be used for many of the add-on packages as well as for R itself. This
means that it is better to use a shared/dynamic BLAS library, as most of a static library will be
compiled into the R executable and each BLAS-using package.
R offers the option of compiling the BLAS into a dynamic library libRblas stored in R_
HOME/lib and linking both R itself and all the add-on packages against that library.
This is the default on all platforms except AIX unless an external BLAS is specified and
found: for the latter it can be used by specifying the option --enable-BLAS-shlib, and it can
always be disabled via --disable-BLAS-shlib.
This has both advantages and disadvantages.
• It saves space by having only a single copy of the BLAS routines, which is helpful if there
is an external static BLAS (as used to be standard for ATLAS).
• There may be performance disadvantages in using a shared BLAS. Probably the most
likely is when R’s internal BLAS is used and R is not built as a shared library, when it is
possible to build the BLAS into R.bin (and libR.a) without using position-independent
code. However, experiments showed that in many cases using a shared BLAS was as fast,
provided high levels of compiler optimization are used.
• It is easy to change the BLAS without needing to re-install R and all the add-on packages,
since all references to the BLAS go through libRblas, and that can be replaced. Note
though that any dynamic libraries the replacement links to will need to be found by the
linker: this may need the library path to be changed in R_HOME/etc/ldpaths.
Another option to change the BLAS in use is to symlink a single dynamic BLAS library to
R_HOME/lib/libRblas.so. For example, just
mv R_HOME/lib/libRblas.so R_HOME/lib/libRblas.so.keep
ln -s /usr/lib64/libopenblasp.so.0 R_HOME/lib/libRblas.so
on ‘x86_64’ Fedora will change the BLAS used to multithreaded OpenBLAS. A similar link
works for most versions of the Goto BLAS, OpenBLAS and ACML (provided the appropriate
lib directory is in the run-time library path or ld.so cache). It can also be used for a single-
library ATLAS, so on ‘x86_64’ Fedora
ln -s /usr/lib64/atlas/libsatlas.so.3 R_HOME/lib/libRblas.so
ln -s /usr/lib64/atlas/libtatlas.so.3 R_HOME/lib/libRblas.so
can be used with its distributed ATLAS libraries. (If you have the ‘-devel’ RPMS installed you
can omit the .0/.3.)
Note that rebuilding or symlinking libRblas.so will not suffice if the intention is to use a
modified LAPACK contained in an external BLAS: the latter could even cause conflicts.
A.3.2 LAPACK
Provision is made for using an external LAPACK library, principally to cope with BLAS libraries
which contain a copy of LAPACK (such as sunperf on Solaris, Accelerate on macOS and
ATLAS and MKL on ‘ix86’/‘x86_64’ Linux). At least LAPACK version 3.2 is required. This
can only be done if --with-blas has been used.
However, the likely performance gains are thought to be small (and may be negative), and the
default is not to search for a suitable LAPACK library, and this is definitely not recommended.
You can specify a specific LAPACK library or a search for a generic library by the configuration
option --with-lapack. The default for --with-lapack is to check the BLAS library and then
look for an external library ‘-llapack’. Sites searching for the fastest possible linear algebra
may want to build a LAPACK library using the ATLAS-optimized subset of LAPACK: this is
simplest with a dynamic ATLAS library which contains a full LAPACK, when --with-lapack
suffices.
A value for --with-lapack can be set via the environment variable LAPACK_LIBS, but this
will only be used if --with-lapack is specified (as the default value is no) and the BLAS library
does not contain LAPACK.
Since ACML contains a full LAPACK, if selected as the BLAS it can be used as the LAPACK
via --with-lapack.
If you do use --with-lapack, be aware of potential problems with bugs in the LAPACK
sources (or in the posted corrections to those sources). In particular, bugs in DGEEV and DGESDD
have resulted in error messages such as
DGEBRD gave error code -10
. Other potential problems are incomplete versions of the libraries, seen several times in Linux
distributions over the years.
Please do bear in mind that using --with-lapack is ‘definitely not recommended’: it is pro-
vided only because it is necessary on some platforms and because some users want to experiment
with claimed performance improvements. Reporting problems where it is used unnecessarily will
simply irritate the R helpers.
Note too the comments about ISO/IEC 60559 compliance in the section of external BLAS:
these apply equally to an external LAPACK, and for example the Intel MKL documentation
has said
LAPACK routines assume that input matrices do not contain IEEE 754 special
values such as INF or NaN values. Using these special values may cause LAPACK
to return unexpected results or become unstable.
We rely on limited support in LAPACK for matrices with 231 or more elements: it is possible
that an external LAPACK will not have that support.
If you have a pure FORTRAN 77 compiler which cannot compile LAPACK it may be possible
to use CLAPACK from http://www.netlib.org/clapack/ by something like
-with-lapack="-lclapack -lf2c"
provided these were built with position-independent code and the calling conventions for double
complex function return values match those in the BLAS used, so it may be simpler to use
CLAPACK built to use CBLAS and
-with-lapack="-lclapack -lcblas -lf2c"
A.3.3 Caveats
As with all libraries, you need to ensure that they and R were compiled with compatible compilers
and flags. For example, this has meant that on Sun Sparc using the native compilers the flag
-dalign is needed if sunperf is to be used.
On some systems it has been necessary that an external BLAS/LAPACK was built with the
same FORTRAN compiler used to build R.
49
Appendix B Configuration on a Unix-alike
B.1 Configuration options

configure has many options: running
./configure --help
will give a list. Probably the most important ones not covered elsewhere are (defaults in brackets)
--with-x use the X Window System [yes]
--x-includes=DIR
X include files are in DIR
--x-libraries=DIR
X library files are in DIR
--with-readline
use readline library (if available) [yes]
--enable-R-profiling
attempt to compile support for Rprof() [yes]
--enable-memory-profiling
attempt to compile support for Rprofmem() and tracemem() [no]
--enable-R-shlib
build R as a shared/dynamic library [no]
--enable-BLAS-shlib
build the BLAS as a shared/dynamic library [yes, except on AIX]
You can use --without-foo or --disable-foo for the negatives.
You will want to use --disable-R-profiling if you are building a profiled executable of R
(e.g. with ‘-pg)’.
Flag --enable-R-shlib causes the make process to build R as a dynamic (shared) library,
typically called libR.so, and link the main R executable R.bin against that library. This can
only be done if all the code (including system libraries) can be compiled into a dynamic library,
and there may be a performance1 penalty. So you probably only want this if you will be using
an application which embeds R. Note that C code in packages installed on an R system linked
with --enable-R-shlib is linked against the dynamic library and so such packages cannot be
used from an R system built in the default way. Also, because packages are linked against R
they are on some OSes also linked against the dynamic libraries R itself is linked against, and
this can lead to symbol conflicts.
For maximally effective use of valgrind, R should be compiled with valgrind instrumentation.
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.) The system headers for valgrind can
be requested by option --with-system-valgrind-headers: they will be used if present (on
Linux they may be in a separate package such as valgrind-devel). Note though that there is no
guarantee that the code in R will be compatible with very old2 or future valgrind headers.
If you need to re-configure R with different options you may need to run make clean or even
make distclean before doing so.
The configure script has other generic options added by autoconf and which are not sup-
ported for R: in particular building for one architecture on a different host is not possible.
1
We have measured 15–20% on ‘i686’ Linux and around 10% on ‘x86_64’ Linux.
2
We believe that versions 3.4.0 to 3.13.0 are compatible.
Appendix B: Configuration on a Unix-alike 50
B.2 Internationalization support

Translation of messages is supported via GNU gettext unless disabled by the configure option
--disable-nls. The configure report will show NLS as one of the ‘Additional capabilities’
if support has been compiled in, and running in an English locale (but not the C locale) will
include
Natural language support but running in an English locale
in the greeting on starting R.
B.3 Configuration variables

If you need or want to set certain configure variables to something other than their default, you
can do that by either editing the file config.site (which documents many of the variables you
might want to set: others can be seen in file etc/Renviron.in) or on the command line as
./configure VAR=value
If you are building in a directory different from the sources, there can be copies of config.site
in the source and the build directories, and both will be read (in that order). In addition, if
there is a file ~/.R/config, it is read between the config.site files in the source and the build
directories.
There is also a general autoconf mechanism for config.site files, which are read before any
of those mentioned in the previous paragraph. This looks first at a file specified by the environ-
ment variable CONFIG_SITE, and if not is set at files such as /usr/local/share/config.site
and /usr/local/etc/config.site in the area (exemplified by /usr/local) where R would be
installed.
These variables are precious, implying that they do not have to be exported to the environ-
ment, are kept in the cache even if not specified on the command line, checked for consistency
between two configure runs (provided that caching is used), and are kept during automatic
reconfiguration as if having been passed as command line arguments, even if no cache is used.
See the variable output section of configure --help for a list of all these variables.
If you find you need to alter configure variables, it is worth noting that some settings may
be cached in the file config.cache, and it is a good idea to remove that file (if it exists)
before re-configuring. Note that caching is turned off by default: use the command line option
--config-cache (or -C) to enable caching.
B.3.1 Setting paper size

One common variable to change is R_PAPERSIZE, which defaults to ‘a4’, not ‘letter’. (Valid
values are ‘a4’, ‘letter’, ‘legal’ and ‘executive’.)
This is used both when configuring R to set the default, and when running R to override the
default. It is also used to set the paper size when making PDF manuals.
The configure default will most often be ‘a4’ if R_PAPERSIZE is unset. (If the (Debian Linux)
program paperconf is found or the environment variable PAPERSIZE is set, these are used to
produce the default.)
B.3.2 Setting the browsers

Another precious variable is R_BROWSER, the default HTML browser, which should take a value
of an executable in the user’s path or specify a full path.
Its counterpart for PDF files is R_PDFVIEWER.
B.3.3 Compilation flags

If you have libraries and header files, e.g., for GNU readline, in non-system directories, use
the variables LDFLAGS (for libraries, using ‘-L’ flags to be passed to the linker) and CPPFLAGS
(for header files, using ‘-I’ flags to be passed to the C/C++ preprocessors), respectively, to
specify these locations. These default to ‘-L/usr/local/lib’ (LDFLAGS, ‘-L/usr/local/lib64’
on most 64-bit Linux OSes) and ‘-I/usr/local/include’ (CPPFLAGS, but note that on most
systems /usr/local/include is regarded as a system include directory and so instances in that
macro will be skipped) to catch the most common cases. If libraries are still not found, then
maybe your compiler/linker does not support re-ordering of -L and -l flags (years ago this was
reported to be a problem on HP-UX with the native cc). In this case, use a different compiler
(or a front-end shell script which does the re-ordering).
These flags can also be used to build a faster-running version of R. On most platforms
using gcc, having ‘-O3’ in CFLAGS and FFLAGS produces worthwhile performance gains with
gcc and gfortran, but may result in a less reliable build (both segfaults and incorrect nu-
meric computations have been seen). On systems using the GNU linker (especially those using
R as a shared library), it is likely that including ‘-Wl,-O1’ in LDFLAGS is worthwhile, and
‘’-Bdirect,--hash-style=both,-Wl,-O1’’ is recommended at https://lwn.net/Articles/
192624/. Tuning compilation to a specific CPU family (e.g. ‘-mtune=native’ for gcc) can give
worthwhile performance gains, especially on older architectures such as ‘ix86’.
B.3.4 Making manuals

The default settings for making the manuals are controlled by R_RD4PDF and R_PAPERSIZE.
B.4 Setting the shell

By default the shell scripts such as R will be ‘#!/bin/sh’ scripts (or using the SHELL chosen by
configure). This is almost always satisfactory, but on a few systems /bin/sh is not a Bourne
shell or clone, and the shell to be used can be changed by setting the configure variable R_SHELL
to a suitable value (a full path to a shell, e.g. /usr/local/bin/bash).
B.5 Using make

To compile R, you will most likely find it easiest to use GNU make, although the Sun make works
on Solaris. The native make has been reported to fail on SGI Irix 6.5 and Alpha/OSF1 (aka
Tru64).
To build in a separate directory you need a make that supports the VPATH variable, for
example GNU make and Sun make.
dmake has also been used. e.g, on Solaris 10.
If you want to use a make by another name, for example if your GNU make is called ‘gmake’,
you need to set the variable MAKE at configure time, for example
./configure MAKE=gmake
B.6 Using FORTRAN

To compile R, you need a FORTRAN compiler. The default is to search for f95, fort, xlf95,
ifort, ifc, efc, pgf95 lf95, gfortran, ftn, g95, f90, xlf90, pghpf, pgf90, epcf90, g77, f77,
xlf, frt, pgf77, cf77, fort77, fl32, af77 (in that order)3 , and use whichever is found first; if
none is found, R cannot be compiled. However, if CC is gcc, the matching FORTRAN compiler
(g77 for gcc 3 and gfortran for gcc 4) is used if available.
3
On HP-UX fort77 is the POSIX compliant FORTRAN compiler, and comes after g77.
The search mechanism can be changed using the configure variable F77 which specifies the
command that runs the FORTRAN 77 compiler. If your FORTRAN compiler is in a non-
standard location, you should set the environment variable PATH accordingly before running
configure, or use the configure variable F77 to specify its full path.
If your FORTRAN libraries are in slightly peculiar places, you should also look at LD_
LIBRARY_PATH or your system’s equivalent to make sure that all libraries are on this path.
Note that only FORTRAN compilers which convert identifiers to lower case are supported.
You must set whatever compilation flags (if any) are needed to ensure that FORTRAN
integer is equivalent to a C int pointer and FORTRAN double precision is equivalent to a
C double pointer. This is checked during the configuration process.
Some of the FORTRAN code makes use of COMPLEX*16 variables, which is a Fortran 90
extension. This is checked for at configure time4 , but you may need to avoid compiler flags
asserting FORTRAN 77 compliance.
Compiling the version of LAPACK in the R sources also requires some Fortran 90 extensions,
but these are not needed if an external LAPACK is used.
It might be possible to use f2c, the FORTRAN-to-C converter (http://www.netlib.org/
f2c), via a script. (An example script is given in scripts/f77_f2c: this can be customized by
setting the environment variables F2C, F2CLIBS, CC and CPP.) You will need to ensure that the
FORTRAN type integer is translated to the C type int. Normally f2c.h contains ‘typedef
long int integer;’, which will work on a 32-bit platform but needs to be changed to ‘typedef
int integer;’ on a 64-bit platform. If your compiler is not gcc you will need to set FPICFLAGS
appropriately. Also, the included LAPACK sources contain constructs that f2c is unlikely to
be able to process, so you would need to use an external LAPACK library (such as CLAPACK
from http://www.netlib.org/clapack/).
B.7 Compile and load flags

A wide range of flags can be set in the file config.site or as configure variables on the command
line. We have already mentioned
CPPFLAGS header file search directory (-I) and any other miscellaneous options for the C and
C++ preprocessors and compilers
LDFLAGS path (-L), stripping (-s) and any other miscellaneous options for the linker
and others include
CFLAGS debugging and optimization flags, C
MAIN_CFLAGS
ditto, for compiling the main program
SHLIB_CFLAGS
for shared objects
FFLAGS debugging and optimization flags, FORTRAN
SAFE_FFLAGS
ditto for source files which need exact floating point behaviour
MAIN_FFLAGS
ditto, for compiling the main program
SHLIB_FFLAGS
for shared objects
4
as well as its equivalence to the Rcomplex structure defined in R_ext/Complex.h.
MAIN_LDFLAGS
additional flags for the main link
SHLIB_LDFLAGS
additional flags for linking the shared objects
LIBnn the primary library directory, lib or lib64
CPICFLAGS
special flags for compiling C code to be turned into a shared object
FPICFLAGS
special flags for compiling Fortran code to be turned into a shared object
CXXPICFLAGS
special flags for compiling C++ code to be turned into a shared object
FCPICFLAGS
special flags for compiling Fortran 95 code to be turned into a shared object
DEFS defines to be used when compiling C code in R itself
Library paths specified as -L/lib/path in LDFLAGS are collected together and prepended to
LD_LIBRARY_PATH (or your system’s equivalent), so there should be no need for -R or -rpath
flags.
Variables such as CPICFLAGS are determined where possible by configure. Some systems
allows two types of PIC flags, for example ‘-fpic’ and ‘-fPIC’, and if they differ the first allows
only a limited number of symbols in a shared object. Since R as a shared library has about 6200
symbols, if in doubt use the larger version.
To compile a profiling version of R, one might for example want to use ‘MAIN_CFLAGS=-pg’,
‘MAIN_FFLAGS=-pg’, ‘MAIN_LDFLAGS=-pg’ on platforms where ‘-pg’ cannot be used with position-
independent code.
Beware: it may be necessary to set CFLAGS and FFLAGS in ways compatible with the libraries
to be used: one possible issue is the alignment of doubles, another is the way structures are
passed.
On some platforms configure will select additional flags for CFLAGS, CPPFLAGS, FFLAGS,
CXXFLAGS and LIBS in R_XTRA_CFLAGS (and so on). These are for options which are always
required, for example to force IEC 60559 compliance.
B.8 Maintainer mode

There are several files that are part of the R sources but can be re-generated from their own
sources by configuring with option --enable-maintainer-mode and then running make in the
build directory. This requires other tools to be installed, discussed in the rest of this section.
File configure is created from configure.ac and the files under m4 by autoconf and
aclocal (part of the automake package). There is a formal version requirement on autoconf
of 2.62 or later, but it is unlikely that anything other than the most recent versions5 have been
thoroughly tested.
File src/include/config.h is created by autoheader (part of autoconf).
Grammar files *.y are converted to C sources by an implementation of yacc, usually bison
-y: these are found in src/main and src/library/tools/src. It is known that earlier versions
of bison generate code which reads (and in some cases writes) outside array bounds: bison
2.6.1 was found to be satisfactory.
5
at the time of revision of this para in 2017, autoconf-2.69 from 2012 and automake-1.15 from 2015.
The ultimate sources for package compiler are in its noweb directory. To re-create the sources
from src/library/compiler/noweb/compiler.nw, the command notangle is required. Some
Linux distributions include this command in package noweb. It can also be installed from the
sources at https://www.cs.tufts.edu/~nr/noweb/6 . The package sources are only re-created
even in maintainer mode if src/library/compiler/noweb/compiler.nw has been updated.
It is likely that in future creating configure will need the GNU ‘autoconf archive’ installed.
This can be found at https://www.gnu.org/software/autoconf-archive/ and as a package
(usually called autoconf-archive) in most packaged distributions, for example Debian, Fedora,
OpenCSW, Homebrew and MacPorts.
6
The links there have proved difficult to access, in which case either point an FTP client at ftp://www.eecs.
harvard.edu/pub/nr/ or grab the copy made available at http://developer.r-project.org/noweb-2.11b.
tgz.
55
Appendix C Platform notes

This section provides some notes on building R on different Unix-alike platforms. These notes
are based on tests run on one or two systems in each case with particular sets of compilers and
support libraries. Success in building R depends on the proper installation and functioning of
support software; your results may differ if you have other versions of compilers and support
libraries.
Older versions of this manual (for R < 2.10.0) contain notes on platforms such as HP-UX,
IRIX and Alpha/OSF1 for which we have had no recent reports.
C macros to select particular platforms can be tricky to track down (there is a fair amount
of misinformation on the Web). The Wiki (currently) at http: / / sourceforge . net / p /
predef / wiki / Home / can be helpful. The R sources have used (often in included software
under src/extra)
AIX: _AIX
Cygwin: __CYGWIN__
FreeBSD: __FreeBSD__
HP-UX: __hpux__, __hpux
IRIX: sgi, __sgi
Linux: __linux__
macOS: __APPLE__
NetBSD: __NetBSD__
OpenBSD: __OpenBSD__
Solaris: __sun, sun
Windows: _WIN32, _WIN64
C.1 X11 issues

The ‘X11()’ graphics device is the one started automatically on Unix-alikes when plotting. As
its name implies, it displays on a (local or remote) X server, and relies on the services provided
by the X server.
The ‘modern’ version of the ‘X11()’ device is based on ‘cairo’ graphics and (in most im-
plementations) uses ‘fontconfig’ to pick and render fonts. This is done on the server, and
although there can be selection issues, they are more amenable than the issues with ‘X11()’
discussed in the rest of this section.
When X11 was designed, most displays were around 75dpi, whereas today they are of the
order of 100dpi or more. If you find that X11() is reporting1 missing font sizes, especially larger
ones, it is likely that you are not using scalable fonts and have not installed the 100dpi versions
of the X11 fonts. The names and details differ by system, but will likely have something like
Fedora’s
xorg-x11-fonts-75dpi
xorg-x11-fonts-100dpi
xorg-x11-fonts-ISO8859-2-75dpi
xorg-x11-fonts-Type1
xorg-x11-fonts-cyrillic
and you need to ensure that the ‘-100dpi’ versions are installed and on the X11 font path (check
via xset -q). The ‘X11()’ device does try to set a pointsize and not a pixel size: laptop users
may find the default setting of 12 too large (although very frequently laptop screens are set to
a fictitious dpi to appear like a scaled-down desktop screen).
1
for example, X11 font at size 14 could not be loaded.
Appendix C: Platform notes 56
More complicated problems can occur in non-Western-European locales, so if you are using
one, the first thing to check is that things work in the C locale. The likely issues are a failure to
find any fonts or glyphs being rendered incorrectly (often as a pair of ASCII characters). X11
works by being asked for a font specification and coming up with its idea of a close match. For
text (as distinct from the symbols used by plotmath), the specification is the first element of
the option "X11fonts" which defaults to
"-adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*"
If you are using a single-byte encoding, for example ISO 8859-2 in Eastern Europe or KOI8-R
in Russian, use xlsfonts to find an appropriate family of fonts in your encoding (the last field
in the listing). If you find none, it is likely that you need to install further font packages, such
as ‘xorg-x11-fonts-ISO8859-2-75dpi’ and ‘xorg-x11-fonts-cyrillic’ shown in the listing
above.
Multi-byte encodings (most commonly UTF-8) are even more complicated. There are few
fonts in ‘iso10646-1’, the Unicode encoding, and they only contain a subset of the available
glyphs (and are often fixed-width designed for use in terminals). In such locales fontsets are
used, made up of fonts encoded in other encodings. If the locale you are using has an entry in
the ‘XLC_LOCALE’ directory (typically /usr/share/X11/locale), it is likely that all you need
to do is to pick a suitable font specification that has fonts in the encodings specified there. If
not, you may have to get hold of a suitable locale entry for X11. This may mean that, for
example, Japanese text can be displayed when running in ‘ja_JP.UTF-8’ but not when running
in ‘en_GB.UTF-8’ on the same machine (although on some systems many UTF-8 X11 locales are
aliased to ‘en_US.UTF-8’ which covers several character sets, e.g. ISO 8859-1 (Western Euro-
pean), JISX0208 (Kanji), KSC5601 (Korean), GB2312 (Chinese Han) and JISX0201 (Kana)).
On some systems scalable fonts are available covering a wide range of glyphs. One source is
TrueType/OpenType fonts, and these can provide high coverage. Another is Type 1 fonts: the
URW set of Type 1 fonts provides standard typefaces such as Helvetica with a larger coverage
of Unicode glyphs than the standard X11 bitmaps, including Cyrillic. These are generally not
part of the default install, and the X server may need to be configured to use them. They might
be under the X11 fonts directory or elsewhere, for example,
/usr/share/fonts/default/Type1
/usr/share/fonts/ja/TrueType
C.2 Linux
Linux is the main development platform for R, so compilation from the sources is normally
straightforward with the standard compilers and libraries.2
Remember that some package management systems (such as RPM and deb) make a distinction
between the user version of a package and the developer version. The latter usually has the same
name but with the extension ‘-devel’ or ‘-dev’: you need both versions installed. So please check
the configure output to see if the expected features are detected: if for example ‘readline’
is missing add the developer package. (On most systems you will also need ‘ncurses’ and its
developer package, although these should be dependencies of the ‘readline’ package(s).) You
should expect to see in the configure summary
Interfaces supported: X11, tcltk
External libraries: readline, curl
Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU
When R has been installed from a binary distribution there are sometimes problems with
missing components such as the FORTRAN compiler. Searching the ‘R-help’ archives will
normally reveal what is needed.
2
For example, glibc: other C libraries such as musl have been used but are not routinely tested.
It seems that ‘ix86’ Linux accepts non-PIC code in shared libraries, but this is not necessarily
so on other platforms, in particular on 64-bit CPUs such as ‘x86_64’. So care can be needed
with BLAS libraries and when building R as a shared library to ensure that position-independent
code is used in any static libraries (such as the Tcl/Tk libraries, libpng, libjpeg and zlib)
which might be linked against. Fortunately these are normally built as shared libraries with the
exception of the ATLAS BLAS libraries.
The default optimization settings chosen for CFLAGS etc are conservative. It is likely that
using -mtune will result in significant performance improvements on recent CPUs: one possibility
is to add -mtune=native for the best possible performance on the machine on which R is being
installed. It is also possible to increase the optimization levels to -O3: however for many versions
of the compilers this has caused problems in at least one CRAN package.
As from g++ 6 the default C++ standard is C++14. Compatibility with earlier releases can be
obtained by using
CXXSTD=-std=gnu++98
in config.site. This is desirable when checking packages, to ensure as far as possible that
features from later C++ standards are not used unintentionally.
For platforms with both 64- and 32-bit support, it is likely that
LDFLAGS="-L/usr/local/lib64 -L/usr/local/lib"
is appropriate since most (but not all) software installs its 64-bit libraries in /usr/local/lib64.
To build a 32-bit version of R on ‘x86_64’ with Fedora 26 we used
CC="gcc -m32"
CXX="g++ -m32"
F77="gfortran -m32"
FC=${F77}
OBJC=${CC}
LDFLAGS="-L/usr/local/lib"
LIBnn=lib
Note the use of ‘LIBnn’: ‘x86_64’ Fedora installs its 64-bit software in /usr/lib64 and 32-bit
software in /usr/lib. Linking will skip over inappropriate binaries, but for example the 32-bit
Tcl/Tk configure scripts are in /usr/lib. It may also be necessary to set the pkg-config path,
e.g. by
export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:/usr/lib/pkgconfig
The 32-bit system libcurl did not work with the system CA certificates: this is worked around
in R’s test suite.
64-bit versions on Linux are built with support for files > 2Gb, and 32-bit versions will be if
possible unless --disable-largefile is specified.
Note that 32-bit glibc currently uses a 32-bit time_t type, so to pass all the date-time
checks needs R built with flag --with-internal-tzcode.
To build a 64-bit version of R on ‘ppc64’ (also known as ‘powerpc64’) with gcc 4.1.1, Ei-ji
Nakama used
CC="gcc -m64"
CXX="gxx -m64"
F77="gfortran -m64"
FC="gfortran -m64"
CFLAGS="-mminimal-toc -fno-optimize-sibling-calls -g -O2"
FFLAGS="-mminimal-toc -fno-optimize-sibling-calls -g -O2"
the additional flags being needed to resolve problems linking against libnmath.a and when
linking R as a shared library.
The setting of the macro ‘SAFE_FFLAGS’ may need some help. It should not need additional
flags on platforms other than ‘68000’ (not likely to be encountered) and ‘ix86’. For the latter,
if the FORTRAN compiler is GNU (gfortran or possibly g77) the flags
-msse2 -mfpmath=sse
are added: earlier versions of R added -ffloat-store and this might still be needed if a ‘ix86’
CPU is encountered without SSE2 support. Note that it is a replacement for ‘FFLAGS’, so should
include all the flags in that macro (except perhaps the optimization level).
C.2.1 Clang
R has been built with Linux ‘ix86’ and ‘x86_64’ C and C++ compilers (http://clang.llvm.
org) based on the Clang front-ends, invoked by CC=clang CXX=clang++, together with gfortran.
These take very similar options to the corresponding GCC compilers.
This has to be used in conjunction with a Fortran compiler: the configure code will remove
-lgcc from FLIBS, which is needed for some versions of gfortran.
The current out-of-the-box default for clang++ is to use the C++ runtime from the installed
g++. Using the runtime from the libc++ project (http://libcxx.llvm.org/, Fedora RPM
libcxx-devel) via -stdlib=libc++ has also been tested.
As from clang++ 6.0.0 the default C++ standard is C++14, which R’s configure also uses
when C++11 is requested. Compatibility with earlier releases can be obtained by using
CXXSTD=-std=gnu++98
CX11STD=-std=gnu++11
in config.site. These are desirable when checking packages, to ensure as far as possible that
features from later C++ standards are not used unintentionally.
Recent versions have (optional when built) OpenMP support.3
There is a project called flang (https://github.com/flang-compiler/flang)) to develop
a Fortran compiler similar to clang but based on the Portland Group’s front end. This needs
something like
FC=/usr/local/flang/bin/flang
F77=/usr/local/flang/bin/flang
LDFLAGS="-L/usr/local/flang/lib -L/usr/local/lib64"
and in earlier versions of R it may be necessary to set
FCPICFLAGS=-fpic
FPICFLAGS=-fpic
Note that flang accepts all the flags which clang does (the driver is a modified version of
clang, and flang is a symbolic link to clang), but does not implement all of them for Fortran
compilation: it also accepts most PGI-style flags such as -mp for OpenMP. It currently produces
few diagnostics even with -Wall -pedantic.
flang’s Fortran runtime is compiled against OpenMP and it seems this conflicts with using
OpenMP in R. So it may be necessary to disable the latter by configuring using --without-
openmp.
It is not clear what architectures flang intends to support: our experiments were done on
‘x86_64’.
3
This also needs the OpenMP runtime which has sometimes been distributed separately.
C.2.2 Intel compilers

Intel compilers have been used under ‘ix86’ and ‘x86_64’ Linux. Brian Ripley used version 9.0
of the compilers for ‘x86_64’ on Fedora Core 5 with
CC=icc
CFLAGS="-g -O3 -wd188 -ip -mp"
F77=ifort
FLAGS="-g -O3 -mp"
CXX=icpc
CXXFLAGS="-g -O3 -mp"
FC=ifort
FCFLAGS="-g -O3 -mp"
ICC_LIBS=/opt/compilers/intel/cce/9.1.039/lib
IFC_LIBS=/opt/compilers/intel/fce/9.1.033/lib
LDFLAGS="-L$ICC_LIBS -L$IFC_LIBS -L/usr/local/lib64"
SHLIB_CXXLD=icpc
configure will add ‘-c99’ to CC for C99-compliance. This causes warnings with icc 10 and
later, so use CC="icc -std=c99" there. The flag -wd188 suppresses a large number of warnings
about the enumeration type ‘Rboolean’. Because the Intel C compiler sets ‘__GNUC__’ without
complete emulation of gcc, we suggest adding CPPFLAGS=-no-gcc.
To maintain correct IEC 60559 arithmetic you most likely need add flags to CFLAGS, FFLAGS
and CXXFLAGS such as -mp (shown above) or -fp-model precise -fp-model source, depending
on the compiler version.
~
Others have reported success with versions 10.x and 11.x. BjA¸rn-Helge Mevik reported
success with version 2015.3 of the compilers, using (for a SandyBridge CPU on Centos 6.x)
fast="-fp-model precise -ip -O3 -opt-mem-layout-trans=3 -xHost -mavx"
CC=icc
CFLAGS="$fast -wd188"
F77=ifort
FFLAGS="$fast"
CXX=icpc
CXXFLAGS="$fast"
FC=$F77
FCFLAGS=$F77FLAGS
It is possible that 32-builds need to force the use of SSE2 instructions in SAFE_FFLAGS, e.g.
by
SAFE_FFLAGS=-axsse2
C.3 macOS
(‘macOS’ was known as ‘OS X’ from 2012–2016.)
The instructions here are for ‘x86_64’ builds on 10.11 (El Capitan) or later. R can be built
for 10.9 and 10.10 and in principle4 for 10.6 to 10.8.
To build R you need Apple’s ‘Command Line Tools’: these can be (re-)installed by
xcode-select --install. (If you have a fresh OS installation, running e.g. make in a terminal
will offer the installation of the command-line tools. If you have installed Xcode, this provides
the command-line tools. The tools will need to be reinstalled when macOS is upgraded, as
upgrading partially removes them.)
4
It will be necessary to install later versions of software such as libcurl.
You need GNU readline5 That and other binary components are available from https://
r.research.att.com/libs: you will need pcre and xz (for libzma) as recent macOS versions
provide libraries but not headers for these (and the system pcre is too old at 8.02 for versions
up to Sierra, although High Sierra has 8.40).
An X sub-system is required unless configuring using --without-x: see https://xquartz.
macosforge.org/. R’s configure script can be told to look for X11 in XQuartz’s main location
of /opt/X11, e.g. by
--x-includes=/opt/X11/include --x-libraries=/opt/X11/lib
although linked versions under /usr/X11 will be found.
To use the quartz() graphics device you need to configure with --with-aqua (which is the
default): quartz() then becomes the default device when running R at the console and X11
would only be used for the command-line-R data editor/viewer and one version of Tcl/Tk. (This
option needs an Objective-C compiler6 which can compile the source code of quartz().)
Use --without-aqua if you want a standard Unix-alike build: apart from disabling quartz()
and the ability to use the build with R.app, it also changes the default location of the personal
library (see ?.libPaths).
Various compilers can be used. One could use
CC=clang
CXX=clang++
F77=/usr/local/gfortran/bin/gfortran
FC=$F77
OBJC=clang
CFLAGS=’-Wal -g -O2’
CXXFLAGS=’-Wall -g -O2’
OBJCFLAGS=’-Wall -g -O2’
F77FLAGS=’-Wall -g -O2 -mtune=generic’
FCFLAGS=$F77FLAGS
with clang and clang++ from the ‘Command Line Tools’ and the Fortran compiler from one of
the packages described in the next paragraph.
There are installers7 for Fortran compilers for El Capitan and Sierra at http://coudert.
name / software / gfortran-6 . 1-ElCapitan . dmg and http: / / coudert . name / software /
gfortran-6.3-Sierra.dmg. (An Apple package for 6.1 is also available at https://cran.
r-project.org/bin/macosx/tools/gfortran-6.1.pkg.) One way to use these builds with a
binary distribution of R is to have a ~/.R/Makevars file similar to (El Capitan)
FC = $F77
or (Sierra or High Sierra)
FC = $F77
(with lines broken here for legibility).
5
Apple provides a partial emulation of GNU readline 4.2 based on the NetBSD editline library. That is not
recommended but for the time being R’s installation scripts will make use of it if GNU readline is not found.
6
These days that is defined by Apple’s implementation of clang, so it is strongly recommended to use that.
7
Some of these are unsigned packages: to install them you may need to right-click and select Open with ->
Installer.
Current CRAN binary distributions use the build of clang 6.0.0 contained in https://cran.
r-project.org/bin/macosx/tools/clang-6.0.0.pkg. Other recent distributions of clang
are often available from http://llvm.org/releases/: for example at the time of writing8 of
5.0.1 and 6.0.0. In particular, all of these include support for OpenMP which Apple builds of
clang do not. Suppose one of these distributions is installed under /usr/local/clang6. Then
R could be configured by something like
./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib \
PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/lib/pkgconfig \
DYLD_FALLBACK_LIBRARY_PATH=/usr/local/clang6/lib:/usr/local/lib
with config.site containing
CC=/usr/local/clang6/bin/clang
OBJC=$CC
F77=/usr/local/gfortran/bin/gfortran
FC=$F77
CXX=/usr/local/clang6/bin/clang++
LDFLAGS="-L/usr/local/clang6/lib -L/usr/local/lib"
R_LD_LIBRARY_PATH=/usr/local/clang6/lib:/usr/local/lib
The care to specify library paths is to ensure that the OpenMP runtime library, here
/usr/local/clang6/lib/libomp.dylib, is found when needed. If this works, you should see
the line
checking whether OpenMP SIMD reduction is supported... yes
in the configure output. Also, ‘R_LD_LIBRARY_PATH’ needs to be set to find the latest version
of the C++ run-time libraries rather than the system ones.
Pre-compiled versions of many of the Section A.2 [Useful libraries and programs], page 41,
are available from https://r.research.att.com/libs/. You will most likely want at least
jpeg and tiff. The pkg-config utility is not provided by Apple and used for the installation
from source of many packages: it will also be used if present when configuring the X11() and
bitmap devices.
Support for cairo (without Pango) can be enabled if pkg-config and XQuartz are available.
Make sure the XQuartz’s pkg-config files are found first on the configuration path: for example
by setting
export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/lib/pkgconf
or appending that variable to the configure command.
The Accelerate library9 can be used via the configuration options
--with-blas="-framework Accelerate"
to provide potentially higher-performance versions of the BLAS and LAPACK routines.10 This
also includes a full LAPACK which can be used via --with-lapack: however, the version of
LAPACK it contains is currently seriously old (‘3.2.1’ in macOS 10.13.2).
In recent versions of macOS, threading in Accelerate is controlled by ‘Grand Central Dispatch’
and is said not to need user control.
Looking at the top of /Library/Frameworks/R.framework/Resources/etc/Makeconf will
show the compilers and configuration options used for the CRAN binary package for R: at the
time of writing the non-default options
--enable-memory-profiling --enable-R-framework --x-libraries=/opt/X11/lib
8
It is unstated what the minimum OS requirement is for these: the distribution of 5.0.0 required Sierra or later.
9
https://developer.apple.com/documentation/accelerate.
10
It was reported that for some non-Apple toolchains CPPFLAGS needed to contain -D__ACCELERATE__: not
needed for clang 6.0.0, though.
were used.
Configure option --with-internal-tzcode is the default on macOS, as the system imple-
mentation of time zones does not work correctly for times before 1902 or after 2037 (despite
using a 64-bit time_t).
The TEX implementation used by the developers is MacTeX (https: / / www . tug . org /
mactex/): the full installation is about 5GB, but a smaller version (‘Basic TeX’) is available at
https://www.tug.org/mactex/morepackages.html to which you will need to add some pack-
ages, e.g. for the 2017 version we needed to add11 cm-super, helvetic, inconsolata and texinfo
which brought this to about 310MB. ‘TeX Live Utility’ (available via the MacTeX front page)
provides a graphical means to manage TEX packages.
One macOS quirk is that the default path has /usr/local/bin after /usr/bin, contrary to
common practice on Unix-alikes. This means that if you install tools from the sources they will
by default be installed under /usr/local and not supersede the system versions.
If you upgrade your OS you should re-install the ‘Command Line Tools’ and may need to
re-install XQuartz and Java (this has been needed for some upgrades but not others).
C.3.1 Tcl/Tk headers and libraries

If you plan to use the tcltk package for R, you need to install a distribution of Tcl/Tk. There
are two alternatives. If you use R.app you will want to use X11-based Tcl/Tk (as used on other
Unix-alikes), which is installed as part of the CRAN binary for R and available as separate tcl
and tk components from https://r.research.att.com/libs/. This may need configure
options
-with-tcltk=/usr/local/lib
or
--with-tcl-config=/usr/local/lib/tclConfig.sh
--with-tk-config=/usr/local/lib/tkConfig.sh
Note that this requires a matching XQuartz installation.
There is also a native (‘Aqua’) version of Tcl/Tk which produces widgets in the native macOS
style: this will not work with R.app because of conflicts over the macOS menu, but for those
only using command-line R this provides a much more intuitive interface to Tk for experienced
Mac users. Most versions of macOS come with Aqua Tcl/Tk libraries, but these are not at
all recent versions of Tcl/Tk (8.5.9 in Sierra, which is not even the latest patched version in
that series). It is better to install Tcl/Tk 8.6.x from the sources or a binary distribution from
https://www.activestate.com/activetcl/downloads. Configure R with
--with-tcl-config=/Library/Frameworks/Tcl.framework/tclConfig.sh
--with-tk-config=/Library/Frameworks/Tk.framework/tkConfig.sh
If you need to find out which distribution of Tk is in use at run time, use
library(tcltk)
tclvalue(.Tcl("tk windowingsystem")) # "x11" or "aqua"
C.3.2 Java
The situation with Java support on macOS is messy,12 and distribution of Java for all platforms
is changing during 2018.
macOS no longer comes with an installed Java runtime (JRE), and a macOS upgrade may
remove one if already installed: it is intended to be installed at first use. Check if a JRE is
11
E.g. via tlmgr install cm-super helvetic inconsolata texinfo .
12
For more details see http://www.macstrategy.com/article.php?3.
installed by running java -version in a Terminal window: if Java is not installed13 this should
prompt you to install it. You can also install directly a recent Java from Oracle (currently from
http://www.oracle.com/technetwork/java/javase/downloads/index.html: note that Java
9 and 10 have a limited lifetime and at the time of writing rJava (https://CRAN.R-project.
org/package=rJava)14 did not install with Java 10). Builds of OpenJDK may also be available,
e.g. from http://jdk.java.net/.
Binary distributions of R are built against a specific version (e.g. 1.8.0 161) of Oracle Java
so sudo R CMD javareconf may be needed before using Java-using packages.
To see what compatible versions of Oracle Java are currently installed, run
/usr/libexec/java_home -V -a x86_64. If needed, set the environment variable JAVA_HOME
to choose between these, both when R is built from the sources and when R CMD javareconf is
run.
Configuring and building R both looks for a JRE and for support for compiling JNI pro-
grams (used by packages rJava (https://CRAN.R-project.org/package=rJava) and JavaGD
(https://CRAN.R-project.org/package=JavaGD)); the latter requires a JDK (Java SDK) and
not just a JRE.
The build process tries to fathom out what JRE/JDK to use, but it may need some help,
e.g. by setting JAVA_HOME. An Oracle JDK can be specified explicitly by something like
JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home
JAVA_CPPFLAGS="-I/${JAVA_HOME}/include -I/${JAVA_HOME}/include/darwin"
JAVA_LD_LIBRARY_PATH="${JAVA_HOME}/jre/lib/server"
JAVA_LIBS="-L/${JAVA_HOME}/jre/lib/server -ljvm"
or
JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk-9.jdk/Contents/Home
JAVA_CPPFLAGS="-I/${JAVA_HOME}/include -I/${JAVA_HOME}/include/darwin"
JAVA_LD_LIBRARY_PATH="${JAVA_HOME}/lib/server"
JAVA_LIBS="-L/${JAVA_HOME}/lib/server -ljvm"
in config.site.
To use the builds of OpenJDK from http://jdk.java.net/, set JAVA_HOME:
JAVA_HOME=/path/to/JDK/jdk-10.jdk/Contents/Home
where /path/to/JDK is wherever the distribution tarball was unpacked. Java 10 JDKs do not
contain javah, but R configuration / R CMD javareconf can use one from an earlier installation
if JAVAH is set, e.g.,
JAVAH=/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/bin/javah
Note that it is necessary to set the environment variable NOAWT to 1 to install many of the
Java-using packages.
C.3.3 Frameworks
The CRAN build of R is installed as a framework, which is selected by the option
./configure --enable-R-framework
(This is intended to be used with an Apple toolchain: others may not support frameworks
correctly but those from llvm.org do.)
It is only needed if you want to build R for use with the R.app console, and implies
--enable-R-shlib to build R as a dynamic library. This option configures R to be built and
installed as a framework called R.framework. The default installation path for R.framework
13
In the unlikely event that the version reported does not start with 1.8.0 or 9 you need to update your Java.
14
the current version 0.9-9.
is /Library/Frameworks but this can be changed at configure time by specifying the flag
--enable-R-framework[=DIR] (or --prefix) or at install time via
make prefix=/where/you/want/R.framework/to/go install
Note that installation as a framework is non-standard (especially to a non-standard location)
and Unix utilities may not support it (e.g. the pkg-config file libR.pc will be put somewhere
unknown to pkg-config).
C.3.4 Building R.app

Note that building the R.app GUI console is a separate project, using Xcode. Before compiling
R.app make sure the current version of R is installed in /Library/Frameworks/R.framework
and working at the command-line (this can be a binary install).
The current sources can be checked out by
svn co https://svn.r-project.org/R-packages/trunk/Mac-GUI
and built by loading the R.xcodeproj project (select the R target and a suitable configuration),
or from the command-line by e.g.
xcodebuild -target R -configuration Release
See also the INSTALL file in the checkout or directly at https: / / svn . r-project . org /
R-packages/trunk/Mac-GUI/INSTALL.
R.app does not need to be installed in any specific way. Building R.app results in the R.app
bundle which appears as one R icon. This application bundle can be run anywhere and it is
customary to place it in the /Applications folder.
C.4 Solaris
R has been built successfully on Solaris 10 using the (zero cost) Oracle Developer Studio15
compilers: there has been some success with gcc/gfortran. (Recent Sun machines are AMD
Opterons or Intel Xeons (‘amd64’) rather than ‘x86’, but 32-bit ‘x86’ executables are the default.)
How these compilers identify16 themselves is slightly confusing: Solaris Studio versions 12.3 and
12.4 report C++ 5.12 and 5.13, and Developer Studio 12.5 reports C++ 5.14. We will only consider
12.5 (May 2016): instructions for 12.3 can be found in versions of this manual for R 3.3.x.
There have been few reports on Solaris 11, with no known extra issues.
Solaris was last tested on Sparc machines in June 2017.
The Solaris versions of several of the tools needed to build R (e.g. make, ar and ld) are in
/usr/ccs/bin, so if using those tools ensure this is in your path. A version of the preferred
GNU tar is (if installed) in /usr/sfw/bin. It may be necessary to avoid the tools in /usr/ucb:
POSIX-compliant versions of some tools can be found in /usr/xpg4/bin and /usr/xpg6/bin.
A large selection of Open Source software can be installed from https://www.opencsw.org,
by default installed under /opt/csw. Solaris 10 ships with bzlib version 1.0.6 (sufficient) but
zlib version 1.2.3 (too old): OpenCSW has 1.2.8.
At least when compiling with Oracle compilers, Solaris uses far more stack space than other
platforms. This makes it desirable to build PCRE with the option --disable-stack-for-
recursion: the OpenCSW distribution was at the time of writing.
The Oracle compilers are unusual in not including /usr/local/include in the default in-
clude search path: R’s default CPPFLAGS=-I/usr/local/include remedies this. If you rely on
OpenCSW software you may need CPPFLAGS=-I/opt/csw/include (or both).
15
Oracle Solaris Studio prior to 2016, and previously Sun Studio.
16
using the -V flag.
You will need GNU libiconv and readline: the Solaris version of iconv is not sufficiently
powerful.
The native make suffices to build R but a small number of packages require GNU make (some
without good reason and without declaring it as ‘SystemRequirements’ in the DESCRIPTION
file).
The support for the C99 long double type on Sparc hardware uses quad-precision arithmetic,
and this is usually slow because it is done by software emulation. On such systems the configure
option --disable-long-double can be used for faster but less accurate computations.
The Solaris time-zone conversion services seem to be unreliable pre-1916 in Europe (when
daylight-savings time was first introduced): most often reporting in the non-existent DST vari-
ant. Using configure option --with-internal-tzcode is recommended, and required if you
find time-zone abbreviations being given odd values (as has been seen on 64-bit builds without
it).
When using the Oracle compilers do not specify -fast, as this disables IEEE arithmetic and
make check will fail.
A little juggling of paths was needed to ensure GNU libiconv (in /usr/local) was used
rather than the Solaris iconv:
CC="cc -xc99"
CFLAGS="-O -xlibmieee"
F77=f95
FFLAGS=-O
CXX=CC
CXXSTD="-library=stlport4"
CXXFLAGS=-O
FC=$F77
FCFLAGS=$FFLAGS
FCLIBS="-lfsu /opt/developerstudio12.5/lib/libfui.so.2"
R_LD_LIBRARY_PATH="/opt/developerstudio12.5/lib:/usr/local/lib:/opt/csw/lib"
The Oracle compilers do not by default conform to the C99 standard (appendix F 8.9) on
the return values of functions such as log: use -xlibmieee to ensure this.
A peculiarity of the Fortran compiler is that when asked to link a shared object it does not
link against the Fortran runtime libraries. In R this is only used for packages with F9x code,
hence the FCLIBS definition (which sufficed for CRAN packages with 12.5).
Using -xlibmil in CFLAGS or -xlibmil in FFLAGS allows more system mathematical functions
to be inlined.
On ‘x86’ you will get marginally higher performance via
CFLAGS="-xO5 -xlibmieee -xlibmil -nofstore -xtarget=native"
FFLAGS="-xO5 -libmil -nofstore -xtarget=native"
CXXFLAGS="-xO5 -xlibmil -nofstore -xtarget=native"
SAFE_FFLAGS="-O -libmil -fstore -xtarget=native"
but the use of -nofstore can be less numerically stable, and some packages have in the past
failed to compile at optimization level 5.
The Oracle compilers provide several implementations of the C++98 standard which select
both the set of headers and a C++ runtime library. These are selected by the -library flag,
which as it is needed for both compiling and linking is best specified as part of the compiler.
The examples above use ‘stlport4’, currently the most modern of the options: the default (but
still needed to be specified as it is needed for linking) is ‘Cstd’: see http://www.oracle.com/
technetwork/server-storage/solaris/cmp-stlport-libcstd-142559.html. Note though
that most external Solaris C++ libraries will have been built with ‘Cstd’ and so an R package
using such libraries also needs to be. Occasionally the option -library=stlport4,Crun has
been needed.
The performance library sunperf is available for use with the Oracle compilers. If selected
as a BLAS, it must also be selected as LAPACK via
./configure --with-blas=’-library=sunperf’ --with-lapack
This has often given test failures in the past, in several different places.17
Parsing very complex R expressions needs a lot of stack space when the Oracle compilers are
used: several packages require the stack increased to at least 20MB.
Some people have reported that the Solaris libintl needs to be avoided, for example by
using --disable-nls or --with-included-gettext or using libintl from OpenCSW. (On
the other hand, there have been many successful installs which automatically detected libintl
from OpenCSW or selected the included gettext.)
It has been reported that some Solaris installations need
INTERNET_LIBS="-lsocket -lnsl"
on the configure command line or in file config.site; however, there have been many suc-
cessful installs without this.
C.4.1 64-bit builds

On both ‘x86’ and ‘Sparc’ platforms the compilers default to 32-bit code.
For a 64-bit target add -m64 to the compiler macros and use something like
LDFLAGS=-L/usr/local/lib/amd64 or LDFLAGS=-L/usr/local/lib/sparcv9 as appropriate
(and other 64-bit library directories if used, e.g. -L/opt/csw/lib/arm64). It will also be
necessary to point pkg-config at the 64-bit directories, e.g. by something like
PKG_CONFIG_PATH=/opt/csw/lib/64/pkgconfig:/usr/lib/64/pkgconfig
and to specify a 64-bit Java VM by e.g.
JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/solaris"
JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/lib/amd64/server
JAVA_LIBS="-L${JAVA_HOME}/lib/amd64/server \
-R${JAVA_HOME}/lib/amd64/server -ljvm"
C.4.2 Using gcc

If using gcc, ensure that the compiler was compiled for the version of Solaris in use. (This
can be ascertained from gcc -v.) gcc makes modified versions of some header files, and several
reports of problems were due to using gcc compiled on one version of Solaris on a later version.
Note that this can even apply to OS patches: some 2016 patches to Solaris 10 changed its C
header files in way incompatible18 with the modified versions included with OpenCSW’s binary
distribution.
The notes here are for gcc set up to use the Solaris linker: it can also be set up to use GNU
ld, but that has not been tested. The tests were for compilers from the OpenCSW repository:
Solaris systems often come with much older compilers installed under /usr/sfw/bin. One of
-m32 or -m64 will be the default and could be omitted, but it is not easy to find out which. (For
OpenCSW it is -m32.)
Compilation for an ‘x86’ target with gcc 4.9.2 or gcc 5.2.0 needed
CC="gcc -m32"
17
When last checked it failed in tests/reg-BLAS.R, and on some builds, including for ‘amd64’, it failed in
example(eigen).
18
In particular, header cmath in C++11 mode includes math.h and iso/math_c99.h and gcc had ‘fixed’ an earlier
version of the latter.
CPPFLAGS="-I/opt/csw/include -I/usr/local/include"
F77="gfortran -m32"
CXX="g++ -m32"
FC=$F77
LDFLAGS="-L/opt/csw/lib -L/usr/local/lib"
For an ‘amd64’ target we used
CC="gcc -m64"
CPPFLAGS="-I/opt/csw/include -I/usr/local/include"
F77="gfortran -m64"
CXX="g++ -m64"
FC=$F77
LDFLAGS="-L/opt/csw/lib/amd64 -L/usr/local/lib/amd64"
Note that paths such as /opt/csw/lib, /usr/local/lib/amd64 and /opt/csw/lib/amd64
may need to be in the LD_LIBRARY_PATH during configuration.
C.5 AIX
We no longer support AIX prior to 4.2, and configure will throw an error on such systems.
Ei-ji Nakama was able to build under AIX 5.2 on ‘powerpc’ with GCC 4.0.3 in several
configurations. 32-bit versions could be configured with --without-iconv as well as --enable-
R-shlib. For 64-bit versions he used
OBJECT_MODE=64
CC="gcc -maix64"
CXX="g++ -maix64"
F77="gfortran -maix64"
FC="gfortran -maix64"
and was also able to build with the IBM xlc and Hitachi f90 compilers by
OBJECT_MODE=64
CC="xlc -q64"
CXX="g++ -maix64"
F77="f90 -cpu=pwr4 -hf77 -parallel=0 -i,L -O3 -64"
FC="f90 -cpu=pwr4 -hf77 -parallel=0 -i,L -O3 -64"
FLIBS="-L/opt/ofort90/lib -lhf90vecmath -lhf90math -lf90"
Some systems have f95 as an IBM compiler that does not by default accept FORTRAN 77.
It needs the flag -qfixed=72, or to be invoked as xlf_r.
The AIX native iconv does not support encodings ‘latin1’ nor ‘""’ and so cannot be used.
(As far as we know GNU libiconv could be installed.)
Fan Long reported success on AIX 5.3 using
OBJECT_MODE=64
LIBICONV=/where/libiconv/installed
CC="xlc_r -q64"
CFLAGS="-O -qstrict"
CXX="xlC_r -q64"
CXXFLAGS="-O -qstrict"
F77="xlf_r -q64"
AR="ar -X64"
CPPFLAGS="-I$LIBICONV/include -I/usr/lpp/X11/include/X11"
LDFLAGS="-L$LIBICONV/lib -L/usr/lib -L/usr/X11R6/lib"
On one AIX 6.x system it was necessary to use R_SHELL to set the default shell to be Bash
rather than Zsh.
Kurt Hornik and Stefan Theussl at WU (Wirtschaftsuniversität Wien) successfully built R

on a ‘powerpc’ (8-CPU Power6 system) running AIX 6.1, configuring with or without --enable-
R-shlib (Ei-ji Nakama’s support is gratefully acknowledged).
It helps to describe the WU build environment first. A small part of the software needed
to build R and/or install packages is available directly from the AIX Installation DVDs, e.g.,
Java 6 and X11. Additional open source software (OSS) is packaged for AIX in .rpm files and
available from both IBM’s “AIX Toolbox for Linux Applications” (http://www-03.ibm.com/
systems/power/software/aix/linux/) and http://www.oss4aix.org/download/. The
latter website typically offers more recent versions of the available OSS. All tools needed and
libraries downloaded from these repositories (e.g., GCC, Make, libreadline, etc.) are typically
installed to /opt/freeware, hence corresponding executables are found in /opt/freeware/bin
which thus needs to be in PATH for using these tools. As on other Unix systems one needs GNU
libiconv as the AIX version of iconv is not sufficiently powerful. Additionally, for proper Uni-
code compatibility one should install the corresponding package from the ICU project (http://
www.icu-project.org/download/), which offers pre-compiled binaries for various platforms
which in case of AIX can be installed via unpacking the tarball to the root file system. For full
LATEX support one can install the TEX Live DVD distribution (https://www.tug.org/texlive/
): it is recommended to update the distribution using the tlmgr update manager. For 64-bit
R builds supporting Tcl/Tk this needs to installed from the sources as available pre-compiled
binaries supply only 32-bit shared objects.
The recent WU testing was done using compilers from both the GNU Compiler Collec-
tion (version 4.2.4) which is available from one of the above OSS repositories, and the IBM
C/C++ (XL C/C++ 10.01) as well as FORTRAN (XL Fortran 12.01) compilers (http://www14.
software.ibm.com/webapp/download/byproduct.jsp#X).
To compile for a 64-bit ‘powerpc’ (Power6 CPU) target one can use
CC ="gcc -maix64 -pthread"
CXX="g++ -maix64 -pthread"
FC="gfortran -maix64 -pthread"
F77="gfortran -maix64 -pthread"
CFLAGS="-O2 -g -mcpu=power6"
FFLAGS="-O2 -g -mcpu=power6"
FCFLAGS="-O2 -g -mcpu=power6"
for the GCC and
CC=xlc
CXX=xlc++
FC=xlf
F77=xlf
CFLAGS="-qarch=auto -qcache=auto -qtune=auto -O3 -qstrict -ma"
FFLAGS="-qarch=auto -qcache=auto -qtune=auto -O3 -qstrict"
FCFLAGS="-qarch=auto -qcache=auto -qtune=auto -O3 -qstrict"
CXXFLAGS="-qarch=auto -qcache=auto -qtune=auto -O3 -qstrict"
for the IBM XL compilers. For the latter, it is important to note that the decision for generating
32-bit or 64-bit code is done by setting the OBJECT_MODE environment variable appropriately
(recommended) or using an additional compiler flag (-q32 or -q64). By default the IBM XL
compilers produce 32 bit code. Thus, to build R with 64-bit support one needs to either export
OBJECT_MODE=64 in the environment or, alternatively, use the -q64 compiler options.
It is strongly recommended to install Bash and use it as the configure shell, e.g., via
setting CONFIG_SHELL=/usr/bin/bash in the environment, and to use GNU Make (e.g., via
(MAKE=/opt/freeware/bin/make).
Further installation instructions to set up a proper R development environment can be found

in the “R on AIX” project on R-Forge (https://R-Forge.R-project.org/projects/aix/).
C.6 FreeBSD
There have been few recent reports on FreeBSD: there is a ‘port’ at https://www.freebsd.
org/ports/math.html. Recent versions of FreeBSD use Clang and the libc++ C++ headers
and runtime.
Use of ICU for collation and the configure option --with-internal-tzcode are desirable
workarounds.
C.7 OpenBSD
Ingo Feinerer installed R version 3.2.2 on OpenBSD 5.8 arch ‘amd64’ (their name for ‘x86_64’).
Details of the build (and patches applied) are at http: / / cvsweb . openbsd . org / cgi-bin /
cvsweb/ports/math/R/. (Downgrading the zlib requirement to 1.2.3 is against the advice of
the R developers.)
C.8 Cygwin
The 32-bit version has never worked well enough to pass R’s make check, and residual support
from earlier experiments was removed in R 3.3.0.
The 64-bit version is completely unsupported.
C.9 New platforms

There are a number of sources of problems when installing R on a new hardware/OS platform.
These include
Floating Point Arithmetic: R requires arithmetic compliant with IEC 60559, also known as
IEEE 754. This mandates the use of plus and minus infinity and NaN (not a number) as well as
specific details of rounding. Although almost all current FPUs can support this, selecting such
support can be a pain. The problem is that there is no agreement on how to set the signalling
behaviour; Sun/Sparc, SGI/IRIX and ‘ix86’ Linux require no special action, FreeBSD requires a
call to (the macro) fpsetmask(0) and OSF1 required that computation be done with a -ieee_
with_inexact flag etc. On a new platform you must find out the magic recipe and add some
code to make it work. This can often be done via the file config.site which resides in the top
level directory.
Beware of using high levels of optimization, at least initially. On many compilers these reduce
the degree of compliance to the IEEE model. For example, using -fast on the Oracle compilers
has caused R’s NaN to be set incorrectly, and gcc’s -ffast-math and clang’s -Ofast have given
incorrect results.
Shared Objects: There seems to be very little agreement across platforms on what needs to
be done to build shared objects. there are many different combinations of flags for the compilers
and loaders. GNU libtool cannot be used (yet), as it currently does not fully support FORTRAN:
one would need a shell wrapper for this). The technique we use is to first interrogate the X
window system about what it does (using xmkmf), and then override this in situations where we
know better (for tools from the GNU Compiler Collection and/or platforms we know about).
This typically works, but you may have to manually override the results. Scanning the manual
entries for cc and ld usually reveals the correct incantation. Once you know the recipe you can
modify the file config.site (following the instructions therein) so that the build will use these
options.
70
It seems that gcc 3.4.x and later on ‘ix86’ Linux defeat attempts by the LA-
PACK code to avoid computations entirely in extended-precision registers, so file
src/modules/lapack/dlamc.f may need to be compiled without optimization or with
additional flags. Set the configure variable SAFE_FFLAGS to the flags to be used for this file.
If you do manage to get R running on a new platform please let us know about it so we can
modify the configuration procedures to include that platform.
If you are having trouble getting R to work on your platform please feel free to use the
‘R-devel’ mailing list to ask questions. We have had a fair amount of practice at porting R to
new platforms . . .
71
Appendix D The Windows toolset

If you want to build R or add-on packages from source in Windows, you will need to collect,
install and test an extensive set of tools. See https://CRAN.R-project.org/bin/windows/
Rtools/ for the current locations and other updates to these instructions. (Most Windows users
will not need to build add-on packages from source; see Chapter 6 [Add-on packages], page 23,
for details.)
We have found that the build process for R is quite sensitive to the choice of tools: please
follow our instructions exactly, even to the choice of particular versions of the tools.1 The build
process for add-on packages is somewhat more forgiving, but we recommend using the exact
toolset at first, and only substituting other tools once you are familiar with the process.
This appendix contains a lot of prescriptive comments. They are here as a result of bitter
experience. Please do not report problems to the R mailing lists unless you have followed all the
prescriptions.
We have collected most of the necessary tools (unfortunately not all, due to license or size
limitations) into an executable installer named Rtools*.exe, available from https://CRAN.
R-project.org/bin/windows/Rtools/. You should download and run it, choosing the default
“Package authoring installation” to build add-on packages, or the “full installation” if you intend
to build R.
You will need the following items to build R and packages. See the subsections below for
detailed descriptions.
• The command line tools (in Rtools*.exe)
• The MinGW-w64 32/64-bit toolchain to compile C, Fortran and C++.
For installing simple source packages containing data or R source but no compiled code, none
of these are needed.
A complete build of R including PDF manuals, and producing the installer will also need the
following:
• LATEX
• The Inno Setup installer
• (optional) qpdf
It is important to set your PATH properly. The installer Rtools*.exe optionally sets the path
to components that it installs.
Your PATH may include . first, then the bin directories of the tools, the compiler toolchain
and LATEX. Do not use filepaths containing spaces: you can always use the short forms (found
by dir /x at the Windows command line). Network shares (with paths starting \\) are not
supported.
For example for a 32-bit build, all on one line,
PATH=c:\Rtools\bin;c:\MiKTeX\miktex\bin;
c:\R\R-3.2\bin\i386;c:\windows;c:\windows\system32
It is essential that the directory containing the command line tools comes first or second in the
path: there are typically like-named tools2 in other directories, and they will not work. The
ordering of the other directories is less important, but if in doubt, use the order above.
Our toolset contains copies of Cygwin DLLs that may conflict with other ones on your system
if both are in the path at once. The normal recommendation is to delete the older ones; however,
at one time we found our tools did not work with a newer version of the Cygwin DLLs, so it
may be safest not to have any other version of the Cygwin DLLs in your path.
1
For example, the Cygwin version of make 3.81 fails to work correctly.
2
such as sort, find and perhaps make.
Appendix D: The Windows toolset 72
D.1 LATEX
The ‘MiKTeX’ (http://www.miktex.org/) distribution of LATEX includes a suitable port of
pdftex. This can be set up to install extra packages ‘on the fly’, which is the simplest way
to use it (and the default). The ‘basic’ version of ‘MiKTeX’ almost suffices: when last checked
packages
epsf inconsolata mptopdf url
needed to be added (on the fly or via the ‘MiKTeX’ Package Manager) to install R. In any
case ensure that the inconsolata package is installed—you can check with the ‘MiKTeX’ Package
Manager.
The Rtools*.exe installer does not include any version of LATEX.
It is also possible to use the TeX Live distribution from https://www.tug.org/texlive/.
Please read Section 2.3 [Making the manuals], page 4, about how to make fullrefman.pdf
and set the environment variable R_RD4PDF suitably; ensure you have the required fonts installed
or that ‘MiKTeX’ is set up to install LATEX packages on first use.
D.2 The Inno Setup installer

To make the installer package (R-3.5.1-win.exe) we currently require the Unicode version of
Inno Setup 5.3.7 or later from http://jrsoftware.org/. This is not included in Rtools*.exe.
Copy file src/gnuwin32/MkRules.dist to src/gnuwin32/MkRules.local and edit it to set
ISDIR to the location where Inno Setup was installed.
D.3 The command line tools

This item is installed by the Rtools*.exe installer.
If you choose to install these yourself, you will need suitable versions of at least basename,
cat, cmp, comm, cp, cut, date, diff, du, echo, expr, gzip, ls, make, makeinfo, mkdir, mv,
rm, rsync, sed, sh, sort, tar, texindex, touch and uniq; we use those from the Cygwin
distribution (https://www.cygwin.com/) or compiled from the sources. You will also need zip
and unzip from the Info-ZIP project (http://www.info-zip.org/). All of these tools are in
Rtools*.exe.
Beware: ‘Native’ ports of make are not suitable (including those called ‘MinGW make’ at the
MinGW SourceForge site and mingw32-make in some MinGW-w64 distributions). There were
also problems with other versions of the Cygwin tools and DLLs. To avoid frustration, please
use our tool set, and make sure it is at the front of your path (including before the Windows
system directories). If you are using a Windows shell, type PATH at the prompt to find out.
You may need to set the environment variable CYGWIN to a value including
‘nodosfilewarning’ to suppress messages about Windows-style paths.
D.4 The MinGW-w64 toolchain

Technically you need more than just a compiler so the set of tools is referred to as a ‘toolchain’.
The preferred toolchain is part of Rtools*.exe: this uses a version of gcc 4.9.3 and version
rt v3 of the MinGW-w64 project’s runtime.
This toolchain does not use multilib: separate front-ends are used for 32-bit and 64-bit
compilation. These compilers need to be specified in BINPREF and BINPREF64 make variables as
described previously at the end of Section 6.3.1 [Windows packages], page 24.
To select a 32-bit or 64-bit build of R, set the options in MkRules.local appropriately
(following the comments in the file).
Appendix D: The Windows toolset 73
Some external software libraries will need to be re-compiled under the new toolchain: es-
pecially those providing a C++ interface. Many of those used by CRAN packages are available
from https://www.stats.ox.ac.uk/pub/Rtools/multilib/. Users developing packages with
Rcpp (https://CRAN.R-project.org/package=Rcpp) need to ensure that they use a version
built with exactly the same toolchain as their package: the recommendation is to build Rcpp
(https://CRAN.R-project.org/package=Rcpp) from its sources yourself.
There is support for OpenMP and pthreads in this toolchain. As the performance of OpenMP
on Windows is poor for small tasks, it is not used for R itself.
D.5 Useful additional programs

The process of making the installer will make use of qpdf to compact some of the package
vignettes, if it is available. Windows binaries of qpdf are available from http://sourceforge.
net/projects/qpdf/files/. Set the path to the qpdf installation in file MkRules.local.
Developers of packages will find some of the ‘goodies’ at https://www.stats.ox.ac.uk/
pub/Rtools/goodies useful.
There is a version of the file command that identifies the type of files, and is used by Rcmd
check if available. The binary distribution is included in Rtools*.exe.
The file xzutils.zip contains the program xz which can be used to (de)compress files with
that form of compression.
74
Function and variable index
C R
configure . . . . . . . . . . . . . . . . . . . . . . . . . . 3, 4, 6, 7, 50, 51 R_HOME . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
remove.packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
I
install.packages. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24 U
update.packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
M
make . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
75
Concept index
A O
AIX . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67 Obtaining R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
OpenBSD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
B
BLAS library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43, 61, 66 P
Packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Packages, default . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
F Packages, installing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
FORTRAN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 Packages, removing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
FreeBSD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69 Packages, updating . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
I R
Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Repositories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Installing under Unix-alikes . . . . . . . . . . . . . . . . . . . . . . . . 3
Installing under Windows . . . . . . . . . . . . . . . . . . . . . . . . . 13
Internationalization. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 S
Site libraries. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
L Solaris . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Sources for R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
LAPACK library . . . . . . . . . . . . . . . . . . . . . . . . . . 47, 61, 66 Subversion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1, 40
Libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Libraries, managing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Libraries, site . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 U
Libraries, user . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Linux . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3, 56 User libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Locale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Localization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
V
Vignettes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
M
macOS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3, 19, 59
Manuals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 W
Manuals, installing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 winCairo.dll . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
76
Environment variable index
B O
BINPREF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 OBJECT_MODE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
BINPREF64 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
BLAS_LIBS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
P
C PAPERSIZE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
CC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52 PATH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40, 52, 68, 71
CONFIG_SITE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
CPP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
CYGWIN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72 R
R_ARCH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
D R_BROWSER . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
R_DEFAULT_PACKAGES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
DESTDIR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8, 37 R_DISABLE_HTTPD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
R_GSCMD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
R_INSTALL_TAR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
F R_JAVA_LD_LIBRARY_PATH . . . . . . . . . . . . . . . . . . . . . . . . . 43
F2C . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52 R_LIBS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
F2CLIBS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52 R_LIBS_SITE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
FPICFLAGS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52 R_LIBS_USER . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
R_PAPERSIZE. . . . . . . . . . . . . . . . . . . . . . . . . . . . 5, 22, 50, 51
J R_PDFVIEWER . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
R_RD4PDF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6, 51, 72
JAVA_HOME . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 R_SCRIPT_DEFAULT_PACKAGES . . . . . . . . . . . . . . . . . . . . . 23
R_SHELL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
L R_USER . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
LANG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
LANGUAGE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33, 34
LAPACK_LIBS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
T
LC_ALL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 TAR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
LC_COLLATE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 TAR_OPTIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1, 14
LC_MESSAGES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 TEMP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
LD_LIBRARY_PATH . . . . . . . . . . . . . . . . . . . . . . 37, 52, 53, 67 TMP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
LOCAL_SOFT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 TMPDIR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3, 14, 22, 23

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R Installation and Administration

Version 3.5.1 (2018-07-02)

2 Installing R under Unix-alikes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

3 Installing R under Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

4 Installing R under macOS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

6.3.3 Customizing package compilation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

7 Internationalization and Localization . . . . . . . . . . . . . . . . . . . . . . . . 32

8 Choosing between 32- and 64-bit builds . . . . . . . . . . . . . . . . . . . . 35

9 The standalone Rmath library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Appendix A Essential and useful other

Appendix B Configuration on a Unix-alike . . . . . . . . . . . . . . . . . . . 49

Appendix C Platform notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

Appendix D The Windows toolset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

Function and variable index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

Environment variable index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76

1.1 Getting and unpacking the sources

1.2 Getting patched and development versions

1.2.1 Using Subversion and rsync

2 Installing R under Unix-alikes

2.1 Simple compilation

2.2 Help options

2.3 Making the manuals

‘R-admin’ “R Installation and Administration”, this manual.

tctt1000.600pk and tcrm1000.600pk. Unfortunately, if those files are not avail-

2.7 Other Options

2.7.1 OpenMP Support

2.7.2 C++ Support

2.8 Testing an Installation

3 Installing R under Windows

3.1 Building from source

3.1.1 Getting the tools

3.1.2 Getting the source files

3.1.3 Building the core files

• You can run a parallel make by e.g.

3.1.4 Building the cairo devices

3.1.5 Using ICU for collation

3.1.6 Support for libcurl

3.1.7 Checking the build

Other levels of checking are

3.1.8 Building the manuals

3.1.9 Building the Inno Setup installer

3.1.10 Building the MSI installer

3.1.11 64-bit Windows builds

3.2 Testing an Installation

4 Installing R under macOS

4.1 Running R under macOS

Users of R.app need to be aware of the ‘App Nap’ feature (https://developer.apple.com/

4.2 Uninstalling under macOS

4.3 Multiple versions

6.1 Default packages

6.2 Managing libraries

6.3 Installing packages

6.3.3 Customizing package compilation

6.3.4 Multiple sub-architectures

When a source package is installed by a build of R which supports multiple sub-architectures,

6.3.6 External software

the role of LD_LIBRARY_PATH is replaced on macOS by DYLD_LIBRARY_PATH and latterly DYLD_