R Installation and Administration

Sources, binaries and documentation for R can be obtained via CRAN, the “Comprehensive R Archive Network” whose current members are listed at http://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 ftp://ftp.stat.math.ethz.ch/pub/Software/R/. 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 http://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.

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 packages, 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 ‘http://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 \
  http://CRAN.R-project.org/src/contrib/dir
./tools/link-recommended

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’, ‘ia64’, ‘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’, ‘i386-*-openbsd’ and ‘powerpc-ibm-aix6*’

In addition, binary distributions are available for some common Linux distributions and for OS X (formerly 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.

2.1 Simple compilation

First review the essential and useful tools and libraries in Essential and useful other programs under a Unix-alike, 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.³

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 Setting paper size.) Issue the following commands:

./configure
make

(See Using make if your make is not called ‘make’.) Users of Debian-based 64-bit systems⁴ may need

./configure LIBnn=lib
make

make check

Failures are not necessarily problems as they might be caused by missing functionality,⁵ 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 Running R).

make check-devel

make check-all

see file tests/README and Testing a Unix-alike Installation for the possibilities of doing this in parallel. Note that these checks need the recommended packages to be installed.

If the command 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 Installation. 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.)

Now rehash if necessary, type R, and read the R manuals and the R FAQ (files FAQ or doc/manual/R-FAQ.html, or http://CRAN.R-project.org/doc/FAQ/R-FAQ.html which always has the version for the latest release of R).

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 (including 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

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 makeinfo version 4.7 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).

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:

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 usual ⁷ 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}}{}

\ifthenelse{\boolean{Rd@use@hyper}}{\hypersetup{linktoc=all}}{}

Ebook versions 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 OS X).

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.

./configure
make
make check

(or, when building outside the source, TOP_SRCDIR/configure, etc) have been completed successfully, you can install the complete R tree to your system by typing

make install

where prefix is determined during configuration (typically /usr/local) and can be set by running configure with the option --prefix, as in

./configure --prefix=/where/you/want/R/to/go

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. You can install into another directory tree by using

make prefix=/path/to/here install

at least with GNU make (and current Solaris and FreeBSD 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-3.1.1.

If you want the R home to be something other than libdir/R, use rhome: for example

make install rhome=/usr/local/lib64/R-3.1.1

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.⁹ 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 at least some aspects (such as installing source packages) will not work.

make install-info
make install-pdf

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 http://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

2.5 Uninstallation

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.

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 63Mb, 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

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.

R --arch=name CMD make check[-devel|all]

Sub-architectures are also used on Windows, but by selecting executables within the appropriate bin directory, R_HOME/bin/i386 or R_HOME/bin/x64. For backwards compatibility with R < 2.12.0, there are executables R_HOME/bin/R.exe or R_HOME/bin/Rscript.exe: these will run an executable from one of the subdirectories, which one being taken first from the R_ARCH environment variable, then from the --arch command-line option¹⁰ and finally from the installation default (which is 32-bit for a combined 32/64 bit R installation).

2.6.1 Multilib

On Linux¹¹, there is an alternative mechanism for mixing 32-bit and 64-bit libraries known as multilib. If a 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).

At present 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

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. Normally 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 lazyloaded but not byte-compiled. (Alternatively the (make or environment) variable R_NO_BASE_COMPILE can be set to a non-empty value for the duration of the build.)

Option --with-internal-tzcode makes use of R’s own code and copy of the Olson database 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 directory¹² 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.

2.8 Testing an Installation

make install-tests

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 the 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 Shared BLAS).

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.

Sys.setenv(LC_COLLATE = "C", LC_TIME = "C", LANGUAGE = "en")
library("tools")
testInstalledBasic("both")
testInstalledPackages(scope = "base")
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 slightly fewer tests than the first approach: in particular they do not test Internet access.

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 the 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

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 Windows XP or later on ix86 CPUs (including AMD64/Intel64 cpus and Windows x64).

Your file system must allow long file names (as is likely except perhaps for some network-mounted systems).

Installation is via the installer R-3.1.1-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.

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).

3.1.1 Getting the tools

The Rtools*.exe executable installer described in The Windows toolset 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

The following additional items are normally installed by Rtools31.exe. If instead you choose to do a completely manual build you will also need

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. Look at MkRules.dist and if settings need to be altered, copy it to MkRules.local and edit the settings there. In particular, this is where a 64-bit build is selected. Then run

make all recommended

3.1.4 Building the bitmap files

The file R_HOME/library/grDevices/libs/{i386,x64}Rbitmap.dll is not built automatically.

Running make in R_HOME/src/gnuwin32/bitmap or make bitmapdll in R_HOME/src/gnuwin32 should build Rbitmap.dll and install it under R_HOME/library/grDevices/libs.

3.1.5 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 Rbitmap.dll, by make cairodevices.

To enable the building of these devices you need to install the static cairographics libraries built by Simon Urbanek at http://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.)

3.1.5.1 Using ICU for collation

It is possible (and even recommended) to build R to use ICU (International Components for Unicode, http://site.icu-project.org/) for collation, as is commonly done on Unix-alikes.

# 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 http://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.

3.1.6 Checking the build

make check

make check-recommended

make check-devel

make check-all

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.

3.1.7 Building the manuals

make manuals

cd ../../doc/manual
make -f Makefile.win info

See the Making the manuals section in the Unix-alike section for setting options such as the paper size and the fonts used.

Version 4.x of makeinfo from Rtools is assumed by default. If you have version 5.x of texinfo, makeinfo has been replaced by a Perl script texi2any: file MkRules.dist contains alternative macros to allow that to be used (copy it to MkRules.local before editing). (A package of texinfo 5.x for use on Windows is available at http://www.stats.ox.ac.uk/pub/Rtools/: you will also need to install Perl.)

3.1.8 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, as well as the recommended packages and Inno Setup (see The Inno Setup installer).

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)
bitmapdll (the bitmap support files)
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 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.

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-3.1.1-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-2 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).

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 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.

3.1.9 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://wix.sourceforge.net/ or 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-3.1.1-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-3.1.1) 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-3.1.1-win32.msi) and from a 64-bit build of R (R-3.1.1-win64.msi, optionally including 32-bit files by setting the macro HOME32, when the name is R-3.1.1-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.

3.1.10 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.

3.2 Testing an Installation

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).

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.

4 Installing R under OS X

The front page of a CRAN site has a link ‘Download R for OS X’. Click on that, then download the file R-3.1.1-snowleopard.pkg and install it. This runs on OS X 10.6 and later (Snow Leopard, Lion, Mountain Lion, Mavericks, …); it is a 64-bit (‘x86_64’) build which should run on all Macs from mid-2008 on. For older Intel Macs and some older versions of the OS you can install R from the sources.

There is a separate installer package, R-3.1.1-mavericks.pkg, for use on Mavericks only: the ‘Snow Leopard’ installer package also works there and may have more binary packages available (but there are a few packages using C++11 and only available for the Mavericks build).

It is important that if you use a binary installer package that your OS is fully updated: run ‘Software Update’ from the Apple menu 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 three components. Everyone will need the ‘R Framework’ component: the ‘R GUI’ and ‘Tcl/Tk’ components are optional (the latter being needed to use package tcltk).

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.

If you update your OS X version, you should re-install R: the installer tailors the installation to the current version of the OS.

4.1 Running R under OS X

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). This is usually referred to as R.APP to distinguish it from command-line R: its user manual is currently part of the OS X FAQ at http://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 from a Terminal 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 personal library directory (under ~/Library/R, e.g. ~/Library/R/3.1/library), and that warnings, messages and other output to stderr are highlighted in bold.

4.2 Uninstalling under OS X

R for OS X 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 into 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. This does leave some links in /usr/bin.

If you want to get rid of R more completely using a Terminal, simply run (prepend sudo if needed):

rm -rf /Library/Frameworks/R.framework /Applications/R.app \
   /usr/bin/R /usr/bin/Rscript

The installation consisted of three Apple packages: org.r-project.R.x86_64.fw.pkg, org.r-project.R.x86_64.GUI.pkg and org.r-project.x86_64.tcltk.x11 (not all of which need be installed). You can use pkgutil --unlink (not supported by Lion or later) to remove their files or 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 component (which is installed under /usr/local) is not simple. You can list the files it installed in a Terminal by

pkgutil --files org.r-project.x86_64.tcltk.x11

4.3 Multiple versions

The installer will remove any previous version 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 3.0, 3.1 and so on, so it is not possible to have different ‘3.x.y’ versions installed for the same ‘x’.

/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R

However, R.APP will always run the ‘current’ version, that is the last installed version. A small utility, Rswitch.app (available at http://r.research.att.com/#other), can be used to change the ‘current’ version. However, 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.

5 Running R

How to start R and what command-line options are available is discussed in 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 will have default limits at least as large as these, but apparently NetBSD does 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 Setting paper size). 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 temporary 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.

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

> 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 (and this is done by Rscript). But it can also be used to customize R, e.g. for class use.

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 recommended¹³ 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 setting¹⁴ ‘.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 packages 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.

Ensure that the environment variable TMPDIR is either unset (and /tmp exists and can be written 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.¹⁵ On most systems ‘install.packages()’ will allow packages to be selected from a list box (typically with several thousand items).

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 set the option CRAN to 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 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, Omegahat, 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 OS X) and Windows. On Unix-alikes it consults the list of available source packages on CRAN (or other repository/ies), downloads the latest version of the package sources, and installs them (via R CMD INSTALL). On Windows it looks (by default) at the list of binary versions of packages available for your version of R and downloads the latest versions (if any), although optionally it will also download and install a source package by setting the type argument.

On Windows install.packages can also install a binary package from a local zip 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.

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 The Windows toolset) are in the path). We have seen occasional permission problems after unpacking source packages on some Vista/Windows 7/Server 2008 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 http://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 use¹⁶ 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 the that zip file on Windows. However, such a package can be installed from the sources on Windows without any additional tools.

There is provision to make use of a system-wide library of installed external software by setting the make variable LOCAL_SOFT, to give an equivalent of /usr/local on a Unix-alike. This can be set in src/gnuwin/MkRules.local when R is built from sources (see the comments in src/gnuwin/MkRules.dist), or in file¹⁷ etc/i386/Makeconf or etc/x64/Makeconf for an installed version of R. The version used by CRAN can be downloaded from http://www.stats.ox.ac.uk/pub/Rtools/libs.html.

6.3.2 OS X

On OS X install.packages works as it does on other Unix-alike systems, but there is an additional type mac.binary (the default in the CRAN distribution but not when compiling from source: mac.binary.mavericks for a Mavericks-only build) which can be passed to install.packages in order to download and install binary packages from a suitable repository. These OS X binary package files have the extension ‘.tgz’. The R.APP GUI provides menus for installation of either binary or source packages, from CRAN or local files.

Note that most binary packages including compiled code are tied to a particular series (e.g. R 3.0.x or 3.1.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 OS X. (Note that the Fortran compilers differ for the ‘Snow Leopard’ and ‘Mavericks’ binary installations of R.)

Package rJava and those which depend on it need a Java runtime installed and several packages need X11 installed, including those using Tk. For Mountain Lion and Mavericks see OS X and Java (OS X).

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.

The default compilers specified in /Library/Frameworks/R.framework/Resources/etc/Makeconf depend on the version of OS X under which R was installed, and are appropriate to the latest version of the Xcode command-line tools for that version of OS X. The settings 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’.

So for example you could select clang for both C and C++ with extensive checking by having in ~/.R/Makevars

CC=clang
CXX=clang++
CFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
CXXFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion

FLIBS=-lgfortran

6.3.3 Customizing package compilation

The R system and package-specific compilation flags can be overridden or added to by setting 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. An alternative personal file 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

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 an alternative file can be specified by environment variable R_MAKEVARS_SITE.

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.

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

In those cases only the current architecture is installed. Further sub-architectures can be installed 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 example because they interfere with the sealing of namespaces). For most packages (especially 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.

6.4 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 packages 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 versions 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 repositories). 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 …

> remove.packages(c("pkg1", "pkg2"),
                  lib = file.path("path", "to", "library"))

Finally, in most installations 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.omegahat.org/R/: this must be an URL scheme that download.packages supports (which also includes ‘ftp://’ and ‘file://’, but not on most systems ‘https://’). Under that base URL there should be directory trees for one or more of the following types of package distributions:

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 a PACKAGES.gz file, a gzip-compressed version of PACKAGES—as this will be downloaded in preference to PACKAGES it should be included for large repositories. (If you have a mis-configured server that does not report correctly non-existent files you may need PACKAGES.gz.)

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 packages in subdirectories must include a line of the form

Path: path/to/subdirectory

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 architectures 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
.../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

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

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 XPG¹⁸ 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 http://msdn.microsoft.com/en-us/library/hzz3tw78(v=vs.80) (or if Microsoft moves it yet again, search for ‘Windows language country strings’).

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 OS X

OS X supports locales in its own particular way, but the R GUI tries to make this easier for users. See http://developer.apple.com/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 it remotely and in batch jobs: note whether Terminal sets the LANG environment variable is an (advanced) option, but the default).

Internally OS X 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 then¹⁹ 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, provided²⁰ 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.

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-level and C-level domains are subtly different, for example in the way strings are canonicalized before being passed for translation.

Translations are looked for by domain according to the currently specified language, as specifically as possible, so for example an Austrian (‘de_AT’) translation catalogue will be used in preference to a generic German one (‘de’) for an Austrian user. However, if a specific translation 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.²¹ 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’²² is used.

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 OS X >= 10.6) 64-bit is.

All current versions of R use 32-bit integers and ISO/IEC 60559²³ double-precision reals, and so compute to the same precision²⁴ and with the same limits on the sizes of numerical quantities. The principal difference is in the size of the pointers.

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 Sub-architectures. (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 (especially in FORTRAN code). For example, the dimensions of an array are limited to 2^{31} - 1.

9 The standalone Rmath library

The routines supporting the distribution and special²⁵ 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 "3.1.0".

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

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)

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;

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.

will make standalone libraries libRmath.a and libRmath.so (libRmath.dylib on OS X): ‘make static’ and ‘make shared’ will create just one of them.

#define MATHLIB_STANDALONE
#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_LIBRARY_PATH on OS X).

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.

$(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 up²⁶ 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

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

#define MATHLIB_STANDALONE
#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,dynamic
-Wl,-Bdynamic -lRmath

or by linking to explicit files (as in the ‘test’ target in Makefile.win: this makes two executables, 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 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++.

#define MATHLIB_STANDALONE
#define RMATH_DLL
#include <Rmath.h>

to ensure that the constants like NA_REAL are linked correctly. (Auto-import will probably work with MinGW, but it is better to be sure. This is likely to also work with VC++, Borland and similar compilers.)

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 deb) 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 Using FORTRAN). Your C compiler should be ISO/IEC 60059²⁷, POSIX 1003.1 and C99-compliant.²⁸ R tries to choose suitable flags for the C compilers it knows about, but you may have to set CC or CFLAGS suitably. For recent versions of gcc with glibc this means including -std=gnu99²⁹. If the compiler is detected as gcc, -std=gnu99 will be appended to CC unless it conflicts with a setting of CFLAGS. (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 a Mac) you need ‘X11’ installed, including its headers and client libraries. For recent Fedora distributions it means (at least) RPMs ‘libX11’, ‘libX11-devel’, ‘libXt’ and ‘libXt-devel’. On Debian 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: 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 for glibc but not of most commercial Unixes. However, you can make use of GNU libiconv (possibly as a plug-in replacement: see http://www.gnu.org/software/libiconv/).

The OS needs to have enough support³⁰ for wide-character types: this is checked at configuration. A small number of POSIX functions³¹ are essential, and others³² will be used if available.

A tar program is needed to unpack the sources and packages (including the recommended packages). A version³³ 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 makeinfo version 4.7 or later installed, and if not some of the HTML manuals will be linked to 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.³⁴ Further, the versions of texi2dvi and texinfo.tex need to be compatible: we have seen problems with older TeX distributions (TeXLive 2007 and MiKTeX 2.8) used with texinfo 4.13. It is possible to use texinfo version 5.x, preferably 5.2 or later.

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 fancyvrb, 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 Making the manuals). Note that most versions of inconsolata require package upquote and that hyperref (currently) requires packages kvoptions, ltxcmds and refcount. For distributions based on TeXLive 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): Fedora uses names like texlive-collection-fontsextra and Debian/Ubuntu like texlive-fonts-extra.

If you want to build from the R Subversion repository you need both makeinfo and pdflatex.

The essential programs should be in your PATH at the time configure is run: this will capture the full paths.

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 installed, and are likely to fail if cairo was built statically (unusual). Most systems with Gtk+ 2.8 or later installed will have suitable libraries. OS X comes with none of these libraries (but XQuartz, as used for 10.8 and later, ships cairo), but cairo support (without Pango) has been added to the binary distribution (see http://r.research.att.com/libs/ you need fontconfig, freetype and pixman too): pkg-config is still needed when building R from source and can be installed from its sources.

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 package³⁵ provides TrueType versions of Monotype fonts such as Arial and Times New Roman. Another useful set of fonts is the ‘liberation’ TrueType fonts available at https://fedorahosted.org/liberation-fonts/,³⁶ 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 (http://en.wikipedia.org/wiki/Liberation_fonts). Then there is the ‘Free UCS Outline Fonts’ project (http://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.

If you have them installed (including the appropriate headers and of suitable versions), system versions of zlib, libbz2 and PCRE will be used if specified by --with-system-zlib (version 1.2.5 or later), --with-system-bzlib or --with-system-pcre (version 8.10 or later, preferably 8.34³⁷): otherwise versions in the R sources will be compiled in. As the latter suffice and are tested with R you should not need to change this.

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.).

liblzma from xz-utils version 5.0.3 or later will be used if installed: the version in the R sources can be selected instead by configuring with --with-system-xz=no. Systems differ in what they call the package including this: e.g. on Fedora the library is in ‘xz-libs’ and the headers in ‘xz-devel’.

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. However some builds of glibc hide it with the intention that the TI-RPC library be used instead, 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 OS X 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 (including on OS X >= 10.4): 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 http://www.tcl.tk/. To specify the locations of the Tcl/Tk files you may need the configuration options

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 8.5.12 and 8.6.0 have been tested (including most versions of 8.4.x, but not recently).

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. JAVA_HOME can be set to point to a specific JRE/JDK.

Principal amongst these are setting 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-1.7.0-openjdk-1.7.0.25.x86_64/jre
R_JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/lib/amd64/server

Note that this unfortunately 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 etc/Makeconf and R_HOME/etc/ldpaths. See R CMD javareconf --help for details.

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-1.7.0/jre/lib/amd64/server

It may be possible to avoid this by specifying an invariant link as the path. For example, on that system either of

JAVA_HOME=/usr/lib/jvm/java-1.7.0
JAVA_HOME=/usr/lib/jvm/java-1.7.0/jre

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 most cases this will be a C++98 compiler, and as from R 3.1.0 it is possible to specify an alternative compiler for use with C++11 by the configure variables CXX1X, CXX1XSTD, CXX1XFLAGS and similar. Again, configure will normally find a suitable value for CXX1XSTD 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 (it is for OS X < 10.9 and Solaris, for example).

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.

A.3 Linear algebra

A.3.1 BLAS

The linear algebra routines in R can make use of enhanced BLAS (Basic Linear Algebra Subprograms, 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 Solaris³⁸, libessl on IBM, Accelerate on OS X). The correct incantation for these is usually 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.

Note that under Unix (but not under Windows) if R is compiled against a non-default BLAS and --enable-BLAS-shlib is not used, then all BLAS-using packages must also be. So if R is re-built to use an enhanced BLAS then packages such as quantreg will need to be re-installed.

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.

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 usually built as a static library that on some platforms cannot be used with shared objects such as are used in R packages. Be careful when using pre-built versions of ATLAS (they seem to work on ‘ix86’ platforms, but not always on ‘x86_64’ ones).

--with-blas="-lf77blas -latlas"

--with-blas="-L/path/to/ATLAS/libs -lf77blas -latlas"

--with-blas="-L/usr/lib64/atlas -lf77blas -latlas"

For systems with multiple CPU cores it is possible to use a multi-threaded version of ATLAS, by specifying

--with-blas="-lptf77blas -lpthread -latlas"

Consult its file INSTALL.txt for how to build ATLAS with position-independent code: that file also describes how to build ATLAS as a shared library.

A.3.1.2 ACML

For ‘x86_64’ and ‘i686’ processors under Linux there is the AMD Core Math Library (ACML) http://www.amd.com/acml. For the gcc version we could use

--with-blas="-lacml"

if the appropriate library directory (such as /opt/acml5.1.0/gfortran64/lib) is in the LD_LIBRARY_PATH. For other compilers, see the ACML documentation. There is a multithreaded Linux version of ACML available for recent versions of gfortran. To make use of this you will need something like

--with-blas="-L/opt/acml5.1.0/gfortran64_mp/lib -lacml_mp"

See see Shared BLAS for an alternative (and in many ways preferable) way to use ACML.

The version last tested (5.1.0) failed the reg-BLAS.R test in its handling of NAs.

A.3.1.3 Goto and OpenBLAS

Dr Kazushige Goto wrote another tuned BLAS which is available for several processors and OSes. The final version is known as GotoBLAS2, and was re-released under a much less restrictive licence. Source code can be obtained from http://www.tacc.utexas.edu/tacc-projects/gotoblas2/

--with-blas="-lgoto2"

See see Shared BLAS for an alternative (and in many ways preferable) way to use it.

Our understanding is that this project is now frozen and so will not be updated for CPUs released since mid-2010. However, OpenBLAS (http://xianyi.github.com/OpenBLAS/) is a descendant project with support for some current CPUs (e.g. Intel Sandy Bridge and AMD Bulldozer).

A.3.1.4 Intel MKL

For Intel processors, and perhaps others, and some distributions of Linux, there is Intel’s Math Kernel Library (http://www.intel.com/software/products/mkl/). You are strongly encouraged to read the MKL User’s Guide, which is installed with the library, before attempting to link to MKL. There are also versions of MKL for OS X and Windows, but they did not work with the standard compilers used for R on those platforms.

The MKL interface has changed several times, and may change again: the following notes apply exactly only to version 10.3 but have been used with version 11.1.

Versions 10 and later of MKL support two linking models: the default model (which is backward compatible with version 9 see below) and the layered model. The layered model gives the user fine-grained control over four different library layers: interface, threading, computation, and run-time library support. Some examples of linking to MKL using this layered model are given below. (These examples are for GCC compilers on ‘x86_64’.) The choice of interface layer is important on ‘x86_64’ since the Intel Fortran compiler returns complex values in different registers from the GNU Fortran compiler. You must therefore use the interface layer that matches your compiler (mkl_intel* or mkl_gf*).

MKL_LIB_PATH=/opt/intel/mkl/10.311.339/lib/intel64/
export LD_LIBRARY_PATH=$MKL_LIB_PATH
MKL="-L${MKL_LIB_PATH} -lmkl_gf_lp64 -lmkl_sequential -lmkl_core"
./configure --with-blas="$MKL" --with-lapack

where some versions may need -lmkl_lapack before -lmkl_core. The order of the libraries is important. The option --with-lapack is used since MKL contains a tuned copy of LAPACK as well as BLAS (see LAPACK), although this can be omitted.

Threaded MKL may be used (according to Zhang Zhang of Intel) by replacing the line defining the variable MKL with (Intel OMP)

MKL="-L${MKL_LIB_PATH} -lmkl_gf_lp64 -lmkl_intel_thread \
     -lmkl_core -liomp5 -lpthread"

MKL="-L${MKL_LIB_PATH} -lmkl_gf_lp64 -lmkl_gnu_thread \
     -lmkl_core -fopenmp -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.

MKL="   -L${MKL_LIB_PATH}                               \
        -Wl,--start-group                               \
                ${MKL_LIB_PATH}/libmkl_gf_lp64.a        \
                ${MKL_LIB_PATH}/libmkl_gnu_thread.a     \
                ${MKL_LIB_PATH}/libmkl_core.a           \
        -Wl,--end-group                                 \
        -lgomp -ldl -lpthread"

(Thanks to Ei-ji Nakama. The -ldl was needed on a Centos 5 systems and may not be needed everywhere.)

• Obtaining R:
• Installing R under Unix-alikes:
• Installing R under Windows:
• Installing R under OS X:
• Running R:
• Add-on packages:
• Internationalization:
• Choosing between 32- and 64-bit builds:
• The standalone Rmath library:
• Essential and useful other programs under a Unix-alike:
• Configuration on a Unix-alike:
• Platform notes:
• The Windows toolset:
• Function and variable index:
• Concept index:
• Environment variable index:

• Simple compilation:
• Help options:
• Making the manuals:
• Installation:
• Uninstallation:
• Sub-architectures:
• Other Options:
• Testing a Unix-alike Installation:

• Getting the tools:
• Getting the source files:
• Building the core files:
• Building the bitmap files:
• Building the cairo devices files:
• Checking the build:
• Building the manuals:
• Building the Inno Setup installer:
• Building the MSI installer:
• 64-bit Windows builds:

• Default packages:
• Managing libraries:
• Installing packages:
• Updating packages:
• Removing packages:
• Setting up a package repository:
• Checking installed source packages:

• Windows packages:
• OS X packages:
• Customizing package compilation:
• Multiple sub-architectures:
• Byte-compilation:

• Getting and unpacking the sources:
• Getting patched and development versions:

• Building from source:
• Testing a Windows Installation:

• Running R under OS X:
• Uninstalling under OS X:
• Multiple versions:

• Locales under Unix-alikes:
• Locales under Windows:
• Locales under OS X:

• Essential programs and libraries:
• Useful libraries and programs:
• Linear algebra:

• ATLAS:
• ACML:
• Goto and OpenBLAS:
• MKL:
• Shared BLAS:

R Installation and Administration

Table of Contents

R Installation and Administration

1 Obtaining R

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

2.4 Installation

2.5 Uninstallation

2.6 Sub-architectures

2.6.1 Multilib

2.7 Other Options

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

3.1.4 Building the bitmap files

3.1.5 Building the cairo devices

3.1.5.1 Using ICU for collation

3.1.6 Checking the build

3.1.7 Building the manuals

3.1.8 Building the Inno Setup installer

3.1.9 Building the MSI installer

3.1.10 64-bit Windows builds

3.2 Testing an Installation

4 Installing R under OS X

4.1 Running R under OS X

4.2 Uninstalling under OS X

4.3 Multiple versions

5 Running R

6 Add-on packages

6.1 Default packages

6.2 Managing libraries

6.3 Installing packages

6.3.1 Windows

6.3.2 OS X

6.3.3 Customizing package compilation

6.3.4 Multiple sub-architectures

6.3.5 Byte-compilation

6.4 Updating packages

6.5 Removing packages

6.6 Setting up a package repository

6.7 Checking installed source packages

7 Internationalization and Localization

7.1 Locales

7.1.1 Locales under Unix-alikes

7.1.2 Locales under Windows

7.1.3 Locales under OS X

7.2 Localization of messages

8 Choosing between 32- and 64-bit builds

9 The standalone Rmath library

9.1 Unix-alikes

9.2 Windows

Appendix A Essential and useful other programs under a Unix-alike

A.1 Essential programs and libraries

A.2 Useful libraries and programs

A.2.1 Tcl/Tk

A.2.2 Java support

A.2.3 Other compiled languages

A.3 Linear algebra

A.3.1 BLAS

A.3.1.1 ATLAS

A.3.1.2 ACML

A.3.1.3 Goto and OpenBLAS

A.3.1.4 Intel MKL