R Installation and Administration
R Installation and Administration
R Core Team
This manual is for R, version 3.2.0 (2015-04-16).
Copyright
c 2001–2015 R Core Team
Permission is granted to make and distribute verbatim copies of this manual provided
the copyright notice and this permission notice are preserved on all copies.
Permission is granted to copy and distribute modified versions of this manual under
the conditions for verbatim copying, provided that the entire resulting derived work
is distributed under the terms of a permission notice identical to this one.
Permission is granted to copy and distribute translations of this manual into an-
other language, under the above conditions for modified versions, except that this
permission notice may be stated in a translation approved by the R Core Team.
i
Table of Contents
1 Obtaining R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.1 Getting and unpacking the sources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Getting patched and development versions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2.1 Using Subversion and rsync . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
4 Installing R under OS X . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
4.1 Running R under OS X . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
4.2 Uninstalling under OS X . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
4.3 Multiple versions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
5 Running R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
6 Add-on packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
6.1 Default packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
6.2 Managing libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
6.3 Installing packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
6.3.1 Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
6.3.2 OS X. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
6.3.3 Customizing package compilation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
6.3.4 Multiple sub-architectures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
ii
6.3.5 Byte-compilation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
6.4 Updating packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
6.5 Removing packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
6.6 Setting up a package repository . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
6.7 Checking installed source packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Concept index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
1 Obtaining R
Sources, binaries and documentation for R can be obtained via CRAN, the “Comprehensive R
Archive Network” whose current members are listed at http://CRAN.R-project.org/mirrors.
html.
Note that ‘https:’ is required2 , and that the SSL certificate for the Subversion server of the
R project should be recognized as from a trusted source.
Note that retrieving the sources by e.g. wget -r or svn export from that URL will not work
(and will give a error early in the make process): the Subversion information is needed to build
R.
The Subversion repository does not contain the current sources for the recommended pack-
ages, which can be obtained by rsync or downloaded from CRAN. To use rsync to install the
appropriate sources for the recommended packages, run ./tools/rsync-recommended from the
top-level directory of the R sources.
If downloading manually from CRAN, do ensure that you have the correct versions
of the recommended packages: if the number in the file VERSION is ‘x.y.z’ you need to
download the contents of ‘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
for some Subversion clients ‘http:’ may appear to work, but requires continual redirection.
Chapter 2: Installing R under Unix-alikes 3
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 Section 2.4 [Installation], page 6.
Note: you do not need to install R: you can run it from where it was built.
You do not necessarily have to build R in the top-level source directory (say, TOP_SRCDIR).
To build in BUILDDIR, run
cd BUILDDIR
TOP_SRCDIR/configure
make
and so on, as described further below. This has the advantage of always keeping your source
tree clean and is particularly recommended when you work with a version of R from Subversion.
(You may need GNU make to allow this, and you will need no spaces in the path to the build
directory. It is unlikely to work if the source directory has previously been used for a build.)
Now rehash if necessary, type R, and read the R manuals and the R FAQ (files FAQ or
doc/manual/R-FAQ.html, or http://CRAN.R-project.org/doc/FAQ/R-FAQ.html which al-
ways has the version for the latest release of R).
Note: if you already have R installed, check that where you installed R replaces or comes
earlier in your path than the previous installation. Some systems are set up to have /usr/bin
(the standard place for a system installation) ahead of /usr/local/bin (the default place for
installation of R) in their default path, and some do not have /usr/local/bin on the default
path.
2.4 Installation
To ensure that the installed tree is usable by the right group of users, set umask appropriately
(perhaps to ‘022’) before unpacking the sources and throughout the build process.
After
./configure
make
make check
(or, when building outside the source, TOP_SRCDIR/configure, etc) have been completed suc-
cessfully, you can install the complete R tree to your system by typing
make install
A parallel make can be used (but run make before make install). Those using GNU make 4.0
or later may want to use make -j n -O to avoid interleaving of output.
This will install to the following directories:
prefix/bin or bindir
the front-end shell script and other scripts and executables
prefix/man/man1 or mandir/man1
the man page
4
on a Unix-alike, ‘inconsolata’ is omitted if not found by configure.
Chapter 2: Installing R under Unix-alikes 7
prefix/LIBnn/R or libdir/R
all the rest (libraries, on-line help system, . . . ). Here LIBnn is usually ‘lib’, but may
be ‘lib64’ on some 64-bit Linux systems. This is known as the R home directory.
where prefix is determined during configuration (typically /usr/local) and can be set by run-
ning configure with the option --prefix, as in
./configure --prefix=/where/you/want/R/to/go
where the value should be an absolute path. This causes make install to install the R script
to /where/you/want/R/to/go/bin, and so on. The prefix of the installation directories can be
seen in the status message that is displayed at the end of configure. The installation may need
to be done by the owner of prefix, often a root account.
You can install into another directory tree by using
make prefix=/path/to/here install
at least with GNU make and current Solaris make (but not some older Unix makes).
More precise control is available at configure time via options: see configure --help for
details. (However, most of the ‘Fine tuning of the installation directories’ options are not used
by R.)
Configure options --bindir and --mandir are supported and govern where a copy of the R
script and the man page are installed.
The configure option --libdir controls where the main R files are installed: the default
is ‘eprefix/LIBnn’, where eprefix is the prefix used for installing architecture-dependent files,
defaults to prefix, and can be set via the configure option --exec-prefix.
Each of bindir, mandir and libdir can also be specified on the make install command
line (at least for GNU make).
The configure or make variables rdocdir and rsharedir can be used to install the system-
independent doc and share directories to somewhere other than libdir. The C header files
can be installed to the value of rincludedir: note that as the headers are not installed into a
subdirectory you probably want something like rincludedir=/usr/local/include/R-3.2.0.
If you want the R home to be something other than libdir/R, use rhome: for example
make install rhome=/usr/local/lib64/R-3.2.0
will use a version-specific R home on a non-Debian Linux 64-bit system.
If you have made R as a shared/static library you can install it in your system’s library
directory by
make prefix=/path/to/here install-libR
where prefix is optional, and libdir will give more precise control.5 However, you should not
install to a directory mentioned in LDPATHS (e.g. /usr/local/lib64) if you intend to work with
multiple versions of R, since that directory may be given precedence over the lib directory of
other R installations.
make install-strip
will install stripped executables, and on platforms where this is supported, stripped libraries in
directories lib and modules and in the standard packages.
Note that installing R into a directory whose path contains spaces is not supported, and
some aspects (such as installing source packages) will not work.
To install info and PDF versions of the manuals, use one or both of
5
This will be needed if more than one sub-architecture is to be installed.
Chapter 2: Installing R under Unix-alikes 8
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
which populates a tests directory in the installation.
2.5 Uninstallation
You can uninstall R by
make uninstall
optionally specifying prefix etc in the same way as specified for installation.
This will also uninstall any installed manuals. There are specific targets to uninstall info and
PDF manuals in file doc/manual/Makefile.
Target uninstall-tests will uninstall any installed tests, as well as removing the directory
tests containing the test results.
An installed shared/static libR can be uninstalled by
make prefix=/path/to/here uninstall-libR
2.6 Sub-architectures
Some platforms can support closely related builds of R which can share all but the executables
and dynamic objects. Examples include builds under Linux and Solaris for different CPUs or
32- and 64-bit builds.
R supports the idea of architecture-specific builds, specified by adding ‘r_arch=name’ to the
configure line. Here name can be anything non-empty, and is used to name subdirectories of
lib, etc, include and the package libs subdirectories. Example names from other software
are the use of sparcv9 on Sparc Solaris and 32 by gcc on ‘x86_64’ Linux.
If you have two or more such builds you can install them over each other (and for 32/64-bit
builds on one architecture, one build can be done without ‘r_arch’). The space savings can be
considerable: on ‘x86_64’ Linux a basic install (without debugging symbols) took 74Mb, and
adding a 32-bit build added 6Mb. If you have installed multiple builds you can select which
build to run by
R --arch=name
and just running ‘R’ will run the last build that was installed.
R CMD INSTALL will detect if more than one build is installed and try to install packages with
the appropriate library objects for each. This will not be done if the package has an executable
configure script or a src/Makefile file. In such cases you can install for extra builds by
Chapter 2: Installing R under Unix-alikes 9
2.6.1 Multilib
On Linux7 , 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
to get a suitable setting.
When this mechanism is used, the version of Rscript in e.g. /usr/bin will be the last
installed, but an architecture-specific version will be available in e.g. /usr/lib64/R/bin. Nor-
mally all installed architectures will run on the platform so the architecture of Rscript does
not matter.
6
with possible values ‘i386’, ‘x64’, ‘32’ and ‘64’.
7
mainly on RedHat and Fedora, whose layout is described here.
Chapter 2: Installing R under Unix-alikes 10
home directory and run fewer tests than the first approach: in particular they do not test things
which need Internet access—that can be tested by
testInstalledBasic("internet")
(On Windows that runs the tests using whichever of internal or WinInet internet functions
has been selected for that session: to test both run this twice selecting both options using
setInternet2.)
These tests work best if diff (in Rtools*.exe for Windows users) is in the path.
It is possible to test the installed packages (but not their package-specific tests) by
testInstalledPackages even if make install-tests was not run.
Note that the results may depend on the language set for times and messages: for maximal
similarity to reference results you may want to try setting (before starting the R session)
LANGUAGE=en
and use a UTF-8 or Latin-1 locale.
Chapter 3: Installing R under Windows 12
but this is only likely to be worthwhile on a multi-core machine with ample memory, and
is not 100% reliable.
• It is possible (mainly for those working on R itself) to set the (make or environment) variable
R_NO_BASE_COMPILE to a non-empty value, which inhibits the byte-compilation of the base
and recommended packages.
make check-all
for both check-devel and check-recommended.
If a test fails, there will almost always be a .Rout.fail file in the directory being checked
(often tests/Examples or tests): examine the file to help pinpoint the problem.
Parallel checking of package sources (part of make check-devel and make
check-recommended) is possible: see the environment variable TEST_MC_CORES to the
maximum number of processes to be run in parallel.
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-3.2.0-win.exe, so
please rename it to indicate that it is customized. If you intend to distribute a customized
installer please do check that license requirements are met – note that the installer will state
that the contents are distributed under GPL and this has a requirement for you to supply the
complete sources (including the R sources even if you started with a binary distribution of R, and
also the sources of any extra packages (including their external software) which are included).
The defaults for the startup parameters may also be customized. For example
make myR IMAGEDIR=rootdir MDISDI=1
will create an installer that defaults to installing R to run in SDI mode. See src/
gnuwin32/installer/Makefile for the names and values that can be set.
The standard CRAN distribution of a 32/64-bit installer is made by first building 32-bit R
(just
make 32-bit
is needed), and then (in a separate directory) building 64-bit R with the macro HOME32 set in file
MkRules.local to the top-level directory of the 32-bit build. Then the make rinstaller step
copies the files that differ between architectures from the 32-bit build as it builds the installer
image.
HOME32, when the name is R-3.2.0-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.
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-3.2.0-mavericks.pkg and install it. This runs on OS X 10.9 and later (Mavericks
and Yosemite).
There may be a separate installer package, R-3.2.0-snowleopard.pkg which runs on OS X
10.6 and later (Snow Leopard, Lion, Mountain Lion, Mavericks, Yosemite, . . . ); 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 in principle (it is little tested) install R from the sources.
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, and requires an X sub-system to be installed: see
Section C.3 [OS X], page 54.)
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.
For building R from source, see Section C.3 [OS X], page 54.
5 Running R
How to start R and what command-line options are available is discussed in Section “Invoking
R” in An Introduction to R.
You should ensure that the shell has set adequate resource limits: R expects a stack size
of at least 8MB and to be able to open at least 256 file descriptors. (Any modern OS should
have default limits at least as large as these, but apparently NetBSD may not. Use the shell
command ulimit (sh/bash) or limit (csh/tcsh) to check.)
R makes use of a number of environment variables, the default values of many of which are
set in file R_HOME/etc/Renviron (there are none set by default on Windows and hence no such
file). These are set at configure time, and you would not normally want to change them – a
possible exception is R_PAPERSIZE (see Section B.3.1 [Setting paper size], page 45). The paper
size will be deduced from the ‘LC_PAPER’ locale category if it exists and R_PAPERSIZE is unset,
and this will normally produce the right choice from ‘a4’ and ‘letter’ on modern Unix-alikes
(but can always be overridden by setting R_PAPERSIZE).
Various environment variables can be set to determine where R creates its per-session tem-
porary directory. The environment variables TMPDIR, TMP and TEMP are searched in turn and the
first one which is set and points to a writable area is used. If none do, the final default is /tmp
on Unix-alikes and the value of R_USER on Windows. The path should be an absolute path not
containing spaces (and it is best to avoid non-alphanumeric characters such as +).
Some Unix-alike systems are set up to remove files and directories periodically from /tmp,
for example by a cron job running tmpwatch. Set TMPDIR to another directory before starting
long-running jobs on such a system.
Note that TMPDIR will be used to execute configure scripts when installing packages, so if
/tmp has been mounted as ‘noexec’, TMPDIR needs to be set to a directory from which execution
is allowed.
Chapter 6: Add-on packages 21
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().
1
unless they were excluded in the build.
2
its binding is locked once the startup files have been read, so users cannot easily change it.
Chapter 6: Add-on packages 22
Ensure that the environment variable TMPDIR is either unset (and /tmp exists and can be writ-
ten in and executed from) or is the absolute path to a valid temporary directory, not containing
spaces.
For most users it suffices to call ‘install.packages(pkgname)’ or its GUI equivalent if
the intention is to install a CRAN package and internet access is available.3 On most systems
‘install.packages()’ will allow packages to be selected from a list box (typically with several
thousand items).
To install packages from source on a Unix-alike use in a terminal
R CMD INSTALL -l /path/to/library pkg1 pkg2 ...
The part ‘-l /path/to/library’ can be omitted, in which case the first library of a normal R
session is used (that shown by .libPaths()[1]).
There are a number of options available: use R CMD INSTALL --help to see the current list.
Alternatively, packages can be downloaded and installed from within R. First choose your
nearest CRAN mirror using chooseCRANmirror(). Then download and install packages pkg1
and pkg2 by
> install.packages(c("pkg1", "pkg2"))
The essential dependencies of the specified packages will also be fetched. Unless the library
is specified (argument lib) the first library in the library search path is used: if this is not
writable, R will ask the user (in an interactive session) if the default personal library should be
created, and if allowed to will install the packages there.
If you want to fetch a package and all those it depends on (in any way) that are not already
installed, use e.g.
> install.packages("Rcmdr", dependencies = TRUE)
install.packages can install a source package from a local .tar.gz file (or a URL to such
a file) by setting argument repos to NULL: this will be selected automatically if the name given
is a single .tar.gz file.
install.packages can look in several repositories, specified as a character vector by the ar-
gument repos: these can include a CRAN mirror, Bioconductor, Omegahat, R-forge, rforge.net,
local archives, local files, . . . ). Function setRepositories() can select amongst those reposi-
tories 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) first at the list of binary versions of packages available for your
version of R and downloads the latest versions (if any). If no binary version is available or
the source version is newer, it will install the source versions of packages without compiled
C/C++/Fortran code, and offer to do so for those with, if make is available (and this can be
tuned by option "install.packages.compile.from.source").
On Windows install.packages can also install a binary package from a local zip file (or
the URL of such a file) by setting argument repos to NULL. Rgui.exe has a menu Packages
with a GUI interface to install.packages, update.packages and library.
Windows binary packages for R are distributed as a single binary containing either or both
architectures (32- and 64-bit).
3
If a proxy needs to be set, see ?download.file.
Chapter 6: Add-on packages 23
A few of the binary packages need other software to be installed on your system: see for
example http://CRAN.R-project.org/bin/windows/contrib/3.1/@ReadMe. Packages using
Gtk+ (Cairo, RGtk2, cairoDevice and those that depend on them) need the bin directory of a
bundled distribution from http://www.gtk.org/download/win32.php or http://www.gtk.
org/download/win64.php in the path: it should work to have both 32- and 64-bit Gtk+ bin
directories in the path on a 64-bit version of R.
R CMD INSTALL works in Windows to install source packages. No additional tools are needed
if the package does not contain compiled code, and install.packages(type="source") will
work for such packages (and for those with compiled code if the tools (see Appendix D [The
Windows toolset], page 66) are in the path). We have seen occasional permission problems
after unpacking source packages on some Windows 7 and 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
use4 option --force-biarch: otherwise R CMD INSTALL --merge-multiarch can be applied to
a source tarball to merge separate 32- and 64-bit installs. (This can only be applied to a tarball,
and will only succeed if both installs succeed.)
If you have a package without compiled code and no Windows-specific help, you can zip
up an installation on another OS and install from that zip file on Windows. However, such a
package can be installed from the sources on Windows without any additional tools.
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 file5 etc/i386/Makeconf or etc/x64/Makeconf for an
installed version of R. The version used by CRAN can be installed as described in See Section 3.1
[Building from source], page 12.
6.3.2 OS X
On OS X install.packages works as it does on other Unix-alike systems, but there are addi-
tional types starting with mac.binary (available for the CRAN distribution but not when com-
piling from source: mac.binary.mavericks for a ‘Mavericks’ build with "default" a synonym
for the appropriate variant) which can be passed to install.packages in order to download
and install binary packages from a suitable repository. These 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.
On R builds using binary packages, the default is type both: this looks first at the list of
binary packages available for your version of R and installs the latest versions (if any). If no
binary version is available or the source version is newer, it will install the source versions of
packages without compiled C/C++/Fortran code and offer to do so for those with, if make is
available.
4
for a small number of CRAN packages where this is known to be safe and is needed by the autobuilder this
is the default. Look at the source of tools:::.install_packages for the list. It can also be specified in the
package’s DESCRIPTION file.
5
or by adding it in a file such as etc/i386/Makevars.site, which does not exist by default.
Chapter 6: Add-on packages 24
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.
You should not attempt to mix-and-match binary packages built for the ‘Snow Leopard’ and
‘Mavericks’ CRAN distributions: doing so is likely to lead to crashes or failures to load.
Installing source packages which do not contain compiled code should work with no additional
tools. For others you will need the ‘Command-line Tools’ for Xcode and compilers which match
those used to build R: see Section C.3 [OS X], page 54. (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 pack-
ages need X11 installed, including those using Tk. For Mountain Lion and later see Section C.3
[OS X], page 54 and Section C.3.5 [Java (OS X)], page 57.
Tcl/Tk extensions BWidget and Tktable are part of the Tcl/Tk contained in the R installer.
These are required by a number of CRAN and Bioconductor packages.
A few of the binary packages need other software to be installed on your system. In particular
packages using Gtk+ (RGtk2, cairoDevice and those that depend on them) need the GTK
framework installed from http://r.research.att.com/libs/: the appropriate version at the
time of writing was http://r.research.att.com/libs/GTK_2.24.17-X11.pkg
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
and for a version of gfortran-4.2 we needed
FLIBS=-lgfortran
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.
installed and available packages, the upgrade method offers to fetch and install the latest ver-
sions of outdated packages.
One sometimes-useful additional piece of information that packageStatus() returns is the
status of a package, as "ok", "upgrade" or "unavailable" (in the currently selected reposito-
ries). For example
> inst <- packageStatus()$inst
> inst[inst$Status != "ok", c("Package", "Version", "Status")]
Package Version Status
Biobase Biobase 2.8.0 unavailable
RCurl RCurl 1.4-2 upgrade
Rgraphviz Rgraphviz 1.26.0 unavailable
rgdal rgdal 0.6-27 upgrade
To add your repository to the list offered by setRepositories(), see the help file for that
function.
Incomplete repositories are better specified via a contriburl argument than via being set
as a repository.
A repository can contain subdirectories, when the descriptions in the PACKAGES file of pack-
ages in subdirectories must include a line of the form
Path: path/to/subdirectory
—once again write_PACKAGES is the simplest way to set this up.
7.1 Locales
A locale is a description of the local environment of the user, including the preferred language,
the encoding of characters, the currency used and its conventions, and so on. Aspects of the
locale are accessed by the R functions Sys.getlocale and Sys.localeconv.
The system of naming locales is OS-specific. There is quite wide agreement on schemes, but
not on the details of their implementation. A locale needs to specify
• A human language. These are generally specified by a lower-case two-character abbreviation
following ISO 639 (see e.g. http://en.wikipedia.org/wiki/ISO_639-1).
• A ‘territory’, used mainly to specify the currency. These are generally specified by an
upper-case two-character abbreviation following ISO 3166 (see e.g. http://en.wikipedia.
org/wiki/ISO_3166).
• A charset encoding, which determines both how a byte stream should be divided into charac-
ters, and which characters the subsequences of bytes represent. Sometimes the combination
of language and territory is used to specify the encoding, for example to distinguish between
traditional and simplified Chinese.
• Optionally, a modifier, for example to indicate that Austria is to be considered pre- or
post-Euro. The modifier is also used to indicate the script (@latin, @cyrillic for Serbian,
@iqtelif) or language dialect (e.g. @saaho, a dialect of Afar, and @bokmal and @nynorsk,
dialects of Norwegian regarded by some OSes as separate languages, no and nn).
R is principally concerned with the first (for translations) and third. Note that the charset
may be deducible from the language, as some OSes offer only one charset per language.
catalogue exists but does not contain a translation, the less specific catalogues are consulted.
For example, R has catalogues for ‘en_GB’ that translate the Americanisms (e.g., ‘gray’) in the
standard messages into English.4 Two other examples: there are catalogues for ‘es’, which is
Spanish as written in Spain and these will by default also be used in Spanish-speaking Latin
American countries, and also for ‘pt_BR’, which are used for Brazilian locales but not for locales
specifying Portugal.
Translations in the right language but the wrong charset are made use of by on-the-fly re-
encoding. The LANGUAGE variable (only) can be a colon-separated list, for example ‘se:de’,
giving a set of languages in decreasing order of preference. One special value is ‘en@quot’, which
can be used in a UTF-8 locale to have American error messages with pairs of single quotes
translated to Unicode directional quotes.
If no suitable translation catalogue is found or a particular message is not translated in any
suitable catalogue, ‘English’5 is used.
See http://developer.r-project.org/Translations.html for how to prepare and install
translation catalogues.
4
the language written in England: some people living in the USA appropriate this name for their language.
5
with Americanisms.
Chapter 8: Choosing between 32- and 64-bit builds 31
1
also known as IEEE 754
2
at least when storing quantities: the on-FPU precision is allowed to vary
Chapter 9: The standalone Rmath library 32
9.1 Unix-alikes
If R has not already been made in the directory tree, configure must be run as described in
the main build instructions.
Then (in src/nmath/standalone)
make
will make standalone libraries libRmath.a and libRmath.so (libRmath.dylib on OS X): ‘make
static’ and ‘make shared’ will create just one of them.
To use the routines in your own C or C++ programs, include
1
e.g. Bessel, beta and gamma functions
Chapter 9: The standalone Rmath library 33
#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).
The targets
make install
make uninstall
will (un)install the header Rmath.h and shared and static libraries (if built). Both prefix= and
DESTDIR are supported, together with more precise control as described for the main build.
‘make install’ installs a file for pkg-config to use by e.g.
$(CC) ‘pkg-config --cflags libRmath‘ -c test.c
$(CC) ‘pkg-config --libs libRmath‘ test.o -o test
On some systems ‘make install-strip’ will install a stripped shared library.
9.2 Windows
You need to set up2 almost all the tools to make R and then run (in a Unix-like shell)
(cd ../../gnuwin32; make MkRules)
(cd ../../include; make -f Makefile.win config.h Rconfig.h Rmath.h)
make -f Makefile.win
Alternatively, in a cmd.exe shell use
cd ../../include
make -f Makefile.win config.h Rconfig.h Rmath.h
cd ../nmath/standalone
make -f Makefile.win
This creates a static library libRmath.a and a DLL Rmath.dll. If you want an import
library libRmath.dll.a (you don’t need one), use
make -f Makefile.win shared implib
To use the routines in your own C or C++ programs using MinGW, include
#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 executa-
bles, test.exe which is dynamically linked, and test-static.exe, which is statically linked).
It is possible to link to Rmath.dll using other compilers, either directly or via an import
library: if you make a MinGW import library as above, you will create a file Rmath.def which
can be used (possibly after editing) to create an import library for other systems such as Visual
C++.
If you make use of dynamic linking you should use
2
including copying MkRules.dist to MkRule.local and selecting the architecture.
Chapter 9: The standalone Rmath library 34
#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 35
There need to be suitable versions of the tools grep and sed: the problems are usually with
old AT&T and BSD variants. configure will try to find suitable versions (including looking in
/usr/xpg4/bin which is used on some commercial Unixes).
You will not be able to build most of the manuals unless you have texi2any version 5.1 or
later installed, and if not most of the HTML manuals will be linked to a version on CRAN. To
make PDF versions of the manuals you will also need file texinfo.tex installed (which is part
of the GNU texinfo distribution but is often made part of the TEX package in re-distributions) as
well as texi2dvi.8 Further, the versions of texi2dvi and texinfo.tex need to be compatible:
we have seen problems with older TEX distributions.
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 Section 2.3 [Making
the manuals], page 4). Note that package 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): Fe-
dora uses names like texlive-collection-fontsextra and Debian/Ubuntu like texlive-fonts-extra.
If you want to build from the R Subversion repository then texi2any is highly recommended
as it is used to create files in the tarball but not under Subversion.
The essential programs should be in your PATH at the time configure is run: this will capture
the full paths.
10
ttf-liberation in Debian/Ubuntu.
11
and not PCRE2, which started at version 10.0. PCRE must be built with UTF-8 support (not the default)
and support for Unicode properties is assumed by some R packages. Only the first is tested by configure, but
both can be checked at run-time by calling pcre_config(). JIT support is desirable for the best performance.
Appendix A: Essential and useful other programs under a Unix-alike 38
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.
If libcurl version 7.28.0 or later is available (including its development files), it will be linked
in to support curlGetHeaders and the "libcurl" methods of download.file and url. This
is recommended as it gives access to ‘https://’ and ‘ftps://’ URLs. Information on libcurl
is found from the curl-config script: if that is missing or needs to be overridden12 there are
macros described in file config.site.
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
--with-tcltk
use Tcl/Tk, or specify its library directory
--with-tcl-config=TCL_CONFIG
specify location of tclConfig.sh
--with-tk-config=TK_CONFIG
specify location of tkConfig.sh
or use the configure variables TCLTK_LIBS and TCLTK_CPPFLAGS to specify the flags needed for
linking against the Tcl and Tk libraries and for finding the tcl.h and tk.h headers, respectively.
If you have both 32- and 64-bit versions of Tcl/Tk installed, specifying the paths to the correct
config files may be necessary to avoid confusion between them.
Versions of Tcl/Tk up to 8.5.12 and 8.6.0 have been tested (including most versions of 8.4.x,
but not recently).
JAVA_HOME=/usr/lib/jvm/java-1.7.0
JAVA_HOME=/usr/lib/jvm/java-1.7.0/jre
worked.
BLAS. On a machine running other tasks, there can be contention for CPU caches that reduces
the effectiveness of the optimization of cache use by a BLAS implementation.
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.
External BLAS implementations often make less use of extended-precision floating-point reg-
isters and will almost certainly re-order computations. This can result in less accuracy than
using the internal BLAS, and may result in different solutions, e.g. different signs in SVD and
eigendecompositions.
The URIs for several of these BLAS are subject to frequent gratuitous changes, so you will
need to search for their current locations.
A.3.1.1 ATLAS
ATLAS (http://math-atlas.sourceforge.net/) is a “tuned” BLAS that runs on a wide range
of Unix-alike platforms. Unfortunately it is built by default as a static library that on some
platforms 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).
The usual way to specify ATLAS will be via
--with-blas="-lf77blas -latlas"
if the libraries are in the library path, otherwise by
--with-blas="-L/path/to/ATLAS/libs -lf77blas -latlas"
For example, ‘x86_64’ Fedora needs
--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 installation guide for how to build ATLAS with position-independent code, and
as a shared library.
A.3.1.2 ACML
For ‘x86_64’ processors14 under Linux there is the AMD Core Math Library (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"
(and you may need to arrange for the directory to be in ld.so cache).
See see Section A.3.1.5 [Shared BLAS], page 42 for an alternative (and in many ways prefer-
able) way to use ACML.
The version last tested (5.1.0) failed the reg-BLAS.R test in its handling of NAs.
14
and ‘i686’ for earlier versions.
Appendix A: Essential and useful other programs under a Unix-alike 41
${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.)
The MKL documentation includes a ‘link line advisor’ which will suggest appropriate incan-
tations.
A.3.2 LAPACK
Provision is made for using an external LAPACK library, principally to cope with BLAS libraries
which contain a copy of LAPACK (such as sunperf on Solaris, Accelerate on OS X and ACML
and MKL on ‘ix86’/‘x86_64’ Linux). At least LAPACK version 3.2 is required. This can only
be done if --with-blas has been used.
However, the likely performance gains are thought to be small (and may be negative), and the
default is not to search for a suitable LAPACK library, and this is definitely not recommended.
You can specify a specific LAPACK library or a search for a generic library by the configuration
option --with-lapack. The default for --with-lapack is to check the BLAS library and then
look for an external library ‘-llapack’. Sites searching for the fastest possible linear algebra
Appendix A: Essential and useful other programs under a Unix-alike 43
may want to build a LAPACK library using the ATLAS-optimized subset of LAPACK. To do
so specify something like
--with-lapack="-L/path/to/ATLAS/libs -llapack -lcblas"
since the ATLAS subset of LAPACK depends on libcblas. A value for --with-lapack can be
set via the environment variable LAPACK_LIBS, but this will only be used if --with-lapack is
specified (as the default value is no) and the BLAS library does not contain LAPACK.
Since ACML contains a full LAPACK, if selected as the BLAS it can be used as the LAPACK
via --with-lapack.
If you do use --with-lapack, be aware of potential problems with bugs in the LAPACK
sources (or in the posted corrections to those sources). In particular, bugs in DGEEV and DGESDD
have resulted in error messages such as
DGEBRD gave error code -10
. Other potential problems are incomplete versions of the libraries, seen several times in Linux
distributions over the years.
Please do bear in mind that using --with-lapack is ‘definitely not recommended’: it is pro-
vided only because it is necessary on some platforms and because some users want to experiment
with claimed performance improvements. Reporting problems where it is used unnecessarily will
simply irritate the R helpers.
Note too the comments about ISO/IEC 60559 compliance in the section of external BLAS:
these apply equally to an external LAPACK, and for example the Intel MKL documentation
says
LAPACK routines assume that input matrices do not contain IEEE 754 special
values such as INF or NaN values. Using these special values may cause LAPACK
to return unexpected results or become unstable.
We rely on limited support in LAPACK for matrices with 231 or more elements: it is quite
possible that an external LAPACK will not have that support.
If you have a pure FORTRAN 77 compiler which cannot compile LAPACK it may be possible
to use CLAPACK from http://www.netlib.org/clapack/ by something like
-with-lapack="-lclapack -lf2c"
provided these were built with position-independent code and the calling conventions for double
complex function return values match those in the BLAS used, so it may be simpler to use
CLAPACK built to use CBLAS and
-with-lapack="-lclapack -lcblas -lf2c"
A.3.3 Caveats
As with all libraries, you need to ensure that they and R were compiled with compatible compilers
and flags. For example, this has meant that on Sun Sparc using the native compilers the flag
-dalign is needed if sunperf is to be used.
On some systems it is necessary that an external BLAS/LAPACK was built with the same
FORTRAN compiler used to build R: known problems are with R built with gfortran, see
Section B.6.1 [Using gfortran], page 47.
Appendix B: Configuration on a Unix-alike 44
standard location, you should set the environment variable PATH accordingly before running
configure, or use the configure variable F77 to specify its full path.
If your FORTRAN libraries are in slightly peculiar places, you should also look at LD_
LIBRARY_PATH or your system’s equivalent to make sure that all libraries are on this path.
Note that only FORTRAN compilers which convert identifiers to lower case are supported.
You must set whatever compilation flags (if any) are needed to ensure that FORTRAN
integer is equivalent to a C int pointer and FORTRAN double precision is equivalent to a
C double pointer. This is checked during the configuration process.
Some of the FORTRAN code makes use of COMPLEX*16 variables, which is a Fortran 90
extension. This is checked for at configure time3 , but you may need to avoid compiler flags
asserting FORTRAN 77 compliance.
Compiling the version of LAPACK in the R sources also requires some Fortran 90 extensions,
but these are not needed if an external LAPACK is used.
It might be possible to use f2c, the FORTRAN-to-C converter (http://www.netlib.org/
f2c), via a script. (An example script is given in scripts/f77_f2c: this can be customized by
setting the environment variables F2C, F2CLIBS, CC and CPP.) You will need to ensure that the
FORTRAN type integer is translated to the C type int. Normally f2c.h contains ‘typedef
long int integer;’, which will work on a 32-bit platform but needs to be changed to ‘typedef
int integer;’ on a 64-bit platform. If your compiler is not gcc you will need to set FPICFLAGS
appropriately. Also, the included LAPACK sources contain constructs that f2c is unlikely to
be able to process, so you would need to use an external LAPACK library (such as CLAPACK
from http://www.netlib.org/clapack/).
SHLIB_CFLAGS
for shared objects
FFLAGS debugging and optimization flags, FORTRAN
SAFE_FFLAGS
ditto for source files which need exact floating point behaviour
MAIN_FFLAGS
ditto, for compiling the main program
SHLIB_FFLAGS
for shared objects
MAIN_LDFLAGS
additional flags for the main link
SHLIB_LDFLAGS
additional flags for linking the shared objects
LIBnn the primary library directory, lib or lib64
CPICFLAGS
special flags for compiling C code to be turned into a shared object
FPICFLAGS
special flags for compiling Fortran code to be turned into a shared object
CXXPICFLAGS
special flags for compiling C++ code to be turned into a shared object
FCPICFLAGS
special flags for compiling Fortran 95 code to be turned into a shared object
DEFS defines to be used when compiling C code in R itself
Library paths specified as -L/lib/path in LDFLAGS are collected together and prepended to
LD_LIBRARY_PATH (or your system’s equivalent), so there should be no need for -R or -rpath
flags.
Variables such as CPICFLAGS are determined where possible by configure. Some systems
allows two types of PIC flags, for example ‘-fpic’ and ‘-fPIC’, and if they differ the first allows
only a limited number of symbols in a shared object. Since R as a shared library has about 6200
symbols, if in doubt use the larger version.
To compile a profiling version of R, one might for example want to use ‘MAIN_CFLAGS=-pg’,
‘MAIN_FFLAGS=-pg’, ‘MAIN_LDFLAGS=-pg’ on platforms where ‘-pg’ cannot be used with position-
independent code.
Beware: it may be necessary to set CFLAGS and FFLAGS in ways compatible with the libraries
to be used: one possible issue is the alignment of doubles, another is the way structures are
passed.
On some platforms configure will select additional flags for CFLAGS, CPPFLAGS, FFLAGS,
CXXFLAGS and LIBS in R_XTRA_CFLAGS (and so on). These are for options which are always
required, for example to force IEC 60559 compliance.
File configure is created from configure.ac and the files under m4 by autoconf and
aclocal. There is a formal version requirement on autoconf of 2.62 or later, but it is un-
likely that anything other than the most recent versions have been thoroughly tested.
File src/include/config.h is created by autoheader.
Grammar files *.y are converted to C sources by an implementation of yacc, usually bison
-y: these are found in src/main and src/library/tools/src. It is known that earlier versions
of bison generate code which reads (and in some cases writes) outside array bounds: bison
2.6.1 was found to be satisfactory.
The ultimate sources for package compiler are in its noweb directory. To re-create the sources
from src/library/compiler/noweb/compiler.nw, the command notangle is required. This
is likely to need to be installed from the sources at http://www.cs.tufts.edu/~nr/noweb/
(and can also be found on CTAN). The package sources are only re-created even in maintainer
mode if src/library/compiler/noweb/compiler.nw has been updated.
It is likely that in future creating configure will need the GNU ‘autoconf archive’ installed.
This can be found at http://www.gnu.org/software/autoconf-archive/ and as a package
(usually called autoconf-archive) in most packaged distributions, for example Debian, Fedora,
OpenCSW, Homebrew and MacPorts.
Appendix C: Platform notes 50
find any fonts or glyphs being rendered incorrectly (often as a pair of ASCII characters). X11
works by being asked for a font specification and coming up with its idea of a close match. For
text (as distinct from the symbols used by plotmath), the specification is the first element of
the option "X11fonts" which defaults to
"-adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*"
If you are using a single-byte encoding, for example ISO 8859-2 in Eastern Europe or KOI8-R
in Russian, use xlsfonts to find an appropriate family of fonts in your encoding (the last field
in the listing). If you find none, it is likely that you need to install further font packages, such
as ‘xorg-x11-fonts-ISO8859-2-75dpi’ and ‘xorg-x11-fonts-cyrillic’ shown in the listing
above.
Multi-byte encodings (most commonly UTF-8) are even more complicated. There are few
fonts in ‘iso10646-1’, the Unicode encoding, and they only contain a subset of the available
glyphs (and are often fixed-width designed for use in terminals). In such locales fontsets are
used, made up of fonts encoded in other encodings. If the locale you are using has an entry
in the ‘XLC_LOCALE’ directory (typically /usr/share/X11/locale, it is likely that all you need
to do is to pick a suitable font specification that has fonts in the encodings specified there. If
not, you may have to get hold of a suitable locale entry for X11. This may mean that, for
example, Japanese text can be displayed when running in ‘ja_JP.UTF-8’ but not when running
in ‘en_GB.UTF-8’ on the same machine (although on some systems many UTF-8 X11 locales are
aliased to ‘en_US.UTF-8’ which covers several character sets, e.g. ISO 8859-1 (Western Euro-
pean), JISX0208 (Kanji), KSC5601 (Korean), GB2312 (Chinese Han) and JISX0201 (Kana)).
On some systems scalable fonts are available covering a wide range of glyphs. One source is
TrueType/OpenType fonts, and these can provide high coverage. Another is Type 1 fonts: the
URW set of Type 1 fonts provides standard typefaces such as Helvetica with a larger coverage
of Unicode glyphs than the standard X11 bitmaps, including Cyrillic. These are generally not
part of the default install, and the X server may need to be configured to use them. They might
be under the X11 fonts directory or elsewhere, for example,
/usr/share/fonts/default/Type1
/usr/share/fonts/ja/TrueType
C.2 Linux
Linux is the main development platform for R, so compilation from the sources is normally
straightforward with the standard compilers.
Remember that some package management systems (such as RPM and deb) make a distinction
between the user version of a package and the developer version. The latter usually has the same
name but with the extension ‘-devel’ or ‘-dev’: you need both versions installed. So please check
the configure output to see if the expected features are detected: if for example ‘readline’
is missing add the developer package. (On most systems you will also need ‘ncurses’ and its
developer package, although these should be dependencies of the ‘readline’ package(s).) You
should expect to see in the configure summary
Interfaces supported: X11, tcltk
External libraries: readline, zlib, bzlib, lzma, PCRE, curl
Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU
When R has been installed from a binary distribution there are sometimes problems with
missing components such as the FORTRAN compiler. Searching the ‘R-help’ archives will
normally reveal what is needed.
It seems that ‘ix86’ Linux accepts non-PIC code in shared libraries, but this is not necessarily
so on other platforms, in particular on 64-bit CPUs such as ‘x86_64’. So care can be needed
with BLAS libraries and when building R as a shared library to ensure that position-independent
Appendix C: Platform notes 52
code is used in any static libraries (such as the Tcl/Tk libraries, libpng, libjpeg and zlib)
which might be linked against. Fortunately these are normally built as shared libraries with the
exception of the ATLAS BLAS libraries.
The default optimization settings chosen for CFLAGS etc are conservative. It is likely that
using -mtune will result in significant performance improvements on recent CPUs (especially
for ‘ix86’): one possibility is to add -mtune=native for the best possible performance on the
machine on which R is being installed: if the compilation is for a site-wide installation, it
may still be desirable to use something like -mtume=core2.2 It is also possible to increase the
optimization levels to -O3: however for many versions of the compilers this has caused problems
in at least one CRAN package.
For platforms with both 64- and 32-bit support, it is likely that
LDFLAGS="-L/usr/local/lib64 -L/usr/local/lib"
is appropriate since most (but not all) software installs its 64-bit libraries in /usr/local/lib64.
To build a 32-bit version of R on ‘x86_64’ with Fedora 18 we used
CC="gcc -m32"
CXX="g++ -m32"
F77="gfortran -m32"
FC=${F77}
OBJC=${CC}
LDFLAGS="-L/usr/local/lib"
LIBnn=lib
Note the use of ‘LIBnn’: ‘x86_64’ Fedora installs its 64-bit software in /usr/lib64 and 32-bit
software in /usr/lib. Linking will skip over inappropriate binaries, but for example the 32-bit
Tcl/Tk configure scripts are in /usr/lib. It may also be necessary to set the pkg-config path,
e.g. by
export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:/usr/lib/pkgconfig
64-bit versions of Linux are built with support for files > 2Gb, and 32-bit versions will be if
possible unless --disable-largefile is specified.
To build a 64-bit version of R on ‘ppc64’ (also known as ‘powerpc64’) with gcc 4.1.1, Ei-ji
Nakama used
CC="gcc -m64"
CXX="gxx -m64"
F77="gfortran -m64"
FC="gfortran -m64"
CFLAGS="-mminimal-toc -fno-optimize-sibling-calls -g -O2"
FFLAGS="-mminimal-toc -fno-optimize-sibling-calls -g -O2"
the additional flags being needed to resolve problems linking against libnmath.a and when
linking R as a shared library.
C.2.1 Clang
R has been built with Linux ‘ix86’ and ‘x86_64’ C and C++ compilers (http://clang.llvm.
org) based on the Clang front-ends, invoked by CC=clang CXX=clang++, together with gfortran.
These take very similar options to the corresponding GCC compilers.
This has to be used in conjunction with a Fortran compiler: the configure code will remove
-lgcc from FLIBS, which is needed for some versions of gfortran.
The current default for clang++ is to use the C++ runtime from the installed g++. Using the
runtime from the libc++ project (http://libcxx.llvm.org/) has also been tested: for some
R packages only the variant using libcxxabi was successful.
2
or -mtune=corei7 for Intel Core i3/15/17 with gcc >= 4.6.0.
Appendix C: Platform notes 53
C.3 OS X
You can build R using Apple’s ‘Command-line Tools for Xcode’ and and suitable compilers. You
will also need readline (or to configure with --without-readline), and a Fortran compiler.
Those and other binary components are available from http://r.research.att.com/libs.
You may also need to install an X sub-system (or you will need to configure using option
--without-x): X is part of the standard OS X distribution in versions prior to Mountain Lion,
but not always installed. For Mountain Lion and later, see http://xquartz.macosforge.org/
. (Note that XQuartz will likely need to be re-installed after an OS upgrade.)
The instructions here are for ‘x86_64’ builds on 10.6 (Snow Leopard) or later. In principle
R can be built for 10.4.x, 10.5.x and for PowerPC or 32-bit Intel Macs but these has not been
tested recently.
To use the quartz() graphics device you need to configure with --with-aqua (which is the
default): quartz() then becomes the default device when running R at the console and X11
would only be used for the command-line-R data editor/viewer. (This needs an Objective-C
compiler3 which can compile the source code of quartz().)
Use --without-aqua if you want a standard Unix-alike build: apart from disabling quartz()
and the ability to use the build with R.app, it also changes the default location of the personal
library (see ?.libPaths()). Also use --disable-R-framework to install in the standard layout.
Various compilers can be used. The current CRAN ‘Mavericks’ distribution of R is built using
CC=clang
CXX=clang++
F77=gfortran-4.8
FC=$F77
OBJC=clang
CFLAGS=-Wall -mtune=core2 -g -O2
CXXFLAGS=-Wall -mtune=core2 -g -O2’
OBJCFLAGS=-Wall -mtune=core2 -g -O2
F77FLAGS=-Wall -g -O2
FCFLAGS=$F77FLAGS
with clang and clang++ from Xcode 5, and the Fortran compiler from http://r.research.
att.com/libs/gfortran-4.8.2-darwin13.tar.bz2.4 Apple’s builds of clang currently have
little or no OpenMP support.
The CRAN ‘Snow Leopard’ distribution of R was built using
• gcc from an Xcode distribution prior to version 5. This is a version of gcc 4.2.1 with an
LLVM backend.
• gfortran from http://cran.r-project.org/bin/macosx/tools/gfortran-4.2.3.pkg.
Note that this installs into /usr/local/bin, so make sure that is on your path. Other
compilers from http://r.research.att.com/tools/ can also be used.
• clang from the Xcode distribution, to compile the Objective-C parts of the quartz()
device.
To use these, have in config.site something like
CC="llvm-gcc-4.2"
CXX="llvm-g++-4.2"
F77="gfortran-4.2 -arch x86_64"
FC=$F77
3
These days that is defined by Apple’s implementation of clang, so it is strongly recommended to use that.
4
This is a tarball which needs to be unpacked in the Terminal by e.g. sudo tar -zxf gfortran-4.8.2-
darwin13.tar.bz2 -C /.
Appendix C: Platform notes 55
OBJC="clang"
Full names help to ensure that the intended compilers are used. In particular gcc is a copy
of llvm-gcc-4.2 for Xcode < 5 but of clang in Xcode 5. The recommended Fortran compiler
defaults to 32-bit, so -arch x86_64 is needed. (For a 32-bit build, use -arch i386 for all
compiler commands.)
The OpenMP support in this version of gcc is problematic, so the CRAN build is configured
with --disable-openmp.
Pre-compiled versions of many of the Section A.2 [Useful libraries and programs], page 36 are
available from http://r.research.att.com/libs/. You will most likely want at least pcre,
xz, jpeg, libpng and readline (and perhaps tiff). pkg-config is not provided by Apple and
useful for many packages: it will also be used if present when configuring the X11() device.
Recent versions of OS X ship with zlib version 1.2.8 and bzlib version 1.0.6, sufficient for
the default configure checks. Mavericks has a recent enough version of libcurl: Snow Leopard
does not.
The Accelerate library can be used via the configuration options
--with-blas="-framework Accelerate" --with-lapack
to provide potentially higher-performance versions of the BLAS and LAPACK routines. (Use of
Accelerate with --with-lapack does not work on Snow Leopard: it may work there without.)5
Looking at the top of /Library/Frameworks/R.framework/Resources/etc/Makeconf will
show the compilers and configuration options used for the CRAN binary package for R: at the
time of writing
--enable-memory-profiling
was used for ‘Mavericks’.
Configure option --with-internal-tzcode is the default, as a 64-bit time_t is available
but the system implementation of time zones does not work correctly for times before 1902 or
after 2037.
The TEX implementation used by the developers is MacTeX (http://www.tug.org/mactex/
): the full installation is about 4GB, but a smaller version is available at http://www.tug.org/
mactex/morepackages.html: you will need to add some packages, e.g. for the 2014 version we
needed to add cm-super, ec, helvetic, inconsolata and texinfo which brought this to about 380MB
(or package texinfo and the collections collection-fontsrecommended, collection-fontsextra and
collection-latexextra which will take this up to about 1GB). ‘TeX Live Utility’ (available via
the MacTeX front page) provides a graphical means to manage TEX packages.
One OS X quirk is that the default path has /usr/local/bin after /usr/bin, contrary to
common practice on Unix-alikes. This means that if you install tools from the sources they will
by default be installed under /usr/local and not supersede the system versions.
To use the compilers from the command-line tools for Xcode 5 or 6 with the recommended
Fortran compiler, have in config.site something like
CC=clang
CXX=clang++
F77=gfortran-4.8
FC=$F77
OBJC=clang
(CC=gcc and CXX=g++ are slightly different front-ends to the same compilers.) Recent versions
of the CRAN binary package installer for ‘Snow Leopard’ change the settings in etc/Makeconf
to
CC = gcc -arch x86_64 -std=gnu99
CXX g++ -arch x86_64
F77 = gfortran-4.2 -arch x86_64
OBJC = gcc -arch x86_64
OBJCXX = g++ -arch x86_64
when installing on Mavericks.
See the comments under Mountain Lion about X11 and GTK.
If you upgrade to Yosemite you should re-install any of XQuartz, the ‘Command-line Tools for
Xcode’ and Java which you have installed. (Upgrading may partially remove previous versions
which can be confusing.)
There are some problems with the recommended gfortran builds under Yosemite. They
give warnings and gfortran-4.8 is reported to be unable to link packages containing Fortran
9x code. (The solution is to use a compiler built under Yosemite.)
The CRAN binaries are built using Xcode 4.2, a version available only to subscribing devel-
opers. It is believed that 3.2.6 (the last public free version for Snow Leopard) will work.
C.3.5 Java
The situation with Java support on OS X is messy, with Apple essentially no longer supporting
Java (and what it does support is Java 6, which has reached end-of-life). Snow Leopard and
Lion shipped with a Java 6 runtime (JRE).
Mountain Lion and later do not come with an installed JRE, and an OS X upgrade removes
one if already installed: it is intended to be installed at first use. Check if a JRE is installed by
running java -version in a Terminal window: if Java is not installed this should prompt you
to install it.
You may want/need to install the latest Java from Oracle (currently Java 8 from http://
www.oracle.com/technetwork/java/javase/downloads/index.html); this is for Lion and
later.
You may need to install what Apple calls ‘legacy Java’6 to suppress pop-up messages, at least
under Yosemite, even if you have a current version installed.
To see what compatible versions of Java are currently installed, run /usr/libexec/java_
home -V -a x86_64. If needed, set the environment variable JAVA_HOME to choose between these,
both when R is built from the sources and when R CMD javareconf is run.
Configuring and building R both looks for a JRE and for support for compiling JNI programs
(used by packages rJava and JavaGD); the latter requires a JDK (Java SDK) and not just a
JRE.
6
e.g. Java For OS X 2014-001.
Appendix C: Platform notes 58
The build process tries to fathom out what JRE/JDK to use, but it may need some help,
e.g. by setting JAVA_HOME. The Apple JRE can be specified explicitly by something like
JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Home
JAVA_CPPFLAGS="-I/System/Library/Frameworks/JavaVM.framework/Headers"
JAVA_LD_LIBRARY_PATH=
JAVA_LIBS="-framework JavaVM"
The Apple developer versions of the JDK install somewhere like
JAVA_HOME=/Library/Java/JavaVirtualMachines/1.6.0_43-b01-447.jdk/Contents/Home
The Oracle JDK can be specified explicitly by something like
JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home
JAVA_CPPFLAGS="-I/${JAVA_HOME}/include -I/${JAVA_HOME}/include/darwin"
JAVA_LD_LIBRARY_PATH="${JAVA_HOME}/jre/lib/server"
JAVA_LIBS="-L/${JAVA_HOME}/jre/lib/server -ljvm"
in config.site.
Note that it is necessary to set the environment variable NOAWT to 1 to install many of the
Java-using packages.
C.3.6 Frameworks
The CRAN build of R is installed as a framework, which is selected by the default option
./configure --enable-R-framework
(This is intended to be used with an Apple toolchain: other compilers may not support
frameworks correctly.)
It is only needed if you want to build R for use with the R.app console, and implies
--enable-R-shlib to build R as a dynamic library. This option configures R to be built and
installed as a framework called R.framework. The default installation path for R.framework
is /Library/Frameworks but this can be changed at configure time by specifying the flag
--enable-R-framework[=DIR] or at install time as
make prefix=/where/you/want/R.framework/to/go install
Note that installation as a framework is non-standard (especially to a non-standard loca-
tion) and utilities may not support it (e.g. the pkg-config file libR.pc will be put somewhere
unknown to pkg-config).
C.4 Solaris
R has been built successfully on Solaris 10 (both Sparc and ‘x86’) using the (zero cost) Oracle
Solaris Studio compilers: there has been some success with gcc 4/gfortran. (Recent Sun ma-
chines are AMD Opterons or Intel Xeons (‘amd64’) rather than ‘x86’, but 32-bit ‘x86’ executables
are the default.)
There have been few reports on Solaris 11, with no known extra issues. Solaris 9 and earlier
are now so old that it is unlikely that R is still used with them, and they will not be considered
here.
The Solaris versions of several of the tools needed to build R (e.g. make, ar and ld) are in
/usr/ccs/bin, so if using those tools ensure this is in your path. A version of the preferred
GNU tar is (if installed) in /usr/sfw/bin. It may be necessary to avoid the tools in /usr/ucb:
POSIX-compliant versions of some tools can be found in /usr/xpg4/bin and /usr/xpg6/bin.
A large selection of Open Source software can be installed from http://www.opencsw.org,
by default installed under /opt/csw. Solaris 10 ships with bzlib version 1.0.6 (sufficient for
the default --with-system-bzlib) but zlib version 1.2.3 (too old for --with-system-zlib):
OpenCSW has 1.2.8.
You will need GNU libiconv and readline: the Solaris version of iconv is not sufficiently
powerful.
The native make suffices to build R but a small number of packages require GNU make (some
without good reason and without declaring it as ‘SystemRequirements’ in the DESCRIPTION
file).
Some people have reported that the Solaris libintl needs to be avoided, for example by
using --disable-nls or --with-included-gettext or using libintl from OpenCSW.
The support for the C99 long double type on Sparc hardware uses quad-precision arithmetic,
and this is usually slow because it is done by software emulation. On such systems configure
option --disable-long-double can be used for faster but less accurate computations.
The Solaris time-zone conversion services seem to be unreliable pre-1916 in Europe (when
daylight-savings time was first introduced): most often reporting in the non-existent DST vari-
ant. Using configure option --with-internal-tzcode is recommended, and required if you
find time-zone abbreviations being given odd values (as has been seen on 64-bit builds without
it).
When using the Oracle compilers7 do not specify -fast, as this disables IEEE arithmetic and
make check will fail.
It has been reported that some Solaris installations need
INTERNET_LIBS="-lsocket -lnsl"
on the configure command line or in file config.site; however, there have been many suc-
cessful installs without this.
A little juggling of paths was needed to ensure GNU libiconv (in /usr/local) was used
rather than the Solaris iconv:
CC="cc -xc99"
CFLAGS="-O -xlibmieee"
F77=f95
FFLAGS=-O
CXX="CC -library=stlport4"
CXXFLAGS=-O
FC=f95
7
including gcc for Sparc from Oracle.
Appendix C: Platform notes 60
FCFLAGS=$FFLAGS
FCLIBS="-lfai -lfsu"
R_LD_LIBRARY_PATH="/usr/local/lib:/opt/csw/gcc4/lib:/opt/csw/lib"
For a 64-bit target add -m64 to the compiler macros and use something like
LDFLAGS=-L/usr/local/lib/sparcv9 or LDFLAGS=-L/usr/local/lib/amd64 as appropriate.
It will also be necessary to point pkg-config at the 64-bit directories, e.g. one of
PKG_CONFIG_PATH=/opt/csw/lib/amd64/pkgconfig:/usr/lib/amd64/pkgconfig
PKG_CONFIG_PATH=/opt/csw/lib/sparcv9/pkgconfig:/usr/lib/sparcv9/pkgconfig
and to specify a 64-bit Java VM by e.g.
JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/solaris"
JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/lib/amd64/server
JAVA_LIBS="-L${JAVA_HOME}/lib/amd64/server \
-R${JAVA_HOME}/lib/amd64/server -ljvm"
With Solaris Studio 12.[23] on Sparc, FCLIBS needs to be
FCLIBS="-lfai -lfai2 -lfsu"
(and possibly other Fortran libraries, but this suffices for the packages currently on CRAN).
Currently ‘amd64’ and ‘sparcv9’ builds work out-of-the-box with Sun Studio 12u1 but not
Solaris Studio 12.2 and 12.3: libRblas.so and lapack.so are generated with code that causes
relocation errors (which is being linked in from the Fortran libraries). This means that building
64-bit R as a shared library may be impossible with Solaris Studio >= 12.2. For a standard build
the trick seems to be to manually set FLIBS to avoid the troublesome libraries. For example, on
‘amd64’ set in config.site something like
FLIBS_IN_SO="-R/opt/solarisstudio12.3/lib/amd64
/opt/solarisstudio12.3/lib/amd64/libfui.so
/opt/solarisstudio12.3/lib/amd64/libfsu.so"
For 64-bit Sparc, set in config.site something like
FLIBS="-R/opt/solarisstudio12.3/prod/lib/sparc/64
-lifai -lsunimath -lfai -lfai2 -lfsumai -lfprodai -lfminlai -lfmaxlai
-lfminvai -lfmaxvai -lfui -lsunmath -lmtsk
/opt/solarisstudio12.3/prod/lib/sparc/64/libfsu.so.1"
By default the Solaris Studio compilers do not by default conform to the C99 standard
(appendix F 8.9) on the return values of functions such as log: use -xlibmieee to ensure this.
You can target specific Sparc architectures for (slightly) higher performance:
-xtarget=native (in CFLAGS etc) tunes the compilation to the current machine.
Using -xlibmil in CFLAGS and -xlibmil in FFLAGS allows more system mathematical func-
tions to be inlined.
On ‘x86’ you will get marginally higher performance via
CFLAGS="-xO5 -xc99 -xlibmieee -xlibmil -nofstore -xtarget=native"
FFLAGS="-O5 -libmil -nofstore -xtarget=native"
CXXFLAGS="-xO5 -xlibmil -nofstore -xtarget=native"
SAFE_FFLAGS="-libmil -fstore -xtarget=native"
but the use of -nofstore can be less numerically stable, and some packages (notably mgcv on
‘x86’) failed to compile at higher optimization levels with version 12.3.
The Solaris Studio compilers provide several implementations of the C++98 standard which
select both the set of headers and a C++ runtime library. These are selected by the -library
flag, which as it is needed for both compiling and linking is best specified as part of the compiler.
The examples above use ‘stlport4’, currently the most modern of the options: the default (but
still needed to be specified as it is needed for linking) is ‘Cstd’: see http://developers.sun.
Appendix C: Platform notes 61
FC=$F77
FCPICFLAGS=$FPICFLAGS
LDFLAGS="-L/opt/csw/gcc4/lib/amd64 -L/opt/csw/lib/amd64"
C.5 AIX
We no longer support AIX prior to 4.2, and configure will throw an error on such systems.
Ei-ji Nakama was able to build under AIX 5.2 on ‘powerpc’ with GCC 4.0.3 in several
configurations. 32-bit versions could be configured with --without-iconv as well as --enable-
R-shlib. For 64-bit versions he used
OBJECT_MODE=64
CC="gcc -maix64"
CXX="g++ -maix64"
F77="gfortran -maix64"
FC="gfortran -maix64"
and was also able to build with the IBM xlc and Hitachi f90 compilers by
OBJECT_MODE=64
CC="xlc -q64"
CXX="g++ -maix64"
F77="f90 -cpu=pwr4 -hf77 -parallel=0 -i,L -O3 -64"
FC="f90 -cpu=pwr4 -hf77 -parallel=0 -i,L -O3 -64"
FLIBS="-L/opt/ofort90/lib -lhf90vecmath -lhf90math -lf90"
Some systems have f95 as an IBM compiler that does not by default accept FORTRAN 77.
It needs the flag -qfixed=72, or to be invoked as xlf_r.
The AIX native iconv does not support encodings ‘latin1’ nor ‘""’ and so cannot be used.
(As far as we know GNU libiconv could be installed.)
Fan Long reports success on AIX 5.3 using
OBJECT_MODE=64
LIBICONV=/where/libiconv/installed
CC="xlc_r -q64"
CFLAGS="-O -qstrict"
CXX="xlC_r -q64"
CXXFLAGS="-O -qstrict"
F77="xlf_r -q64"
AR="ar -X64"
CPPFLAGS="-I$LIBICONV/include -I/usr/lpp/X11/include/X11"
LDFLAGS="-L$LIBICONV/lib -L/usr/lib -L/usr/X11R6/lib"
On one AIX 6.x system it was necessary to use R_SHELL to set the default shell to be Bash
rather than Zsh.
Kurt Hornik and Stefan Theussl at WU (Wirtschaftsuniversität Wien) successfully built R
on a ‘powerpc’ (8-CPU Power6 system) running AIX 6.1, configuring with or without --enable-
R-shlib (Ei-ji Nakama’s support is gratefully acknowledged).
It helps to describe the WU build environment first. A small part of the software needed
to build R and/or install packages is available directly from the AIX Installation DVDs, e.g.,
Java 6 and X11. Additional open source software (OSS) is packaged for AIX in .rpm files and
available from both IBM’s “AIX Toolbox for Linux Applications” (http://www-03.ibm.com/
systems/power/software/aix/linux/) and http://www.oss4aix.org/download/. The
latter website typically offers more recent versions of the available OSS. All tools needed and
libraries downloaded from these repositories (e.g., GCC, Make, libreadline, etc.) are typically
installed to /opt/freeware, hence corresponding executables are found in /opt/freeware/bin
Appendix C: Platform notes 63
which thus needs to be in PATH for using these tools. As on other Unix systems one needs GNU
libiconv as the AIX version of iconv is not sufficiently powerful. Additionally, for proper Uni-
code compatibility one should install the corresponding package from the ICU project (http://
www.icu-project.org/download/), which offers pre-compiled binaries for various platforms
which in case of AIX can be installed via unpacking the tarball to the root file system. For full
LATEX support one can install the TEX Live DVD distribution (http://www.tug.org/texlive/
): it is recommended to update the distribution using the tlmgr update manager. For 64-bit
R builds supporting Tcl/Tk this needs to installed from the sources as available pre-compiled
binaries supply only 32-bit shared objects.
The recent WU testing was done using compilers from both the GNU Compiler Collec-
tion (version 4.2.4) which is available from one of the above OSS repositories, and the IBM
C/C++ (XL C/C++ 10.01) as well as FORTRAN (XL Fortran 12.01) compilers (http://www14.
software.ibm.com/webapp/download/byproduct.jsp#X).
To compile for a 64-bit ‘powerpc’ (Power6 CPU) target one can use
CC ="gcc -maix64 -pthread"
CXX="g++ -maix64 -pthread"
FC="gfortran -maix64 -pthread"
F77="gfortran -maix64 -pthread"
CFLAGS="-O2 -g -mcpu=power6"
FFLAGS="-O2 -g -mcpu=power6"
FCFLAGS="-O2 -g -mcpu=power6"
for the GCC and
CC=xlc
CXX=xlc++
FC=xlf
F77=xlf
CFLAGS="-qarch=auto -qcache=auto -qtune=auto -O3 -qstrict -ma"
FFLAGS="-qarch=auto -qcache=auto -qtune=auto -O3 -qstrict"
FCFLAGS="-qarch=auto -qcache=auto -qtune=auto -O3 -qstrict"
CXXFLAGS="-qarch=auto -qcache=auto -qtune=auto -O3 -qstrict"
for the IBM XL compilers. For the latter, it is important to note that the decision for generating
32-bit or 64-bit code is done by setting the OBJECT_MODE environment variable appropriately
(recommended) or using an additional compiler flag (-q32 or -q64). By default the IBM XL
compilers produce 32 bit code. Thus, to build R with 64-bit support one needs to either export
OBJECT_MODE=64 in the environment or, alternatively, use the -q64 compiler options.
It is strongly recommended to install Bash and use it as the configure shell, e.g., via
setting CONFIG_SHELL=/usr/bin/bash in the environment, and to use GNU Make (e.g., via
(MAKE=/opt/freeware/bin/make).
Further installation instructions to set up a proper R development environment can be found
in the “R on AIX” project on R-Forge (http://R-Forge.R-project.org/projects/aix/).
C.6 FreeBSD
There have been no reports for R 3.0.0 or later.
C.7 Cygwin
The Cygwin emulation layer on Windows can be treated as a Unix-alike OS. This is unsupported,
but experiments have been conducted and a few workarounds added. Cygwin has not been tested
for R 3.0.0 or later.
Appendix C: Platform notes 64
The 64-bit version is completely unsupported. The 32-bit version has never worked well
enough to pass R’s make check.
R requires C99 complex type support, which is available as from Cygwin 1.7.8 (March 2011).
However, the (then) implementation of cacos gives incorrect results, so we undefine HAVE_
CACOS in src/main/complex.c on that platform. It has been reported that some C99 long
double mathematical functions are missing, so configuring with --disable-long-double was
required.
Only building as a shared library can possibly work,8 so use e.g.
./configure --disable-nls --enable-R-shlib FLIBS=-lgfortran
make
Enabling NLS does work if required, although adding --with-included-gettext is preferable.
You will see many warnings about the use of auto-import. Setting ‘FLIBS’ explicitly seems
needed currently as the auto-detection gives an incorrect value.
You will need the tetex-extra Cygwin package to build NEWS.pdf and the vignettes.
Note that this gives you a command-line application using readline for command editing.
The ‘X11’ graphics device will work if a suitable X server is running, and the standard Unix-alike
ways of installing source packages work. There was a bug in the /usr/lib/tkConfig.sh script
in the version we looked at, which needs to have
TK_LIB_SPEC=’-ltk84’
The overhead of using shell scripts makes this noticeably slower than a native build of R on
Windows.
Even when R could be built, not all the tests passed: there were incorrect results from
wide-character regular expressions code and from sourcing CR-delimited files.
Do not use Cygwin’s BLAS library: it is known to give incorrect results.
know better (for tools from the GNU Compiler Collection and/or platforms we know about).
This typically works, but you may have to manually override the results. Scanning the manual
entries for cc and ld usually reveals the correct incantation. Once you know the recipe you can
modify the file config.site (following the instructions therein) so that the build will use these
options.
It seems that gcc 3.4.x and later on ‘ix86’ Linux defeat attempts by the LA-
PACK code to avoid computations entirely in extended-precision registers, so file
src/modules/lapack/dlamc.f may need to be compiled without optimization. Set the
configure variable SAFE_FFLAGS to the flags to be used for this file. If configure detects GNU
FORTRAN it adds flag -ffloat-store to FFLAGS. (Other settings are needed when using icc
on ‘ix86’ Linux, for example. Using -mpc64 is preferable on more recent GCC compilers.)
If you do manage to get R running on a new platform please let us know about it so we can
modify the configuration procedures to include that platform.
If you are having trouble getting R to work on your platform please feel free to use the
‘R-devel’ mailing list to ask questions. We have had a fair amount of practice at porting R to
new platforms . . .
Appendix D: The Windows toolset 66
at one time we found our tools did not work with a newer version of the Cygwin DLLs, so it
may be safest not to have any other version of the Cygwin DLLs in your path.
D.1 LATEX
The ‘MiKTeX’ (http://www.miktex.org/) distribution of LATEX includes a suitable port of
pdftex. This can be set up to install extra packages ‘on the fly’, which is the simplest way
to use it (and the default). The ‘basic’ version of ‘MiKTeX’ almost suffices: when last tested
packages
epsf fancyvrb inconsolata listings mptopdf natbib url
needed to be added (on the fly or via the ‘MiKTeX’ Package Manager) to install R. In any
case ensure that the inconsolata package is installed—you can check with the ‘MiKTeX’ Package
Manager.
The Rtools*.exe installer does not include any version of LATEX.
It is also possible to use the TeXLive distribution from http://www.tug.org/texlive/.
Please read Section 2.3 [Making the manuals], page 4 about how to make fullrefman.pdf
and set the environment variable R_RD4PDF suitably; ensure you have the required fonts installed
or that ‘MiKTeX’ is set up to install LATEX packages on first use.
and -m64 respectively. The tools are all 32-bit Windows executables and should be able to run
on any current version of Windows—however you do need a 64-bit version of Windows to build
64-bit R as the build process runs R.
To select a 32-bit or 64-bit build of R, set the options in MkRules.local appropriately
(following the comments in the file).
Some external software libraries will need to be re-compiled under the new toolchain: espe-
cially those providing a C++ interface. Many of those used by CRAN packages are available from
http://www.stats.ox.ac.uk/pub/Rtools/multilib/. Users developing packages with Rcpp
need to ensure that they use a version built with exactly the same toolchain as their package:
the recommendation is to build Rcpp from its sources yourself.
There is support for OpenMP and pthreads in this toolchain. As the performance of OpenMP
on Windows is poor for small tasks, it is not used for R itself.
C R
configure . . . . . . . . . . . . . . . . . . . . . . . . . . 3, 4, 6, 7, 45, 46
R_HOME . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
remove.packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
I
install.packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
M U
make . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 update.packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Concept index 70
Concept index
A O
AIX . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62 Obtaining R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
OS X . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3, 18, 54
B
BLAS library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39, 55, 61 P
Packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Packages, default . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
F Packages, installing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
FORTRAN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 Packages, removing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
FreeBSD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63 Packages, updating . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
I R
Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Repositories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Installing under Unix-alikes . . . . . . . . . . . . . . . . . . . . . . . 3
Installing under Windows . . . . . . . . . . . . . . . . . . . . . . . . 12
Internationalization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28 S
Site libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Solaris . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
L Sources for R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
LAPACK library. . . . . . . . . . . . . . . . . . . . . . . . . . 42, 55, 61 Subversion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1, 36
Libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Libraries, managing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Libraries, site . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 U
Libraries, user . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 User libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Linux . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3, 51
Locale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Localization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28 V
Vignettes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
M
Manuals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 W
Manuals, installing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
winCairo.dll. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Environment variable index 71
B O
BLAS_LIBS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39 OBJECT_MODE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
C P
CC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 PAPERSIZE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
CONFIG_SITE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45 PATH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36, 47, 62, 66
CPP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
CYGWIN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
R
D R_ARCH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
DESTDIR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8, 33 R_BROWSER . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
R_DEFAULT_PACKAGES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
R_DISABLE_HTTPD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
F R_GSCMD. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
F2C . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 R_INSTALL_TAR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
F2CLIBS. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 R_JAVA_LD_LIBRARY_PATH . . . . . . . . . . . . . . . . . . . . . . . . 38
FPICFLAGS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 R_LIBS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
R_LIBS_SITE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
R_LIBS_USER . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
J R_PAPERSIZE . . . . . . . . . . . . . . . . . . . . . . . . . . . 5, 20, 45, 46
JAVA_HOME . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 R_PDFVIEWER . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
R_RD4PDF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6, 46, 67
R_SHELL. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
L R_USER . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
LANG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
LANGUAGE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29, 30
LAPACK_LIBS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 T
LC_ALL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 TAR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
LC_COLLATE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 TAR_OPTIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1, 13
LC_MESSAGES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 TEMP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
LD_LIBRARY_PATH . . . . . . . . . . . . . . . . . . 33, 40, 47, 48, 61 TMP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
LOCAL_SOFT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 TMPDIR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3, 13, 20, 21