This is a guide to installation and administration for R.
The current version of this document is 1.4.0 (2001-08-07).
Sources, binaries and documentation for R can be obtained via
CRAN, the "Comprehensive R Archive Network". See the file
RESOURCES for information on CRAN.
The simplest way is to download the most recent
R-x.y.z.tgz file, and unpack it with
tar xvfz R-x.y.z.tgz
on systems that have GNU tar installed. On other systems you
need at least to have the gzip program installed. Then you
can use
gzip -dc R-x.y.z.tgz | tar xvf -
If you need to transport the sources on floppy disks, you can download
the R-x.y.z.tgz-split.* files and paste them
together at the destination with (Unix)
cat R-x.y.z-split.* > R-x.y.z.tgz
and proceed as above. If you want the build to be usable by a group of
users, set umask before unpacking so that the files will be
readable by the target group (e.g., umask 022 to be usable by all
users).
Finally, for minor-minor releases (x.y.z with
z != 0), a patch against the preceding release is made available
in
R-x.y.{z-1}-x.y.z.diff.gz
(e.g., R-1.2.2-1.2.3.diff.gz), which is generally a much smaller
file that the .tgz files. Such a file can be applied to the
sources of the previous version by changing to the top directory of it
and
gzip -dc /path/to/it/R-x.y.{z-1}-x.y.z.diff.gz | patch -E -p1
Beware that this does not necessarily work if the older sources have been modified (e.g., by building in their directories).
Sources are also available via anonymous rsync. Use
rsync -rC rsync.r-project.org::module R
to create a copy of the source tree specified by module in the
subdirectory R of the current directory, where module
specifies one of the three existing flavours of the R sources, and be
one of r-release (current released version), r-patched
(patched released version), and r-pre-release (pre-release
development version). The rsync trees are created directly from the
master CVS archive and are updated hourly. The -C option in
the rsync command is to cause it to skip the CVS directories.
Further information on rsync is available at
http://rsync.samba.org/rsync/.
R will configure and build from source under a number of common
Unix-like platforms, including i386-freebsd, i386-linux,
i386-sun-solaris, ppc-linux, mips-sgi-irix,
alpha-linux, alpha-dec-osf4, rs6000-ibm-aix,
hppa-hp-hpux, sparc-linux and sparc-sun-solaris.
In addition, binary distributions are available for most common Linux distributions, Compaq Alpha systems running OSF/Tru64, and for MacOS X (Darwin) with X11. See the FAQ for current details. These are installed in platform-specific ways. So for the rest of this chapter we consider only building from the sources.
First review the essential and useful tools and libraries in Essential and useful other programs, and install those you want or need.
Choose a place to install the R tree (R is not just a binary, but
has additional data sets, help files, font metrics etc). Let us call
this place R_HOME. Untar the source code. This should create
directories src, doc, and several more. Issue the
following commands:
./configure make
(See Using make if your make is not called make.)
Then check the built system works correctly, by
make check
Failures are not necessarily problems as they might be caused by missing functionality, but you should look carefully at any reported discrepancies. To re-run the tests you would need
make check FORCE=FORCE
If these commands execute successfully, the R binary will be copied
to the ${R_HOME}/bin directory. In addition, a shell-script
front-end called R will be created and copied to the same
directory. You can copy this script to a place where users can invoke
it, for example to /usr/local/bin/R. You could also copy the man
page R.1 to a place where your man reader finds it,
such as /usr/local/man/man1. If you want to install the complete
R tree to, e.g., /usr/local/lib/R, see Installation.
Note: you do not need to install R: you can run it from where
it was built.
You do not necessarily have to build R in the top-level source
directory (say, TOP_SRCDIR). To build in BUILDDIR, run
cd BUILDDIR TOP_SRCDIR/configure make
and so on, as described further below. This has the advantage of always
keeping your source tree "clean". (You may need GNU make to
allow this.)
Make will also build plain text help pages as well as HTML and
LaTeX versions of the R object documentation (the three kinds can
also be generated separately using make help, make html
and make latex). Note that you need Perl version 5: if this is
not available on your system, you can obtain PDF versions of the
documentation files via CRAN.
Now rehash if necessary, type R, and read the R manuals
and the R FAQ (files FAQ or
doc/html/faq.html, or
http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html which always has
the latest version).
There is a set of manuals that can be built from the sources,
refman
R-FAQ
R-intro
R-data
R-admin
R-exts
R-lang
To make these, use
make dvi to create DVI versions
make pdf to create PDF versions
make info to create info files (not refman).
You will not be able to build the info files unless you have
makeinfo version 4 or later installed (and some Linux
distributions have 3.12).
The DVI versions can be previewed and printed using standard programs
such as xdvi and dvips. The PDF versions can be
viewed using Acrobat Reader or (recent versions of) ghostscript: they
have hyperlinks that can be followed in Acrobat Reader. The info files
are suitable for reading online with Emacs or the standalone GNU Info.
After
./configure make make check
have been completed successfully, you can install the complete R tree to your system by typing
make install
This will install to the following directories:
${prefix}/bin
${prefix}/man/man1
${prefix}/lib/R
where prefix is determined during configuration (typically
/usr/local) and can be set by running configure with
the option --prefix, as in
./configure --prefix=/where/you/want/R/to/go
This causes make install to install the R executable to
/where/you/want/R/to/go/bin, and so on. The prefix of the
installation directories can be seen in the status message that is
displayed at the end of configure. You can install into
another directory by using
make prefix=/path/to/here install
To install DVI, info and PDF versions of the manuals, use one or more of
make install-dvi make install-info make install-pdf
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.
The bin/windows directory of a CRAN site contains
binaries for a base distribution and a large number of add-on packages
from CRAN to run on Windows 95, 98, NT4, 2000 and ME (at
least) on Intel and clones (but not on other platforms).
You do need one of those Windows versions: Windows 3.11+win32s will not work.
Your file system must allow long file names (as is likely except perhaps for some network-mounted systems).
The simplest way is to use SetupR.exe or miniR.exe. Just
double-click on the icon and follow the instructions. If you installed
R this way you can uninstall it from the Control Panel or Start Menu
(unless you suppressed making a group for R).
See the R Windows FAQ for more details.
If you want to build this port from the sources, see the file
src/gnuwin32/INSTALL in the source distribution. You will need
to collect, install and test an extensive set of tools: see
http://www.stats.ox.ac.uk/pub/Rtools/ for the current locations.
You may need to compile under a case-honouring file system: we found
that a samba-mounted file system (which maps all file names to
lower case) did not work. Open a commands window at a directory whose
path does not contain spaces, and run something like
tar zxvf R-1.3.0.tgz cd R-1.3.0\src\gnuwin32 make
sit back and wait (for about 5 minutes on 1GHz PIII with a fast local disc).
For further details, including how to make the documentation and how to
cross-compile, see src/gnuwin32/INSTALL.
The bin/macos directory of a CRAN site contains
bin-hexed (hqx) and stuffit (sit)
archives for a base distribution and a large number of add-on packages
to run under MacOS 8.6 to MacOS 9.1 or MacOS X natively. Just extract
one of these archives in a suitable folder using standard utilities like
Aladdin Stuffit Expander (tm).
There is also a port to MacOS X which is considered to be a Unix variant
in this document. You can find it in the bin/macosx directory at
of a CRAN site.
This chapter applies to Unix-like and Windows versions of R, but not to the Classic MacOS port.
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 the R object
.lib.loc.
Note that you need to specify implicitly or explicitly the library to which the package is to be installed. This is only an issue if you have more than one library, of course.
To install packages from source on Unix use
R CMD INSTALL -l /path/to/library pkg1 pkg2 ...
The part -l /path/to/library can be omitted, when the first
library in R_LIBS is used if set, otherwise the main library
R_HOME/library.
The Windows equivalent is1
Rcmd INSTALL -l /path/to/library pkg1 pkg2 ...
Alternatively, packages can be downloaded and installed from within
R. First set the option CRAN to your nearest CRAN
mirror, for example
> options(CRAN = "http://cran.us.r-project.org/")
Then download and install package foo by
> install.packages("foo")
Unless the library is specified (argument lib) the first library
in .lib.loc is used.
What this does is different on Unix and Windows. On Unix it consults
the list of available source packages on CRAN, downloads the
latest version of the foo sources, and installs it (via R
CMD INSTALL). On Windows it looks at the list of binary
versions of packages and downloads the latest version (if any).
On Windows install.packages can also install a binary package
from a local zip file by setting argument CRAN to
NULL. RGui.exe has a menu Packages with a GUI
interface to install.packages, update.packages and
library.
The command update.packages() is the simplest way to ensure that
all the packages on your system are up to date. Set the CRAN
option as in the previous section. The update.packages()
downloads the list of available packages and their current versions,
compares it with those installed and offers to fetch and install any
that have later versions on CRAN.
Packages can be removed in a number of ways. From a command prompt they can be removed by
R CMD REMOVE -l /path/to/library pkg1 pkg2 ...
(Unix) or
Rcmd REMOVE -l /path/to/library pkg1 pkg2 ...
(Windows).
From a running R process they can be removed by
> remove.packages(c("pkg1", "pkg2"), lib="/path/to/library")
Finally, in most installations one can just remove the package directory from the library.
This appendix gives details of programs you will need to build R on
Unix-like platforms, or which will be used by R if found by
./configure.
You need a means of compiling C and FORTRAN (see Using FORTRAN). Some add-on packages also need a C++ compiler.
You will need Perl version 5, available via http://www.perl.com/CPAN/, to build any of the on-line documentation.
You will not be able to build the info files unless you have
makeinfo version 4 or later installed (and some Linux
distributions have 3.12).
The typeset documentation needs tex and latex, or
pdftex and pdflatex.
You can build R as a Unix application on MacOS X. You will need the
DevTools, f2c
(ftp://netlib.bell-labs.com/netlib/f2c.tar2) and the dlcompat libraries3.
You will also need to install a X sub-system or configure with
--without-x.
The command-line editing depends on the readline library
available from any GNU mirror: you will need a fairly recent version.
Use of gzfile connections needs zlib (version 1.1.3 or later).
The bitmapped graphics devices jpeg() and png() need the
appropriate libraries installed: jpeg (version 6b or later) or
libpng (version 1.0.5 or later)
and zlib (version 1.1.3 or later) respectively.
The bitmap and dev2bitmap devices make use of ghostscript
(http://www.cs.wisc.edu/~ghost).
The tcltk package needs Tcl/Tk installed: the sources are available at http://dev.scriptics.com/. To specify the locations of the Tcl/Tk files you may need the configuration options
--with-tcltk
--with-tcl-config=TCL_CONFIG
tclConfig.sh
--with-tk-config=TK_CONFIG
tkConfig.sh
The linear algebra routines in R can make use of enhanced BLAS (Basic
Linear Algebra Subprograms, http://www.netlib.org/blas/faq.html)
routines. Some are compiler-system-specific (libsunperf on Sun
Sparc4, libessl on IBM) but ATLAS
(http://www.netlib.org/atlas/) is a `tuned' BLAS that runs on a
wide range of platforms. If no more specific library is found, a
libblas library in the library path will be used. You can
specify a specific BLAS library by the configuration option
--with-blas and not to use an external BLAS library by
--without-blas.
Note that the BLAS library will be used for several add-on packages as well as for R itself. This means that it is better to use a shared BLAS library, as most of a static library will be compiled into the R executable and each BLAS-using package.
You will need double-precision and double-complex versions of the BLAS, but not single-precision nor complex routines.
Optimized versions of LAPACK are available, but no provision is made for using them with R as the likely performance gains are thought to be small.
As with all libraries, you need to ensure that they and R were
compiled with compatible compilers and flags. For example, this means
that on Sun Sparc using the native compilers the flag -dalign is
needed so libsunperf can be used.
configure has many options: running
./configure --help
will give a list. Probably the most important ones not covered elsewhere are (defaults in brackets)
--with-x
--x-includes=DIR
--x-libraries=DIR
--with-readline
--enable-R-profiling
Rprof() [yes]
--enable-R-shlib
You can use --without-foo or --disable-foo for the
negatives.
You will want to use --disable-R-profiling if you are building
a profiled executable of R (e.g. with -pg).
Flag --enable-R-shlib causes the make process to build R as a
shared library, typically called libR.so, and to take
considerably longer, so you probably only want this if you will be using
an application which embeds R.
If you need or want to set certain configure variables to something
other than their default, you can do that by either editing the file
config.site (which documents all the variables you might want to
set) or on the command line as
VAR="..." ./configure # Bourne shell compatibles (setenv VAR "..."; ./configure) # C shell
One common variable to change is R_PAPERSIZE, which defaults to
a4, not letter.
If you have libraries and header files, e.g., for GNU readline, in
non-system directories, use the variables LIBS (for libraries)
and CPPFLAGS (for header files), respectively, to specify these
locations. These default to /usr/local/lib and
/usr/local/include to catch the most common cases. If libraries
are still not found, then maybe your compiler/linker does not support
re-ordering of -L and -l flags (this has been reported
to be a problem on HP-UX with the native cc). In this case,
use a different compiler (or a front end shell script which does the
re-ordering).
If you find you need to alter configure variables, it is worth noting
that some settings are cached in the file config.cache, and it is
a good idea to remove that file before re-configuring.
To compile R, you will most likely find it easiest to use GNU
make. On Solaris 2.6/7/8 in particular, you need a version of
GNU make different from 3.77; 3.79 works fine, as does the Sun
make.
To build in a separate directory you need a make that uses the
VPATH variable, for example GNU make, or Sun
make on Solaris 2.7/8 (but not earlier).
If you want to use a make by another name, for example if your
GNU make is called gmake, you need to set the
environment variable MAKE at configure time, for example
MAKE=gmake ./configure (sh, bash) env MAKE=gmake ./configure (csh)
To compile R, you need a FORTRAN compiler or f2c, the
FORTRAN-to-C converter (http://www.netlib.org/f2c). The default
is to search for g77, f77, xlf,
cf77, cft77, pgf77, fl32,
af77, fort77, f90, xlf90,
pgf90, epcf90, f95, xlf95,
lf95, g95, and fc (in that order), and
then for f2c, and use whichever is found first; if none is
found, R cannot be compiled. The search mechanism can be changed
using the --with-g77, --with-f77, and
--with-f2c command line options to configure. If
your FORTRAN compiler is in a non-standard location, you should set the
environment variable PATH accordingly before running
configure.
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.
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
time5, but you may need to avoid
compiler flags6 asserting
FORTRAN 77 compliance.
For performance reasons7 you may want to choose a FORTRAN 90/95 compiler.
A wide range of flags can be set in the file config.site or via
environment variables. We have already mentioned
CPPFLAGS
LIBS
-L/lib/path flags
and others include
CFLAGS
MAIN_CFLAGS
SHLIB_CFLAGS
FFLAGS
MAIN_FFLAGS
SHLIB_FFLAGS
MAIN_LDFLAGS
SHLIB_LDFLAGS
Library paths specified as -L/lib/path in LIBS 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.
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.
This interface is experimental, incomplete and not currently being
developed. It provides a console and a graphics device (gtk();
the x11() device can also be used). Many of the `features' of
the console are currently stubs.
The GNOME interface for R will only be built if you specify
it by running configure with the --with-gnome option. For
example, you might run
./configure --with-gnome
but please check you have all the requirements first. It is advisable
to have reasonably-up-to-date versions of the gnome and
gtk+ libraries. You can find the versions you have by
gnome-config --version gtk-config --version
We know 1.0.10 and 1.2.3 suffice. On Red Hat systems, you need the following RPMs and their dependencies installed:
gnome-libs gnome-libs-devel gtk+ gtk+-devel glib glib-devel
You will need also libglade 0.5 or later for correct behaviour.
For more information on libglade and to download the source, see
http://www.daa.com.au/~james/gnome/. The sources are also
available from the GNOME ftp site (ftp://ftp.gnome.org/
and mirrors). RPMs are in RedHat 6.1 and later.
Library libglade needs libxml 1.4 or later, the source for
which is available from the GNOME ftp site
(ftp://ftp.gnome.org/ and mirrors).
The locations of some of these libraries can be set as configuration options, by (defaults in brackets)
--with-gnome
--with-gnome-includes=DIR
--with-gnome-libs=DIR
--with-libglade-config=LIBGLADE_CONFIG
libglade-config
There are a number of sources of problems when installing R on a new hardware/OS platform. These include
Floating Point Arithmetic: R supports the POSIX,
SVID and IEEE models for floating point arithmetic. The
POSIX and SVID models provide no problems. The IEEE
model however can be a pain. The problem is that there is no agreement
on how to set the signalling behaviour; Sun/Sparc, SGI/IRIX and ix86
Linux require no special action, FreeBSD requires a call to (the macro)
fpsetmask(0) and OSF1 requires that computation be done with a
-ieee_with_inexact flag etc. On a new platform you must find
out the magic recipe and add some code to make it work. This can often
be done via the file config.site which resides in the top level
directory.
Beware of using high levels of optimization, at least initially. On
many compilers these reduce the degree of compliance to the
IEEE model. For example, using -fast on the Solaris
SunPro compilers causes R's NaN to be set incorrectly.
Shared Libraries: There seems to be very little agreement
across platforms on what needs to be done to build shared libraries.
there are many different combinations of flags for the compilers and
loaders. The technique we use is to first interrogate the X window
system about what it does (using xmkmf), and maybe override
this in situations where we know better. This often works, but you may
have to manually override the results. Scanning the cc(1) and
ld(1) manual entries 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.
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 get in touch to ask questions. We've had a fair amount of practice at porting R to new platforms ....
configure: Using make, Configuration variables, Installation, Simple compilation
install.packages: Installing packages
make: Using make
R_HOME: Simple compilation
remove.packages: Removing packages
rsync: Using rsync
update.packages: Updating packages
if you have Perl and the source-code package files installed
compile with
c++ or comment out sigcatch(0) in line 520 of
main.c
e.g. http://fink.sourceforge.net/files/dlcompat-20010123.tar.gz
Using the SunPro cc and f95
compilers
as well as its equivalence to the Rcomplex
structure defined in R_ext/Complex.h.
In particular, avoid g77's
-pedantic, which gives confusing error messages.
e.g., to use an optimized BLAS on Sun/Sparc