     [file R-defs.texi not included]
     [file version.texi not included]

This is a guide to installation and administration for R.

2001

permission

R Installation and Administration
*********************************

This is a guide to installation and administration for R.

The current version of this document is VERSION.

Obtaining R
***********

Sources, binaries and documentation for R can be obtained via CRAN, the ``Comprehensive R Archive Network''.  See the file RESOURCES for information on CRAN.

Getting and unpacking the sources
=================================

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).

Using rsync
===========

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 can be one of r-release (latest released version), r-release-patched (latest released version with patches applied), and r-devel (current 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/.

Installing R under Unix
***********************

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 OSF1, and for MacOS X.  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.

Simple compilation
==================

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).

Making the manuals
==================

There is a set of manuals that can be built from the sources,

refman
     Printed versions of all the help pages.

R-FAQ
     R FAQ (which is already built for you).

R-intro
     ``An Introduction to R''.

R-data
     ``R Data Import/Export''.

R-admin
     ``R Installation and Administration'', this manual.

R-exts
     ``Writing R Extensions''.

R-lang
     ``The R Language Definition''.

To make these, 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.

Installation
============

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
     the front-end shell script

${prefix}/man/man1
     the man page

${prefix}/lib/R
     all the rest (libraries, on-line help system, ...)

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.

Installing R under Windows
**************************

The bin/windows directory of a CRAN site contains binaries for a base distribution and a large number of add-on packages from CRAN to run on Windows 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 (http://www.stats.ox.ac.uk/pub/R/rw-FAQ.html) for more details.

Building from source
====================

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.

Installing R on Classic MacOS
*****************************

The bin/macos directory of a CRAN site contains bin-hexed (hqx) and stuffit (sit) self-extracting binaries 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 under Classic Environment.

Just extract one of these self-extracting binaries in a suitable folder.

There is also a port to MacOS X which is considered to be a Unix variant in this document.

Add-on packages
***************

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.

Installing packages
===================

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 is (if you have Perl and the source-code package files installed)

     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.

Updating packages
=================

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.

Removing packages
=================

Packages can be removed in a number of ways.  From a command prompt they can be removed by

     R CMD REMOVE -l /path/to/library pkg1 pkg2 ...

(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.

Essential and useful other programs
***********************************

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.

Essential programs
==================

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.

Building on MacOS X
-------------------

You can build R as a Unix application on MacOS X.  You will need the DevTools, f2c (ftp://netlib.bell-labs.com/netlib/f2c.tar (compile with c++ or comment out sigcatch(0) in line 520 of main.c)) and the dlcompat libraries (e.g. http://fink.sourceforge.net/files/dlcompat-20010123.tar.gz).

You will also need to install a X sub-system or configure with --without-x.

Useful libraries and programs
=============================

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).

Tcl/Tk
------

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
     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

Linear algebra
--------------

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 Sparc (Using the SunPro cc and f95 compilers), libscs and libcomplib.sgimath on SGI, 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 are 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.

Configuration on Unix
*********************

Configuration options
=====================

configure has many options: running

     ./configure --help

will give a list.  Probably the most important ones not covered elsewhere are (defaults in brackets)

--with-x
     use the X Window System

--x-includes=DIR
     X include files are in DIR

--x-libraries=DIR
     X library files are in DIR

--with-readline
     use readline library (if available) [yes]

--enable-R-profiling
     attempt to compile support for Rprof() [yes]

--enable-R-shlib
     build R as a shared library [no]

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.

Configuration variables
=======================

If you need or want to set certain configure variables to something other than their default, you can do that by either editing the file config.site (which documents 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.

Using make
==========

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)

Using FORTRAN
=============

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 time (as well as its equivalence to the Rcomplex structure defined in R_ext/Complex.h.), but you may need to avoid compiler flags (In particular, avoid g77's -pedantic, which gives confusing error messages.) asserting FORTRAN 77 compliance.

For performance reasons (e.g., to use an optimized BLAS on Sun/Sparc) you may want to choose a FORTRAN 90/95 compiler.

Compile and load flags
======================

A wide range of flags can be set in the file config.site or via environment variables.  We have already mentioned

CPPFLAGS
     extra include flags

LIBS
     libraries and -L/lib/path flags

and others include

CFLAGS
     debugging and optimization flags, C

MAIN_CFLAGS
     ditto, for compiling the main program

SHLIB_CFLAGS
     for shared libraries

FFLAGS
     debugging and optimization flags, FORTRAN

MAIN_FFLAGS
     ditto, for compiling the main program

SHLIB_FFLAGS
     for shared libraries

MAIN_LDFLAGS
     additional flags for the main link

SHLIB_LDFLAGS
     additional flags for linking the shared libraries

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.

Building the GNOME interface
============================

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
     use GNOME, or specify its prefix [no]

--with-gnome-includes=DIR
     specify location of GNOME headers

--with-gnome-libs=DIR
     specify location of GNOME libs

--with-libglade-config=LIBGLADE_CONFIG
     specify location of libglade-config

New platforms
*************

There are a number of sources of problems when installing R on a new hardware/OS platform. These include

Floating Point Arithmetic: R 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 ...