\input texinfo @c %**start of header @setfilename R-admin.info @settitle R Installation and Administration @defcodeindex en @c %**end of header @syncodeindex fn vr @dircategory Programming @direntry * R Administration: (R-admin). R Installation and Administration. @end direntry @finalout @include R-defs.texi @include version.texi @copying This manual is for R, version @value{VERSION}. @Rcopyright{2001} @quotation @permission{} @end quotation @end copying @titlepage @title R Installation and Administration @subtitle Version @value{VERSION} @author R Core Team @page @vskip 0pt plus 1filll @insertcopying @end titlepage @ifplaintext @insertcopying @end ifplaintext @c @ifnothtml @contents @c @end ifnothtml @ifnottex @node Top @top R Installation and Administration This is a guide to installation and administration for R. @insertcopying @end ifnottex @node Obtaining R @chapter Obtaining R @cindex Obtaining R Sources, binaries and documentation for @R{} can be obtained via @acronym{CRAN}, the ``Comprehensive R Archive Network'' whose current members are listed at @uref{https://CRAN.R-project.org/mirrors.html}. @node Getting and unpacking the sources @section Getting and unpacking the sources @cindex Sources for R The simplest way is to download the most recent @file{R-@var{x}.@var{y}.@var{z}.tar.gz} file, and unpack it with @example tar -xf R-@var{x}.@var{y}.@var{z}.tar.gz @end example @noindent on systems that have a suitable@footnote{e.g.@: @acronym{GNU} @command{tar} version 1.15 or later, or that from the @samp{libarchive} (as used on macOS) or `@I{Heirloom Toolchest}' distributions.} @command{tar} installed. On other systems you need to have the @command{gzip} program installed, when you can use @example gzip -dc R-@var{x}.@var{y}.@var{z}.tar.gz | tar -xf - @end example The pathname of the directory into which the sources are unpacked should not contain spaces, as most @command{make} programs (and specifically @acronym{GNU} @command{make}) do not expect spaces. If you want the build to be usable by a group of users, set @code{umask} before unpacking so that the files will be readable by the target group (e.g.,@: @code{umask 022} to be usable by all users). Keep this setting of @code{umask} whilst building and installing. If you use a fairly recent @acronym{GNU} version of @command{tar} and do this as a root account (which on Windows includes accounts with administrator privileges) you may see many warnings about changing ownership. In which case you can use @example tar --no-same-owner -xf R-@var{x}.@var{y}.@var{z}.tar.gz @end example @noindent and perhaps also include the option @option{--no-same-permissions}. @enindex TAR_OPTIONS (These options can also be set in the @env{TAR_OPTIONS} environment variable: if more than one option is included they should be separated by spaces.) @node Getting patched and development versions @section Getting patched and development versions A patched version of the current release, @samp{r-patched}, and the current development version, @samp{r-devel}, are available as daily tarballs and via access to the @R{} Subversion repository. (For the two weeks prior to the release of a minor (4.x.0) version, @samp{r-patched} tarballs may refer to beta/release candidates of the upcoming release, the patched version of the current release being available via Subversion.) The tarballs are available from @uref{https://cran.r-project.org/src/base-prerelease/}. Download @file{R-patched.tar.gz} or @file{R-devel.tar.gz} (or the @file{.tar.bz2} versions) and unpack as described in the previous section. They are built in exactly the same way and on the same platform as distributions of @R{} releases. Notice, that you probably want to use the CRAN master site for this, due to propagation delays. An alternative source of daily snapshots is maintained at @uref{https://stat.ethz.ch/R/daily/}. @c Keep this single-item menu to avoid a spurious warning about @c an unreferenced node when making info with Texinfo 6.8 and 7.0. @menu * Using Subversion and rsync:: @end menu @node Using Subversion and rsync @subsection Using Subversion and @I{rsync} @cindex Subversion Sources are also available via @uref{https://svn.R-project.org/R/}, the R Subversion repository. If you have a Subversion client (see @uref{https://subversion.apache.org/}), you can check out and update the current @samp{r-devel} from @uref{https://svn.r-project.org/R/trunk/} and the current @samp{r-patched} from @samp{https://svn.r-project.org/@/R/@/branches/@/R-@var{x}-@var{y}-branch/} (where @var{x} and @var{y} are the major and minor number of the current released version of R). E.g., use @example svn checkout https://svn.r-project.org/R/trunk/ @var{path} @end example @noindent to check out @samp{r-devel} into directory @var{path} (which will be created if necessary). The alpha, beta and RC versions of an upcoming @var{x.y.0} release are available from @samp{https://svn.r-project.org/R/branches/R-@var{x}-@var{y}-branch/} in the four-week period prior to the release. Note that @samp{https:} is required@footnote{for some Subversion clients @samp{http:} may appear to work, but requires continual redirection.}, and that the @abbr{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.@: @command{wget -r} or @command{svn export} from that URL will not work (and will give a error early in the @command{make} process): the Subversion information is needed to build @R{}. The Subversion repository does not contain the current sources for the recommended packages, which can be obtained by @command{rsync} or downloaded from @acronym{CRAN}. To use @code{rsync} to install the appropriate sources for the recommended packages, run @code{./tools/rsync-recommended} from the top-level directory of the @R{} sources. If downloading manually from @acronym{CRAN}, do ensure that you have the correct versions of the recommended packages: if the number in the file @file{VERSION} is @samp{@var{x}.@var{y}.@var{z}} you need to download the contents of @samp{https://CRAN.R-project.org/src/contrib/@var{dir}}, where @var{dir} is @samp{@var{x}.@var{y}.@var{z}/Recommended} for r-devel or @file{@var{x}.@var{y}-patched/Recommended} for r-patched, respectively, to directory @file{src/library/Recommended} in the sources you have unpacked. After downloading manually you need to execute @command{tools/link-recommended} from the top level of the sources to make the requisite links in @file{src/library/Recommended}. A suitable incantation from the top level of the @R{} sources using @command{wget} might be (for the correct value of @file{@var{dir}}) @example wget -r -l1 --no-parent -A\*.gz -nd -P src/library/Recommended \ https://CRAN.R-project.org/src/contrib/@var{dir} ./tools/link-recommended @end example @node Installing R under Unix-alikes @chapter Installing R under Unix-alikes @cindex Installing under Unix-alikes @R{} will configure and build under most common Unix and Unix-alike platforms including @samp{@var{cpu}-*-linux-gnu} for the @cputype{alpha}, @cputype{arm64} (also known as @cputype{aarch64}, @cputype{ix86}, @cputype{mips}, @cputype{mipsel}#, @cputype{ppc64}, @cputype{riscv64}, @cputype{s390x}, @cputype{sparc64}, and @cputype{x86_64} @acronym{CPU}s, @c (see e.g.@: @uref{https://buildd.debian.org/build.php?&pkg=r-base}), @c Actually, see https://packages.debian.org/unstable/math/r-base-core as @c the build daemon is not used for all platforms; note also that Debian @c has x86_64 <=> amd64, ix86 <=> i386. @samp{aarch64-@/apple-@/darwin}@footnote{aka `Apple Silicon', known to some as @samp{arm64-@/apple-@/darwin}.} and @samp{x86_64-@/apple-@/darwin} as well as perhaps (it is tested less frequently on these platforms) @samp{x86_64-@/*-@/freebsd}, @samp{x86_64-@/*-@/openbsd} and @samp{powerpc-@/ibm-@/aix6*} Only 64-bit platforms are tested regularly, and @command{configure} will warn if it encounters a 32-bit one. @cindex Linux @cindex macOS In addition, binary distributions are available for some common Linux distributions (see the @acronym{FAQ} for current details) and for macOS. These are installed in platform-specific ways, so for the rest of this chapter we consider only building from the sources. Cross-building is not possible: installing @R{} builds a minimal version of @R{} and then runs many @R{} scripts to complete the build. @node Simple compilation @section Simple compilation First review the essential and useful tools and libraries in @ref{Essential and useful other programs under a Unix-alike}, and install those you @enindex TMPDIR want or need. Ensure that either the environment variable @env{TMPDIR} is either unset (and @file{/tmp} exists and can be written in and scripts can be executed from) or points to the absolute path to a valid temporary directory (one from which execution of scripts is allowed) which does not contain spaces. @findex R_HOME Choose a directory to install the @R{} tree (@R{} is not just a binary, but has additional data sets, help files, font metrics etc). Let us call this place @var{R_HOME}. Untar the source code. This should create directories @file{src}, @file{doc}, and several more under a top-level directory: change to that top-level directory (At this point readers in North American should consult @ref{Setting paper size}.) Issue the following commands: @findex configure @example ./configure make @end example @noindent (See @ref{Using make} if your make is not called @samp{make}.) Users of Debian-based 64-bit systems@footnote{such as Ubuntu. These use @file{lib} rather than @file{lib64} for their primary 64-bit library directories: attempts are made to detect such systems.} may need @example ./configure LIBnn=lib make @end example Then check the built system works correctly by @example make check @end example @noindent Failures are not necessarily problems as they might be caused by missing functionality, but you should look carefully at any reported discrepancies. (Some non-fatal errors are expected in locales that do not support Latin-1, in particular in true @code{C} locales and non-UTF-8 non-Western-European locales.) A failure in @file{tests/ok-errors.R} may indicate inadequate resource limits (@pxref{Running R}). More comprehensive testing can be done by @example make check-devel @end example @noindent or @example make check-all @end example @noindent see @ref{Testing a Unix-alike Installation} for the possibilities of doing this in parallel. Note that these checks are only run completely if the recommended packages are installed (the default) . If you have a local CRAN mirror, these checks can be speeded up by either setting environment variable @env{R_CRAN_WEB} to its URL, or having a file @file{.R/repositories} specifying it (see @code{?setRepositories}). @command{make check-devel} checks the included packages' @file{tests} directories. For @pkg{grDevices} more complete checks will be run if the environment variable @env{R_GRDEVICES_COMPARE_PS_PDF} is set: those checks are skipped on platforms using @code{musl} such as Alpine Linux, and it knows about differences from transliterations in macOS 14 and later. Parallel make is supported for building @R{} but not for the @samp{check} targets (as the output is likely to be unreadably interleaved, although where supported@footnote{not by the version supplied by macOS.} GNU make's @option{-O} may help). If the @command{configure} and @command{make} commands execute successfully, a shell-script front-end called @file{R} will be created and copied to @file{@var{R_HOME}/bin}. You can link or copy this script to a place where users can invoke it, for example to @file{/usr/local/bin/R}. You could also copy the man page @file{R.1} to a place where your @command{man} reader finds it, such as @file{/usr/local/man/man1}. If you want to install the complete @R{} tree to, e.g., @file{/usr/local/lib/R}, see @ref{Installation}. Note: you do not @emph{need} to install @R{}: you can run it from where it was built. You do not have to build @R{} in the top-level source directory (say, @file{@var{TOP_SRCDIR}}). To build in @file{@var{BUILDDIR}}, run @findex configure @example cd @var{BUILDDIR} @var{TOP_SRCDIR}/configure make @end example @noindent 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 @acronym{GNU} @command{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.) There are many settings which can be customized when building @R{} and most are described in the file @file{config.site} in the top-level source directory. This can be edited, but for an installation using @file{@var{BUILDDIR}} it is better to put the changed settings in a newly-created file @file{config.site} in the build directory. @c For those obtaining @R{} @emph{via} Subversion, one additional step is @c necessary: @c @cindex Vignettes @c @cindex Subversion @c @example @c make vignettes @c @end example @c @noindent @c which makes the @pkg{grid} vignettes (which are contained in the @c tarballs): it make take several minutes. Now @code{rehash} if necessary, type @kbd{R}, and read the @R{} manuals and the @R{} @acronym{FAQ} (files @file{FAQ} or @file{doc/manual/R-FAQ.html}, or @uref{https://CRAN.R-project.org/doc/FAQ/R-FAQ.html} which always has the version for the latest release of @R{}). Note: if you already have @R{} installed, check that where you installed @R{} replaces or comes earlier in your path than the previous installation. Some systems are set up to have @file{/usr/bin} (the standard place for a system installation) ahead of @file{/usr/local/bin} (the default place for a source installation of @R{}) in their default path, and some do not have @file{/usr/local/bin} on the default path. @node Help options @section Help options @R{} by default provides help pages as plain text displayed in a pager, with the options (see the help for @code{help}) of displaying help as HTML or PDF. By default @HTML{} help pages are created when needed rather than being built at install time. If you need to disable its server and want @HTML{} help, there is the option to build @HTML{} pages when packages are installed (including those installed with @R{}). This is enabled by the @command{configure} option @option{--enable-prebuilt-html}. Whether @command{R CMD INSTALL} (and hence @code{install.packages}) pre-builds @HTML{} pages is determined by looking at the @R{} installation and is reported by @command{R CMD INSTALL --help}: it can be overridden by specifying one of the @command{INSTALL} options @option{--html} or @option{--no-html}. The server is disabled by setting the environment variable @enindex R_DISABLE_HTTPD @env{R_DISABLE_HTTPD} to a non-empty value, either before @R{} is started or within the @R{} session before @HTML{} help (including @code{help.start}) is used. It is also possible that system security measures will prevent the server from being started, for example if the loopback interface has been disabled. See @code{?tools::startDynamicHelp} for more details. @node Making the manuals @section Making the manuals @cindex Manuals There is a set of manuals that can be built from the sources, @table @samp @item fullrefman Printed versions of all the help pages for base and recommended packages (around 3900 pages). @item refman Printed versions of the help pages for selected base packages (around 2300 pages) @item R-FAQ R @acronym{FAQ} @item R-intro ``An Introduction to R''. @item R-data ``R Data Import/Export''. @item R-admin ``R Installation and Administration'', this manual. @item R-exts ``Writing R Extensions''. @item R-ints ``R Internals''. @item R-lang ``The R Language Definition''. @end table @noindent To make these (with @samp{fullrefman} rather than @samp{refman}), use @c FIXME: mention HTML versions built by default from make docs @example make pdf @r{to create PDF versions} make info @r{to create info files (not @samp{refman} nor @samp{fullrefman}).} @end example @c texi2any from Feb 2016. You will not be able to build any of these unless you have @command{texi2any} version 6.1 or later installed, and for PDF you must have @command{texi2dvi} and @file{texinfo.tex} installed (which are part of the @acronym{GNU} @I{Texinfo} distribution but are, especially @file{texinfo.tex}, often made part of the @TeX{} package @pkg{texinfo} in re-distributions). The path to @command{texi2any} can be set by macro @samp{TEXI2ANY} in @file{config.site}. NB: @command{texi2any} requires @command{perl}. The PDF versions can be viewed using any recent PDF viewer: they have hyperlinks that can be followed. The info files are suitable for reading online with Emacs or the standalone @acronym{GNU} @command{info} program. The PDF versions will be created using the paper size selected at configuration (default ISO a4): this can be overridden by setting @env{R_PAPERSIZE} @enindex R_PAPERSIZE on the @command{make} command line, or setting @env{R_PAPERSIZE} in the environment and using @command{make -e}. (If re-making the manuals for a different paper size, you should first delete the file @file{doc/manual/version.texi}. The usual value for North America would be @samp{letter}.) There are some issues with making the PDF reference manual, @file{fullrefman.pdf} or @file{refman.pdf}. The help files contain both non-ASCII characters (e.g.@: in @file{text.Rd}) and upright quotes, neither of which are contained in the standard @LaTeX{} Computer Modern fonts. We have provided the following alternatives: @table @code @item times (The default.) Using standard PostScript fonts, Times Roman, Helvetica and Courier. This works well both for on-screen viewing and for printing. One disadvantage is that the Usage and Examples sections may come out rather wide: this can be overcome by using @emph{in addition} either of the options @code{inconsolata} (on a Unix-alike only if found by @command{configure}) or @code{beramono}, which replace the Courier monospaced font by @I{Inconsolata} or @I{Bera Sans Mono} respectively. (You will need the @LaTeX{} package @pkg{inconsolata}@footnote{Instructions on how to install the latest version are at @uref{https://www.ctan.org/tex-archive/fonts/inconsolata/}. TeX Live bundles @pkg{inconsolata} in @pkg{collection-fontsextra}.} or @pkg{bera} installed.) Note that in most @LaTeX{} installations this will not actually use the standard fonts for PDF, but rather embed the URW clones @I{NimbusRom}, @I{NimbusSans} and (for Courier, if used) @I{NimbusMon}. This needs @LaTeX{} packages @pkg{times}, @pkg{helvetic} and (if used) @pkg{courier} installed. @item lm Using the @emph{Latin Modern} (@emph{aka} @pkg{lmodern}) fonts, usually installed even in basic @TeX{} distributions. @c E.g.: scheme-basic / collection-latex will have it installed. This uses fonts rather similar to Computer Modern, but is not so good on-screen as @code{times} and produces larger PDF files. @c @item cm-super @c Using type-1 versions of the Computer Modern fonts by Vladimir Volovich. @c This is a large installation, obtainable from @c @uref{https://www.ctan.org/tex-archive/fonts/ps-type1/cm-super/} @c and its mirrors. These type-1 fonts have poor hinting and so are @c nowhere near as readable on-screen as the other three options. @end table The default can be overridden by setting the environment variable @enindex R_RD4PDF @env{R_RD4PDF}. (On Unix-alikes, this will be picked up at install time and stored in @file{etc/Renviron}, but can still be overridden when the manuals are built, using @command{make -e}.) The usual@footnote{on a Unix-alike, @samp{inconsolata} is omitted if not found by @command{configure}.} default value for @env{R_RD4PDF} is @samp{times,inconsolata,hyper}: omit @samp{inconsolata} if you do not have @LaTeX{} package @pkg{inconsolata} installed. @samp{hyper} is always enabled (with a fallback if @LaTeX{} package @pkg{hyperref} is not installed). Further options, e.g@: for @pkg{hyperref}, can be included in a file @file{Rd.cfg} somewhere on your @LaTeX{} search path. For example, if you prefer to hyperlink the text and not the page number in the table of contents use @example \ifthenelse@{\boolean@{Rd@@use@@hyper@}@}@{\hypersetup@{linktoc=section@}@}@{@} @end example @noindent or @example \ifthenelse@{\boolean@{Rd@@use@@hyper@}@}@{\hypersetup@{linktoc=all@}@}@{@} @end example @noindent to hyperlink both text and page number. Any generated PDF manuals can be compacted by @example make compact-pdf @end example @noindent provided @command{qpdf} and @command{gs} are available (see @code{?tools::compactPDF} for how to specify them if not on the path). E-book versions of most of the manuals in one or both of @file{.epub} and @file{.mobi} formats can be made by running in @file{doc/manual} one of @example make ebooks make epub make mobi @end example @noindent This requires @command{ebook-convert} from @uref{https://calibre-ebook.com/download, @command{Calibre}}, or from most Linux distributions. If necessary the path to @command{ebook-convert} can be set as make macro @env{EBOOK} by editing @file{doc/manual/Makefile} (which contains a commented value suitable for macOS) or using @command{make -e}. @node Installation @section Installation @cindex Installation To ensure that the installed tree is usable by the right group of users, set @code{umask} appropriately (perhaps to @samp{022}) before unpacking the sources and throughout the build process. After @findex configure @example ./configure make make check @end example @noindent (or, when building outside the source, @code{@var{TOP_SRCDIR}/configure}, etc) have been completed successfully, you can install the complete @R{} tree to your system by typing @example make install @end example @noindent A parallel make can be used (but run @command{make} before @command{make install}). Those using GNU @command{make} 4.0 or later may want to use @command{make -j @var{n} -O} to avoid interleaving of output. This will install to the following directories: @table @asis @item @file{@var{prefix}/bin} or @file{@var{bindir}} the front-end shell script and other scripts and executables @item @file{@var{prefix}/man/man1} or @file{@var{mandir}/man1} the man page @item @file{@var{prefix}/@var{LIBnn}/R} or @file{@var{libdir}/R} all the rest (libraries, on-line help system, @dots{}). Here @var{LIBnn} is usually @samp{lib}, but may be @samp{lib64} on some 64-bit Linux systems. This is known as the @R{} home directory. @end table @noindent where @var{prefix} is determined during configuration (typically @file{/usr/local}) and can be set by running @command{configure} with the option @option{--prefix}, as in @findex configure @example ./configure --prefix=/where/you/want/R/to/go @end example @noindent where the value should be an absolute path. This causes @command{make install} to install the @R{} script to @file{/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 @command{configure}. The installation may need to be done by the owner of @file{@var{prefix}}, often a root account. There is the option of using @command{make install-strip} (@pxref{Debugging Symbols}). You can install into another directory tree by using @example make prefix=/path/to/here install @end example @noindent at least with @acronym{GNU} @command{make} (but not some other Unix makes). More precise control is available at configure time via options: see @command{configure --help} for details. (However, most of the `Fine tuning of the installation directories' options are not used by @R{}.) Configure options @option{--bindir} and @option{--mandir} are supported and govern where a copy of the @command{R} script and the @command{man} page are installed. The configure option @option{--libdir} controls where the main @R{} files are installed: the default is @samp{@var{eprefix}/@var{LIBnn}}, where @var{eprefix} is the prefix used for installing architecture-dependent files, defaults to @var{prefix}, and can be set via the configure option @option{--exec-prefix}. Each of @code{bindir}, @code{mandir} and @code{libdir} can also be specified on the @command{make install} command line (at least for @acronym{GNU} @command{make}). The @command{configure} or @command{make} variables @code{rdocdir} and @code{rsharedir} can be used to install the system-independent @file{doc} and @file{share} directories to somewhere other than @code{libdir}. The C header files can be installed to the value of @code{rincludedir}: note that as the headers are not installed into a subdirectory you probably want something like @code{rincludedir=/usr/local/include/R-@value{VERSIONno}}. If you want the @R{} home to be something other than @file{@var{libdir}/R}, use @option{rhome}: for example @example make install rhome=/usr/local/lib64/R-@value{VERSIONno} @end example @noindent 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 @example make prefix=/path/to/here install-libR @end example @noindent where @code{prefix} is optional, and @code{libdir} will give more precise control.@footnote{This will be needed if more than one sub-architecture is to be installed.} However, you should not install to a directory mentioned in @env{LDPATHS} (e.g.@: @file{/usr/local/lib64}) if you intend to work with multiple versions of @R{}, since that directory may be given precedence over the @file{lib} directory of other @R{} installations. @example make install-strip @end example @noindent will install stripped executables, and on platforms where this is supported, stripped libraries in directories @file{lib} and @file{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. @c The main problem is the Makefile include in etc/Makeconf @cindex Manuals, installing To install info and PDF versions of the manuals, use one or both of @example make install-info make install-pdf @end example @noindent Once again, it is optional to specify @code{prefix}, @code{libdir} or @code{rhome} (the PDF manuals are installed under the @R{} home directory). More precise control is possible. For info, the setting used is that of @code{infodir} (default @file{@var{prefix}/info}, set by configure option @option{--infodir}). The PDF files are installed into the @R{} @file{doc} tree, set by the @command{make} variable @code{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 @code{prefix} (and so on) should reflect the @enindex DESTDIR final destination, and @env{DESTDIR} should be used: see @uref{https://www.gnu.org/prep/standards/html_node/DESTDIR.html}. You can optionally install the run-time tests that are part of @command{make check-all} by @example make install-tests @end example @noindent which populates a @file{tests} directory in the installation. @node Uninstallation @section @I{Uninstallation} You can uninstall @R{} by @example make uninstall @end example @noindent optionally specifying @code{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 @file{doc/manual/Makefile}. Target @code{uninstall-tests} will uninstall any installed tests, as well as removing the directory @file{tests} containing the test results. An installed shared/static @code{libR} can be uninstalled by @example make prefix=/path/to/here uninstall-libR @end example @node Sub-architectures @section Sub-architectures Now 32-bit builds are unsupported, this section is only of historical interest, although in future the mechanisms could be used for different CPU types on the same OS (e.g. @cputype{x86_64} and @cputype{aarch64}). Some platforms can support closely related builds of @R{} which can share all but the executables and dynamic objects. Examples include builds under Linux for different @acronym{CPU}s or 32- and 64-bit builds. @R{} supports the idea of architecture-specific builds, specified by adding @samp{r_arch=@var{name}} to the @command{configure} line. Here @var{name} can be anything non-empty, and is used to name subdirectories of @file{lib}, @file{etc}, @file{include} and the package @file{libs} subdirectories. Example names from other software are the use of @file{sparcv9} on @I{Sparc} Solaris and @file{32} by @command{gcc} on @cputype{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 @samp{r_arch}). The space savings can be considerable: on @cputype{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 @example R --arch=@var{name} @end example @noindent and just running @samp{R} will run the last build that was installed. @code{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 @code{configure} script or a @file{src/Makefile} file. In such cases you can install for extra builds by @example R --arch=@var{name} CMD INSTALL --libs-only @var{pkg1} @var{pkg2} @dots{} @end example If you want to mix sub-architectures compiled on different platforms (for example @cputype{x86_64} Linux and @cputype{i686} Linux), it is wise to use explicit names for each, and you may also need to set @option{libdir} to ensure that they install into the same place. When sub-architectures are used the version of @command{Rscript} in e.g.@: @file{/usr/bin} will be the last installed, but architecture-specific versions will be available in e.g.@: @file{/usr/lib64/R/bin/exec$@{@var{R_ARCH}@}}. Normally all installed architectures will run on the platform so the architecture of @command{Rscript} itself does not matter. The executable @command{Rscript} will run the @command{R} script, and at that time the @enindex R_ARCH setting of the @env{R_ARCH} environment variable determines the architecture which is run. When running post-install tests with sub-architectures, use @example R --arch=@var{name} CMD make check[-devel|all] @end example @noindent to select a sub-architecture to check. Sub-architectures were also used on Windows, but by selecting executables within the appropriate @file{bin} directory such as @file{@var{R_HOME}/bin/x64}. As from @R{} 4.2.0 only the @samp{x64} subdirectory is used. @node Other Options @section Other Options There are many other installation options, most of which are listed by @command{configure --help}. Almost all of those not listed elsewhere in this manual are either standard @command{autoconf} options not relevant to @R{} or intended for specialist uses by the @R{} developers. @command{configure} will select a C23 compiler if it finds one: to circumvent this use option @option{--without-C23}. This will only have an effect if the compiler in use does not default to C23: GCC 15 does and might be selected as @command{gcc} if macro @code{CC} is not specified in @file{config.site}. (A compiler is considered to be a `C23 compiler' if it supports C23 by default or if such support can be selected by a flag such as @option{-std=gnu23} or @option{-std=gnu2x} and it supports the new C23 keywords such as @code{bool}, @code{false} and @code{true}.) One that may be useful when working on @R{} itself is the option @option{--disable-byte-compiled-packages}, which ensures that the base and recommended packages are not byte-compiled. (Alternatively the (make or environment) variable @env{R_NO_BASE_COMPILE} can be set to a non-empty value for the duration of the build.) Option @option{--with-internal-tzcode} makes use of @R{}'s own code and copy of the @abbr{IANA} database for managing timezones. This will be preferred where there are issues with the system implementation, usually involving times after 2037 or before 1916. An alternative time-zone directory@footnote{How to prepare such a directory is described in file @file{src/extra/tzone/Notes} in the @R{} sources.} can be used, pointed to by environment variable @env{TZDIR}: this should contain files such as @file{Europe/London}. On all recently tested OSes the system timezone was deduced correctly, but if necessary it can be set as the value of environment variable @env{TZ}. Options @option{--with-internal-iswxxxxx}, @option{--with-internal-towlower} and @option{--with-internal-wcwidth} control the replacement of the system wide-character classification (such as @code{iswprint}), case-changing (@code{wctrans}) and width (@code{wcwidth} and @code{wcswidth}) functions by ones contained in the @R{} sources. Replacement of the classification functions has been done for many years on macOS and @abbr{AIX} (and Windows): option @option{--with-internal-iswxxxxx} allows this to be suppressed on those platforms or used on others. Replacing the case-changing functions is the default on macOS and Windows. Replacement of the width functions has also been done for many years and remains the default. These options will only matter to those working with non-ASCII character data, especially in languages written in a non-Western script@footnote{But on Windows problems have been seen with case-changing functions on accented Latin-1 characters.} (which includes `symbols' such as emoji). Note that one of those @code{iswxxxxx} is @code{iswprint} which is used to decide whether to output a character as a glyph or as a @samp{\U@{xxxxxx@}} escape---for example, try @samp{"\U1f600"}, an emoji. The width functions are of most importance in East Asian locale: their values differ between such locales. (Replacing the system functions provides a degree of platform-independence (including to OS updates) but replaces it with a dependence on the @R{} version.) @node Debugging Symbols @subsection Debugging Symbols By default, @command{configure} adds a flag (usually @option{-g}) to the compilation flags for C, Fortran and C++ sources. This will slow down compilation and increase object sizes of both @R{} and packages, so it may be a good idea to change those flags (set @samp{CFLAGS} etc in @file{config.site} before configuring, or edit files @file{Makeconf} and @file{etc/Makeconf} between running @command{configure} and @command{make}). Having debugging symbols available is useful both when running @R{} under a debugger (e.g., @command{R -d gdb}) and when using sanitizers and @command{valgrind}, all things intended for experts. Debugging symbols (and some others) can be `stripped' on installation by using @example make install-strip @end example @noindent How well this is supported depends on the platform: it works best on those using GNU @code{binutils}. On @cputype{x86_64} Linux a typical reduction in overall size was from 92MB to 66MB. On macOS debugging symbols are not by default included in @file{.dylib} and @file{.so} files, so there is negligible difference. @node OpenMP Support @subsection @abbr{OpenMP} Support By default @command{configure} searches for suitable flags@footnote{for example, @option{-fopenmp}, @option{-fiopenmp}, @option{-xopenmp} or @option{-qopenmp}. This includes for @command{clang} and the Intel and Oracle compilers.} for @abbr{OpenMP} support for the C, C++ (default standard) and Fortran compilers. Only the C result is currently used for @R{} itself, and only if @code{MAIN_LD}/@code{DYLIB_LD} were not specified. This can be overridden by specifying @example R_OPENMP_CFLAGS @end example Use for packages has similar restrictions (involving @code{SHLIB_LD} and similar: note that as Fortran code is by default linked by the C (or C++) compiler, both need to support @abbr{OpenMP}) and can be overridden by specifying some of @example SHLIB_OPENMP_CFLAGS SHLIB_OPENMP_CXXFLAGS SHLIB_OPENMP_FFLAGS @end example @noindent Setting these to an empty value will disable @abbr{OpenMP} for that compiler (and configuring with @option{--disable-openmp} will disable all detection@footnote{This does not necessarily disable @emph{use} of @abbr{OpenMP} -- the @command{configure} code allows for platforms where @abbr{OpenMP} is used without a flag. For the @command{flang} compiler in late 2017, the Fortran runtime always used @abbr{OpenMP}.} of @abbr{OpenMP}). The @command{configure} detection test is to compile and link a standalone @abbr{OpenMP} program, which is not the same as compiling a shared object and loading it into the C program of @R{}'s executable. Note that overridden values are not tested. @node C++ Support @subsection C++ Support C++ is not used by @R{} itself, but support is provided for installing packages with C++ code via @command{make} macros defined in file @file{etc/Makeconf} (and with explanations in file @file{config.site}): @example CXX CXXFLAGS CXXPICFLAGS CXXSTD CXX11 CXX11STD CXX11FLAGS CXX11PICFLAGS CXX14 CXX14STD CXX14FLAGS CXX14PICFLAGS CXX17 CXX17STD CXX17FLAGS CXX17PICFLAGS CXX20 CXX20STD CXX20FLAGS CXX20PICFLAGS CXX23 CXX23STD CXX23FLAGS CXX23PICFLAGS CXX26 CXX26STD CXX26FLAGS CXX26PICFLAGS @end example @noindent The macros @code{CXX} etc are those used by default for C++ code. @command{configure} will attempt to set the rest suitably, choosing for @code{CXXSTD} and @code{CXX11STD} a suitable flag such as @option{-std=gnu++17} for C++17 support (which is required if C++ is to be supported by default). Inferred values can be overridden in file @file{config.site} or on the @command{configure} command line: user-supplied values will be tested by compiling some C++11/14/17/20/23/26 code. It may be that there is no suitable flag for C++14/17/20/23/26 support with the default compiler, in which case a different compiler could be selected for @code{CXX14}/@code{CXX17}/@code{CXX20}/@code{CXX23}/@code{CXX236} with its corresponding flags. If no suitable compiler/flag is found for the default C++ compiler, one can be set in file @file{config.site} @emph{via} macros @code{CXX} and @code{CXXSTD}. A user-specified compiler does not need to pass the C++17 tests, so do this at your own risk as some packages may not compile. The @option{-std} flag is supported by the GCC, @command{clang++} and Intel compilers. Currently accepted values are (plus some synonyms) @example g++: c++11 gnu+11 c++14 gnu++14 c++17 gnu++17 c++2a gnu++2a (from 8) c++20 gnu++20 (from 10) c++23 gnu++23 c++2b gnu++2b (from 11) c++2c gnu++2c Intel: c++11 gnu+11 c++14 gnu++14 c++17 gnu++17 c++20 gnu++20 (from 2021.1) c++2b gnu++2b (from 2022.2) c++23 gnu++23 (at least from 2024.0) @end example @noindent (Those for @I{LLVM} @command{clang++} are documented at @uref{https://clang.llvm.org/cxx_status.html}, and follow @code{g++}: @code{-std=c++20} is supported from Clang 10, @code{-std=c++2b} from Clang 13 and @code{-std=c++23} and @code{-std=c++2c} from Clang 17. Apple Clang supports @code{-std=c++2b} from 13.1.6 and @code{-std=c++23} and @code{-std=c++2c} from 16.0.0.) @c c++1y does not pass the configure test in gcc 4.9.3 @c , with @option{-std=c++1y} (introduced@footnote{See @c @uref{https://gcc.gnu.org/projects/cxx-status.html#cxx14} for which @c C++14 features it supported.} in version 4.9.x) remaining as a deprecated @c synonym. `Standards' for @command{g++} starting with @samp{gnu} enable `GNU extensions': what those are is hard to track down. For the use of C++ in @R{} packages, @pxref{, , , R-exts, Writing R Extensions}. @c Prior to @R{} 3.6.0 the default C++ standard was @c that of the compiler used: currently it is C++17. @uref{https://en.cppreference.com/w/cpp/compiler_support} indicates which versions of common compilers support (parts of) which C++ standards. @node C standards @subsection C standards Compiling @R{} requires some POSIX features (such as @code{strdup}@footnote{this is part of C23, but part of the C library not the compiler.} and the @code{ssize_t} type) not in the C standards. Typically compilers make these available, but @strong{not} if strict C compliance is specified by for example @option{-std=c17}. So if you want to specify a non-default standard use something like @option{-std=gnu17}. Compiling @R{} requires C99 or later: C11 and C17 are minor updates, but the substantial update `C23' (finally published in October 2024) is also supported for recent versions of GCC@footnote{At least 13--15: 15 defaults to C23}, @command{clang}@footnote{including @I{LLVM} clang 18--20 and Apple clang 15/16.} and Intel @command{icx}. @R{} 4.5.0 defaults to C23 if supported by the chosen compiler. As from @R{} 4.3.0 there is support for packages to indicate their preferred C version. Macros @code{CC17}, @code{C17FLAGS}, @code{CC23} and @code{C23FLAGS} can be set in @file{config.site} (there are examples there). Those for C17 should support C17 or earlier and not allow C23 additions so for example @code{bool}, @code{true} and @code{false} can be used as identifiers. Those for C23 should support the new keywords such as @code{bool}. There is also support for requesting earlier standards @emph{via} @code{CC99} and @code{CC90}: however these are very rarely needed as compilers accept legacy (even K&R) code in C17 mode (but not C23 mode). Some compilers warn enthusiastically about prototypes. For most, omitting @option{-Wstrict-prototypes} in @code{C17FLAGS} suffices. However, versions 15 and later of @I{LLVM} @command{clang} and 14.0.3 and later of Apple clang warn by default in all modes if @option{-Wall} or @option{-pedantic} is used, and may need @option{-Wno-strict-prototypes}. @node Link-Time Optimization @subsection Link-Time Optimization There is support for using link-time optimization (@abbr{LTO}) if the toolchain supports it: configure with flag @option{--enable-lto}. When @abbr{LTO} is enabled it is also used for compiled code in add-on packages unless the flag @option{--enable-lto=R} is used@footnote{Then all add-on packages, including recommended packages are not installed with @abbr{LTO}.}. The main benefit seen to date from @abbr{LTO} has been detecting long-standing bugs in the ways packages pass arguments to compiled code and between compilation units. @I{Benchmarking} in 2020 with @command{gcc}/@command{gfortran}@tie{}10 showed gains of a few percent in increased performance and reduction in installed size for builds without debug symbols, but large size reductions for some packages@footnote{A complete @acronym{CRAN} installation reduced from 50 to 35GB.} with debug symbols. (Performance and size gains are said to be most often seen in complex C++ builds.) Whether toolchains support @abbr{LTO} is often unclear: all of the C compiler, the Fortran compiler@footnote{although there is the possibility to exclude Fortran but that misses some of the benefits.} and linker have to support it, and support it by the same mechanism (so mixing compiler families may not work and a non-default linker may be needed). It has been supported by the GCC and @I{LLVM} projects for some years with diverging implementations. @abbr{LTO} support was added in 2011 for GCC@tie{}4.5 on Linux but was little used before 2019: compiler support has steadily improved over those years and @option{--enable-lto=R} is nowadays used for some routine @acronym{CRAN} checking. Unfortunately @option{--enable-lto} may be accepted but silently do nothing useful if some of the toolchain does not support @abbr{LTO}: this is less common than it once was. Various macros can be set in file @file{config.site} to customize how @abbr{LTO} is used. If the Fortran compiler is not of the same family as the C/C++ compilers, set macro @samp{LTO_FC} (probably to empty). Macro @samp{LTO_LD} can be used to select an alternative linker should that be needed. @node LTO with GCC @subsubsection @abbr{LTO} with GCC This has been tested on Linux with @command{gcc}/@command{gfortran}@tie{}8 and later: that needed setting (e.g.@: in @file{config.site}) @example AR=gcc-ar RANLIB=gcc-ranlib @end example @noindent For non-system compilers or if those wrappers have not been installed one may need something like @example AR="ar --plugin=/path/to/liblto_plugin.so" RANLIB="ranlib --plugin=/path/to/liblto_plugin.so" @end example @noindent and @code{NM} may be needed to be set analogously. (If using an @abbr{LTO}-enabled build to check packages, set environment variable @env{UserNM}@footnote{not @env{NM} as we found @command{make} overriding that.} to @samp{gcc-nm}.) @c http://hubicka.blogspot.com/2019/05/gcc-9-link-time-and-inter-procedural.html It is possible to parallelize parts of the @abbr{LTO} linking process: set the make macro @samp{LTO} to something like @samp{LTO=-flto=8} (to use 8 threads), for example in file @file{config.site}. Under some circumstances and for a few packages, the PIC flags have needed overriding on Linux with GCC 9: e.g@: use in @file{config.site}: @example CPICFLAGS=-fPIC CXXPICFLAGS=-fPIC CXX11PICFLAGS=-fPIC CXX14PICFLAGS=-fPIC CXX17PICFLAGS=-fPIC CXX20PICFLAGS=-fPIC FPICFLAGS=-fPIC @end example @noindent We suggest only using these if the problem is encountered (it had not been seen on @acronym{CRAN} with GCC 10--15 at the time of writing). Note that @R{} will usually need to be re-compiled after even a minor update to the compiler (e.g.@: from 13.1 to 13.2). @node LTO with LLVM @subsubsection @abbr{LTO} with @I{LLVM} @I{LLVM} supports another type of @abbr{LTO} called `Thin @abbr{LTO}' as well as a similar implementation to GCC, sometimes called `Full @abbr{LTO}'. (See @uref{https://clang.llvm.org/docs/ThinLTO.html}.) Currently the @I{LLVM} compilers relevant to @R{} are @command{clang} and @command{flang} (formerly @command{Flang-new}) for which this can be selected by setting macro @samp{LTO=-flto=thin}. @I{LLVM} has @example AR=llvm-ar RANLIB=llvm-ranlib @end example @noindent (but macOS does not, and these are not needed there). Where the linker supports a parallel backend for Thin @abbr{LTO} this can be specified @emph{via} the macro @samp{LTO_LD}: see the URL above for per-linker settings and further linking optimizations.) For example, on macOS one might use @example LTO=-flto=thin LTO_FC= LTO_LD=-Wl,-mllvm,-threads=4 @end example to use Thin @abbr{LTO} with 4 threads for C/C++ code, but skip @abbr{LTO} for Fortran code compiled with @command{gfortran}. It is said to be particularly beneficial to use @option{-O3} for @command{clang} in conjunction with @abbr{LTO}. It seems that @command{flang} may in future support @abbr{LTO}. The 2020s versions of Intel's C/C++ compilers are based on @I{LLVM} and as such support @I{LLVM}-style @abbr{LTO}, both `full' and `thin'. This might use something like @example LTO=-flto=thin -flto-jobs=8 @end example @node LTO for package checking @subsubsection @abbr{LTO} for package checking @abbr{LTO} effectively compiles all the source code in a package as a single compilation unit and so allows the compiler (with sufficient diagnostic flags such as @option{-Wall}) to check consistency between what are normally separate compilation units. With @command{gcc}/@command{gfortran} 9.x and later@footnote{probably also 8.4 and later.} @abbr{LTO} will flag inconsistencies in calls to Fortran subroutines/functions, both between Fortran source files and between Fortran and C/C++. @command{gfortran} 8.4, 9.2 and later can help understanding these by extracting C prototypes from Fortran source files with option @option{-fc-prototypes-external}, e.g.@: that (at the time of writing) Fortran @code{LOGICAL} corresponds to @code{int_least32_t *} in C. @c This worked in 2019 but with Fedora 32 did not export dpotrf from dlapack.o @c On some systems it is possible to build the BLAS, LINPACK and LAPACK @c support as static libraries containing intermediate-level code that @abbr{LTO} @c will compile for all objects linked against these libraries, by @c configuring @R{} with @option{--enable-lto=check}. This checks the @c consistency of calls to BLAS/LINPACK/LAPACK in any packages installed @c using the build. @strong{NB:} as its name suggests, this option is @c intended only for checking installation of @R{} and packages: it @c includes these library routines (those called directly and all they @c depend on) in each package. This is unlikely to work in conjunction @c with non-default options for BLAS and LAPACK, and `linking' against @c these libraries may be very slow. @node Testing a Unix-alike Installation @section Testing an Installation Full post-installation testing is possible only if the test files have been installed with @example make install-tests @end example @noindent which populates a @file{tests} directory in the installation. If this has been done, two testing routes are available. The first is to move to the home directory of the @R{} installation (as given by @command{R RHOME} or from @R{} as @code{R.home()}) and run @example cd tests ## followed by one of ../bin/R CMD make check ../bin/R CMD make check-devel ../bin/R CMD make check-all @end example @noindent and other useful targets are @code{test-BasePackages} and @code{test-Recommended} to run tests of the standard and recommended packages (if installed) respectively. This re-runs all the tests relevant to the installed @R{} (including for example the code in the package vignettes), but not for example the ones checking the example code in the manuals nor making the standalone @I{Rmath} library. This can occasionally be useful when the operating environment has been changed, for example by OS updates or by substituting the @acronym{BLAS} (@pxref{Shared BLAS}). Parallel checking of packages may be possible: set the environment variable @env{TEST_MC_CORES} to the maximum number of processes to be run in parallel. This affects both checking the package examples (part of @command{make check}) and package sources (part of @command{make check-devel} and @command{make check-recommended}). It does require a @command{make} command which supports the @command{make -j @var{n}} option: most do. Alternatively, the installed @R{} can be run, preferably with @option{--vanilla}. Then @enindex LC_COLLATE @example pdf("tests.pdf") ## optional, but prevents flashing graphics windows Sys.setenv(LC_COLLATE = "C", LC_TIME = "C", LANGUAGE = "en") tools::testInstalledBasic("both") tools::testInstalledPackages(scope = "base") tools::testInstalledPackages(scope = "recommended") @end example @noindent runs the basic tests and then all the tests on the standard and recommended packages. These tests can be run from anywhere: the basic tests write their results in the @file{tests} folder of the @R{} home directory and run fewer tests than the first approach: in particular they do not test things which need Internet access---that can be tested by @example tools::testInstalledBasic("internet") @end example It is possible to test the installed packages (but not their package-specific tests) by @code{testInstalledPackages} even if @command{make install-tests} was not run. The outputs are written under the current directory unless a different one is specified by @code{outDir}. 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) @example LANGUAGE=en @end example @noindent and use a UTF-8 or Latin-1 locale. @node Installing R under Windows @chapter Installing R under Windows @cindex Installing under Windows [The rest of this paragraph is only relevant after release.] The @file{bin/windows} directory of a @acronym{CRAN} site contains binaries for a base distribution and a large number of add-on packages from @acronym{CRAN} to run on 64-bit @cputype{x86_64} Windows. R is most tested on current versions of Windows 10 and Windows Server 2022 with UTF-8 as the charset encoding. It works also on Windows 11. It runs on older versions of Windows, but normally with other charset encoding and may require manual installation of the Universal C Runtime (@abbr{UCRT}). Your file system must allow long file names (as is likely except perhaps for some network-mounted systems). If it does not also support conversion to short name equivalents (a.k.a. DOS 8.3 names), then @R{} @emph{must} be installed in a path that does not contain spaces. Installation is @emph{via} the installer @file{@value{RWVERSION}-win.exe}. Just double-click on the icon and follow the instructions. You can uninstall @R{} from the Control Panel. You will be asked to choose a language for installation: that choice applies to both installation and @I{un-installation} but not to running @R{} itself. See the @uref{https://CRAN.R-project.org/bin/windows/base/rw-FAQ.html, R Windows @acronym{FAQ}} for more details on the binary installer and for information on use on older Windows systems. @node Building from source @section Building from source It is possible to use other 64-bit toolchains (including `MSYS2') with @abbr{UCRT} support to build @R{}, but this manual only documents that used for recent binary distributions of @R{}. When using other toolchains, makefiles of @R{} and packages may need to be adapted. @node The Windows toolset @subsection The Windows toolset The binary distribution of @R{} is currently built with tools from @uref{https://CRAN.R-project.org/bin/windows/Rtools/rtools44/rtools.html,Rtools44 for Windows}. See @uref{https://CRAN.R-project.org/bin/windows/base/howto-@value{RWTVERSION}.html, Building @value{RWTVERSION} and packages on Windows} for more details on how to use it. The toolset includes compilers (currently GCC version 13.2.0 with selected additional patches) and runtime libraries from @uref{http://mingw-w64.org/,the `@I{MinGW-w64}' project} and a number of pre-compiled static libraries and headers used by @R{} and @R{} packages, compiled by @uref{https://mxe.cc/,'MXE'} (M cross environment, with updates maintained by @I{Tomas Kalibera}). The toolset also includes build tools from the @uref{https://www.msys2.org/, the 'MSYS2' project}. Additional build tools packaged by 'MSYS2' may be installed via a package manager (@samp{pacman}). There is also an experimental variant of @I{Rtools44} with support for 64-bit ARM CPUs (@I{aarch64}) via @I{LLVM} 17 toolchain using @command{clang}/@command{flang} compilers, @command{lld} linker, and @I{libc++}. The toolsets used for 64-bit Windows from 2008 to 2022 were based on @I{MinGW-w64}. The assistance of @I{Yu Gong} at a crucial step in porting @R{} to @I{MinGW-w64} is gratefully acknowledged, as well as help from @I{Kai Tietz}, the lead developer of the @I{MinGW-w64} project and from @I{Martin Storsjo}. @node LaTeX on Windows @subsection @LaTeX{} Both building @R{} and checking packages need a distribution of @LaTeX{} installed, with the directory containing @command{pdflatex} on the path. The @samp{MiKTeX} (@uref{https://miktex.org/}) distribution of @LaTeX{} is that used on @acronym{CRAN}. This can be set up to install extra packages `on the fly' (without asking), which is the simplest way to use it. The `basic' version of @samp{MiKTeX} will need to add some packages.@footnote{There are reports of segfaults when @samp{MiKTeX} installs additional packages when making @file{NEWS.pdf}: re-running @command{make} seems to solve this.} In any case ensure that the @pkg{inconsolata} package is installed---you can check with the @samp{MiKTeX} Package Manager. It is also possible to use the TeX Live distribution from @uref{https://www.tug.org/texlive/}. (The @acronym{CRAN} package @CRANpkg{tinytex} can install and manage a subset of TeX Live.) @node Checking the build @section Checking the build You can test a build by running @example make check @end example @noindent The recommended packages can be checked by @example make check-recommended @end example @noindent Other levels of checking are @example make check-devel @end example @noindent for a more thorough check of the @R{} functionality, and @example make check-all @end example @noindent for both @code{check-devel} and @code{check-recommended}. If a test fails, there will almost always be a @file{.Rout.fail} file in the directory being checked (often @file{tests/Examples} or @file{tests}): examine the file to help pinpoint the problem. Parallel checking of package sources (part of @command{make check-devel} and @command{make check-recommended}) is possible: see the environment variable @env{TEST_MC_CORES} to the maximum number of processes to be run in parallel. @node Testing a Windows Installation @section Testing an Installation The Windows installer contains a set of test files used when building @R{}. The toolset is not needed to run these tests, but more comprehensive analysis of errors will be given if @command{diff} is in the path. Launch either @code{Rgui} or @code{Rterm} (preferred), preferably with @option{--vanilla}. Then run @example Sys.setenv(LC_COLLATE = "C", LC_TIME="C", LANGUAGE = "en") tools::testInstalledBasic("both") tools::testInstalledPackages(scope = "base") tools::testInstalledPackages(scope = "recommended") @end example @noindent runs the basic tests and then all the tests on the standard and recommended packages. These tests can be run from anywhere: @code{testInstalledBasic} writes results in the @file{tests} folder of the @R{} home directory (as given by @code{R.home()}) and @code{testInstalledPackages} under the current directory unless a different one is specified by @code{outDir}. For the @file{tests} folder to be writeable, one normally needs to install @R{} to a directory other than the default @file{C:\Program Files}. The installer also allows to install @R{} without Administrator privileges, see the @uref{https://CRAN.R-project.org/bin/windows/base/rw-FAQ.html, R Windows @acronym{FAQ}} for more details. The results of @code{example(md5sums)} when testing @pkg{tools} may differ from the reference output as some files are installed with Windows' CRLF line endings. Also, expect differences in @file{reg-plot-latin1.pdf}. One can also run tests from the toolset shell (e.g. @command{bash}) similarly to a Unix-like installation. Move to the home directory of the @R{} installation (as given by @command{R RHOME} or from @R{} as @code{R.home()}) and run @example cd tests ## followed by one of ../bin/R CMD make check ../bin/R CMD make check-devel ../bin/R CMD make check-all @end example Remember that @LaTeX{} needs to be on the path. @node Installing R under macOS @chapter Installing R under macOS @cindex macOS @macro Rapp{} @sc{R.app} @end macro [The rest of this paragraph is only relevant after release.] @c The front page of a @acronym{CRAN} site has a link `Download R for (Mac) OS X' which takes you to a new page. Two files are offered for download, @file{R-@value{VERSIONno}-arm64.pkg} and @file{R-@value{VERSIONno}-x86_64.pkg}. Both are for macOS 11 or later (@I{Big Sur}, @I{Monterey}, @I{Ventura}, @I{Sonoma}, @dots{}). The first is for `Apple Silicon' (@emph{aka} `M1', `M2', @dots{}) Macs, the second for older Macs with an @cputype{x86_64} (Intel) CPU. @c Package @file{R-@value{VERSIONno}.pkg} also be installed on `Apple @c Silicon' CPUs using `Rosetta' emulation@footnote{You may be asked to @c install Rosetta at first use -- @c @url{https://support.apple.com/en-us/102527} -- which may need @c administrator privileges.}, but the native build is preferred. It is a @c little faster (and for some tasks, considerably so) but may give @c different numerical results from the more common @cputype{x86_64} @c platforms (on Windows, Linux, @dots{} as well as macOS) as ARM hardware @c lacks extended-precision floating-point operations. It is important that if you use a binary installer package that your OS is fully updated: look at `Software Update' in 'System Preferences' to be sure. To install, just double-click on the icon of the file you downloaded. At the `Installation Type' stage, note the option to `Customize'. This currently shows four components: everyone will need the `R Framework' component: the remaining components are optional. (The `Tcl/Tk' component is needed to use package @pkg{tcltk}. The `@I{Texinfo}' component is only needed by those installing source packages or @R{} from its sources.) Note for @I{Ventura} users: installation from the @file{Downloads} folder may not be allowed or may require additional authorization, so we suggest you download somewhere else such as your desktop or home folder. These are Apple Installer packages. If you encounter any problem during the installation, please check the Installer log by clicking on the ``Window'' menu and item ``Installer Log''. The full output (select ``Show All Log'') is useful for tracking down problems. Note that the installer is clever enough to try to upgrade the last-installed version of the application where you installed it (which may not be where you want this time @dots{}). Various parts of the build require @I{XQuartz} to be installed: see @uref{https://www.xquartz.org/releases/}.@footnote{At the time of writing, version 2.8.5 or later.} These include the @pkg{tcltk} package and the @code{X11} graphics device: attempting to use these without @I{XQuartz} will remind you. This is also needed for some @cindex Cairo builds of the @I{cairographics}-based devices (which are not often used on macOS) such as @code{png(type = "cairo")} and @code{svg()} and some third-party packages (e.g.@: @CRANpkg{rgl}). If you update your macOS version, you should re-install @R{} (and perhaps @I{XQuartz}): the installer may tailor the installation to the current version of the OS. Installers for R-patched and R-devel are usually available from @uref{https://mac.R-project.org}. (Some of these packages may be unsigned/not notarized: to install those Control/right/two-finger click, select @samp{Open With} and @samp{Installer}.) For building @R{} from source, see @ref{macOS}. @node Running R under macOS @section Running R under macOS There are two ways to run @R{} on macOS from a @acronym{CRAN} binary distribution. There is a GUI console normally installed with the @R{} icon in @file{/Applications} which you can run by double-clicking (e.g.@: from Launchpad or Finder). (If you cannot find it there it was possibly installed elsewhere so try searching for it in Spotlight.) This is usually referred to as @Rapp{} to distinguish it from command-line @R{}: its user manual is currently part of the macOS FAQ at @uref{https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html} and can be viewed from @Rapp{}'s `Help' menu. You can run command-line @R{} and @command{Rscript} from a Terminal@footnote{The installer puts links to @command{R} and @command{Rscript} in @file{/usr/local/bin}. If these are missing or that is not on your path, you can run directly the copies in @file{/Library/Frameworks/R.framework/Resources/bin} or link those yourself to somewhere on your path.} so these can be typed as commands as on any other Unix-alike: see the next chapter of this manual. There are some small differences which may surprise users of @R{} on other platforms, notably the default location of the personal library directory (under @file{~/Library/R}, e.g.@: @file{~/Library/R/arm64/4.4/library}), and that warnings, messages and other output to @file{stderr} are highlighted in bold. @c https://ryanhomer.github.io/posts/build-openmp-macos-catalina-complete Those using the @command{zsh} shell (the default for new user accounts) might find the command @command{R} being masked by the @command{zsh} builtin @command{r} (which recalls commands). One can use a full path to @R{} in an alias, or add @code{disable r} to @file{~/.zshrc}. @c If you have installed both installer packages on an @code{arm64} Mac, @c the last installed will be used. @c https://stat.ethz.ch/pipermail/r-sig-mac/2014-October/011131.html It has been reported that running @Rapp{} may fail if no preferences are stored, so if it fails when launched for the very first time, try it again (the first attempt will store some preferences). Users of @Rapp{} need to be aware of the `App Nap' feature (@uref{https://developer.apple.com/library/archive/releasenotes/MacOSX/WhatsNewInOSX/Articles/MacOSX10_9.html}) which can cause @R{} tasks to appear to run very slowly when not producing output in the console. Here are ways to avoid it: @itemize @item Ensure that the console is completely visible (or at least the activity indicator at the top right corner is visible). @item In a Terminal, run @example defaults write org.R-project.R NSAppSleepDisabled -bool YES @end example @noindent (see @uref{https://developer.apple.com/library/archive/releasenotes/MacOSX/WhatsNewInOSX/Articles/MacOSX10_9.html}). @end itemize Using the @code{X11} graphics device or the X11-based versions of @code{View()} and @code{edit()} for data frames and matrices (the latter are the default for command-line @R{} but not @Rapp{}) requires @uref{https://www.xquartz.org/, XQuartz} to be installed. Under some rather nebulous circumstances messages have been seen from @code{fontconfig} about missing/unreadable configuration files when using @I{cairo}-based devices, especially @code{X11(type = "cairo")}. With @I{XQuartz} installed there are two @code{fontconfig} areas from different versions and it can help to set @example setenv FONTCONFIG_PATH /opt/X11/lib/X11/fontconfig @end example @noindent Another symptom has been that italic/oblique fonts are replaced by upright ones. @node Uninstalling under macOS @section Uninstalling under macOS @R{} for macOS consists of two parts: the GUI (@Rapp{}) and the R framework. @I{Un-installation} is as simple as removing those folders (e.g.@: by dragging them onto the Bin@footnote{Formerly known as the Trash.}). The typical installation will install the GUI into the @file{/Applications/R.app} folder and the R framework into the @file{/Library/Frameworks/R.framework} folder. The links to @file{R} and @file{Rscript} in @file{/usr/local/bin} should also be removed. If you want to get rid of @R{} more completely using a Terminal, simply run: @example sudo rm -Rf /Library/Frameworks/R.framework /Applications/R.app \ /usr/local/bin/R /usr/local/bin/Rscript @end example The installation consists of up to four Apple packages:@footnote{At the time of writing: use @command{pkgutil --pkgs | grep -i org.r-project} to check.} for the `Apple Silicon' build, @code{org.R-project.arm64.R.fw.pkg}, @code{org.R-project.arm64.R.GUI.pkg}, @code{org.r-project.arm64.tcltk} and @code{org.r-project.arm64.texinfo}. You can use @code{sudo pkgutil --forget} if you want the Apple Installer to forget about the package without deleting its files (useful for the @R{} framework when installing multiple @R{} versions in parallel), or after you have deleted the files. @strong{NB:} the package names are case-sensitive and the @R{} domain is named inconsistently. Uninstalling the Tcl/Tk and @I{Texinfo} components (which are installed under @file{/opt/R/arm64} on a @cputype{arm64} build and @file{/opt/R/x86_64} for an @cputype{x86_64} one) is not as simple. You can list the files they installed in a Terminal by e.g.@: @example pkgutil --files org.r-project.arm64.tcltk pkgutil --files org.r-project.arm64.texinfo @end example @noindent (For the `Intel build, replace @code{arm64} by @code{x86_64}.) These are paths relative to @file{/}, the root of the file system. @c Maybe too dangerous for naive users. @c file.remove removes empty directories on Unix. @c The second could be uninstalled by an @R{} script like @c @example @c lis <- system2("pkgutil", "--files org.r-project.x86_64.texinfo", stdout = TRUE) @c setwd("/") @c file.remove(rev(lis)) @c @end example @c @noindent @c run as the owner of @file{/usr/local}. If you are not compiling @R{} nor installing packages from source you could remove all of @file{/opt/R/arm64} or @file{/opt/R/x86_64}. @node Multiple versions @section Multiple versions The installer will remove any previous version@footnote{More precisely, of the Apple package of the same name: this means that ARM and Intel versions can be installed together.} of the @R{} framework which it finds installed. This can be avoided by using @command{pkgutil --forget} (see the previous section). However, note that different versions are installed under @file{/Library/Frameworks/R.framework/Versions} as @file{4.4-arm64} (or @file{4.4-x86_64}), @file{4.3} and so on, so it is not possible to have different @samp{4.x.y} versions installed for the same @samp{x} and CPU type. @Rapp{} will always run the `current' version of @R{}, that is the last installed version. @node Running R @chapter Running R How to start @R{} and what command-line options are available is discussed in @ref{Invoking R, , , R-intro, 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 @I{NetBSD} may not. Use the shell command @command{ulimit} (@command{sh}/@command{bash}) or @command{limit} (@command{csh}/@command{tcsh}) to check.) For some compilers@footnote{Including GCC 9 on Linux.} and packages a larger stack size has been needed: 20-25MB has sufficed to date. @R{} makes use of a number of environment variables, the default values of many of which are set in file @file{@var{R_HOME}/etc/Renviron} (there are none set by default on Windows and hence no such file). These are set at @command{configure} time, and you would not normally want to @enindex R_PAPERSIZE change them -- a possible exception is @env{R_PAPERSIZE} (@pxref{Setting paper size}). The paper size will be deduced from the @samp{LC_PAPER} locale category if it exists and @env{R_PAPERSIZE} is unset, and this will normally produce the right choice from @samp{a4} and @samp{letter} on modern Unix-alikes (but can always be overridden by setting @env{R_PAPERSIZE}). Various environment variables can be set to determine where @R{} creates its per-session temporary directory. The environment variables @enindex TMPDIR @enindex TMP @enindex TEMP @env{TMPDIR}, @env{TMP} and @env{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 @file{/tmp} on Unix-alikes and the value of @enindex R_USER @env{R_USER} on Windows. The path should be an absolute path not containing spaces@footnote{On Windows a path containing spaces will be replaced by the `short path' version if available and that does not contain spaces.} (and it is best to avoid non-alphanumeric characters such as @code{+} or quotes). Some Unix-alike systems are set up to remove files and directories periodically from @file{/tmp}, for example by a @command{cron} job @enindex TMPDIR running @command{tmpwatch}. Set @env{TMPDIR} to another directory before starting long-running jobs on such a system. Note that @env{TMPDIR} will be used to execute @command{configure} scripts when installing packages, so if @file{/tmp} has been mounted as @samp{noexec}, @env{TMPDIR} needs to be set to a directory from which execution is allowed. @node Add-on packages @chapter Add-on packages @cindex Packages @cindex Libraries It is helpful to use the correct terminology. A @emph{package} is loaded from a @emph{library} by the function @code{library()}. Thus a library is a directory containing installed packages; the main library is @file{@var{R_HOME}/library}, but others can be used, for example by @enindex R_LIBS setting the environment variable @env{R_LIBS} or using the @R{} function @code{.libPaths()}. To avoid any confusion you will often see a library directory referred to as a `library tree'. @node Default packages @section Default packages @cindex Packages, default The set of packages loaded on startup is by default @example > getOption("defaultPackages") [1] "datasets" "utils" "grDevices" "graphics" "stats" "methods" @end example @noindent (plus, of course, @pkg{base}) and this can be changed by setting the option in startup code (e.g.@: in @file{~/.Rprofile}). It is initially @enindex R_DEFAULT_PACKAGES set to the value of the environment variable @env{R_DEFAULT_PACKAGES} if set (as a comma-separated list). Setting @env{R_DEFAULT_PACKAGES=NULL} ensures that only package @pkg{base} is loaded. Changing the set of default packages is normally used to reduce the set for speed when scripting: in particular not using @pkg{methods} will reduce the start-up time by a factor of up to two. But it can also be used to customize @R{}, e.g.@: for class use. @command{Rscript} also checks the environment variable @env{R_SCRIPT_DEFAULT_PACKAGES}; @enindex R_SCRIPT_DEFAULT_PACKAGES if set, this takes precedence over @env{R_DEFAULT_PACKAGES}. @node Managing libraries @section Managing libraries @cindex Libraries, managing @R{} packages are installed into @emph{libraries}, which are directories in the file system containing a subdirectory for each package installed there. @R{} comes with a single library, @file{@var{R_HOME}/library} which is the value of the @R{} object @samp{.Library} containing the standard and recommended@footnote{unless they were excluded in the build.} packages. Both sites and users can create others and make use of them (or not) in an @R{} session. At the lowest level @samp{.libPaths()} can be used to add paths to the collection of libraries or to report the current collection. @cindex Libraries, site @cindex Site libraries @R{} will automatically make use of a site-specific library @file{@var{R_HOME}/site-library} if this exists (it does not in a vanilla @R{} installation). This location can be overridden by setting@footnote{its binding is locked once the startup files have been read, so users cannot easily change it. See @code{?.libPaths} for how to make use of the new value.} @samp{.Library.site} in @file{@var{R_HOME}/etc/Rprofile.site}, or (not recommended) by setting the @enindex R_LIBS_SITE environment variable @env{R_LIBS_SITE}. @cindex Libraries, user @cindex User libraries @enindex R_LIBS_USER Users can have one or more libraries, normally specified by the environment variable @env{R_LIBS_USER}. This has a default value (to see it, use @samp{Sys.getenv("R_LIBS_USER")} within an @R{} session), but that is only used if the corresponding directory actually exists (which by default it will not). Both @env{R_LIBS_USER} and @env{R_LIBS_SITE} can specify multiple library paths, separated by colons (semicolons on Windows). @node Installing packages @section Installing packages @cindex Packages, installing Packages may be distributed in source form or compiled binary form. Installing source packages which contain C/C++/Fortran code requires that compilers and related tools be installed. Binary packages are platform-specific and generally need no special tools to install, but see the documentation for your platform for details. Note that you may need to specify implicitly or explicitly the library to which the package is to be installed. This is only an issue if you have more than one library, of course. @c If installing packages on a Unix-alike to be used by other users, ensure @c that the system @code{umask} is set to give sufficient permissions (see @c also @code{Sys.umask} in @R{}). (To a large extent this is unnecessary @c in recent versions of @R{}, which install packages as if @code{umask = 022}.) @enindex TMPDIR Ensure that the environment variable @env{TMPDIR} is either unset (and @file{/tmp} exists and can be written in and executed from) or is the absolute path to a valid temporary directory, not containing spaces. For most users it suffices to call @samp{install.packages(@var{pkgname})} or its GUI equivalent if the intention is to install a @acronym{CRAN} package and Internet access is available.@footnote{If a proxy needs to be set, see @command{?download.file}.} On most systems @samp{install.packages()} will allow packages to be selected from a list box (typically with tens of thousands of items). To install packages from source on a Unix-alike use in a terminal @example R CMD INSTALL -l /path/to/library @var{pkg1} @var{pkg2} @dots{} @end example @noindent The part @samp{-l /path/to/library} can be omitted, in which case the first library of a normal @R{} session is used (that shown by @code{.libPaths()[1]}). There are a number of options available: use @code{R CMD INSTALL --help} to see the current list. @findex install.packages Alternatively, packages can be downloaded and installed from within @R{}. First choose your nearest @acronym{CRAN} mirror using @command{chooseCRANmirror()}. Then download and install packages @pkg{pkg1} and @pkg{pkg2} by @example > install.packages(c("pkg1", "pkg2")) @end example @noindent The essential dependencies of the specified packages will also be fetched. Unless the library is specified (argument @code{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. @example > install.packages("Rcmdr", dependencies = TRUE) @end example @code{install.packages} can install a source package from a local @file{.tar.gz} file (or a URL to such a file) by setting argument @code{repos} to @code{NULL}: this will be selected automatically if the name given is a single @file{.tar.gz} file. @code{install.packages} can look in several repositories, specified as a character vector by the argument @code{repos}: these can include a @acronym{CRAN} mirror, Bioconductor, R-forge, @I{rforge.net}, local archives, local files, @dots{}). Function @code{setRepositories()} can select amongst those repositories that the @R{} installation is aware of. Something which sometimes puzzles users is that @code{install.packages()} may report that a package which they believe should be available is not found. Some possible reasons: @itemize @item The package, such as @pkg{grid} or @pkg{tcltk}, is part of @R{} itself and not otherwise available. @item The package is not in the available repositories, so check which have been selected by @example getOption("repos") @end example @item The package is available, but not for the current version of @R{} or for the type of OS (Unix/Windows). To retrieve the information on available versions of package @code{@var{pkg}}, use @example av <- available.packages(filters=list()) av[av[, "Package"] == @var{pkg}, ] @end example @noindent in your @R{} session, and look at the @samp{Depends} and @samp{OS_type} fields (there may be more than one matching entry). If the package depends on a version of @R{} later than the one in use, it is possible that an earlier version is available which will work with your version of @R{}: for @acronym{CRAN} look for `Old sources' on the package's @acronym{CRAN} landing page and manually retrieve an appropriate version (of comparable age to your version of @R{}). @end itemize Naive users sometimes forget that as well as installing a package, they have to use @code{library} to make its functionality available. @node Windows packages @subsection Windows What @code{install.packages} does by default is different on Unix-alikes (except macOS) and Windows. On Unix-alikes it consults the list of available @emph{source} packages on @acronym{CRAN} (or other repositories), downloads the latest version of the package sources, and installs them (via @code{R CMD INSTALL}). On @cputype{x86_64} Windows it looks (by default) first at the list of @emph{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 @command{make} is available (and this can be tuned by option @code{"install.packages.compile.from.source"}). [At present binary packages are not distributed for @cputype{aarch64} Windows, so most of this subsection only applies to @cputype{x86_64}.] On Windows @code{install.packages} can also install a binary package from a local @file{zip} file (or the URL of such a file) by setting argument @code{repos} to @code{NULL}. @code{Rgui.exe} has a menu @code{Packages} with a GUI interface to @code{install.packages}, @code{update.packages} and @code{library}. Windows binary packages for @R{} were distributed as a single binary containing either or both architectures (32- and 64-bit). Prior to @R{} 4.2.0, they might contain only the 32-bit architecture. @c A few of the binary packages need other software to be installed on your @c system. @c Packages using Gtk+ (@CRANpkg{Cairo}, @CRANpkg{RGtk2}, @c @CRANpkg{cairoDevice} and those that depend on them) need the @file{bin} @c directory of a bundled distribution of Gtk2 from @c @uref{http://ftp.gnome.org/pub/gnome/binaries/win32/gtk+} or @c @uref{http://ftp.gnome.org/pub/gnome/binaries/win64/gtk+} in @c the path: it should work to have both 32- and 64-bit Gtk+ @file{bin} @c directories in the path on a 64-bit version of @R{}. @command{R CMD INSTALL} works in Windows to install source packages. No additional tools are needed if the package does not contain compiled code, and @code{install.packages(type="source")} will work for such packages. Those with compiled code need the tools (see @ref{The Windows toolset}). The tools are found automatically by @R{} when installed by the toolset installer. See @uref{https://cran.r-project.org/bin/windows/base/howto-@value{RWTVERSION}.html, Building @value{RWTVERSION} and packages on Windows} for more details. Occasional permission problems after unpacking source packages have been seen on some systems: these have been circumvented by setting the environment variable @env{R_INSTALL_TAR} to @samp{tar.exe}. @enindex R_INSTALL_TAR 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 @uref{https://win-builder.r-project.org/}. For almost all packages @command{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{} (only 64-bit builds and installs are supported since @R{} 4.2.0). It will report success if the installation of the architecture of the running @command{R} succeeded, whether or not the other architecture was successfully installed. The exceptions are packages with a non-empty @file{configure.win} script or which make use of @file{src/Makefile.win}. If @file{configure.win} does something appropriate to both architectures use@footnote{for a small number of @acronym{CRAN} packages where this is known to be safe and is needed by the @I{autobuilder} this is the default. Look at the source of @file{tools:::.install_packages} for the list. It can also be specified in the package's @file{DESCRIPTION} file.} option @option{--force-biarch}: otherwise @command{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. @node macOS packages @subsection macOS On macOS @code{install.packages} works as it does on other Unix-alike systems, but there is an additional type @code{binary} (available for the @acronym{CRAN} distribution but not when compiling @R{} from source) which can be passed to @code{install.packages} in order to download and install binary packages from a suitable repository. These binary package files for macOS have the extension @samp{.tgz}. The @Rapp{} GUI provides menus for installation of either binary or source packages, from @acronym{CRAN}, other repositories or local files. On @R{} builds using binary packages, the default is type @code{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 @command{make} is available. Note that most binary packages which include compiled code are tied to a particular series (e.g.@: @R{} 4.5.x or 4.4.x) of @R{}. Installing source packages which do not contain compiled code should work with no additional tools. For others you will need the `Command Line Tools' for @command{Xcode} and compilers which match those used to build @R{}, plus a Fortran compiler for packages which contain Fortran code: see @ref{macOS}. Packages with C/C++ source code which link to Fortran libraries (which include the @acronym{BLAS} and @acronym{LAPACK} libraries) will need either the Fortran compiler or, for @acronym{CRAN} binary distributions of @R{}, to specify @example FLIBS = -L/Library/Frameworks/R.framework/Resources/lib -lgfortran -lquadmath @end example @noindent in a @file{Makevars} file (see the next section) to point to the Fortran libraries in the binary distribution. Package @CRANpkg{rJava} and those which depend on it need a Java runtime installed and several packages need X11 installed, including those using Tk. See @ref{macOS} and @ref{Java (macOS)}. Package @CRANpkg{rjags} needs a build of JAGS installed under @file{/usr/local}, such as those at @uref{https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Mac%20OS%20X/}. Tcl/Tk extension @code{BWidget} used to be distributed with @R{} but no longer is; @code{Tktable} has been distributed with recent versions of @R{}. @c (but not 4.0.0 and not @cputype{arm64} builds of 4.1.0 or 4.1.1). @c A few of the binary packages need other software to be installed on your @c system. In particular packages using Gtk+ (@CRANpkg{RGtk2}, @c @CRANpkg{cairoDevice} and those that depend on them) need the GTK @c framework installed from @uref{https://mac.R-project.org/libs/}: the @c appropriate version at the time of writing was @c @uref{https://mac.R-project.org/libs/GTK_2.24.17-X11.pkg}. @c The same instructions apply when installing binary packages into the @c @acronym{CRAN} distribution of @R{} running on an @cputype{arm64} (aka @c `Apple Silicon' aka `M1') Mac. The default compilers specified are shown in file @file{/Library/Frameworks/@/R.framework/@/Resources/etc/Makeconf}. At the time of writing those settings assumed that the C, Fortran and C++ compilers were on the path (see @ref{macOS}). The settings can be changed, either by editing that file or in a file such as @file{~/.R/Makevars} (see the next section). Entries which may need to be changed include @samp{CC}, @samp{CXX}, @samp{FC}, @samp{FLIBS} and the corresponding flags, and perhaps @samp{CXXCPP}, @samp{DYLIB_LD}, @samp{MAIN_LD}, @samp{SHLIB_CXXLD} and @samp{SHLIB_LD}, as well as their @samp{CXX11}, @samp{CXX14}, @samp{CXX17} and @samp{CXX20} variants. So for example you could select a specific @I{LLVM} @command{clang} for both C and C++ with extensive checking by having in @file{~/.R/Makevars} @example SDK=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk CC = /usr/local/clang/bin/clang -isysroot $(SDK) CXX = /usr/local/clang/bin/clang++ -isysroot $(SDK) CXX11 = $CXX CXX14 = $CXX CXX17 = $CXX CXX20 = $CXX CXX23 = $CXX CFLAGS = -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion CXXFLAGS = -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion CXX11FLAGS = $CXXFLAGS CXX14FLAGS = $CXXFLAGS CXX17FLAGS = $CXXFLAGS CXX20FLAGS = $CXXFLAGS CXX23FLAGS = $CXXFLAGS @end example @noindent (the current @I{SDK} can be found by running @command{xcrun -show-sdk-path}) and for the current macOS distribution of @command{gfortran} at @uref{https://mac.r-project.org/tools/} @example FC = /opt/gfortran/bin/gfortran (arm64) FLIBS = -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lheapt_w -lquadmath (Intel) FLIBS = -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath @end example @noindent (line broken here for the manual only). If that @command{clang} build supports @abbr{OpenMP}, you can add @example SHLIB_OPENMP_CFLAGS = -fopenmp SHLIB_OPENMP_CXXFLAGS = -fopenmp @end example @noindent to compile @abbr{OpenMP}-using packages. It will also be necessary to arrange for the @code{libomp.dylib} library to be found at both install time and run time, for example by copying/linking it somewhere that is searched such as @file{/usr/local/lib}. Apple includes many Open Source libraries in macOS but increasingly without the corresponding headers (not even in @I{Xcode} nor the Command Line Tools): they are often rather old versions. If installing packages from source using them it is usually easiest to install a statically-linked up-to-date copy of the Open Source package from its sources or from @uref{https://mac.r-project.org/bin/}. But sometimes it is desirable/necessary to use Apple's dynamically linked library, in which case appropriate headers could be extracted from the sources@footnote{Note that capitalization and versioning may differ from the Open Source project.} available @emph{via} @uref{https://opensource.apple.com/releases} -- this has been used for @code{iodbc}. Some care may be needed with selecting compilers when installing external software for use with packages. The `system' compilers as used when building @R{} are @command{clang} and @command{clang++}, but the Apple toolchain also provides compilers called @command{gcc} and @command{g++} which despite their names are based on @I{LLVM} and @code{libc++} like the system ones and which behave in almost the same way as the system ones. Most Open Source software has a @command{configure} script developed using GNU @command{autoconf} and hence will select @command{gcc} and @command{g++} as the default compilers: this usually works fine. For consistency one can use @example ./configure CC=clang CFLAGS=-O2 CXX=clang++ CXXFLAGS=-O2 @end example @noindent (avoiding @command{autoconf}'s default @option{-g}). @command{R CMD INSTALL} and @code{install.packages()} try to invoke @command{configure} with the same compilers and flags used to build @R{}. @c For @cputype{arm64}, not all configure scripts have been updated to @c recognize the platform and so might need the flag @c @option{--build=aarch64-apple-darwin20.1.0}. @c Also, be aware that @c running the compilers from a @cputype{x86_64} application switches them @c to generating code for that CPU: this applies to a Terminal, a shell, @c older @command{cmake} or (non-system) @command{make}, and from @c @command{R CMD INSTALL} or @code{install.packages()}. One can use @c @example @c ./configure CC="clang -arch arm64" CFLAGS=-O2 CXX="clang++ -arch arm64" CXXFLAGS=-O2 @c @end example @c @noindent @c to force @cputype{arm64} code. @node Customizing package compilation @subsection Customizing package compilation The @R{} system and package-specific compilation flags can be overridden or added to by setting the appropriate Make variables in the personal file @file{@var{HOME}/.R/Makevars-@var{R_PLATFORM}} (but @file{@var{HOME}/.R/Makevars.win} or @file{@var{HOME}/.R/Makevars.win64} on Windows), or if that does not exist, @file{@var{HOME}/.R/Makevars}, where @samp{R_PLATFORM} is the platform for which @R{} was built, as available in the @code{platform} component of the @R{} variable @code{R.version}. The full path to an alternative personal file@footnote{using a path containing spaces is likely to cause problems} can be specified @emph{via} the environment variable @env{R_MAKEVARS_USER}. Package developers are encouraged to use this mechanism to enable a reasonable amount of diagnostic messaging (``warnings'') when compiling, such as e.g.@: @option{-Wall -pedantic} for tools from GCC, the GNU Compiler Collection, and for @I{LLVM} (@command{clang} and @command{flang}). Note that this mechanism can also be used when it is necessary to change the optimization level whilst installing a particular package. For example @example ## @r{for C code} CFLAGS = -g -O -mtune=native ## @r{for C++ code} CXXFLAGS = -g -O -mtune=native ## @r{for C++11 code} CXX11FLAGS = -g -O -mtune=native ## @r{for fixed-form Fortran code} FFLAGS = -g -O -mtune=native ## @r{for C17 code} C17FLAGS = -g -O -mtune=native -Wno-strict-prototypes @end example @noindent Note that if you have specified a non-default C++ or C standard, you need to set the flag(s) appropriate to that standard. Another use is to override the settings in a binary installation of R. For example, for the current distribution of @command{gfortran} at @uref{https://mac.r-project.org/tools/} @example FC = /opt/gfortran/bin/gfortran FLIBS = -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath @end example @noindent (line broken here for the manual only). There is also provision for a site-wide @file{Makevars.site} file under @file{@var{R_HOME}/etc} (in a sub-architecture-specific directory if appropriate). This is read immediately after @file{Makeconf}, and the path to an alternative file can be specified by environment variable @env{R_MAKEVARS_SITE}. Note that these mechanisms do not work with packages which fail to pass settings down to sub-makes, perhaps reading @file{etc/Makeconf} in makefiles in subdirectories. Fortunately such packages are unusual. @node Multiple sub-architectures @subsection Multiple sub-architectures When installing packages from their sources, there are some extra considerations on installations which use sub-architectures. These were commonly used on Windows prior to @R{} 4.2.0 but can in principle be used on other platforms. When a source package is installed by a build of @R{} which supports multiple sub-architectures, the normal installation process installs the packages for all sub-architectures. The exceptions are @table @emph @item Unix-alikes where there is an @file{configure} script, or a file @file{src/Makefile}. @item Windows where there is a non-empty @file{configure.win} script, or a file @file{src/Makefile.win} (with some exceptions where the package is known to have an architecture-independent @file{configure.win}, or if @option{--force-biarch} or field @samp{Biarch} in the @file{DESCRIPTION} file is used to assert so). @end table @noindent In those cases only the current architecture is installed. Further sub-architectures can be installed by @example R CMD INSTALL --libs-only @var{pkg} @end example @noindent using the path to @command{R} or @command{R --arch} to select the additional sub-architecture. There is also @command{R CMD INSTALL --merge-multiarch} to build and merge the two architectures, starting with a source tarball. @node Byte-compilation @subsection Byte-compilation Packages are by default byte-compiled on installation. Byte-compilation can be controlled on a per-package basis by the @samp{ByteCompile} field in the @file{DESCRIPTION} file. @node External software @subsection External software Some @R{} packages contain compiled code which links to external software libraries. Unless the external library is statically linked (which is done as much as possible for binary packages on Windows and macOS), the libraries have to be found when the package is loaded and not just when it is installed. How this should be done depends on the OS (and in some cases the version). For Unix-alikes except macOS the primary mechanism is the @code{ld.so} cache controlled by @command{ldconfig}: external dynamic libraries recorded in that cache will be found. Standard library locations will be covered by the cache, and well-designed software will add its locations (as for example @pkg{openmpi} does on Fedora). The secondary mechanism is to consult the environment variable @env{LD_LIBRARY_PATH}. The @R{} script controls that variable, and sets it to the concatenation of @env{R_LD_LIBRARY_PATH}, @env{R_JAVA_LD_LIBRARY_PATH} and the environment value of @env{LD_LIBRARY_PATH}. The first two have defaults which are normally set when @R{} is installed (but can be overridden in the environment) so @env{LD_LIBRARY_PATH} is the best choice for a user to set. On macOS the primary mechanism is to embed the absolute path to dependent dynamic libraries into an object when it is compiled. Few @R{} packages arrange to do so, but it can be edited@footnote{They need to have been created using @option{-headerpad_max_install_names}, which is the default for an @R{} package.} @emph{via} @command{install_name_tool} --- that only deals with direct dependencies and those would also need to be compiled to include the absolute paths of their dependencies. If the choice of absolute path is to be deferred to load time, how they are resolved is described in @command{man dyld}: the role of @env{LD_LIBRARY_PATH} is replaced on macOS by @env{DYLD_LIBRARY_PATH} and @env{DYLD_FALLBACK_LIBRARY_PATH}. Running @command{R CMD otool -L} on the package shared object will show where (if anywhere) its dependencies are resolved. @env{DYLD_FALLBACK_LIBRARY_PATH} is preferred (and it is that which is manipulated by the @R{} script), but as from 10.11 (`@I{El Capitan}') the default behaviour had been changed for security reasons to discard these environment variables when invoking a shell script (and @file{R} is a shell script). That makes the only portable option to set @env{R_LD_LIBRARY_PATH} in the environment, something like @example export R_LD_LIBRARY_PATH="`R RHOME`/lib:/opt/local/lib" @end example The precise rules for where Windows looks for DLLs are complex and depend on the version of Windows. But for present purposes the main solution is to put the directories containing the DLLs the package links to (and any those DLLs link to) on the @env{PATH}. @c 64-bit versions of Windows will ignore 32-bit DLLs from 64-bit @R{} and @c @emph{vice versa}. The danger with any of the methods which involve setting environment variables is of inadvertently masking a system library. This is less for @env{DYLD_FALLBACK_LIBRARY_PATH} and for @emph{appending} to @env{PATH} on Windows (as it should already contain the system library paths). @node Updating packages @section Updating packages @findex update.packages @cindex Packages, updating The command @code{update.packages()} is the simplest way to ensure that all the packages on your system are up to date. It downloads the list of available packages and their current versions, compares it with those installed and offers to fetch and install any that have later versions on the repositories. An alternative interface to keeping packages up-to-date is provided by the command @code{packageStatus()}, which returns an object with information on all installed packages and packages available at multiple repositories. The @code{print} and @code{summary} methods give an overview of installed and available packages, the @code{upgrade} method offers to fetch and install the latest versions of outdated packages. One sometimes-useful additional piece of information that @code{packageStatus()} returns is the status of a package, as @code{"ok"}, @code{"upgrade"} or @code{"unavailable"} (in the currently selected repositories). For example @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 @end example @node Removing packages @section Removing packages @findex remove.packages @cindex Packages, removing Packages can be removed in a number of ways. From a command prompt they can be removed by @example R CMD REMOVE -l /path/to/library @var{pkg1} @var{pkg2} @dots{} @end example From a running @R{} process they can be removed by @example > remove.packages(c("pkg1", "pkg2"), lib = file.path("path", "to", "library")) @end example Finally, one can just remove the package directory from the library. @node Setting up a package repository @section Setting up a package repository @cindex Repositories Utilities such as @code{install.packages} can be pointed at any @acronym{CRAN}-style repository, and @R{} users may want to set up their own. The `base' of a repository is a URL such as @uref{https://www.stats.ox.ac.uk/pub/RWin/}: this must be an URL scheme that @code{download.packages} supports (which also includes @samp{https://}, @samp{ftp://} and @samp{file://}). Under that base URL there should be directory trees for one or more of the following types of package distributions: @itemize @item @code{"source"}: located at @file{src/contrib} and containing @file{.tar.gz} files. Other forms of compression can be used, e.g.@: @file{.tar.bz2} or @file{.tar.xz} files. Complete repositories contain the sources corresponding to any binary packages, and in any case it is wise to have a @file{src/contrib} area with a possibly empty @file{PACKAGES} file. @item @code{"binary"}: binary packages are located under @file{bin/@var{os}/@var{build}/contrib/@var{x.y}} for @R{} versions @var{x.y.z}, where @var{os} is either @file{windows} for Windows or @file{macosx} for macOS and OS X. The @var{build} variable is defined by the third part of the @code{type} value after @code{binary} and may be empty. For example, in @R{} 4.4.1 @code{"mac.binary.big-sur-arm64"} specifies the @file{bin/macosx/big-sur-arm64/4.4} location, while @code{"win.binary"} specifies @file{bin/windows/contrib/4.4}. The platform and build specification in @acronym{CRAN} @R{} binaries can be obtained from @code{.Platform$pkgType}. Windows binary package files use @file{.zip} extension while Mac files use @file{.tgz}. @end itemize Each terminal directory must also contain a @file{PACKAGES} file. This can be a concatenation of the @file{DESCRIPTION} files of the packages separated by blank lines, but only a few of the fields are needed. The simplest way to set up such a file is to use function @code{write_PACKAGES} in the @pkg{tools} package, and its help explains which fields are needed. Optionally there can also be @file{PACKAGES.rds} and @file{PACKAGES.gz} files, downloaded in preference to @file{PACKAGES}. (If you have a @I{mis-configured} server that does not report correctly non-existent files you may need these files.) To add your repository to the list offered by @code{setRepositories()}, see the help file for that function. Incomplete repositories are better specified @emph{via} a @code{contriburl} argument than @emph{via} being set as a repository. A repository can contain subdirectories, when the descriptions in the @file{PACKAGES} file of packages in subdirectories must include a line of the form @example Path: @var{path/to/subdirectory} @end example @noindent ---once again @code{write_PACKAGES} is the simplest way to set this up. @node Checking installed source packages @section Checking installed source packages It can be convenient to run @command{R CMD check} on an installed package, particularly on a platform which uses sub-architectures. The outline of how to do this is, with the source package in directory @file{@var{pkg}} (or a tarball filename): @example R CMD INSTALL -l @var{libdir} @var{pkg} > @var{pkg}.log 2>&1 R CMD check -l @var{libdir} --install=check:@var{pkg}.log @var{pkg} @end example @noindent Where sub-architectures are in use the @command{R CMD check} line can be repeated with additional architectures by @example R --arch @var{arch} CMD check -l @var{libdir} --extra-arch --install=check:@var{pkg}.log @var{pkg} @end example @noindent where @option{--extra-arch} selects only those checks which depend on the installed code and not those which analyse the sources. (If multiple sub-architectures fail only because they need different settings, e.g.@: environment variables, @option{--no-multiarch} may need to be added to the @code{INSTALL} lines.) On Unix-alikes the architecture to run is selected by @option{--arch}: this can also be used on Windows with @file{@var{R_HOME}/bin/R.exe}, but it is more usual to select the path to the @command{Rcmd.exe} of the desired architecture. So on Windows to install, check and package for distribution a source package from a tarball which has been tested on another platform one might use @example .../bin/x64/Rcmd INSTALL -l @var{libdir} @var{tarball} --build > @var{pkg}.log 2>&1 @end example @node Internationalization @chapter Internationalization and Localization @cindex Internationalization @cindex Localization @emph{Internationalization} refers to the process of enabling support for many human languages, and @emph{localization} to adapting to a specific country and language. Current builds of @R{} support all the character sets that the underlying OS can handle. These are interpreted according to the @cindex Locale current @code{locale}, a sufficiently complicated topic to merit a separate section. Note though that @R{} has no built-in support for right-to-left languages and bidirectional output, relying on the OS services. For example, how character vectors in UTF-8 containing both English digits and Hebrew characters are printed is OS-dependent (and perhaps locale-dependent). The other aspect of the internationalization is support for the translation of messages. This is enabled in almost all builds of @R{}. @node Locales @section Locales @cindex Locale A @emph{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 @code{Sys.getlocale} and @code{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 @itemize @item A human language. These are generally specified by a lower-case two-character abbreviation following ISO 639 (see e.g.@: @uref{https://en.wikipedia.org/wiki/ISO_639-1}). @item 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.@: @uref{https://en.wikipedia.org/wiki/ISO_3166}). @item A charset encoding, which determines both how a byte stream should be divided into characters, 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. @item 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 (@code{@@latin}, @code{@@cyrillic} for Serbian, @code{@@iqtelif}) or language dialect (e.g.@: @code{@@saaho}, a dialect of Afar, and @code{@@bokmal} and @code{@@nynorsk}, dialects of Norwegian regarded by some OSes as separate languages, @code{no} and @code{nn}). @end itemize @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. @node Locales under Unix-alikes @subsection Locales under Unix-alikes Modern Linux uses the @abbr{XPG}@footnote{`X/Open Portability Guide', which has had several versions.} locale specifications which have the form @samp{en_GB}, @samp{en_GB.UTF-8}, @samp{aa_ER.UTF-8@@saaho}, @samp{de_AT.iso885915@@euro}, the components being in the order listed above. (See @command{man locale} and @command{locale -a} for more details.) Similar schemes are used by most Unix-alikes: some (including some distributions of Linux) use @samp{.utf8} rather than @samp{.UTF-8}. Note that whereas UTF-8 locales are nowadays almost universally used, locales such as @samp{en_GB} use 8-bit encodings for backwards compatibility. @node Locales under Windows @subsection Locales under Windows Windows also uses locales, but specified in a rather less concise way. Most users will encounter locales only via drop-down menus, but more information and lists can be found by searching for @samp{Windows language country strings}). It offers only one encoding per language. Some care is needed with Windows' locale names. For example, @code{chinese} is Traditional Chinese and not Simplified Chinese as used in most of the Chinese-speaking world. @node Locales under macOS @subsection Locales under macOS macOS supports locales in its own particular way, but the @R{} GUI tries to make this easier for users. See @uref{https://developer.apple.com/library/archive/documentation/MacOSX/Conceptual/BPInternational/} for how users can set their locales. End users will generally only see lists of languages/territories. Users of @R{} in a terminal may need to set the locale to something like @samp{en_GB.UTF-8} if it defaults to @samp{C} (as it sometimes does when logging in remotely and for batch jobs: note whether @command{Terminal} sets the @env{LANG} environment variable is an (advanced) preference, but does so by default). Internally macOS uses a form similar to Linux: the main difference from other Unix-alikes is that where a character set is not specified it is assumed to be @code{UTF-8}. @node Localization of messages @section Localization of messages The preferred language for messages is by default taken from the locale. This can be overridden first by the setting of the environment variable @enindex LANGUAGE @enindex LC_ALL @enindex LC_MESSAGES @enindex LANG @env{LANGUAGE} and then@footnote{On some systems setting @env{LC_ALL} or @env{LC_MESSAGES} to @samp{C} disables @env{LANGUAGE}.} by the environment variables @env{LC_ALL}, @env{LC_MESSAGES} and @env{LANG}. (The last three are normally used to set the locale and so should not be needed, but the first is only used to select the language for messages.) The code tries hard to map locales to languages, but on some systems (notably Windows) the locale names needed for the environment variable @env{LC_ALL} do not all correspond to @abbr{XPG} language names and so @env{LANGUAGE} may need to be set. (One example is @samp{LC_ALL=es} on Windows which sets the locale to Estonian and the language to Spanish.) It is usually possible to change the language once @R{} is running @emph{via} (not Windows) @code{Sys.setlocale("LC_MESSAGES", "new_locale")}, or by setting an environment variable such as @env{LANGUAGE}, @emph{provided}@footnote{If you try changing from French to Russian except in a UTF-8 locale, you may find messages change to English.} the language you are changing to can be output in the current character set. But this is OS-specific, and has been known to stop working on an OS upgrade. Note that translated messages may be cached, so attempting to change the language of an error that has already been output in another language may not work. Messages are divided into @emph{domains}, and translations may be available for some or all messages in a domain. @R{} makes use of the following domains. @itemize @item Domain @code{R} for the C-level error and warning messages from the @R{} interpreter. @item Domain @code{R-@var{pkg}} for the @R{} @code{stop}, @code{warning} and @code{message} messages in each package, including @code{R-base} for the @pkg{base} package. @item Domain @code{@var{pkg}} for the C-level messages in each package. @item Domain @code{RGui} for the menus etc of the @R{} for Windows GUI front-end. @end itemize Dividing up the messages in this way allows @R{} to be extensible: as packages are loaded, their message translation catalogues can be loaded too. @R{} can be built without support for translations, but it is enabled by default. R-level and C-level domains are subtly different, for example in the way strings are canonicalized before being passed for translation. Translations are looked for by domain according to the currently specified language, as specifically as possible, so for example an Austrian (@samp{de_AT}) translation catalogue will be used in preference to a generic German one (@samp{de}) for an Austrian user. However, if a specific translation catalogue exists but does not contain a translation, the less specific catalogues are consulted. For example, @R{} has catalogues for @samp{en_GB} that translate the Americanisms (e.g., @samp{gray}) in the standard messages into English.@footnote{the language written in England: some people living in the USA appropriate this name for their language.} Two other examples: there are catalogues for @samp{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 @samp{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 @enindex LANGUAGE by on-the-fly re-encoding. The @env{LANGUAGE} variable (only) can be a colon-separated list, for example @samp{se:de}, giving a set of languages in decreasing order of preference. One special value is @samp{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'@footnote{with Americanisms.} is used. See @uref{https://developer.r-project.org/Translations30.html} for how to prepare and install translation catalogues. @node Choosing between 32- and 64-bit builds @chapter Choosing between 32- and 64-bit builds As from @R{} 4.4.0 32-bit builds are unsupported. @node The standalone Rmath library @chapter The standalone @I{Rmath} library The routines supporting the distribution and special@footnote{e.g.@: Bessel, beta and gamma functions} functions in @R{} and a few others are declared in C header file @file{Rmath.h}. These can be compiled into a standalone library for linking to other applications. (Note that they are not a separate library when @R{} is built, and the standalone version differs in several ways.) The makefiles and other sources needed are in directory @file{src/nmath/standalone}, so the following instructions assume that is the current working directory (in the build directory tree on a Unix-alike if that is separate from the sources). @file{Rmath.h} contains @samp{R_VERSION_STRING}, which is a character string containing the current @R{} version, for example @code{"4.4.0"}. There is full access to @R{}'s handling of @code{NaN}, @code{Inf} and @code{-Inf} via special versions of the macros and functions @example ISNAN, R_FINITE, R_log, R_pow and R_pow_di @end example @noindent and (extern) constants @code{R_PosInf}, @code{R_NegInf} and @code{NA_REAL}. There is no support for @R{}'s notion of missing values, in particular not for @code{NA_INTEGER} nor the distinction between @code{NA} and @code{NaN} for doubles. A little care is needed to use the random-number routines. You will need to supply the uniform random number generator @example double unif_rand(void) @end example @noindent or use the one supplied (and with a shared library or DLL you may have to use the one supplied, which is the @I{Marsaglia}-@I{multicarry} with an entry point @example set_seed(unsigned int, unsigned int) @end example @noindent to set its seeds). The facilities to change the normal random number generator are available through the constant @code{N01_kind}. This takes values from the enumeration type @example typedef enum @{ BUGGY_KINDERMAN_RAMAGE, AHRENS_DIETER, BOX_MULLER, USER_NORM, INVERSION, KINDERMAN_RAMAGE @} N01type; @end example @noindent (and @samp{USER_NORM} is not available). @node Unix-alike standalone @section Unix-alikes If @R{} has not already been made in the directory tree, @command{configure} must be run as described in the main build instructions. Then (in @file{src/nmath/standalone}) @example make @end example @noindent will make standalone libraries @file{libRmath.a} and @file{libRmath.so} (@file{libRmath.dylib} on macOS): @samp{make static} and @samp{make shared} will create just one of them. To use the routines in your own C or C++ programs, include @example #define MATHLIB_STANDALONE #include @end example @noindent and link against @samp{-lRmath} (and @samp{-lm} if needed on your OS). The example file @file{test.c} does nothing useful, but is provided to test the process (via @command{make test}). Note that you will probably not be able to run it unless you add the directory containing @enindex LD_LIBRARY_PATH @file{libRmath.so} to the @env{LD_LIBRARY_PATH} environment variable (@file{libRmath.dylib}, @env{DYLD_FALLBACK_LIBRARY_PATH} on macOS). The targets @example make install make uninstall @end example @noindent will @I{(un)install} the header @file{Rmath.h} and shared and static @enindex DESTDIR libraries (if built). Both @code{prefix=} and @env{DESTDIR} are supported, together with more precise control as described for the main build. @samp{make install} installs a file for @command{pkg-config} to use by e.g. @example $(CC) `pkg-config --cflags libRmath` -c test.c $(CC) `pkg-config --libs libRmath` test.o -o test @end example On some systems @samp{make install-strip} will install a stripped shared library. @node Windows standalone @section Windows You need to set up@footnote{including copying @file{MkRules.dist} to @file{MkRule.local} and selecting the architecture.} almost all the tools to make @R{} and then run (in a Unix-like shell) @example (cd ../../gnuwin32; make MkRules) (cd ../../include; make -f Makefile.win config.h Rconfig.h Rmath.h) make -f Makefile.win @end example @noindent Alternatively, in a @file{cmd.exe} shell use @example cd ../../include make -f Makefile.win config.h Rconfig.h Rmath.h cd ../nmath/standalone make -f Makefile.win @end example This creates a static library @file{libRmath.a} and a DLL @file{Rmath.dll}. If you want an import library @file{libRmath.dll.a} (you don't need one), use @example make -f Makefile.win shared implib @end example To use the routines in your own C or C++ programs using @I{MinGW-w64}, include @example #define MATHLIB_STANDALONE #include @end example @noindent and link against @samp{-lRmath}. This will use the first found of @file{libRmath.dll.a}, @file{libRmath.a} and @file{Rmath.dll} in that order, so the result depends on which files are present. You should be able to force static or dynamic linking @emph{via} @example -Wl,-Bstatic -lRmath -Wl,Bdynamic -Wl,-Bdynamic -lRmath @end example @noindent or by linking to explicit files (as in the @samp{test} target in @file{Makefile.win}: this makes two executables, @file{test.exe} which is dynamically linked, and @file{test-static.exe}, which is statically linked). It is possible to link to @file{Rmath.dll} using other compilers, either directly or via an import library: if you make a @I{MinGW-w64} import library as above, you will create a file @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 @example #define MATHLIB_STANDALONE #define RMATH_DLL #include @end example @noindent to ensure that the constants like @code{NA_REAL} are linked correctly. (Auto-import will probably work with @I{MinGW-w64}, but it is better to be sure. This is likely to also work with @I{VC++}, @I{Borland} and similar compilers.) @node Essential and useful other programs under a Unix-alike @appendix Essential and useful other programs under a Unix-alike This appendix gives details of programs you will need to build @R{} on Unix-like platforms, or which will be used by @R{} if found by @command{configure}. Remember that some package management systems (such as @abbr{RPM} and Debian/Ubuntu's) make a distinction between the user version of a package and the development version. The latter usually has the same name but with the extension @samp{-devel} or @samp{-dev}: you need both versions installed. @node Essential programs and libraries @section Essential programs and libraries You need a means of compiling C and Fortran 90 (see @ref{Using Fortran}). Your C compiler should be @acronym{ISO}/@acronym{IEC}@tie{}60059@footnote{also known as @acronym{IEEE}@tie{}754}, POSIX 1003.1 and C99-compliant.@footnote{Note that C11 compilers need not be C99-compliant: @R{} requires support for @code{double complex} and variable-length arrays which are optional in C11 but are mandatory in C99. C17 (also known as C18 as it was published in 2018) is a `bugfix release' of C11, clarifying the standard. However, all known recent compilers in C11 or C17 mode are C99-compliant, and most default to C17.} @R{} tries to choose suitable flags@footnote{Examples are @option{-std=gnu99}, @option{-std=c99} and @option{-c99}.} for the C compilers it knows about, but you may have to set @code{CC} or @code{CFLAGS} suitably. (Note that options essential to run the compiler even for linking, such as those to set the architecture, should be specified as part of @code{CC} rather than in @code{CFLAGS}.) Unless you do not want to view graphs on-screen (or use macOS) you need @samp{X11} installed, including its headers and client libraries. For recent Fedora/@I{RedHat} distributions it means (at least) @abbr{RPM}s @samp{libX11}, @samp{libX11-devel}, @samp{libXt} and @samp{libXt-devel}. On Debian/Ubuntu we recommend the meta-package @samp{xorg-dev}. If you really do not want these you will need to explicitly configure @R{} without X11, using @option{--with-x=no}. The command-line editing (and command completion) depends on the @acronym{GNU} @code{readline} library (including its headers): version 6.0 or later is needed for all the features to be enabled. Otherwise you will need to configure with @option{--with-readline=no} (or equivalent). A suitably comprehensive @code{iconv} function is essential. The @R{} usage requires @code{iconv} to be able to translate between @code{"latin1"} and @code{"UTF-8"}, to recognize @code{""} (as the current encoding) and @code{"ASCII"}, and to translate to and from the Unicode wide-character formats @code{"UCS-[24][BL]E"} --- this is true by default for @code{glibc}@footnote{However, it is possible to break the default behaviour of @code{glibc} by re-specifying the @code{gconv} modules to be loaded.} but not of most commercial Unixes. However, you can make use of @acronym{GNU} @code{libiconv} (as used on macOS: see @uref{https://www.gnu.org/software/libiconv/}). The OS needs to have enough support@footnote{specifically, the C99 functionality of headers @file{wchar.h} and @file{wctype.h}, types @code{wctans_t} and @code{mbstate_t} and functions @code{mbrtowc}, @code{mbstowcs}, @code{wcrtomb}, @code{wcscoll}, @code{wcstombs}, @code{wctrans}, @code{wctype}, and @code{iswctype}.} for wide-character types: this is checked at configuration. Some C99 functions@footnote{including @code{expm1}, @code{hypot}, @code{log1p}, @code{nearbyint} and @code{va_copy}.} are required and checked for at configuration. A small number of POSIX functions@footnote{including @code{opendir}, @code{readdir}, @code{closedir}, @code{popen}, @code{stat}, @code{glob}, @code{access}, @code{getcwd} and @code{chdir} system calls, @code{select} on a Unix-alike, and either @code{putenv} or @code{setenv}.} are essential, and others@footnote{such as @code{realpath}, @code{symlink}.} will be used if available. @c zlib 1.2.5 is from July 2010, bzip2 1.0.6 from Sept 2010 @c xz 5.0.3 is from May 2011 Installations of @code{zlib} (version 1.2.5 or later), @code{libbz2} (version 1.0.6 or later: called @pkg{bzip2-libs}/@pkg{bzip2-devel} or @pkg{libbz2-1.0}/@pkg{libbz2-dev} by some Linux distributions) and @code{liblzma}@footnote{most often distributed as part of @code{xz}: possible names in Linux distributions include @code{xz-devel}/@code{xz-libs} and @code{liblzma-dev}.} version 5.0.3 or later are required. Some software distributions@footnote{for example, Fedora 40} replace @code{zlib} by @code{zlib-ng}@footnote{@uref{https://github.com/zlib-ng/zlib-ng}} which has an optional compatibility interface. @c PCRE[1] 8.32 is from Nov 2012. @c Debian Wheezy had 8.30, Ubuntu 14.04LTS had 8.31 but both are EOL. @c PCRE2: Ubuntu 16.04LTS (EOL Apr 2021) and RHEL/Centos 6 have 10.21, @c OpenCSW has 10.20. @c PCRE2 10.30 is from Aug 2017. Ubuntu 18.04LTS has 10.31. Either PCRE1 (version 8.32 or later, formerly known as just PCRE) or PCRE2 is required: PCRE2 is preferred and using PCRE1 requires @command{configure} option @option{--with-pcre1}. Only the 8-bit library and headers are needed if these are packaged separately. @abbr{JIT} support (optional) is desirable for the best performance. For PCRE2 >= 10.30 (which is desirable as matching has been re-written not to use recursion and the Unicode tables were updated to version 10) @example ./configure --enable-jit @end example @noindent suffices. If building PCRE1 for use with @R{} a suitable @command{configure} command might be @example ./configure --enable-utf --enable-unicode-properties --enable-jit --disable-cpp @end example @noindent The @option{--enable-jit} flag is supported for most common CPUs but does not work (well or at all) for @cputype{arm64} macOS. Some packages require the `Unicode properties' which are optional for PCRE1: support for this and @abbr{JIT} can be checked at run-time by calling @code{pcre_config()}. @c libcurl 7.22.0 was released in Sep 2011, in Ubuntu 12.04 LTS, @c end-of-life Apr 2017 @c libcurl 7.26.0 was released in May 2012, still in Debian 7 Wheezy LTS, @c end-of-life May 2018. @c libcurl 7.28.0 was released in Oct 2012 @c libcurl 7.32.0 was released in Aug 2013 @c Ubuntu 14.04LTS has 7.35.0 RHEL/Centos 7 has 7.29.0 (we are told) Library @code{libcurl} (version 7.28.0 or later) is required. Information on @code{libcurl} is found from the @command{curl-config} script: if that is missing or needs to be overridden@footnote{for example to specify static linking with a build which has both shared and static libraries.} there are macros to do so described in file @file{config.site}. A @command{tar} program is needed to unpack the sources and packages (including the recommended packages). A version@footnote{Such as @acronym{GNU} @command{tar} 1.15 or later, @command{bsdtar} (from @uref{https://github.com/libarchive/libarchive/}, used as @command{tar} by FreeBSD and macOS 10.6 and later) or @command{tar} from the @I{Heirloom Toolchest} (@uref{https://heirloom.sourceforge.net/tools.html}), although the latter does not support @command{xz} compression.} that can automagically detect compressed archives is preferred for use with @code{untar()}: the configure script looks for @command{gtar} and @command{gnutar} before @enindex TAR @command{tar} -- use environment variable @env{TAR} to override this. (On @I{NetBSD}/@I{OpenBSD} systems set this to @command{bsdtar} if that is installed.) There need to be suitable versions of the tools @command{grep} and @command{sed}: the problems are usually with old AT&T and BSD variants. @command{configure} will try to find suitable versions (including looking in @file{/usr/xpg4/bin} which is used on some commercial Unixes). You will not be able to build most of the manuals unless you have @command{texi2any} version 6.1 or later installed (which requires @command{perl}), and if not most of the @HTML{} manuals will be linked to a version on @acronym{CRAN}. To make PDF versions of the manuals you will also need file @file{texinfo.tex} installed (which is part of the @acronym{GNU} @I{Texinfo} distribution but is often made part of the @TeX{} package @pkg{texinfo} in re-distributions) as well as @command{texi2dvi}.@footnote{@command{texi2dvi} is normally a shell script. Some of the issues which have been observed with broken versions of @command{texi2dvi} can be circumvented by setting the environment variable @env{R_TEXI2DVICMD} to the value @code{emulation}.} Further, the versions of @command{texi2dvi} and @file{texinfo.tex} need to be compatible: we have seen problems with older @TeX{} distributions. @cindex Subversion If you want to build from the @R{} Subversion repository then @command{texi2any} is highly recommended as it is used to create files which are in the tarball but not stored in the Subversion repository. @cindex Vignettes The PDF documentation (including @file{doc/NEWS.pdf}) and building vignettes needs @command{pdftex} and @command{pdflatex}. We require @LaTeX{} version @code{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 @pkg{hyperref} and we recommend that the @TeX{} distribution used is kept up-to-date. A number of standard @LaTeX{} packages are required for the PDF manuals (including @pkg{url} and some of the font packages such as @pkg{times} and @pkg{helvetic} and also @pkg{amsfonts}) and others such as @pkg{hyperref} and @pkg{inconsolata} are desirable (and without them you may need to change @R{}'s defaults: @pxref{Making the manuals}). Note that package @pkg{hyperref} (currently) requires packages @pkg{etoolbox}, @pkg{kvoptions}, @pkg{ltxcmds} and @pkg{refcount}, and @pkg{inconsolata} requires @pkg{xkeyval}. Building the base vignettes requires @pkg{hyperref}, @pkg{fancyvrb}, @pkg{natbib}, @pkg{parskip} and @pkg{listings}. For distributions based on TeX Live the simplest approach may be to install collections @pkg{collection-latex}, @pkg{collection-fontsrecommended}, @pkg{collection-latexrecommended}, @pkg{collection-fontsextra} and @pkg{collection-latexextra} (assuming they are not installed by default): Fedora uses names like @pkg{texlive-collection-fontsextra} and Debian/Ubuntu like @pkg{texlive-fonts-extra}. Programs @command{qpdf} and @I{Ghostscript} (@command{gs}) are desirable as these will be used to compact the installed PDF vignettes and any PDF manuals. @enindex PATH The essential programs should be in your @env{PATH} at the time @command{configure} is run: this will capture the full paths. For date-times to work correctly it is essential that the tables defining time zones are installed: these are usually in an OS component named something like @code{tzdata}. On most OSes they are required @c with glibc by glibc-common but installations of Alpine Linux have been seen without them. There is a @command{configure} check that recent date-times to work correctly in different time zones which catches this when installing from source (but not for binary distributions). Those distributing binary versions of @R{} may need to be aware of the licences of the external libraries it is linked to (including `useful' libraries from the next section). The @code{liblzma} library is in the public domain and X11, @code{libbzip2}, @code{libcurl} and @code{zlib} have MIT-style licences. PCRE and PCRE2 have a BSD-style licence which requires distribution of the licence (included in @R{}'s @file{COPYRIGHTS} file) in binary distributions. GNU @code{readline} is licensed under GPL (which version(s) of GPL depends on the @code{readline} version). @node Useful libraries and programs @section Useful libraries and programs The ability to use translated messages makes use of @code{gettext} and most likely needs @acronym{GNU} @code{gettext}: you do need this to work with new translations, but otherwise the version of the @code{gettext} runtime contained in the R sources will be used if no suitable external @code{gettext} is found. @cindex Cairo @cindex @I{Pango} The `modern' version of the @code{X11()}, @code{jpeg()}, @code{png()} and @code{tiff()} graphics devices uses the Cairo and @I{Pango} libraries. Cairo version 1.2.0 or later and @I{Pango} version 1.10 or later are required (but much later versions are current). @R{} checks for @command{pkg-config}, and uses that to check first that the @samp{pangocairo} package is installed (and if not, @samp{cairo}) then if suitable code can be compiled. These tests will fail if @command{pkg-config} is not installed@footnote{If necessary the path to @command{pkg-config} can be specified by setting @env{PKG_CONFIG} in @file{config.site}, on the @command{configure} command line or in the environment. There is a compatible re-implementation of @command{pkg-config} called @command{pkgconf} which can be used in the unlikely event that is installed but not linked to @command{pkg-config}.}, and might fail if @code{cairo} was built statically unless @command{configure} option @option{--with-static-cairo} is used. Most systems with @code{Gtk+} 2.8 or later installed will have suitable libraries: for Fedora users the @code{pango-devel} @abbr{RPM} and its dependencies suffice. @c arm64 Homebrew did in early 2021. It is possible (but very unusual on a platform with X11) to build Cairo without its @code{cairo-xlib} module in which case @code{X11(type = "cairo")} will not be available. @I{Pango} is optional but highly desirable as it is likely to give much better text rendering, including kerning. For the best font experience with these devices you need suitable fonts installed: Linux users will want the @code{urw-fonts} package. On platforms which have it available, the @code{msttcorefonts} package@footnote{also known as @code{ttf-mscorefonts-installer} in the Debian/Ubuntu world: see also @uref{https://en.wikipedia.org/wiki/Core_fonts_for_the_Web}.} provides @I{TrueType} versions of @I{Monotype} fonts such as @I{Arial} and Times New Roman. Another useful set of fonts is the `liberation' @I{TrueType} fonts available at @uref{https://pagure.io/liberation-fonts},@footnote{@code{ttf-liberation} in Debian/Ubuntu.} which cover the Latin, Greek and Cyrillic alphabets plus a fair range of signs. These share metrics with @I{Arial}, Times New Roman and Courier New, and contain fonts rather similar to the first two (@uref{https://en.wikipedia.org/wiki/Liberation_fonts}). Then there is the `Free @I{UCS} Outline Fonts' project (@uref{https://www.gnu.org/software/freefont/}) which are @I{OpenType}/@I{TrueType} fonts based on the URW fonts but with extended Unicode coverage. See the @R{} help on @code{X11} on selecting such fonts. The bitmapped graphics devices @code{jpeg()}, @code{png()} and @code{tiff()} need the appropriate headers and libraries installed: @code{jpeg} (version 6b or later, or @code{libjpeg-turbo}) or @code{libpng} (version 1.2.7 or later) and @code{zlib} or @code{libtiff} respectively. @command{pkg-config} is used if available and so needs the appropriate @file{.pc} file (which requires @code{libtiff} version 4.x and is not available on all platforms for @code{jpeg} before version 9c). They also need support for either @code{X11} or @code{cairo} (see above). Should support for these devices @strong{not} be required or broken system libraries need to be avoided there are @command{configure} options @option{--without-libpng}, @option{--without-jpeglib} and @option{--without-libtiff}. The TIFF library has many optional features such as @code{jpeg}, @code{libz}, @code{zstd}, @code{lzma}, @code{webp}, @code{jbig} and @code{jpeg12}, none of which is required for the @code{tiff()} devices but may need to be present to link the library (usually only an issue for static linking). @command{pkg-config} can tell you what other libraries are required for linking, for example by @code{pkg-config libtiff-4 --static --libs}. @c --print-requires and --print-requires-private are not recursive. Option @option{--with-system-tre} is also available: it needs a recent version of @I{TRE}. (The latest sources are in the @command{git} repository at @url{https://github.com/laurikari/tre/}, but at the time of writing the resulting build did not complete its checks, nor did @R{} built against the version supplied by Fedora.) An implementation of @acronym{XDR} is required, and the @R{} sources contain one which is likely to suffice (although a system version may have higher performance). @acronym{XDR} is part of @acronym{RPC} and historically has been part of @file{libc} on a Unix-alike. (In principle @command{man xdr_string} should tell you which library is needed, but it often does not: on some OSes it is provided by @code{libnsl}.) However some builds@footnote{Including that used by Fedora 28 and later} of @code{glibc} omit or hide it with the intention that the @acronym{TI-RPC} library be used, in which case @code{libtirpc} (and its development version) should be installed, and its headers@footnote{@R{} uses @file{rpc/xdr.h} but that includes @file{netconfig.h} from the top @file{tirpc} directory.} need to be on the C include path or under @file{/usr/include/tirpc}. Library @code{libdeflate} (@url{https://github.com/ebiggers/libdeflate}) is used by @code{memCompress()} and @code{memDecompress()} if available. Use of the X11 clipboard selection requires the @code{Xmu} headers and libraries. These are normally part of an X11 installation (e.g.@: the Debian meta-package @samp{xorg-dev}), but some distributions have split this into smaller parts, so for example recent versions of Fedora require the @samp{libXmu} and @samp{libXmu-devel} @abbr{RPM}s. Some systems (notably macOS and at least some FreeBSD systems) have inadequate support for collation in multibyte locales. It is possible to replace the OS's collation support by that from ICU (International Components for Unicode, @uref{https://icu.unicode.org/}), and this provides much more precise control over collation on all systems. ICU is available as sources and as binary distributions for (at least) most Linux distributions, FreeBSD, macOS and @abbr{AIX}, usually as @code{libicu} or @code{icu4c}. It will be used by default where available: should a very old or broken version of ICU be found this can be suppressed by @option{--without-ICU}. The @code{bitmap} and @code{dev2bitmap} devices and function @code{embedFonts()} use @I{Ghostscript} (@uref{https://www.ghostscript.com/}). This should either be in your path when the command is run, or its full path specified by the environment variable @env{R_GSCMD} at that time. @enindex R_GSCMD At the time of writing a full installation on Fedora Linux used the following packages and their development versions, and this may provide a useful checklist for other systems: @example bzip2 cairo fontconfig freetype fribidi gcc gcc-gfortran gcc-c++ glib2 glibc harfbuzz lapack libX11 libXext libXt libcurl libdeflate libicu libjpeg libpng libtiff libtirpc libxcrypt ncurses pango pkgconf-pkg-config pcre2 readline tcl tk xz zlib @end example @noindent plus, preferably a TeX installation and Java. @node Tcl/Tk @subsection Tcl/Tk The @pkg{tcltk} package needs Tcl/Tk @geq{} 8.4 installed: the sources are available at @uref{https://www.tcl-lang.org/}. To specify the locations of the Tcl/Tk files you may need the configuration options @table @option @item --with-tcltk use Tcl/Tk, or specify its library directory @item --with-tcl-config=@var{TCL_CONFIG} specify location of @file{tclConfig.sh} @item --with-tk-config=@var{TK_CONFIG} specify location of @file{tkConfig.sh} @end table @noindent or use the configure variables @code{TCLTK_LIBS} and @code{TCLTK_CPPFLAGS} to specify the flags needed for linking against the Tcl and Tk libraries and for finding the @file{tcl.h} and @file{tk.h} headers, respectively. If you have both 32- and 64-bit versions of Tcl/Tk installed, specifying the paths to the correct config files may be necessary to avoid confusion between them. Versions of Tcl/Tk up to 8.5.19 and 8.6.12 have been tested (including most versions of 8.4.x, but not recently). Note that the @file{tk.h} header includes@footnote{This is true even for the `Aqua' version of Tk on macOS, but distributions of that include a copy of the X11 files needed.} X11 headers, so you will need X11 and its development files installed. @node Java support @subsection Java support The build process looks for Java support on the host system, and if it finds it sets some settings which are useful for Java-using packages (such as @CRANpkg{rJava} and @CRANpkg{JavaGD}: installing these from source requires a full @abbr{JDK}). This check can be suppressed by configure option @option{--disable-java}. @enindex JAVA_HOME Configure variable @env{JAVA_HOME} can be set to point to a specific @abbr{JRE}/@abbr{JDK}, on the @command{configure} command line or in the environment. Principal amongst these settings are some paths to the Java libraries and JVM, which are stored in environment variable @enindex R_JAVA_LD_LIBRARY_PATH @env{R_JAVA_LD_LIBRARY_PATH} in file @file{@var{R_HOME}/etc/ldpaths} (or a sub-architecture-specific version). A typical setting for @cputype{x86_64} Linux is @example JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.322.b06-6.fc34.x86_64/jre R_JAVA_LD_LIBRARY_PATH=$@{JAVA_HOME@}/lib/amd64/server @end example Unfortunately this depends on the exact version of the @abbr{JRE}/@abbr{JDK} installed, and so may need updating if the Java installation is updated. This can be done by running @code{R CMD javareconf} which updates settings in both @file{@var{R_HOME}/etc/Makeconf} and @file{@var{R_HOME}/etc/ldpaths}. See @code{R CMD javareconf --help} for details: note that this needs to be done by the account owning the @R{} installation. Another way of overriding those settings is to set the environment variable @enindex R_JAVA_LD_LIBRARY_PATH @env{R_JAVA_LD_LIBRARY_PATH} (before @R{} is started, hence not in @file{~/.Renviron}), which suffices to run already-installed Java-using packages. For example @example R_JAVA_LD_LIBRARY_PATH=/usr/lib/jvm/java-1.8.0/jre/lib/amd64/server @end example It may be possible to avoid this by specifying an invariant link as the path when configuring. For example, on that system any of @example JAVA_HOME=/usr/lib/jvm/java JAVA_HOME=/usr/lib/jvm/java-1.8.0 JAVA_HOME=/usr/lib/jvm/java-1.8.0/jre JAVA_HOME=/usr/lib/jvm/jre-1.8.0 @end example @noindent worked (since the `auto' setting of @command{/etc/alternatives} chose Java 8 aka 1.8.0). `Non-server' Oracle distributions of Java as from version 11 are of a full @abbr{JDK}. However, Linux distributions can be confusing: for example Fedora 38 had @example java-1.8.0-openjdk java-1.8.0-openjdk-devel java-11-openjdk java-11-openjdk-devel java-17-openjdk java-17-openjdk-devel java-latest-openjdk java-latest-openjdk-devel @end example @noindent where the @code{-devel} @abbr{RPM}s are needed to complete the @abbr{JDK}. Debian/Ubuntu use @samp{-jre} and @samp{-jdk}, e.g. @example sudo apt install default-jdk @end example @c https://www.digitalocean.com/community/tutorials/how-to-install-java-with-apt-on-ubuntu-22-04 @node Other compiled languages @subsection Other compiled languages Some add-on packages need a C++ compiler. This is specified by the configure variables @code{CXX}, @code{CXXFLAGS} and similar. @command{configure} will normally find a suitable compiler. It is possible to specify an alternative C++17 compiler by the configure variables @code{CXX17}, @code{CXX17STD}, @code{CXX17FLAGS} and similar (@pxref{C++ Support}). Again, @command{configure} will normally find a suitable value for @code{CXX17STD} if the compiler given by @code{CXX} is capable of compiling C++17 code, but it is possible that a completely different compiler will be needed. (Similar macros are provided for C++20.) For source files with extension @file{.f90} or @file{.f95} containing free-form Fortran, the compiler defined by the macro @code{FC} is used by @command{R CMD INSTALL}. Note that it is detected by the name of the command without a test that it can actually compile Fortran 90 code. Set the configure variable @code{FC} to override this if necessary: variables @code{FCFLAGS} and @code{FCLIBS_XTRA} might also need to be set. See file @file{config.site} in the @R{} source for more details about these variables. @node Linear algebra @section Linear algebra @cindex BLAS library The linear algebra routines in @R{} make use of @acronym{BLAS} (Basic Linear Algebra Subprograms, @uref{https://netlib.org/blas/faq.html}) routines, and most make use of routines from @acronym{LAPACK} (@I{Linear Algebra PACKage}, @uref{https://netlib.org/lapack/}). The @R{} sources contain reference (Fortran) implementations of these, but they can be replaced by external libraries, usually those tuned for speed on specific CPUs. These libraries normally contain all of the BLAS routines and some tuned LAPACK routines and perhaps the rest of LAPACK from the reference implementation. Because of the way linking works, using an external BLAS library may necessitate using the version of LAPACK it contains. Note that the alternative implementations will not give identical numeric results. Some differences may be benign (such the signs of @abbr{SVD}s and eigenvectors), but the optimized routines can be less accurate and (particularly for LAPACK) can be from older versions with fewer corrections. However, @R{} relies on @acronym{ISO}/@acronym{IEC}@tie{}60559 compliance. 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 @code{x*0} can be @code{NaN}. The internal BLAS has been extensively patched to avoid this whereas @I{MKL}'s documentation has warned @quotation 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. @end quotation Some of the external libraries are multi-threaded. One issue is that @R{} profiling (which uses the @code{SIGPROF} signal) may cause problems, and you may want to disable profiling if you use a multi-threaded @acronym{BLAS}. Note that using a multi-threaded @acronym{BLAS} can result in taking more @acronym{CPU} time and even more elapsed time (occasionally dramatically so) than using a similar single-threaded @acronym{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 @acronym{BLAS} implementation: some people warn that this is especially problematic for hyper-threaded CPUs. BLAS and LAPACK routines may be used inside threaded code, for example in @abbr{OpenMP} sections in packages such as @CRANpkg{mgcv}. The reference implementations are thread-safe but external ones may not be (even single-threaded ones): this can lead to hard-to-track-down incorrect results or segfaults. @c Seen for OpenBLAS 0.3.2 in 2018. There is a tendency for re-distributors of @R{} to use `enhanced' linear algebra libraries without explaining their downsides. @node BLAS @subsection BLAS An external BLAS library has to be explicitly requested at configure time. You can specify a particular @acronym{BLAS} library @emph{via} a value for the configuration option @option{--with-blas}. If this is given with no @code{=}, its value is taken from the @enindex BLAS_LIBS environment variable @env{BLAS_LIBS}, set for example in @file{config.site}. If neither the option nor the environment variable supply a value, a search is made for a suitable@footnote{The search order is currently @I{OpenBLAS}, @I{BLIS}, ATLAS, platform-specific choices (see below) and finally a generic @file{libblas}.} @acronym{BLAS}. If the value is not obviously a linker command (starting with a dash or giving the path to a library), it is prefixed by @samp{-l}, so @example --with-blas="foo" @end example @noindent is an instruction to link against @samp{-lfoo} to find an external @acronym{BLAS} (which needs to be found both at link time and run time). The configure code checks that the external @acronym{BLAS} is complete (as of LAPACK 3.9.1: it must include all double precision and double complex routines, as well as @code{LSAME}), and appears to be usable. However, an external @acronym{BLAS} has to be usable from a shared object (so must contain position-independent code), and that is not checked. Also, the BLAS can be switched after configure is run, either as a symbolic link or by the mechanisms mentioned below, and this can defeat the completeness check. Some enhanced @acronym{BLAS}es are compiler-system-specific (@code{Accelerate} on macOS, @code{sunperf} on Solaris@footnote{Using the Oracle Developer Studio @command{cc} and @command{f95} compilers}, @code{libessl} on IBM). The correct incantation for these is often found @emph{via} @option{--with-blas} with no value on the appropriate platforms. Note that under Unix (but not under Windows) if @R{} is compiled against a non-default @acronym{BLAS} and @option{--enable-BLAS-shlib} is @strong{not} used (it is the default on all platforms except @abbr{AIX}), then all @acronym{BLAS}-using packages must also be. So if @R{} is re-built to use an enhanced @acronym{BLAS} then packages such as @CRANpkg{quantreg} will need to be re-installed. Debian/Ubuntu systems provide a system-specific way to switch the BLAS in use: Build @R{} with @option{--with-blas} to select the OS version of the reference BLAS, and then use @command{update-alternatives} to switch between the available BLAS libraries. See @uref{https://wiki.debian.org/DebianScience/LinearAlgebraLibraries}. Fedora 33 and later offer `@I{FlexiBLAS}', a similar mechanism for switching the BLAS in use (@uref{https://www.mpi-magdeburg.mpg.de/projects/flexiblas}). However, rather than overriding @code{libblas}, this requires configuring @R{} with option @option{--with-blas=flexiblas}. `Backend' wrappers are available for the reference BLAS, ATLAS and serial, threaded and @abbr{OpenMP} builds of @I{OpenBLAS} and @I{BLIS}, and perhaps others@footnote{for example, Intel @I{MKL} not packaged by Fedora.}. This can be controlled from a running @R{} session by package @CRANpkg{flexiblas}. BLAS implementations which use parallel computations can be non-deterministic: this is known for ATLAS. @node ATLAS @subsubsection ATLAS ATLAS (@uref{https://math-atlas.sourceforge.net/}) is a ``tuned'' @acronym{BLAS} that runs on a wide range of Unix-alike platforms. Unfortunately it is built by default as a static library that on some platforms may not be able to be used with shared objects such as are used in @R{} packages. Be careful when using pre-built versions of ATLAS static libraries (they seem to work on @cputype{ix86} platforms, but not always on @cputype{x86_64} ones). ATLAS contains replacements for a small number of LAPACK routines, but can be built to merge these with the reference LAPACK sources to include a full LAPACK library. Recent versions of ATLAS can be built as a single shared library, either @code{libsatlas} or @code{libtatlas} (serial or threaded respectively): these may even contain a full LAPACK. Such builds can be used by one of @example --with-blas=satlas --with-blas=tatlas @end example @noindent or, as on @cputype{x86_64} Fedora where a path needs to be specified, @example --with-blas="-L/usr/lib64/atlas -lsatlas" --with-blas="-L/usr/lib64/atlas -ltatlas" @end example @noindent Distributed ATLAS libraries cannot be tuned to your machine and so are a compromise: for example Fedora tunes@footnote{The only way to see exactly which CPUs the distributed libraries have been tuned for is to read the @file{atlas.spec} file.} @cputype{x86_64} @abbr{RPM}s for CPUs with SSE3 extensions, and separate @abbr{RPM}s may be available for specific CPU families. Note that building @R{} on Linux against distributed shared libraries may need @samp{-devel} or @samp{-dev} packages installed. Linking against multiple static libraries requires one of @example --with-blas="-lf77blas -latlas" --with-blas="-lptf77blas -lpthread -latlas" --with-blas="-L/path/to/ATLAS/libs -lf77blas -latlas" --with-blas="-L/path/to/ATLAS/libs -lptf77blas -lpthread -latlas" @end example Consult its installation guide@footnote{@uref{https://math-atlas.sourceforge.net/atlas_install/}} for how to build ATLAS as a shared library or as a static library with position-independent code (on platforms where that matters). According to the ATLAS FAQ@footnote{@uref{https://math-atlas.sourceforge.net/faq.html#tnum}} the maximum number of threads used by multi-threaded ATLAS is set at compile time. Also, the author advises against using multi-threaded ATLAS on hyper-threaded CPUs without restricting affinities at compile-time to one virtual core per physical CPU. (For the Fedora libraries the compile-time flag specifies 4 threads.) @c https://math-atlas.sourceforge.net/atlas_install/node21.html @node OpenBLAS and BLIS @subsubsection @I{OpenBLAS} and @I{BLIS} @I{Dr Kazushige Goto} wrote a tuned @acronym{BLAS} for several processors and OSes, which was frozen in 2010. @I{OpenBLAS} (@uref{https://www.openblas.net/}) is a descendant project with support for some later CPUs. This can be used by configuring @R{} with something like @example --with-blas="openblas" @end example @noindent See @pxref{Shared BLAS} for an alternative (and in many ways preferable) way to use them. Some platforms provide multiple builds of @I{OpenBLAS}: for example Fedora has @abbr{RPM}s@footnote{(and more, e.g.@: for 64-bit ints and static versions).} @example openblas openblas-threads openblas-openmp @end example @noindent providing shared libraries @example libopenblas.so libopenblasp.so libopenblaso.so @end example @noindent respectively, each of which can be used as a shared BLAS. For the second and third the number of threads is controlled by @env{OPENBLAS_NUM_THREADS} and @env{OMP_NUM_THREADS} (as usual for @abbr{OpenMP}) respectively. These and their Debian equivalents contain a complete LAPACK implementation. Note that building @R{} on Linux against distributed libraries may need @samp{-devel} or @samp{-dev} packages installed. @c https://wiki.debian.org/DebianScience/LinearAlgebraLibraries For @cputype{ix86} and @cputype{x86_64} CPUs most distributed libraries contain several alternatives for different CPU microarchitectures with the choice being made at run time. Another descendant project is @I{BLIS} (@uref{https://github.com/flame/blis}). This has (in Fedora) shared libraries @example libblis.so libblisp.so libbliso.so @end example @noindent (@code{p} for `threads', @code{o} for @abbr{OpenMP} as for @I{OpenBLAS}) which can also be used as a shared BLAS. The Fedora builds do not include LAPACK in the @I{BLIS} libraries. @node MKL @subsubsection Intel @I{MKL} For Intel processors (and perhaps others) and some distributions of Linux, there is Intel's Math Kernel Library@footnote{Nowadays known as `@I{Intel oneAPI Math Kernel Library}' or even `@I{oneMKL}'.}. You are encouraged to read the documentation which is installed with the library before attempting to link to @I{MKL}. This includes a `link line advisor' which will suggest appropriate incantations: its use is recommended. Or see @uref{https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl-link-line-advisor.html#gs.vpt6qp} (which at the time of writing selected the Intel library for linking with GCC). There are also versions of @I{MKL} for macOS@footnote{The issue for macOS has been the use of double-complex routines.} and Windows, but when these have been tried they did not work with the default compilers used for @R{} on those platforms. The following examples have been used with @I{MKL} versions 10.3 to 2023.2.0, for GCC compilers on @cputype{x86_64} CPUs. (See also @ref{Intel compilers}.) To use a sequential version of @I{MKL} we used @example MKL_LIB_PATH=/path/to/intel_mkl/mkl/lib/intel64 export LD_LIBRARY_PATH=$MKL_LIB_PATH MKL="-L$@{MKL_LIB_PATH@} -lmkl_gf_lp64 -lmkl_core -lmkl_sequential" ./configure --with-blas="$MKL" --with-lapack @end example @noindent The option @option{--with-lapack} is used since @I{MKL} contains a tuned copy of LAPACK (often older than the current version) as well as the @acronym{BLAS} (@pxref{LAPACK}), although this can be omitted. Threaded @I{MKL} may be used by replacing the line defining the variable @code{MKL} by @example MKL="-L$@{MKL_LIB_PATH@} -lmkl_gf_lp64 -lmkl_core \ -lmkl_gnu_thread -dl -fopenmp" @end example @R{} can also be linked against a single shared library, @code{libmkl_rt.so}, for both BLAS and LAPACK, but the correct @abbr{OpenMP} and @I{MKL} interface layer then has to be selected via environment variables. With 64-bit builds and the GCC compilers, we used @example export MKL_INTERFACE_LAYER=GNU,LP64 export MKL_THREADING_LAYER=GNU @end example On Debian/Ubuntu, @I{MKL} is provided by package @code{intel-mkl-full} and one can set @code{libmkl_rt.so} as the system-wide implementation of both BLAS and LAPACK during installation of the package, so that also @R{} installed from Debian/Ubuntu package @code{r-base} would use it. It is, however, still essential to set @code{MKL_INTERFACE_LAYER} and @code{MKL_THREADING_LAYER} before running @R{}, otherwise @I{MKL} computations will produce incorrect results. @R{} does not have to be rebuilt to use @I{MKL}, but @code{configure} includes tests which may discover some errors such as a failure to set the correct @abbr{OpenMP} and @I{MKL} interface layer. Note that the Debian/Ubuntu distribution can be quite old (for example @code{2020.4} in mid-2023 when @code{2023.1} was current): this can be important for the LAPACK version included. @noindent The default number of threads will be chosen by the @abbr{OpenMP} software, but can be controlled by setting @code{OMP_NUM_THREADS} or @code{MKL_NUM_THREADS}, and in recent versions seems to default to a sensible value for sole use of the machine. (Parallel @I{MKL} has not always passed @command{make check-all}, but did with @I{MKL} 2019.4 and later.) @I{MKL} includes a partial implementation of @I{FFTW3}, which causes trouble for applications that require some of the @I{FFTW3} functionality unsupported in @I{MKL}. Please see the @I{MKL} manuals for description of these limitations and for instructions on how to create a custom version of @I{MKL} which excludes the @I{FFTW3} wrappers. There is Intel documentation for building @R{} with @I{MKL} at @uref{https://www.intel.com/content/www/us/en/developer/articles/technical/using-onemkl-with-r.html}: that includes @example -Wl,--no-as-needed @end example @noindent which we have not found necessary. @c https://stat.ethz.ch/pipermail/r-devel/2015-September/071717.html @c It was reported in 2015 that @c @example @c --with-blas='-mkl=parallel' --with-lapack @c @end example @c @noindent @c worked with the Intel 2015.3 compilers on Centos 6. @node Shared BLAS @subsubsection Shared BLAS The @acronym{BLAS} library will be used for many of the add-on packages as well as for @R{} itself. This means that it is better to use a shared/dynamic @acronym{BLAS} library, as most of a static library will be compiled into the @R{} executable and each @acronym{BLAS}-using package. @R{} offers the option of compiling the @acronym{BLAS} into a dynamic library @code{libRblas} stored in @file{@var{R_HOME}/lib} and linking both @R{} itself and all the add-on packages against that library. This is the default on all platforms except @abbr{AIX} unless an external @acronym{BLAS} is specified and found: for the latter it can be used by specifying the option @option{--enable-BLAS-shlib}, and it can always be disabled via @option{--disable-BLAS-shlib}. This has both advantages and disadvantages. @itemize @item It saves space by having only a single copy of the @acronym{BLAS} routines, which is helpful if there is an external static @acronym{BLAS} (as used to be standard for ATLAS). @item There may be performance disadvantages in using a shared @acronym{BLAS}. Probably the most likely is when @R{}'s internal @acronym{BLAS} is used and @R{} is @emph{not} built as a shared library, when it is possible to build the @acronym{BLAS} into @file{R.bin} (and @file{libR.a}) without using position-independent code. However, experiments showed that in many cases using a shared @acronym{BLAS} was as fast, provided high levels of compiler optimization are used. @item It is easy to change the @acronym{BLAS} without needing to re-install @R{} and all the add-on packages, since all references to the @acronym{BLAS} go through @code{libRblas}, and that can be replaced. Note though that any dynamic libraries the replacement links to will need to be found by the linker: this may need the library path to be changed in @file{@var{R_HOME}/etc/ldpaths}. @end itemize Another option to change the @acronym{BLAS} in use is to symlink a single dynamic @acronym{BLAS} library to @file{@var{R_HOME}/lib/libRblas.so}. For example, just @example mv @var{R_HOME}/lib/libRblas.so @var{R_HOME}/lib/libRblas.so.keep ln -s /usr/lib64/libopenblasp.so.0 @var{R_HOME}/lib/libRblas.so @end example @noindent on @cputype{x86_64} Fedora will change the @acronym{BLAS} used to multithreaded @I{OpenBLAS}. A similar link works for most versions of the @I{OpenBLAS} (provided the appropriate @file{lib} directory is in the run-time library path or @command{ld.so} cache). It can also be used for a single-library ATLAS, so on @cputype{x86_64} Fedora either of @example ln -s /usr/lib64/atlas/libsatlas.so.3 @var{R_HOME}/lib/libRblas.so ln -s /usr/lib64/atlas/libtatlas.so.3 @var{R_HOME}/lib/libRblas.so @end example @noindent can be used with its distributed ATLAS libraries. (If you have the @samp{-devel} @abbr{RPM}s installed you can omit the @code{.0}/@code{.3}.) Note that rebuilding or symlinking @file{libRblas.so} may not suffice if the intention is to use a modified LAPACK contained in an external BLAS: the latter could even cause conflicts. However, on Fedora where the @I{OpenBLAS} distribution contains a copy of LAPACK, it is the latter which is used. @node LAPACK @subsection LAPACK @cindex LAPACK library If when configuring @R{} a system LAPACK library is found of version 3.9.0 or later (and does not contain BLAS routines) it will be used instead of compiling the LAPACK code in the package sources. This can be prevented by configuring @R{} with @option{--without-lapack}. Using a static @file{liblapack.a} is not supported. It is assumed that @code{-llapack} is the reference LAPACK library but on Debian/Ubuntu it can be switched, including after @R{} is installed. On such a platform it is better to use @option{--without-lapack} or @option{--with-blas --with-lapack} (see below) explicitly. The known examples@footnote{ATLAS, @I{OpenBLAS} and @I{Accelerate}.} of a non-reference LAPACK library found at installation all contain BLAS routines so are not used by a default @command{configure} run. Provision is made for specifying an external LAPACK library with option @option{--with-lapack}, principally to cope with @acronym{BLAS} libraries which contain a copy of LAPACK (such as @code{Accelerate} on macOS and some builds of ATLAS, @I{FlexiBLAS}, @I{MKL} and @I{OpenBLAS} on @cputype{ix86}/@cputype{x86_64} Linux). At least LAPACK version 3.2 is required. This can only be done if @option{--with-blas} has been used. However, the likely performance gains are thought to be small (and may be negative). The default is not to search for a suitable LAPACK library, and this is definitely @strong{not} recommended. You can specify a specific LAPACK library or a search for a generic library by the configuration option @option{--with-lapack} without a value. The default for @option{--with-lapack} is to check the @acronym{BLAS} library (for function @code{DPSTRF}) and then look for an external library @samp{-llapack}. Sites searching for the fastest possible linear algebra may want to build a LAPACK library using the ATLAS-optimized subset of LAPACK. Similarly, @I{OpenBLAS} can be built to contain an optimized subset of LAPACK or a full LAPACK (the latter seeming to be the default). A value for @option{--with-lapack} can be set @emph{via} the environment variable @enindex LAPACK_LIBS @env{LAPACK_LIBS}, but this will only be used if @option{--with-lapack} is specified and the @acronym{BLAS} library does not contain LAPACK. Please bear in mind that using @option{--with-lapack} is provided @strong{only} because it is necessary on some platforms and because some users want to experiment with claimed performance improvements. In practice its main uses are without a value, @itemize @item with an `enhanced' BLAS such as ATLAS, @I{FlexiBLAS}, @I{MKL} or @I{OpenBLAS} which contains a full LAPACK (to avoid possible conflicts), or @item on Debian/Ubuntu systems to select the system @code{liblapack} which can be switched by the `alternatives' mechanism. @end itemize If building LAPACK from its @I{Netlib} sources, be aware that @command{make} with its supplied @file{Makefile} will make a @emph{static} library and @R{} requires a shared/dynamic one. To get one, use @command{cmake} as documented briefly in @file{README.md}. Something like (to build only the double and double complex subroutines with 32-bit array indices), @example mkdir build cd build cmake \ -DCMAKE_INSTALL_PREFIX=/where/you/want/to/install \ -DCMAKE_BUILD_TYPE:STRING=Release \ -DBUILD_DEPRECATED=ON -DBUILD_SHARED_LIBS=ON \ -DBUILD_INDEX64_EXT_API:BOOL=OFF \ -DBUILD_SINGLE:BOOL=OFF -DBUILD_COMPLEX:BOOL=OFF \ -DLAPACKE=OFF -DCBLAS=OFF \ -S .. make -j10 @end example @noindent This builds the reference BLAS and the reference LAPACK linked to it. Note that @command{cmake} files do not provide an @code{uninstall} target, but @file{build/install_manifest.txt} is a list of the files installed, so you can remove them @emph{via} shell commands or from @R{}. If using @option{--with-lapack} to get a generic LAPACK (or allowing the default to select one), consider also using @option{--with-blas} (with a path if an enhanced BLAS is installed). @node Caveats @subsection 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 @I{Sparc} using the Oracle compilers the flag @option{-dalign} is needed if @code{sunperf} is to be used. On some systems it has been necessary that an external @acronym{BLAS}/LAPACK was built with the same Fortran compiler used to build @R{}. BLAS and LAPACK libraries built with recent versions of @command{gfortran} require calls from C/C++ to handle `hidden' character lengths --- @R{} itself does so but many packages used not to and some have segfaulted. This was largely circumvented by using the Fortran flag @option{-fno-optimize-sibling-calls} (formerly set by @command{configure} if it detected @command{gfortran}@tie{}7 or later): however use of the @R{} headers which include those character-length arguments is no longer optional in packages. LAPACK 3.9.0 (and probably earlier) had a bug in which the @code{DCOMBSSQ} subroutine may cause NA to be interpreted as zero. This is fixed in the @R{} 3.6.3 and later sources, but if you use an external LAPACK, you may need to fix it there. (The bug was corrected in 3.9.1 and the routine removed in 3.10.1.) The code (in @code{dlapack.f}) should read @example * .. * .. Executable Statements .. * IF( V1( 1 ).GE.V2( 1 ) ) THEN IF( V1( 1 ).NE.ZERO ) THEN V1( 2 ) = V1( 2 ) + ( V2( 1 ) / V1( 1 ) )**2 * V2( 2 ) ELSE V1( 2 ) = V1( 2 ) + V2( 2 ) END IF ELSE V1( 2 ) = V2( 2 ) + ( V1( 1 ) / V2( 1 ) )**2 * V1( 2 ) V1( 1 ) = V2( 1 ) END IF RETURN @end example (The inner ELSE clause was missing in LAPACK 3.9.0.) If you do use an external LAPACK, be aware of potential problems with other bugs in the LAPACK sources (or in the posted corrections to those sources), seen several times in Linux distributions over the years. We have even seen distributions with missing LAPACK routines from their @code{liblapack}. We rely on limited support in LAPACK for matrices with @math{2^{31}} or more elements: it is possible that an external LAPACK will not have that support. @node Configuration on a Unix-alike @appendix Configuration on a Unix-alike @node Configuration options @section Configuration options @command{configure} has many options: running @example ./configure --help @end example @noindent will give a list. Probably the most important ones not covered elsewhere are (defaults in brackets) @table @option @item --with-x use the X Window System [yes] @item --x-includes=@var{DIR} X include files are in @var{DIR} @item --x-libraries=@var{DIR} X library files are in @var{DIR} @item --with-readline use @I{readline} library (if available) [yes] @item --enable-R-profiling attempt to compile support for @code{Rprof()} [yes] @item --enable-memory-profiling attempt to compile support for @code{Rprofmem()} and @code{tracemem()} [no] @item --enable-R-shlib build @R{} as a shared/dynamic library [no] @item --enable-BLAS-shlib build the @acronym{BLAS} as a shared/dynamic library [yes, except on @abbr{AIX}] @end table @noindent You can use @option{--without-foo} or @option{--disable-foo} for the negatives. You will want to use @option{--disable-R-profiling} if you are building a profiled executable of @R{} (e.g.@: with @samp{-pg)}. Support for @R{} profiling requires OS support for POSIX threads (@emph{aka} @samp{pthreads}), which are available on all mainstream Unix-alike platforms. Flag @option{--enable-R-shlib} causes the make process to build @R{} as a dynamic (shared) library, typically called @file{libR.so}, and link the main @R{} executable @file{R.bin} against that library. This can only be done if all the code (including system libraries) can be compiled into a dynamic library, and there may be a performance@footnote{We have measured 15--20% on @cputype{i686} Linux and around 10% on @cputype{x86_64} Linux.} penalty. So you probably only want this if you will be using an application which embeds @R{}. Note that C code in packages installed on an @R{} system linked with @option{--enable-R-shlib} is linked against the dynamic library and so such packages cannot be used from an @R{} system built in the default way. Also, because packages are linked against @R{} they are on some OSes also linked against the dynamic libraries @R{} itself is linked against, and this can lead to symbol conflicts. For maximally effective use of @command{valgrind}, @R{} should be compiled with @I{Valgrind} instrumentation. The @command{configure} option is @option{--with-valgrind-instrumentation=@var{level}}, where @var{level} is 0, 1 or 2. (Level 0 is the default and does not add anything.) The system headers for @command{valgrind} are required: on Linux they may be in a separate package such as @pkg{valgrind-devel}. If you need to re-configure @R{} with different options you may need to run @code{make clean} or even @code{make distclean} before doing so. The @file{configure} script has other generic options added by @command{autoconf} and which are not supported for @R{}: in particular building for one architecture on a different host is not possible. @node Internationalization support @section Internationalization support Translation of messages is supported via @acronym{GNU} @code{gettext} unless disabled by the configure option @option{--disable-nls}. The @code{configure} report will show @code{NLS} as one of the `Additional capabilities' if support has been compiled in, and running in an English locale (but not the @code{C} locale) will include @example Natural language support but running in an English locale @end example @noindent in the greeting on starting R. @node Configuration variables @section Configuration variables @findex configure 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 @file{config.site} (which documents many of the variables you might want to set: others can be seen in file @file{etc/Renviron.in}) or on the command line as @example ./configure @var{VAR}=@var{value} @end example @noindent If you are building in a directory different from the sources, there can be copies of @file{config.site} in the source and the build directories, and both will be read (in that order). In addition, if there is a file @file{~/.R/config}, it is read between the @file{config.site} files in the source and the build directories. There is also a general @command{autoconf} mechanism for @file{config.site} files, which are read before any of those mentioned in the previous paragraph. This looks first at a file specified by the @enindex CONFIG_SITE environment variable @env{CONFIG_SITE}, and if not is set at files such as @file{/usr/local/share/config.site} and @file{/usr/local/etc/config.site} in the area (exemplified by @file{/usr/local}) where @R{} would be installed. These variables are @emph{precious}, implying that they do not have to be exported to the environment, are kept in the cache even if not specified on the command line, checked for consistency between two configure runs (provided that caching is used), and are kept during automatic reconfiguration as if having been passed as command line arguments, even if no cache is used. See the variable output section of @code{configure --help} for a list of all these variables. If you find you need to alter configure variables, it is worth noting that some settings may be cached in the file @file{config.cache}, and it is a good idea to remove that file (if it exists) before re-configuring. Note that caching is turned @emph{off} by default: use the command line option @option{--config-cache} (or @option{-C}) to enable caching. @node Setting paper size @subsection Setting paper size @enindex R_PAPERSIZE One common variable to change is @env{R_PAPERSIZE}, which defaults to @samp{a4}, not @samp{letter}. (Valid values are @samp{a4}, @samp{letter}, @samp{legal} and @samp{executive}.) This is used both when configuring @R{} to set the default, and when running @R{} to override the default. It is also used to set the paper size when making PDF manuals. The configure default will most often be @samp{a4} if @env{R_PAPERSIZE} is unset. (If the program @command{paperconf} is found, present in many Linux distributions, @enindex PAPERSIZE or the environment variable @env{PAPERSIZE} is set, these are used to produce the default.) @node Setting the browsers @subsection Setting the browsers @enindex R_BROWSER Another precious variable is @env{R_BROWSER}, the default @HTML{} browser, which should take a value of an executable in the user's path or specify a full path. @enindex R_PDFVIEWER Its counterpart for PDF files is @env{R_PDFVIEWER}. @node Compilation flags @subsection Compilation flags If you have libraries and header files, e.g., for @acronym{GNU} @I{readline}, in non-system directories, use the variables @code{LDFLAGS} (for libraries, using @samp{-L} flags to be passed to the linker) and @code{CPPFLAGS} (for header files, using @samp{-I} flags to be passed to the C/C++ preprocessors), respectively, to specify these locations. These default to @samp{-L/usr/local/lib} (@code{LDFLAGS}, @samp{-L/usr/local/lib64} on most 64-bit Linux OSes) and @samp{-I/usr/local/include} (@code{CPPFLAGS}, but note that on most systems @file{/usr/local/include} is regarded as a system include directory and so instances in that macro will be skipped) to catch the most common cases. If libraries are still not found, then maybe your compiler/linker does not support re-ordering of @option{-L} and @option{-l} flags. @c (years ago this was reported to be a problem on HP-UX with the native @c @command{cc}). In this case, use a different compiler (or a front-end shell script which does the re-ordering). These flags can also be used to build a faster-running version of @R{}. On most platforms using @command{gcc}, having @samp{-O3} in @code{CFLAGS} and @code{FFLAGS} produces worthwhile performance gains with @command{gcc} and @command{gfortran}, but may result in a less reliable build (both segfaults and incorrect numeric computations have been seen). On systems using the @acronym{GNU} linker (especially those using @R{} as a shared library), it is likely that including @samp{-Wl,-O1} in @code{LDFLAGS} is worthwhile, and @samp{'-Bdirect,--hash-style=both,-Wl,-O1'} is recommended at @uref{https://lwn.net/Articles/192624/}. Tuning compilation to a specific @acronym{CPU} family (e.g.@: @samp{-mtune=native} for @command{gcc}) can give worthwhile performance gains, especially on older architectures such as @cputype{ix86}. @node Making manuals @subsection Making manuals @enindex R_RD4PDF @enindex R_PAPERSIZE The default settings for making the manuals are controlled by @env{R_RD4PDF} and @env{R_PAPERSIZE}. @node Setting the shell @section Setting the shell By default the shell scripts such as @file{R} will be @samp{#!/bin/sh} scripts (or using the @env{SHELL} chosen by @file{configure}). This is almost always satisfactory, but on a few systems @file{/bin/sh} is not a @I{Bourne} shell or clone, and the shell to be used can be changed by setting the configure variable @env{R_SHELL} to a suitable value (a full path to a shell, e.g.@: @file{/usr/local/bin/bash}). @node Using make @section Using make @findex make To build in a separate directory you need a @command{make} that supports the @code{VPATH} variable, for example @acronym{GNU} @command{make} and @command{dmake}. If you want to use a @command{make} by another name, for example if your @acronym{GNU} @command{make} is called @samp{gmake}, you need to set the variable @code{MAKE} at configure time, for example @findex configure @example ./configure MAKE=gmake @end example @node Using Fortran @section Using Fortran @cindex Fortran To compile @R{}, you need a Fortran 90 compiler. The current default is to search for @c From AC_PROG_FC @command{gfortran}, @command{g95}, @command{xlf95} @command{f95}, @command{fort}, @command{ifort}, @command{ifc}, @command{efc}, @command{pgfortran}, @command{pgf95} @command{lf95}, @command{ftn}, @command{nagfor}, @command{xlf90}, @command{f90}, @command{pgf90}, @command{pghpf}, @command{epcf90}. (Note that these are searched for by name, without checking the standard of Fortran they support.) The command and flags used should support fixed-form Fortran with extension @file{.f}: in the unusual case that a specific flag is needed for free-form Fortran with extension @file{.f90} or @file{.f95}, this can be specified as part of @code{FCFLAGS}. The search mechanism can be changed using the configure variable @code{FC} which specifies the command that runs the Fortran compiler. If your Fortran compiler is in a non-standard location, you @enindex PATH should set the environment variable @env{PATH} accordingly before running @command{configure}, or use the configure variable @code{FC} to specify its full path. If your Fortran libraries are in slightly peculiar places, you should @enindex LD_LIBRARY_PATH also look at @env{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 @code{integer} is equivalent to a C @code{int} pointer and Fortran @code{double precision} is equivalent to a C @code{double} pointer. This is checked during the configuration process. Some of the Fortran code makes use of @code{DOUBLE COMPLEX} and @code{COMPLEX*16} variables. This is checked for at configure time, as well as its equivalence to the @code{Rcomplex} C structure defined in @file{R_ext/Complex.h}. @command{gfortran}@tie{}10 by default gives a compilation error for the previously widespread practice of passing a Fortran array element where an array is expected, or a scalar instead of a length-one array. See @uref{https://gcc.gnu.org/gcc-10/porting_to.html}. @command{gfortran}@tie{}12 errors in more cases of this. @node Compile and load flags @section Compile and load flags A wide range of flags can be set in the file @file{config.site} or as configure variables on the command line. We have already mentioned @table @code @item CPPFLAGS header file search directory (@option{-I}) and any other miscellaneous options for the C and C++ preprocessors and compilers @item LDFLAGS path (@option{-L}), stripping (@option{-s}) and any other miscellaneous options for the linker @end table @noindent and others include @table @code @item CFLAGS debugging and optimization flags, C @item MAIN_CFLAGS ditto, for compiling the main program (e.g.@: when profiling) @item SHLIB_CFLAGS for shared objects (no known examples) @item FFLAGS debugging and optimization flags, fixed-form Fortran @item FCFLAGS debugging and optimization flags, free-form Fortran @item SAFE_FFLAGS ditto for source files which need exact floating point behaviour @item MAIN_FFLAGS ditto, for compiling the main program (e.g.@: when profiling) @item SHLIB_FFLAGS for shared objects (no known examples) @item MAIN_LDFLAGS additional flags for the main link @item SHLIB_LDFLAGS additional flags for linking the shared objects @item LIBnn the primary library directory, @file{lib} or @file{lib64} @item CPICFLAGS special flags for compiling C code to be turned into a shared object @item FPICFLAGS special flags for compiling Fortran code to be turned into a shared object @item CXXPICFLAGS special flags for compiling C++ code to be turned into a shared object @item DEFS defines to be used when compiling C code in @R{} itself @end table @noindent Library paths specified as @option{-L/lib/path} in @code{LDFLAGS} are @enindex LD_LIBRARY_PATH collected together and prepended to @env{LD_LIBRARY_PATH} (or your system's equivalent), so there should be no need for @option{-R} or @option{-rpath} flags. Variables such as @env{CPICFLAGS} are determined where possible by @command{configure}. Some systems allows two types of PIC flags, for example @samp{-fpic} and @samp{-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. Other variables often set by @command{configure} include @samp{MAIN_LDFLAGS}, @samp{SAFE_FFLAGS}, @samp{SHLIB_LDFLAGS} and @samp{SHLIB_CXXLDFLAGS}: see file @file{config.site} in the sources for more documentation on these and others. To compile a profiling version of @R{}, one might for example want to use @samp{MAIN_CFLAGS=-pg}, @samp{MAIN_FFLAGS=-pg}, @samp{MAIN_LDFLAGS=-pg} on platforms where @samp{-pg} cannot be used with position-independent code. @strong{Beware}: it may be necessary to set @code{CFLAGS} and @code{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 @command{configure} will select additional flags for @code{CFLAGS}, @code{CPPFLAGS} and @code{LIBS} in @code{R_XTRA_CFLAGS} (and so on). These are for options which are always required, for example to force @acronym{IEC}@tie{}60559 compliance. @node Maintainer mode @section Maintainer mode There are several files that are part of the @R{} sources but can be re-generated from their own sources by configuring with option @option{--enable-maintainer-mode} and then running @command{make} in the build directory. This requires other tools to be installed, discussed in the rest of this section. File @file{configure} is created from @file{configure.ac} and the files under @file{m4} by @command{autoconf} and @command{aclocal} (part of the @pkg{automake} package). There is a formal version requirement on @command{autoconf} of 2.72 or later, but it is unlikely that anything other than the most recent versions@footnote{at the time of revision of this para in early 2024, @pkg{autoconf-2.72} and @pkg{automake-1.16.5}. Previously @pkg{autoconf-2.71} was used.} have been thoroughly tested. File @file{src/include/config.h} is created by @command{autoheader} (part of @pkg{autoconf}). Grammar files @file{*.y} are converted to C sources by an implementation of @command{yacc}, usually @command{bison -y}: these are found in @file{src/main} and @file{src/library/tools/src}. It is known that earlier versions of @command{bison} generate code which reads (and in some cases writes) outside array bounds: @command{bison} 3.8.2 is currently used. The ultimate sources for package @pkg{compiler} are in its @file{noweb} directory. To re-create the sources from @file{src/library/compiler/noweb/compiler.nw}, the command @command{notangle} is required. Some Linux distributions include this command in package @pkg{noweb}. It can also be installed from the sources at @url{https://www.cs.tufts.edu/~nr/noweb/}@footnote{The links there have proved difficult to access, in which case grab the copy made available at @uref{https://developer.r-project.org/noweb-2.11b.tgz}.}. The package sources are only re-created even in maintainer mode if @file{src/library/compiler/noweb/compiler.nw} has been updated. @c It is likely that in future creating @code{configure} will need the GNU @c `autoconf archive' installed. This can be found at @c @c and it has moved to github! @c @url{https://www.gnu.org/software/autoconf-archive/} and as a package @c (usually called @pkg{autoconf-archive}) in most packaged distributions, @c for example Debian, Fedora, OpenCSW, Homebrew and MacPorts. @node Platform notes @appendix Platform notes This section provides some notes on building @R{} on different Unix-alike platforms. These notes are based on tests run on one or two systems in each case with particular sets of compilers and support libraries. Success in building @R{} depends on the proper installation and functioning of support software; your results may differ if you have other versions of compilers and support libraries. Older versions of this manual contain notes on platforms such as @I{HP-UX}, @abbr{IRIX}, Alpha/@I{OSF1} (for @R{} < 2.10.0, and support has since been removed for all of these) and @abbr{AIX} (for @R{} < = 3.5.x) for which we have had no recent reports. C macros to select particular platforms can be tricky to track down (there is a fair amount of misinformation on the Web). The Wiki (currently) at @uref{https://sourceforge.net/p/predef/wiki/Home/} can be helpful. The @R{} sources have used (often in included software under @file{src/extra}) @example AIX: _AIX Cygwin: __CYGWIN__ FreeBSD: __FreeBSD__ HP-UX: __hpux__, __hpux IRIX: sgi, __sgi Linux: __linux__ macOS: __APPLE__ NetBSD: __NetBSD__ OpenBSD: __OpenBSD__ Windows: _WIN32, _WIN64 Windows on 64-but ARM: _M_ARM64 or _WIN32 plus __aarch64__ @end example Identifying compilers can be very tricky. GCC defines @code{__GNUC__}, but so do other compilers claiming conformance with it, notably (@I{LLVM} and Apple) @command{clang} and Intel compilers. Further, some use the value of @code{__GNUC__} for their version, not the version of GCC they claim to be compatible with.@footnote{Most @command{clang}-based compilers give @code{4}, but not those distributed by FreeBSD. Intel's @command{icx} reported @code{12} in 2023.} @command{clang}-based compilers define @code{__clang__}. Both @I{LLVM} and Apple @command{clang} define @code{__clang_major__} as a string giving their major version, but for example Apple's 13.x.y is very different from @I{LLVM}'s 13.x.y. And compilers based on @I{LLVM} @command{clang}, for example from Intel and IBM, will define these. Some of the included software uses @code{__APPLE_CC__} to identify an Apple compiler (which used to include Apple builds of GCC), but Apple @command{clang} is better identified by the @code{__apple_build_version__} macro. @node X11 issues @section X11 issues The @samp{X11()} graphics device is the one started automatically on Unix-alikes (except most macOS builds) when plotting. As its name implies, it displays on a (local or remote) X server, and relies on the services provided by the X server. @cindex Cairo The `modern' version of the @samp{X11()} device is based on @samp{cairo} graphics and (in most implementations) uses @samp{fontconfig} to pick and render fonts. This is done on the server, and although there can be selection issues, they are more amenable than the issues with @samp{X11()} discussed in the rest of this section. When X11 was designed, most displays were around 75dpi, whereas today they are of the order of 100dpi or more. If you find that X11() is reporting@footnote{for example, @code{X11 font at size 14 could not be loaded}.} missing font sizes, especially larger ones, it is likely that you are not using scalable fonts and have not installed the 100dpi versions of the X11 fonts. The names and details differ by system, but will likely have something like Fedora's @example xorg-x11-fonts-75dpi xorg-x11-fonts-100dpi xorg-x11-fonts-ISO8859-2-75dpi xorg-x11-fonts-Type1 xorg-x11-fonts-cyrillic @end example @noindent and you need to ensure that the @samp{-100dpi} versions are installed and on the X11 font path (check via @command{xset -q}). The @samp{X11()} device does try to set a pointsize and not a pixel size: laptop users may find the default setting of 12 too large (although very frequently laptop screens are set to a fictitious dpi to appear like a scaled-down desktop screen). More complicated problems can occur in non-Western-European locales, so if you are using one, the first thing to check is that things work in the @code{C} locale. The likely issues are a failure to find any fonts or glyphs being rendered incorrectly (often as a pair of @acronym{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 @I{plotmath}), the specification is the first element of the option @code{"X11fonts"} which defaults to @example "-adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*" @end example If you are using a single-byte encoding, for example ISO 8859-2 in Eastern Europe or @I{KOI8-R} in Russian, use @command{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 @samp{xorg-x11-fonts-ISO8859-2-75dpi} and @samp{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 @samp{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 @emph{@I{fontset}s} are used, made up of fonts encoded in other encodings. If the locale you are using has an entry in the @samp{XLC_LOCALE} directory (typically @file{/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 @samp{ja_JP.UTF-8} but not when running in @samp{en_GB.UTF-8} on the same machine (although on some systems many UTF-8 X11 locales are aliased to @samp{en_US.UTF-8} which covers several character sets, e.g.@: ISO 8859-1 (Western European), @I{JISX0208} (Kanji), @I{KSC5601} (Korean), @I{GB2312} (Chinese Han) and @I{JISX0201} (Kana)). On some systems scalable fonts are available covering a wide range of glyphs. One source is @I{TrueType}/@I{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 @file{fonts} directory or elsewhere, for example, @example /usr/share/fonts/default/Type1 /usr/share/fonts/ja/TrueType @end example @node Linux @section Linux @cindex Linux Linux is the main development platform for @R{}, so compilation from the sources is normally straightforward with the most common compilers and libraries.@footnote{For example, @code{glibc}: other C libraries such as @code{musl} (as used by Alpine Linux) have been used but are not routinely tested.} This section is about the GCC compilers: @command{gcc}/@command{gfortran}/@command{g++}. Recall that some package management systems (such as @acronym{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 @samp{-devel} or @samp{-dev}: you need both versions installed. So please check the @code{configure} output to see if the expected features are detected: if for example @samp{readline} is missing add the developer package. (On most systems you will also need @samp{ncurses} and its developer package, although these should be dependencies of the @samp{readline} package(s).) You should expect to see in the @command{configure} summary @example Interfaces supported: X11, tcltk External libraries: pcre2, readline, curl Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU @end example When @R{} has been installed from a binary distribution there are sometimes problems with missing components such as the Fortran compiler. Searching the @samp{R-help} archives will normally reveal what is needed. It seems that @cputype{ix86} Linux accepts non-PIC code in shared libraries, but this is not necessarily so on other platforms, in particular on 64-bit @acronym{CPU}s such as @cputype{x86_64}. So care can be needed with @acronym{BLAS} libraries and when building @R{} as a shared library to ensure that position-independent code is used in any static libraries (such as the Tcl/Tk libraries, @code{libpng}, @code{libjpeg} and @code{zlib}) which might be linked against. Fortunately these are normally built as shared libraries with the exception of the ATLAS @acronym{BLAS} libraries. The default optimization settings chosen for @code{CFLAGS} etc are conservative. It is likely that using @option{-mtune} will result in significant performance improvements on recent CPUs: one possibility is to add @option{-mtune=native} for the best possible performance on the machine on which @R{} is being installed. It is also possible to increase the optimization levels to @option{-O3}: however for many versions of the compilers this has caused problems in at least one @acronym{CRAN} package. Do not use @option{-O3} with @command{gcc} 11.0 or 11.1: it @I{mis-compiles} code resulting in plausible but incorrect results. (This was seen in package @CRANpkg{MASS} but has been worked around there as from version 3.1-57.) For comments on @cputype{ix86} builds (including 32-bit builds on @cputype{x86_64}) see the version of this manual for @R{} 4.3.x. To build a 64-bit version of @R{} on @cputype{ppc64} (also known as @cputype{powerpc64}) with @command{gcc}@tie{}4.1.1, @I{Ei-ji Nakama} used @example CC="gcc -m64" CXX="gxx -m64" FC="gfortran -m64" CFLAGS="-mminimal-toc -fno-optimize-sibling-calls -g -O2" FFLAGS="-mminimal-toc -fno-optimize-sibling-calls -g -O2" @end example @noindent the additional flags being needed to resolve problems linking against @file{libnmath.a} and when linking @R{} as a shared library. @c suggestion of https://gcc.gnu.org/wiki/FloatingPointMath The setting of the macro @samp{SAFE_FFLAGS} may need some help. It should not need additional flags on platforms other than @cputype{68000} (not likely to be encountered) and @cputype{ix86}. For the latter, if the Fortran compiler is GNU (@command{gfortran} or possibly @command{g77}) the flags @example -msse2 -mfpmath=sse @end example @noindent are added: earlier versions of @R{} added @option{-ffloat-store} and this might still be needed if a @cputype{ix86} CPU is encountered without SSE2 support. Note that it is a @emph{replacement} for @samp{FFLAGS}, so should include all the flags in that macro (except perhaps the optimization level). Additional compilation flags can be specified for added safety/security checks. For example Fedora adds @example -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -Fexceptions -fstack-protector-strong -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection @end example @noindent to all the C, C++ and Fortran compiler flags (even though @code{_GLIBCXX_ASSERTIONS} is only for C++ in current GCC and @code{glibc} and none of these are documented for @code{gfortran}). Use of @code{_GLIBCXX_ASSERTIONS} will link @code{abort} and @code{printf} into almost all C++ code, and @command{R CMD check --as-cran} will warn. @node Clang @subsection Clang @R{} has been built with Linux @cputype{ix86} and @cputype{x86_64} C and C++ compilers (@uref{https://clang.llvm.org}) based on the Clang front-ends, invoked by @code{CC=clang CXX=clang++}, together with @command{gfortran}. These take very similar options to the corresponding GCC compilers. This has to be used in conjunction with a Fortran compiler: the @command{configure} code will remove @option{-lgcc} from @env{FLIBS}, which is needed for some versions of @command{gfortran}. The current out-of-the-box default for @command{clang++} is to use the C++ runtime from the installed @command{g++}. Using the runtime from the @url{https://libcxx.llvm.org/, @code{libc++}} project (Fedora @acronym{RPM} @code{libcxx-devel}) @emph{via} @option{-stdlib=libc++} has also been tested. Recent versions have (optional when built) @abbr{OpenMP} support.@footnote{This also needs the @abbr{OpenMP} runtime which has sometimes been distributed separately.} There are problems mixing @command{clang} 15.0.0 and later built as default on Linux to produce PIE code and @command{gfortran} 11 or later, which does not. One symptom is that @command{configure} does not detect @code{FC_LEN_T}, which can be overcome by setting @example FPIEFLAGS=-fPIE @end example @noindent in @file{config.site}. (@command{configure} tries that value if it is unset.) @node flang @subsection @I{flang} The name @command{flang} has been used for two projects: this is about the sub-project of @I{LLVM} which builds a Fortran compiler and runtime libraries. The compiler command was @command{flang-new} prior to version 20. The version in @I{LLVM} 16 and later was able to build @R{} on @cputype{x86_64} Linux with @example FC=/path/to/flang @end example @noindent with the matching @command{clang} used as the C compiler, and the build passed @command{make check-all}. There is also support for @cputype{aarch64} and @cputype{ppc64le} Linux, but these have not been tested with @R{}. @c It is recommended to use C flag @option{-Wno-strict-prototypes} @c (disabling a C23 feature) if using @code{-pedantic} in @command{clang} @c 15.0.0 and later, as @R{} is not yet optimized for C23. For more detail @c see the release notes at @c @uref{https://releases.llvm.org/15.0.0/tools/clang/docs/ReleaseNotes.html#id9}, @c under `improvements to diagnostics'.. @c This was about 'Classic Flang'. The newer version is not @c yet able to compile Fortran. @c There is a project called @command{flang} @c (@uref{https://github.com/flang-compiler/flang})) to develop a @c Fortran compiler similar to clang but based on the Portland Group's front @c end. This needs something like @c @example @c FC=/usr/local/flang/bin/flang @c LDFLAGS="-L/usr/local/flang/lib -L/usr/local/lib64" @c @end example @c Note that @command{flang} accepts all the flags which @command{clang} @c does (the driver is a modified version of @command{clang}, and @c @command{flang} is a symbolic link to @command{clang}), but does not @c implement all of them for Fortran compilation: it also accepts most @c PGI-style flags such as @option{-mp} for @abbr{OpenMP}. It currently produces @c few diagnostics even with @option{-Wall -pedantic}. @c @command{flang}'s Fortran runtime is compiled against @abbr{OpenMP} and it @c seems this conflicts with using @abbr{OpenMP} in @R{}. So it may be necessary @c to disable the latter by configuring @R{} using @option{--disable-openmp}. @c It is not clear what architectures @command{flang} intends to support: @c our experiments were done on @cputype{x86_64}. At the time of writing @c binary `releases' were available for that platform (called by them @c @cputype{x86}) and @cputype{ppc64le}. @node Intel compilers @subsection Intel compilers In late 2020 Intel revamped their C/C++ compilers (and later their Fortran compiler) to use an @I{LLVM} back-end (and for the C/C++ compilers, a modified version of @command{clang} as the front-end). Those compilers are only for @cputype{x86_64}: the earlier (now called `Classic') C/C++ compilers were discontinued in late 2023 (and are covered in the version of this manual for @R{} 4.3.x: the Fortran compiler @command{ifort} remains part of the Fortran distribution).. The compilers are now all under Intel's `@I{oneAPI}' brand. The revamped ones are @command{icx}, @command{icpx} and @command{ifx}; they are identified by the C/C++ macro @code{__INTEL_LLVM_COMPILER} (and do not define @code{__INTEL_COMPILER}: they also define @code{__clang__} and @code{__clang_major__}). The C++ compiler uses the system's @code{libstdc++} as its runtime library rather than @I{LLVM}'s @code{libc++}. Standalone installers (which are free-of-charge) are available from @uref{https://www.intel.com/content/www/us/en/developer/articles/tool/oneapi-standalone-components.html}: they are also part of the @I{oneAPI} Base and HPC (for Fortran) toolkits. We tried the compilers in @I{oneAPI} 2024.2.1 and 2023.x.y using (the paths do differ by compiler version) @example IP=/path/to/compilers/bin/ CC=$IP/icx CXX=$IP/icpx FC=$IP/ifx CFLAGS="-O3 -fp-model precise -Wall -Wstrict-prototypes" C17FLAGS="-O3 -fp-model precise -Wall -Wno-strict-prototypes" FFLAGS="-O3 -fp-model precise -warn all,noexternals" FCFLAGS="-free -O3 -fp-model precise -warn all,noexternals" CXXFLAGS="-O3 -fp-model precise -Wall" LDFLAGS="-L/path/to/compilers/compiler/lib -L/usr/local/lib64" @end example @noindent but the build segfaulted in the checks (in complex arithmetic in @file{tests/lapack.R}). Intel document building @R with @I{MKL}: for the Intel compilers this needed something like @example MKL_LIB_PATH=/path/to/intel_mkl/mkl/lib/intel64 export LD_LIBRARY_PATH="$MKL_LIB_PATH" MKL="-L$@{MKL_LIB_PATH@} -lmkl_intel_lp64 -lmkl_core -lmkl_sequential" ./configure --with-blas="$MKL" --with-lapack @end example @noindent and the build passed its checks with @I{MKL} 2023.2.0 (but not 2024.x on the hardware tested). It may also be possible to use a compiler option like @option{-qmkl=sequential}. One quirk is that the Intel Fortran compilers do not accept @file{.f95} files, only @file{.f90}, for free-format Fortran. @command{configure} adds @option{-Tf} which tells the compiler this is indeed a Fortran file (and needs to immediately precede the file name), but @option{-free} is needed to say it is free-format. Hence setting the @code{FCFLAGS} macro. @c https://www.intel.com/content/www/us/en/docs/fortran-compiler/developer-guide-reference/2023-2/file-extensions.html The compilers have many options: as the C/C++ and Fortran compilers have different origins for their front-ends, there is little consistency in their options. @c https://www.intel.com/content/www/us/en/docs/dpcpp-cpp-compiler/developer-guide-reference/2023-2/compiler-options.html @c https://www.intel.com/content/www/us/en/docs/fortran-compiler/developer-guide-reference/2023-2/compiler-options-001.html (The C/C++ compilers support `all' @command{clang} options even if undocumented for @command{icx}/@command{icpc}, such as @option{-Wno-strict-prototypes} above, However it is unclear for which version of @command{clang}: the Intel manual suggests checking @command{icx -help}.) The C/C++ compilers support clang-style @abbr{LTO}: it is not clear if the Fortran one does. @c https://community.intel.com/t5/Intel-C-Compiler/Troubles-with-getrusage-when-using-icx/m-p/1509374#M41116 For some earlier versions (including 2023.2.0) all CPU times in e.g.@: @code{proc.time()} are reported as zero. If you see this, uncomment the @samp{INTEL_ICX_FIX} setting in @file{config.site} and re-build. @c https://www.intel.com/content/www/us/en/docs/fortran-compiler/developer-guide-reference/2023-2/stand.html The preferred Fortran standard for @command{ifx} can be set by one of @option{-std90}, @option{-std95}, @option{-std03}, @option{-std08} or @option{-std18} (and variants). However, this is documented to only affect warnings on non-standard features: the default is no such warnings. Warning to package maintainers: the Intel Fortran compiler interprets comments intended for Visual Fortran@footnote{as the `Classic' compiler has been known on Windows.} like @c from package tseriesentropy 0.6-0 @example !DEC$ ATTRIBUTES DLLEXPORT,C,REFERENCE,ALIAS:'kdenestmlcvb' :: kdenestmlcvb @end example @noindent The @code{DLLEXPORT} gives a warning but the remainder silently generates incorrectly named entry points. Such comment lines need to be removed from code for use with @R{} (even if using Intel Fortran on Windows). @c What this architecture is known as varies. The kernel is called @c 'Darwin' and so autoconf uses 'apple-darwin' with @c current architectures x86_64 and aarch64. @c OTOH, 'file' reports architectures x86_64, arm64 and arm64e and @c Apple's clang has a -target flag with values like @c x86_64-apple-macos10.12 and arm64-apple-macos11 @c 'Activity monitor' reports the architectures as 'Intel' and 'Apple' @node macOS @section macOS @cindex macOS The instructions here are for `Apple Silicon' (@cputype{arm64}) or Intel 64-bit (@cputype{x86_64}) builds on macOS 11 (@I{Big Sur}), 12 (@I{Monterey)}, 13 (@I{Ventura}), 14 (@I{Sonoma}) and likely later. (They may well work on Intel macOS 10.14 or 10.15, but are untested there.) @node Prerequisites @subsection Prerequisites The Apple silicon components install into @file{/opt/R/arm64}, the Intel ones into @file{/opt/R/x86_64}. That may not exist@footnote{it will if @R{} has been installed from @acronym{CRAN} since @R{} 4.3.0.} so it is simplest to first create the directory and adjust its ownership if desired: for example by @example sudo mkdir -p /opt/R/arm64 sudo chown -R $USER /opt/R @end example @noindent Also, add @file{/opt/R/arm64/bin} or @file{/opt/R/x86_64/bin} to your path. Define an appropriate variable in your Terminal: @example set LOCAL=/opt/R/arm64 # Apple Silicon set LOCAL=/opt/R/x86_64 # Intel @end example @noindent to use the code snippets here. The following are essential to build @R{}: @itemize @item Apple's `Command Line Tools': these can be (re-)installed by running @command{xcode-select --install} in a terminal. If you have a fresh OS installation, running e.g.@: @command{make} in a terminal will offer the installation of the command-line tools. If you have installed @I{Xcode}, this provides the command-line tools. The tools may need to be reinstalled when macOS is upgraded, as upgrading may partially or completely remove them. The Command Line Tools provide C and C++ compilers derived from @I{LLVM}'s @command{clang} but nowadays known as `Apple clang' with different versioning (so Apple clang 15 is unrelated to @I{LLVM} clang 15). @item A Fortran compiler. @xref{Fortran compilers}. @item Binary components @code{pcre2}@footnote{If compiling it from source on @cputype{arm64}, @code{pcre2} (at least up to version 10.39) needs to be built without JIT support (the default) as the @R{} build segfaults if that is enabled, so do run @code{make check} on your build.} and @code{xz} (for @code{liblzma}) from @uref{https://mac.r-project.org/bin/}. There is an @R{} script there to help with installing all the needed components. (At the time of writing @code{install.libs("r-base-dev")} installed neither @code{readline5} nor those needed to support @I{Pango}.) Intel users want the @code{darwin20} components: the @code{darwin17} ones are for macOS 10.13--10.15. Or this can be done manually, by for example @example curl -OL https://mac.r-project.org/bin/darwin20/arm64/pcre2-10.44-darwin.20-arm64.tar.xz sudo tar -xvzf pcre2-10.44-darwin.20-arm64.tar.gz -C / curl -OL https://mac.r-project.org/bin/darwin20/arm64/xz-5.6.3-darwin.20-arm64.tar.xz sudo tar -xvzf xz-5.6.3-darwin.20-arm64.tar.xz -C / @end example @noindent (@command{sudo} is not needed if your account owns @file{/opt/R/arm64} or @file{/opt/R/x86_64} as appropriate.) Messages like @samp{opt/R/: Can't restore time} should be ignored. @end itemize @noindent and desirable @itemize @item Component @code{readline5}.@footnote{For licence reasons this is version 5.2 of @code{readline}: for those who want a more recent version it is straightforward to compile it from its sources.} If @code{readline} is not present, the emulation in Apple's version of @code{libedit} (aka @code{editline}) will be used: if you wish to avoid that, configure with @option{--without-readline}. @item Components @code{jpeg}, @code{libpng}, @code{pkgconfig}, @code{tiff} and @code{zlib-system-stub} from @uref{https://mac.r-project.org/bin//} for the full range of bitmapped graphics devices. (Some builds of @code{tiff} may require @code{libwebp} and/or @code{openjpeg}.) @item An X sub-system unless configuring using @option{--without-x}: see @uref{https://www.xquartz.org/}. @R{}'s @command{configure} script can be told to look for @code{X11} in @I{XQuartz}'s main location of @file{/opt/X11}, e.g.@: by @example --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib @end example Be wary of pre-release versions of @I{XQuartz}, which may be offered as an update. @item An Objective-C compiler, as provided by @command{clang} in the Command Line Tools: this is needed for the @code{quartz()} graphics device. Use @option{--without-aqua} if you want a standard Unix-alike build: apart from disabling @code{quartz()} and the ability to use the build with @Rapp{}, it also changes the default location of the personal library (see @code{?.libPaths}). @item A Tcl/Tk installation, @xref{ Tcl/Tk headers and libraries}. @item Support for Cairo-based graphics devices. @xref{Cairo graphics}. @item A TeX installation. @xref{Other libraries}. @item @command{texi2any} from a @I{Texinfo} distribution, which requires @command{perl} (currently a default part of macOS but it has been announced that it may not be in future). @c macOS 10.15 release notes, but is in 11 @c https://developer.apple.com/documentation/macos-release-notes/macos-catalina-10_15-release-notes A version of @command{texi2any} has been included in the binary distribution of @R{} and there is a @samp{texinfo} component at @uref{https://mac.r-project.org/bin/}. @end itemize To build @R{} itself from the sources with the C/C++ compilers in the Command Line Tools (or @I{Xcode}) and @command{gfortran} from the installer mentioned below, use a file @file{config.site} containing @example CC=clang OBJC=$CC FC="/opt/gfortran/bin/gfortran -mtune=native" CPPFLAGS='-isystem $LOCAL/include' CXX=clang++ @end example @noindent and configure by something like @example ./configure -C \ --enable-R-shlib --enable-memory-profiling \ --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib \ --with-tcl-config=$LOCAL/lib/tclConfig.sh \ --with-tk-config=$LOCAL/lib/tkConfig.sh \ PKG_CONFIG_PATH=$LOCAL/lib/pkgconfig:/usr/lib/pkgconfig @end example @noindent (See below for other options for Tcl/Tk.) For an @cputype{arm64} build further flags are desirable in @file{config.site}: @example CFLAGS="-falign-functions=8 -g -O2" @end example @noindent is needed to inter-work with @command{gfortran} without segfaulting in some packages. Some builds of @command{gfortran} have targetted the current version of macOS (unlike @command{clang}), causing linker warnings: to avoid these use @example FFLAGS="-g -O2 -mmacosx-version-min=11.0" FCFLAGS="-g -O2 -mmacosx-version-min=11.0" @end example @noindent or perhaps @example FFLAGS="-g -O2 -mmacos-version-min=11.0" FCFLAGS="-g -O2 -mmacos-version-min=11.0" @end example @noindent where @code{11.0} can be replaced by @code{12.0}, @code{13.0}, @code{14.0} or @code{15.0} To install packages using compiled code one needs the Command Line Tools (or @I{Xcode}) and appropriate compilers, e.g.@: the C/C++ compilers from those tools and/or @command{gfortran}. Some packages have further requirements such as component @command{pkgconfig} (and to set @env{PKG_CONFIG_PATH=} as above). @c svn was in CLT 11.3.1, even in the opensource.apple.com repository A subversion client can be obtained from @uref{https://mac.r-project.org/tools/}, for example by (Apple Silicon) @example curl -OL https://mac.r-project.org/tools/subversion-1.14.3-darwin.20-arm64.tar.gz tar xf subversion-1.14.3-darwin.20-arm64.tar.gz sudo cp subversion-1.14.3-darwin-20-arm64/svn $LOCAL/bin @end example @noindent or (Intel) @example curl -OL https://mac.r-project.org/tools/subversion-1.14.3-darwin15.6.tar.gz tar xf subversion-1.14.3-darwin15.6.tar.gz sudo cp subversion-1.14.3-darwin15.6/svn $LOCAL/bin @end example If building software or installing source packages with @command{cmake} (or a non-Apple @command{make}) for `Apple Silicon' ensure it contains the @cputype{arm64} architecture (use @command{file} to be sure). Running Apple compilers from an @cputype{x86_64} executable will generate @cputype{x86_64} code @dots{}. @c If you have a build@footnote{For example, some Homebrew @c distributions.} of @code{cairo} with dynamic libraries, you can add @c option @option{--without-static-cairo} to the @command{configure} call @c (it probably would work anyway). Updating an @cputype{arm64} build may fail because of the bug described at @uref{https://openradar.appspot.com/FB8914243} but @emph{ab initio} builds work. This has been far rarer since macOS 13. If you are using the macOS 13 @abbr{SDK}@footnote{@command{ls -l `xcrun -show-sdk-path`} in a terminal will show you which @abbr{SDK} is selected.}, you may need to add something like @code{-mmacos-version-min=12.0} to @samp{CFLAGS}. Linker warnings like @example ld: warning: could not create compact unwind for _sort_: register 26 saved somewhere other than in frame ld: warning: ld: warning: could not create compact unwind for _arcoef_: registers 23 and 24 not saved contiguously in frame ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame @end example @noindent can be ignored. These stem from compiled Fortran code, including its run-time libraries. The default security settings can make it difficult to install Apple packages which have not been `notarized'@footnote{See @uref{https://developer.apple.com/documentation/xcode/notarizing_macos_software_before_distribution}.} by Apple. And not just packages, as this has been seen for executables contained in tarballs/@I{zipfiles} (for example, for @command{pandoc}). Usually one can use @samp{Open With} (Control/right/two-finger-click in Finder), then select @samp{Installer} and @samp{Open} if you get a further warning message. If you run into problems with `quarantine' for tarballs downloaded in a browser, consider using @command{curl -OL} to download (as illustrated above) or @command{xattr -c} to remove extended attributes. @command{configure} defaults to @option{--with-internal-tzcode} on macOS. The native implementation used to be unusable on earlier versions (with a 32-bit @code{time_t} and/or timezone tables missing information beyond the 32-bit range). As from macOS 12.6, option @option{--without-internal-tzcode} can be used to override this and @R{} contains sufficient workarounds (for example, the native code fails to recognize dates with a negative @code{tm_year}, that is dates before 1900) for @R{} to pass its checks. However, there are discrepancies, notably in Europe in the 1900s and 1940s, even though the Olson database contains the correct information. @node Fortran compilers @subsection Fortran compiler There is a `universal' (@code{arm64} and Intel) build of @command{gfortran} 14.2 at @uref{https://mac.r-project.org/tools/gfortran-14.2-universal.pkg}/ This installs into @file{/opt/gfortran}. The @file{/opt/gfortran/SDK} symlink should point to the desired path to the @abbr{SDK} (defaults to the command line tools @abbr{SDK}). This can be updated by running @file{/opt/gfortran/bin/gfortran-update-sdk} or manually. If the symlink is broken, the driver will issue a warning and use @code{xcrun -show-sdk-path} to try to find an @abbr{SDK} and use its path. (The @abbr{SDK} path is used when using @command{gfortran} to link, so not when building @R{} but when installing a few packages.) Other builds of @command{gfortran} for @code{arm64} macOS 14 are available at @uref{https://github.com/fxcoudert/gfortran-for-macOS/releases}. To use one of the pre-built compilers with Apple @command{clang} needs something like @example LDFLAGS="-L/opt/R/arm64/lib -rpath /usr/local/gfortran/lib" @end example @noindent in @file{config.site} to ensure the matching Fortran run-time libraries are found. @node Cairo graphics @subsection Cairo graphics @cindex Cairo Cairo-based graphics devices such as @code{cairo_ps}, @code{cairo_pdf}, @code{X11(type = "cairo")} and the Cairo-based types of devices @code{bmp} @code{jpeg}, @code{png} and @code{tiff} are not the default on macOS, and much less used than the Quartz-based devices. However, the only SVG device in the @R{} distribution, @code{svg}, is based on Cairo. Support for Cairo is optional and can be added in several ways, all of which need @code{pkg-config}. @command{configure} will add Cairo support if @code{pkg-config} finds package @code{cairo} unless @code{--without-cairo} is used. A way to statically link Cairo is by downloading and unpacking components @code{cairo}, @code{fontconfig}, @code{freetype}, @code{pixman} and @code{zlib-system-stub} (and do not have @file{/opt/X11/lib/pkgconfig} in @env{PKG_CONFIG_PATH}). Some static builds of @code{fontconfig} need @code{libxml2} (from component @code{xml2}) and others @code{expat}, supplied by macOS but needing a file @file{$LOCAL/lib/pkgconfig/expat.pc} along the lines of @example Name: expat Version: 2.2.8 Description: expat XML parser URL: http://www.libexpat.org Libs: -lexpat Cflags: @end example @noindent Note that the list of components is liable to change: running @command{pkg-config cairo --exists --print-errors} should tell you if any others are required. @c If you have XQuartz 2.7.x installed (not 2.8.x) and ensure XQuartz's @c @code{pkg-config} files are found first on its configuration path, Cairo @c will be linked dynamically. This can be done by setting something like @c @example @c export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:$LOCAL/lib/pkgconfig:/usr/lib/pkgconfig @c @end example @c @noindent @c or by appending that variable to the @command{configure} command. (Note @c that this uses rather old versions of the graphics software.) @c @c Homebrew is another with dynamic libraries @c If you use XQuartz or another build of @code{cairo} with dynamic @c libraries, you can add option @option{--without-static-cairo} to the @c @command{configure} call (it may work without). @c @c A possible issue is that --static will require the private @c @c dependencies of fontconfig, usually either xml2 or expat, and a @c @c dynamic installation might not have the pkg-config files for those. @c @c Another issue seen in XQuartz 2.8.0 is that pkg-config requires @c @c the private dependencies of cairo of which xproto is not included. @cindex @I{Pango} The best font experience of Cairo graphics will be to use it in combination with @I{Pango} which will match that supported on most other Unix-alikes. @command{configure} uses @command{pkg-config} to determine if all the external software required by both @I{Pango} and Cairo is available: running @command{pkg-config pangocairo --exists --print-errors} should show if the installation suffices and if not, what is missing. At the time of writing using pre-built components @code{cairo}, @code{fontconfig}, @code{freetype}, @code{ffi}, @code{fribidi}, @code{gettext}, @code{icu}, @code{glib}, @code{harfbuzz}, @code{pango}, @code{pcre}, @code{pixman} and @code{xml2} sufficed. @node Other C/C++ compilers @subsection Other C/C++ compilers @c Un May 2024, 18.1.6 was the final release of that series, but the @c latest binary build was 17.0.6. Other pre-compiled distributions of @command{clang} may be available from @uref{https://github.com/llvm/llvm-project/releases/} (recently only for @code{arm64} and usually unsigned/not notarized which makes them hard to use). In particular, these include support for @abbr{OpenMP} which Apple @command{clang} does not. Suppose one of these distributions is installed under @file{$LOCAL/llvm}. Use a file @file{config.site} containing @example SDK=`xcrun -show-sdk-path` CC="$LOCAL/llvm/bin/clang -isysroot $SDK" CXX="$LOCAL/llvm/bin/clang++ -isysroot $SDK" OBJC=$CC FC=/opt/gfortran/bin/gfortran LDFLAGS="-L$LOCAL/llvm/lib -L$LOCAL/lib" R_LD_LIBRARY_PATH=$LOCAL/llvm/lib:$LOCAL/lib @end example The care to specify library paths is to ensure that the @abbr{OpenMP} runtime library, here @file{$LOCAL/llvm/lib/libomp.dylib}, is found when needed. If this works, you should see the line @example checking whether OpenMP SIMD reduction is supported... yes @end example @noindent in the @command{configure} output. Also, @samp{R_LD_LIBRARY_PATH} needs to be set to find the latest version of the C++ run-time libraries rather than the system ones. It is normally possible to build @R{} with GCC (built from the sources, from a @command{gfortran} distribution, from @I{Homebrew}, @dots{}). @c re-trested with GCC 14.1 When last tested it was not possible to use @command{gcc} to build the @code{quartz()} device, so @command{configure --without-aqua} may be required. @R{} was built and tested with the GCC 14.2 compilers in the @code{arm64} @command{gfortran} distribution mentioned above using a @file{config.site} containing @example CC=/opt/gfortran/bin/gcc CXX=/opt/gfortran/bin/g++ FC=/opt/gfortran/bin/gfortran CFLAGS="-g -O2 -Wall -pedantic -Wstrict-prototypes" C17FLAGS="-g -O2 -Wall -pedantic -Wno-strict-prototypes" C90FLAGS=$C17FLAGS C99FLAGS=$C17FLAGS CXXFLAGS="-g -O2 -Wall -pedantic" CPPFLAGS='-isystem /opt/R/arm64/include' LDFLAGS=-L/opt/R/arm64/lib @end example It is usually possible to add some @abbr{OpenMP} support to the Apple @command{clang} compilers: see @uref{https://mac.r-project.org/openmp/}. Note that that approach is somewhat fragile as it needs a @file{libomp.dylib} library matching the version of the compiler used. @node Other libraries @subsection Other libraries Pre-compiled versions of many of the @ref{Useful libraries and programs} are available from @uref{https://mac.r-project.org/bin//}. Looking at the top of @file{/Library/Frameworks/R.framework/Resources/etc/Makeconf} will show the compilers and configuration options used for the @acronym{CRAN} binary package for @R{}: at the time of writing the non-default options @example --enable-memory-profiling --enable-R-framework --x-libraries=/opt/X11/lib --x-includes=/opt/X11/include @end example @noindent were used. (@option{--enable-R-framework} implies @option{--enable-R-shlib}.) The main @TeX{} implementation used by the developers is @I{MacTeX}@footnote{An essentially equivalent @TeX{} installation can be obtained by the Unix TeX Live installation scripts.} (@uref{https://www.tug.org/mactex/}): the full installation is about 8.5GB, but a much smaller version (`Basic TeX') is available at @uref{https://www.tug.org/mactex/morepackages.html} to which you will need to add some packages to build @R{}, e.g.@: for the 2022 version we needed to add@footnote{E.g.@: @emph{via} @command{tlmgr install helvetic inconsolata texinfo} .} @pkg{helvetic}, @pkg{inconsolata} and @pkg{texinfo} which brought this to about 310MB.@footnote{Adding all the packages needed to check @acronym{CRAN} increased this to about 600MB.} @samp{TeX Live Utility} (available @emph{via} the @I{MacTeX} front page) provides a graphical means to manage @TeX{} packages. These contain executables which run natively on both @cputype{arm64} and @cputype{x86_64}. Checking packages thoroughly requires @I{Ghostscript} (part of the full @I{MacTeX} distribution or separately from @uref{https://www.tug.org/mactex/morepackages.html}) and @command{qpdf} (from @uref{https://mac.r-project.org/bin//}, a version of which is in the @file{bin} directory of a binary installation of @R{}, usually @file{/Library/@/Frameworks/@/R.framework/@/Resources/@/bin/@/qpdf}). @command{R CMD check --as-cran} makes use of `HTML Tidy'. macOS at the time of writing has a version in @file{/usr/bin/tidy} dating from 2006 which is far too old. Up-to-date versions can be installed from @uref{http://binaries.html-tidy.org/}. One macOS quirk is that the default path has @file{/usr/local/bin} after @file{/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 @file{/usr/local} and not supersede the system versions. Parallel installation of packages will make use of the utility @command{timeout} if available. A `universal' build can be downloaded from @uref{https://www.stats.ox.ac.uk/pub/bdr/timeout}: make it executable (@code{chmod 755 timeout}) and put it somewhere on your path. @node Accelerate @subsubsection @I{Accelerate} @cindex BLAS library @cindex LAPACK library The @code{Accelerate} library@footnote{@uref{https://developer.apple.com/documentation/accelerate}.} can be used @emph{via} the configuration option @example --with-blas="-framework Accelerate" @end example @noindent @c LAPACK in Accelerate was still 3.2.1 in macOS 13.6 and 14 to provide potentially higher-performance versions of the @acronym{BLAS} and LAPACK routines.@footnote{It has been reported that for some non-Apple toolchains @code{CPPFLAGS} needed to contain @code{-D__ACCELERATE__}: not needed for @command{clang} from @I{LLVM}.} This includes a full LAPACK which can be used @emph{via} @option{--with-lapack}: however, the version of LAPACK it contains has often been seriously old (and is not used unless @option{--with-lapack} is specified). Some @acronym{CRAN} builds of @R{} can be switched@footnote{@url{https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#Which-BLAS-is-used-and-how-can-it-be-changed_003f}} to use @I{Accelerate}'s BLAS. @c https://developer.apple.com/documentation/macos-release-notes/macos-13_3-release-notes @c https://developer.apple.com/documentation/xcode-release-notes/xcode-14_3-release-notes As from macOS 13.3, the BLAS and LAPACK libraries under the @I{Accelerate} framework are `now inline with reference version 3.9.1'.@footnote{Released 2021-04-01.} However, this has been done by naming new entry points and so only accessible @emph{via} their C headers. That version can be used for BLAS calls @emph{via} @command{configure} option @option{--with-newAccelerate}: it requires at least macOS 13.3 and @abbr{SDK} 13.3 (from @I{Xcode CLT} 14.3). To use it for both BLAS and LAPACK calls, configure with @option{--with-newAccelerate=lapack}. These options cannot be used with others such as @option{--with-blas} and @option{--with-lapack}. @c https://developer.apple.com/documentation/accelerate/veclib Threading in @I{Accelerate} is controlled by `Grand Central Dispatch'@footnote{E.g., @url{https://en.wikipedia.org/wiki/Grand_Central_Dispatch} .} and is said not to need user control. Test @file{nls.R} in package @pkg{stats} has often failed with the @I{Accelerate} BLAS on Intel macOS. All versions of @I{Accelerate} show differences from the reference BLAS (and most others) in the use of @code{NA} @emph{vs} @code{NaN} and a substantial number of @R{} packages fail their checks. @node OpenBLAS (macOS) @subsubsection @I{OpenBLAS} @R{} has been built on @cputype{arm64} using @I{OpenBLAS} 0.3.24 (sources from @uref{https://github.com/OpenMathLib/OpenBLAS/releases}) by symlinking @file{/opt/OpenBLAS/lib/libopenblas.dylib} to @file{lib/libRblas.dylib} (see @ref{Shared BLAS}). On macOS, a default build of @I{OpenBLAS} uses @code{pthreads} (as macOS does not have @abbr{OpenMP}) with the number of threads controlled by environment variable @env{OPENBLAS_NUM_THREADS}. On an M1 Pro this defaulted to 10 threads (there are 8 `performance' cores and 2 `efficiency cores`) and we saw a 9x speedup over the reference BLAS on a large SVD (which was slightly faster than @I{Accelerate}). @node Tcl/Tk headers and libraries @subsection Tcl/Tk headers and libraries If you plan to use the @code{tcltk} package for @R{}, you will need to install a distribution of Tcl/Tk. There are two alternatives. If you use @Rapp{} you will want to use X11-based Tcl/Tk (as used on other Unix-alikes), which is installed under @file{$LOCAL/lib} as part of the @acronym{CRAN} binary for @R{}.@footnote{Just that component can be selected from the installer for @R{}: at the `Installation Type' screen select `Customise' and then just the `Tcl/Tk 8.6.11' component.} This may need @command{configure} options @example --with-tcltk=$LOCAL/lib @end example or @example --with-tcl-config=$LOCAL/lib/tclConfig.sh --with-tk-config=$LOCAL/lib/tkConfig.sh @end example Note that this requires a matching @I{XQuartz} installation. There is also a native (`Aqua') version of Tcl/Tk which produces widgets in the native macOS style: this will not work with @Rapp{} because of conflicts over the macOS menu, but for those only using command-line @R{} this provides a much more intuitive interface to Tk for experienced Mac users. Earlier versions of macOS came with an Aqua Tcl/Tk distribution but these were often not at all recent versions of Tcl/Tk. It is better to install Tcl/Tk 8.6.x from the sources@footnote{Configure Tk with @option{--enable-aqua}.} or a binary distribution from @uref{https://www.activestate.com/platform/supported-languages/tcl/}. For the latter, configure @R{} with @example --with-tcl-config=/Library/Frameworks/Tcl.framework/tclConfig.sh --with-tk-config=/Library/Frameworks/Tk.framework/tkConfig.sh @end example If you need to find out which distribution of Tk is in use at run time, use @example library(tcltk) tclvalue(.Tcl("tk windowingsystem")) # "x11" or "aqua" @end example Note that some Tcl/Tk extensions only support the X11 interface: this includes @code{Tktable} and the @acronym{CRAN} package @CRANpkg{tkrplot}. @node Java (macOS) @subsection Java @c The situation with Java support on macOS is messy,@footnote{For more @c details see @uref{https://www.macstrategy.com/article.php?3}.} and @c distribution of Java for all platforms changed in 2018. macOS does not comes with an installed Java runtime (@abbr{JRE}) and a macOS upgrade may remove one if already installed: it is intended to be installed at first use. Check if a @abbr{JRE} is installed by running @command{java -version} in a @command{Terminal} window: if Java is not installed this may prompt you to install it from Oracle@footnote{Oracle Java has a restrictive licence, unlike distributions based on @I{OpenJDK}.} (but see the next paragraph). We recommend you install a version with long-term support, e.g.@: 17 or 21@footnote{The planned next @I{LTS} release is 25 in September 2025. Java 8 @emph{aka} 1.8.0 is still @I{LTS} but some packages require 11 or later.} but not 18--20, 22--24 with a 6-month lifetime. The currently simplest way to install Java is from @uref{https://adoptium.net, Adoptium}@footnote{which website works with Safari but not some other browsers.}: this installs into an Apple-standard location and so works with @command{/usr/bin/java}. Other builds of @I{OpenJDK} are available from @uref{https://www.azul.com/downloads/zulu-community/?os=macos&architecture=arm-64-bit&package=jdk} and from @I{OpenJDK} at @uref{https://jdk.java.net/}, for which @env{JAVA_HOME} may need to be set both when configuring @R{} and at runtime. Note that Java distribution sites may use unusual designations for macOS CPUs such as @code{AArch64}, @code{x64} or @code{x86 64-bit}. Binary distributions of @R{} are built against a specific version (e.g.@: 11.0.18 or 17.0.1) of Java so @example sudo R CMD javareconf @end example @noindent will likely be needed to be run before using Java-using packages. To see what compatible versions of Java are currently installed, run the appropriate one of @example /usr/libexec/java_home -V -a arm64 /usr/libexec/java_home -V -a x86_64 @end example @noindent If needed, set the environment variable @env{JAVA_HOME} to choose between these, both when @R{} is built from the sources and when @command{R CMD javareconf} is run. Configuring and building @R{} both looks for a @abbr{JRE} and for support for compiling @abbr{JNI} programs (used to install packages @CRANpkg{rJava} and @CRANpkg{JavaGD}); the latter requires a @abbr{JDK} (Java @abbr{SDK}). Most distributions of Java 11 or later are of a full @abbr{JDK}. The build process tries to fathom out what @abbr{JRE}/@abbr{JDK} to use, but it may need some help, e.g.@: by setting environment variable @env{JAVA_HOME}. To select a build from @uref{https://adoptium.net, Adoptium} set e.g.@: @example JAVA_HOME=/Library/Java/JavaVirtualMachines/temurin-21.jdk/Contents/Home @end example @noindent in @file{config.site}. For Java 21 from @uref{https://jdk.java.net/} (which might no longer be available), use @example JAVA_HOME=/path/to/jdk-21.jdk/Contents/Home @end example @c For an @cputype{arm64} build, the earliest Java version which is @c officially supported is 17. @c jdk.java.net no longer has Java 11 nor 17 LTS builds. Note that it is necessary to set the environment variable @env{NOAWT} to @code{1} to install many of the Java-using packages. @node Frameworks @subsection Frameworks The @acronym{CRAN} build of @R{} is installed as a framework, which is selected by the option @example ./configure --enable-R-framework @end example @noindent (This is intended to be used with an Apple toolchain: others may not support frameworks correctly but those from @I{LLVM} have done so.) It is only needed if you want to build @R{} for use with the @Rapp{} console, and implies @option{--enable-R-shlib} to build @R{} as a dynamic library. This option configures @R{} to be built and installed as a framework called @file{R.framework}. The default installation path for @file{R.framework} is @file{/Library/Frameworks} but this can be changed at configure time by specifying the flag @option{--enable-R-framework[=@var{DIR}]} (or @option{--prefix}) or at install time @emph{via} @example make prefix=/where/you/want/R.framework/to/go install @end example Note that installation as a framework is non-standard (especially to a non-standard location) and Unix utilities may not support it (e.g.@: the @command{pkg-config} file @file{libR.pc} will be put somewhere unknown to @command{pkg-config}). @node Building R.app @subsection Building R.app Building the @Rapp{} GUI console is a separate project, using @I{Xcode}. Before compiling @Rapp{} make sure the current version of @R{} is installed in @file{/Library/Frameworks/R.framework} and is working at the command-line (this can be a binary install). The current sources can be checked out by @example svn co https://svn.r-project.org/R-packages/trunk/Mac-GUI @end example @noindent and built by loading the @code{R.xcodeproj} project (select the @code{R} target and a suitable configuration), or from the command-line by e.g.@: @example xcodebuild -target R -configuration Release @end example See also the @file{INSTALL} file in the checkout or directly at @uref{https://svn.r-project.org/R-packages/trunk/Mac-GUI/INSTALL}. @Rapp{} does not need to be installed in any specific way. Building @Rapp{} results in the @Rapp{} bundle which appears as one @R{} icon. This application bundle can be run from anywhere and it is customary to place it in the @file{/Applications} folder. @node Building binary packages @subsection Building binary packages @acronym{CRAN} macOS binary packages are distributed as tarballs with suffix @file{.tgz} to distinguish them from source tarballs. One can @command{tar} an existing installed package, or use @command{R CMD INSTALL --build}. However, there are some important details. @itemize @item Current @acronym{CRAN} macOS distributions are targeted at @I{Big Sur} so it is wise to ensure that the compilers generate code that will run on @I{Big Sur} or later. With the recommended compilers we can use @example CC="clang -mmacos-version-min=11.0" CXX="clang++ -mmacos-version-min=11.0" FC="/opt//gfortran/bin/gfortran -mmacosx-version-min=11.0" @end example @noindent or set the environment variable @example export MACOSX_DEPLOYMENT_TARGET=11.0 @end example @item Using the flag @option{-Werror=partial-availability} can help trigger compilation errors on functionality not in @I{Big Sur}. @item Check that any compiled code is not dynamically linked to libraries only on your machine, for example by using @command{otool -L} or @command{objdump -macho -dylibs-used}. This can include C++ and Fortran run-time libraries under @file{/opt/R/x86_64/lib} or @file{/opt/R/arm64/lib}: one can use @command{install_name_tool} to point these at system versions or those shipped with @R{}, for example @example install_name_tool -change /usr/local/llvm/lib/libc++.1.dylib \ /usr/lib/libc++.1.dylib \ @var{pkg}.so install_name_tool -change /opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0/libgfortran.5.dylib \ /Library/Frameworks/R.framework/Resources/lib/libgfortran.5.dylib \ @var{pkg}.so install_name_tool -change /opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0/libquadmath.0.dylib \ /Library/Frameworks/R.framework/Resources/lib/libquadmath.0.dylib \ @var{pkg}.so @end example @noindent (where the details depend on the compilers and @acronym{CRAN} macOS @R{} release). @item For C++ code there is the possibility that calls will be generated to entry points not in the system @file{/usr/lib/libc++.1.dylib}. The previous step allows this to be tested against the system library on the build OS, but not against earlier ones. It may be possible to circumvent that by static linking to @file{libc++.a} and @file{libc++abi.a} by something like @example SHLIB_CXXLD = /usr/local/llvm/bin/clang PKG_LIBS = /usr/local/llvm/lib/libc++.a /usr/local/llvm/lib/libc++abi.a @end example @noindent in @file{src/Makevars}. It would also be possible to static link the Fortran runtime libraries @file{libgfortran.a} and @file{libquadmath.a} should the Fortran compiler have later versions (but @command{gfortran} 8--14 all have version @code{5}). @end itemize @noindent The @acronym{CRAN} binary packages are built with the Apple compiler on the oldest supported version of macOS, which avoids the first two and any issues with C++ libraries. @node Building for Intel on arm64 @subsection Building for Intel on @samp{arm64} Should one want to build @R{} for Intel on an @cputype{arm64} @I{Big Sur} Mac, add the target for the compilers: @example CC="clang -arch x86_64 OBJC=$CC CXX="clang++ -arch x86_64" FC="/opt//gfortran/bin/gfortran -arch x86_64 -mtune=native -mmacosx-version-min=11" @end example @noindent and install the Fortran compiler and external software described above for Intel builds (and have @file{/opt/R/x86_64/bin} before @file{/opt/R/arm64/bin} in your path). To set the correct architecture (which will be auto-detected as @code{aarch64}), use something like @example /path/to/configure --build=x86_64-apple-darwin20 @end example @node Installer @subsection Installer The scripts for the @acronym{CRAN} packaging of @R{} can be found under @uref{https://svn.r-project.org/R-dev-web/trunk/QA/Simon/R4/}: start with the @file{README} file in that directory. @node FreeBSD @section FreeBSD @cindex FreeBSD There have been few recent reports on FreeBSD: there is a `port' at @uref{https://svnweb.freebsd.org/ports/head/math/R}, currently last updated for @R{} 4.0.4. Recent versions of FreeBSD use Clang and the @code{libc++} C++ headers and runtime, but the `port' has been configured to use GCC. Use of ICU for collation and the @command{configure} option @option{--with-internal-tzcode} are desirable workarounds. @node OpenBSD @section @I{OpenBSD} @cindex @I{OpenBSD} @I{Ingo Feinerer} installed @R{} version 3.2.2 on OpenBSD 5.8 arch @cputype{amd64} (their name for @cputype{x86_64}). Details of the build (and patches applied) are at @uref{https://cvsweb.openbsd.org/cgi-bin/cvsweb/ports/math/R/}, currently updated for @R{} 4.2.3. @node Cygwin @section @I{Cygwin} The 32-bit version never worked well enough to pass @R{}'s @command{make check}, and residual support from earlier experiments was removed in @R{} 3.3.0. The 64-bit version was never supported. @node New platforms @section New platforms There are a number of sources of problems when installing @R {} on a new hardware/OS platform. These include @strong{Floating Point Arithmetic}: @R{} requires arithmetic compliant with @acronym{IEC}@tie{}60559, also known as @acronym{IEEE}@tie{}754. This mandates the use of plus and minus infinity and @code{NaN} (not a number) as well as specific details of rounding. Although almost all current @abbr{FPU}s can support this, selecting such support can be a pain. The problem is that there is no agreement on how to set the signalling behaviour; @I{Sun/Sparc}, @I{SGI/IRIX} and @cputype{ix86} Linux require no special action, FreeBSD requires a call to (the macro) @code{fpsetmask(0)} and @I{OSF1} required that computation be done with a @option{-ieee_with_inexact} flag etc. With Intel compilers on 32-bit and 64-bit Intel machines, one has to explicitly disable flush-to-zero and @I{denormals-are-zero} modes. Some ARM processors including A12Z and M1 (Apple Silicon) by default use @I{runfast} mode, which includes flush-to-zero and @I{default-nan} and hence has to be disabled. With @I{default-nan} mode, the NaN payload used for representation of numeric NA values is lost even on simple operations with finite values. 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 @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 @acronym{IEEE} model. For example, using @option{-fast} on the Oracle compilers has caused @R{}'s @code{NaN} to be set incorrectly, and @command{gcc}'s @option{-ffast-math} and @command{clang}'s @option{-Ofast} have given incorrect results. @strong{Shared Objects}: There seems to be very little agreement across platforms on what needs to be done to build shared objects. there are many different combinations of flags for the compilers and loaders. @acronym{GNU} @I{libtool} cannot be used (yet), as it currently does not fully support Fortran: one would need a shell wrapper for this). The technique we use is to first interrogate the X window system about what it does (using @command{xmkmf}), and then override this in situations where we know better (for tools from the @acronym{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 @command{cc} and @command{ld} usually reveals the correct incantation. Once you know the recipe you can modify the file @file{config.site} (following the instructions therein) so that the build will use these options. It seems that @command{gcc}@tie{}3.4.x and later on @cputype{ix86} Linux defeat attempts by the LAPACK code to avoid computations entirely in extended-precision registers, so file @file{src/modules/lapack/dlamc.f} may need to be compiled without optimization or with additional flags. Set the configure variable @env{SAFE_FFLAGS} to the flags to be used for this file. If you do manage to get @R{} running on a new platform please let us know about it so we can modify the configuration procedures to include that platform. If you are having trouble getting @R{} to work on your platform please feel free to use the @samp{R-devel} mailing list to ask questions. We have had a fair amount of practice at porting @R{} to new platforms @enddots{} One thing you might want to add for a new platform is the mapping of C/C++/Fortran calls to entry point names used for @command{R CMD check}. See @uref{https://svn.r-project.org/R-dev-web/trunk/sotools.txt} for how to do so. @node Function and variable index @unnumbered Function and variable index @printindex vr @node Concept index @unnumbered Concept index @printindex cp @node Environment variable index @unnumbered Environment variable index @printindex en @bye @c Local Variables: *** @c mode: TeXinfo *** @c End: ***