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Section “Installing packages” in R Installation and Administration

1. 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 http sourceforge net p predef wiki Home can be helpful The R sources currently use AIX _AIX Cygwin __CYGWIN__ FreeBSD __FreeBSD__ HP UX __hpux__ __hpux IRIX sgi sgi Linux linux OS X APPLE NetBSD NetBSD OpenBSD OpenBSD Solaris sun sun Windows _WIN32 _WIN64 C 1 X11 issues The X11 O graphics device is the one started automatically on Unix alikes 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 The modern version of the X11 device is based on cairo graphics and in most implementations uses 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 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 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 xorg xli fonts 75dpi xorg x11 fonts 100dpi xorg x11 fonts
2. Concept index Environment variable index Chapter 1 Obtaining R 1 1 Obtaining R Sources binaries and documentation for R can be obtained via CRAN the Comprehensive R Archive Network whose current members are listed at http CRAN R project org mirrors html 1 1 Getting and unpacking the sources The simplest way is to download the most recent R x y z tar gz file and unpack it with tar xf R x y z tar gz on systems that have a suitable tar installed On other systems you need to have the gzip program installed when you can use gzip dc R x y z tar gz tar xf The pathname of the directory into which the sources are unpacked should not contain spaces as most make programs and specifically GNU make do not expect spaces If you want the build to be usable by a group of users set umask before unpacking so that the files will be readable by the target group e g umask 022 to be usable by all users Keep this setting of umask whilst building and installing If you use a recent GNU version of tar and do this as a root account which on Windows includes accounts with administrator privileges you may see many warnings about changing ownership In which case you can use tar no same owner xf R x y z tar gz and perhaps also include the option no same permissions These options can also be set in the AR OPTIONS environment variable if more than one option is included they should be
3. MKL with lapack where some versions may need 1mkl lapack before 1mkl core The order of the libraries is important The option with lapack is used since MKL contains a tuned copy of LAPACK as well as BLAS see Section A 3 2 LAPACK page 45 although this can be omitted Threaded MKL may be used according to Zhang Zhang of Intel by replacing the line defining the variable MKL with Intel OMP MKL L MKL LIB PATH 1mkl gf 1p64 1mkl intel thread lmkl core liomp5 lpthread or GNU OMP MKL L MKL LIB PATH 1mkl gf 1p64 1mkl gnu thread lmkl core fopenmp lpthread The default number of threads will be chosen by the OpenMP software but can be controlled by setting OMP NUM THREADS or MEI NUM THREADS and in recent versions seems to default to a sensible value for sole use of the machine Static threaded MKL may be used GNU OpenMP with something like MKL L MKL LIB PATH Wl start group 4MKL LIB PATH libmkl gf lp64 a 4MKL LIB PATH libmkl en thread a MKL LIB PATH libmkl core a Wl end group lgomp ldl lpthread LOO LO a a Thanks to Ei ji Nakama The 1d1 was needed on a Centos 5 systems and may not be needed everywhere The MKL documentation includes a link line advisor which will suggest appropriate incantations an on line version was available at http software intel com en us articles intel mkl link line advisor The default linking model which was also u
4. The results of example md5sums when testing tools will differ from the reference output as some files are installed with Windows CRLF line endings Chapter 4 Installing R under OS X 19 4 Installing R under OS X The front page of a CRAN site has a link Download R for OS X Click on that then download the file R 3 1 1 snowleopard pkg and install it This runs on OS X 10 6 and later Snow Leopard Lion Mountain Lion Mavericks it is a 64 bit x86_64 build which should run on all Macs from mid 2008 on For older Intel Macs and some older versions of the OS you can install R from the sources There is a separate installer package R 3 1 1 mavericks pkg for use on Mavericks only the Snow Leopard installer package also works there and may have more binary packages available but there are a few packages using C 11 and only available for the Mavericks build It is important that if you use a binary installer package that your OS is fully updated run Software Update from the Apple menu to be sure If using XQuartz check that is current To install just double click on the icon of the file you downloaded At the Installation Type stage note the option to Customize This currently shows three components Ev eryone will need the R Framework component the H GUI and Tcl Tk components are optional the latter being needed to use package tcltk This is an Apple Installer packag
5. std gnu99 will be appended to CC unless it conflicts with a setting of CFLAGS Note that options essential to run the compiler even for linking such as those to set the architecture should be specified as part of CC rather than in CFLAGS Unless you do not want to view graphs on screen or use a Mac you need X11 installed including its headers and client libraries For recent Fedora distributions it means at least RPMs 1ibX11 libX11 devel libXt and libXt devel On Debian we recommend the meta package xorg dev If you really do not want these you will need to explicitly configure R without X11 using with x no The command line editing and command completion depends on the GNU readline library version 4 2 or later is needed for all the features to be enabled Otherwise you will need to configure with with readline no or equivalent A suitably comprehensive iconv function is essential The R usage requires iconv to be able to translate between latini and UTF 8 to recognize as the current encoding and ASCII and to translate to and from the Unicode wide character formats UCS 24 BL E this is true for glibc but not of most commercial Unixes However you can make use of GNU libiconv possibly as a plug in replacement see http www gnu org software libiconv The OS needs to have enough support for wide character types this is checked at configuration A small number of POSIX fun
6. usr local lib pkgconfig usr lib pkgconfig in config site For some pre compiled software for example the GTK framework opt X11 include may need to be added to the include paths If you install the command line tools for Xcode 4 6 3 you will get the compilers used for the CRAN binary distribution those for Xcode 5 can be installed afterwards C 3 4 Mavericks Xcode for Mavericks provides different compilers headers and libraries from earlier versions In particular the compilers even those called gcc and g are based on clang and the C headers and runtime are from LLVM s libc project The command line tools can be re installed by xcode select install If you have a fresh installation of Mavericks running e g make in a terminal will offer the installation of the command line tools or perhaps use the versions from Xcode However after an update to Mavericks you are advised to re install them They are not available under the Downloads preference pane in Xcode To use the compilers from the command line tools for Xcode 5 with the recommended Fortran compiler have in config site something like CC clang CXX clang F77 gfortran 4 8 FC F77 OBJC clang CC gcc and CXX g are slightly different front ends to the same compilers Recent versions of the CRAN binary package installer for Snow Leopard change the settings in etc Makeconf to CC gcc arch x86_64 std gnu99 CXX g arch x86_64 F
7. System Library C 3 6 Java The situation with Java support on OS X is messy with Apple essentially no longer sup porting Java and what it does support is Java 6 which has reached end of life Snow Leopard and Lion shipped with a Java 6 runtime JRE Mountain Lion and Mavericks do not come with an installed JRE and an upgrade to either removes one if already installed it is intended to be installed at first use Check if a JRE is installed by running java version in a Terminal window if Java is not installed this should prompt you to install it However you may want need to install the latest Java from Oracle currently Java 7 from http www oracle com technetwork java javase downloads index html this is for Lion and later To see what compatible versions of Java are currently installed run usr libexec java_home V a x86_64 If needed set the environment variable JAVA_HOME to choose between these both when R is built from the sources and when R CMD javareconf is run Configuring and building R both looks for a JRE and for support for compiling JNI programs used by packages rJava and JavaGD the latter requires a JDK Java SDK and not just a JRE The build process tries to fathom out what JRE JDK to use but it may need some help e g by setting JAVA_HOME The Apple JRE can be specified explicitly by something like JAVA_HOME System Library Frameworks JavaVM framework Home JAVA_CPPFLAGS I System Library Frameworks Ja
8. declared in C header file Rmath h These can be compiled into a standalone library for linking to other applications Note that they are not a separate library when R is built and the standalone version differs in several ways The makefiles and other sources needed are in directory src nmath standalone so the following instructions assume that is the current working directory in the build directory tree on a Unix alike if that is separate from the sources Rmath h contains BR VERSION STRING which is a character string containing the current R version for example 3 1 0 There is full access to R s handling of NaN Inf and Inf via special versions of the macros and functions ISNAN R FINITE R log R pow and R pow di and extern constants R_PosInf R NegInf and NA REAL There is no support for R s notion of missing values in particular not for NA INTEGER nor the distinction between NA and NaN for doubles A little care is needed to use the random number routines You will need to supply the uniform random number generator double unif_rand void or use the one supplied and with a shared library or DLL you may have to use the one supplied which is the Marsaglia multicarry with an entry point set seed unsigned int unsigned int to set its seeds The facilities to change the normal random number generator are available through the constant N01 kind This takes values from the enumeration type typedef enum BUGGY_KIN
9. f90 or 95 the compiler defined by the macro FC is used by R CMD INSTALL This is found when R is configured and is often the same as F77 note that it is detected by the name of the command without a test that it can actually compile Fortran 90 code Set the configure variable FC to override this if necessary variables FCFLAGS FCPICFLAGS FCLIBS SHLIB_FCLD and SHLIB FCLDFLAGS might also need to be set See file config site in the R source for more details about these variables A 3 Linear algebra Appendix A Essential and useful other programs under a Unix alike 42 A 3 1 BLAS The linear algebra routines in R can make use of enhanced BLAS Basic Linear Algebra Subprograms http www netlib org blas faq html routines However these have to be explicitly requested at configure time R provides an internal BLAS which is well tested and will be adequate for most uses of R You can specify a particular BLAS library via a value for the configuration option with blas and not to use an external BLAS library by without blas the default If with blas is given with no its value is taken from the environment variable BLAS_ LIBS set for example in config site If neither the option nor the environment variable supply a value a search is made for a suitable BLAS If the value is not obviously a linker command starting with a dash or giving the path to a library it is prefixed by 1 so with blas foo is an instruction t
10. on the return values of functions such as log use xlibmieee to ensure this You can target specific Sparc architectures for slightly higher performance xtarget native in CFLAGS etc tunes the compilation to the current machine Using xlibmil in CFLAGS and xlibmil in FFLAGS allows more system mathematical functions to be inlined On x86 you will get marginally higher performance via CFLAGS x05 xc99 xlibmieee xlibmil nofstore xtarget native FFLAGS 05 libmil nofstore xtarget native CXXFLAGS x05 xlibmil nofstore xtarget native SAFE FFLAGS libmil fstore xtarget native but the use of nofstore can be less numerically stable and some packages notably mgcv on x86 failed to compile at higher optimization levels with version 12 3 The Solaris Studio compilers provide several implementations of the C 98 standard which select both the set of headers and a C runtime library These are selected by the library flag which as it is needed for both compiling and linking is best specified as part of the compiler The examples above use stlport4 currently the most modern of the options the default but still needed to be specified as it is needed for linking is Appendix C Platform notes 65 Cstd see http developers sun com solaris articles cmp stlport libCstd html Note though that most external Solaris C libraries will have been built with Cstd and so an R package using such libra
11. whereas x 0 can be NaN This is checked in the test suite A 3 1 1 ATLAS ATLAS http math atlas sourceforge net is a tuned BLAS that runs on a wide range of Unix alike platforms Unfortunately it is usually built as a static library that on some platforms cannot be used with shared objects such as are used in R packages Be careful when using pre built versions of ATLAS they seem to work on ix86 platforms but not always on x86_64 ones The usual way to specify ATLAS will be via with blas lf77blas latlas if the libraries are in the library path otherwise by 12 Using the Oracle Solaris Studio cc and 95 compilers Appendix A Essential and useful other programs under a Unix alike 43 with blas L path to ATLAS libs 1f77blas latlas For example x86_64 Fedora needs with blas L usr lib64 atlas 1f77blas latlas For systems with multiple CPU cores it is possible to use a multi threaded version of ATLAS by specifying with blas lptf77blas lpthread latlas Consult its file INSTALL txt for how to build ATLAS with position independent code that file also describes how to build ATLAS as a shared library A 3 1 2 ACML For x86_64 and i686 processors under Linux there is the AMD Core Math Library ACML http www amd com acml For the gcc version we could use with blas lacml if the appropriate library directory such as opt acml15 1 0 gfortran64 lib is in the LD LIBRAR
12. you will first need to collect install and test an extensive set of tools See Appendix D The Windows toolset page 70 and perhaps updates in http CRAN R project org bin windows Rtools for details The Rtools exe executable installer described in Appendix D The Windows toolset page 70 also includes some source files in addition to the R source as noted below You should run it first to obtain a working tar and other necessities Choose a Full installation and install the extra files into your intended R source directory e g C R The directory name should not contain spaces We will call this directory R HOME below 3 1 2 Getting the source files You need to collect the following sets of files e Get the R source code tarball R 3 1 1 tar gz from CRAN Open a command window or another shell at directory R HOME and run tar xf R 3 1 1 tar gz to create the source tree in R HOME Beware do use tar to extract the sources rather than tools such as WinZip If you are using an account with administrative privileges you may get a lot of messages which can be suppressed by Chapter 3 Installing R under Windows 13 tar no same owner xf R 3 1 1 tar gz or perhaps better set the environment variable TAR OPTIONS to the value no same owner no same permissions It is also possible to obtain the source code using Subversion see Chapter 1 Obtaining R page 1 for details e If you are not using a tarball you need to o
13. 10 tar gz mv libpng 1 6 10 libpng tar zxf jpegsrc v9a tar gz tar zxf tiff 4 0 3 tar gz mv tiff 4 0 3 libtiff rm rf tiff 4 0 3 V WM WM WM M and see the comment above about no same owner 3 1 3 Building the core files Set the environment variable TMPDIR to the absolute path to a writable directory with a path specified with forward slashes and no spaces The default is tmp which may not be useful on Windows You may need to compile under a case honouring file system we found that a samba mounted file system which maps all file names to lower case did not work Chapter 3 Installing R under Windows 14 Open a command window at R_HOME src gnuwin32 Look at MkRules dist and if settings need to be altered copy it to MkRules local and edit the settings there In particular this is where a 64 bit build is selected Then run make all recommended and sit back and wait while the basic compile takes place Notes e We have had reports that earlier versions of anti virus software locking up the machine but not for several years However aggressive anti virus checking such as the on access scanning of Sophos can slow the build down several fold e By default Doug Lea s malloc in the file R_HOME src gnuwin32 malloc c is used for R s internal memory allocations You can opt out of this by setting LEA MALLOC NO in MkRules dist in which case the malloc in msvcrt d1l is used This does impose a considerable performance pen
14. CXXPICFLAGS Kpic FC sunf95 FCFLAGS FFLAGS FCPICFLAGS Kpic LDFLAGS L opt sunstudio12 1 rtlibs amd64 SHLIB LDFLAGS shared SHLIB CXXLDFLAGS G SHLIB FCLDFLAGS G SAFE FFLAGS 05 libmil m64 could be added but was the default Do not use fast see the warnings under Solaris The C options are also explained under Solaris Others have found on at least some versions of ix86 Linux that the configure flag disable largefile was needed since glob h on that platform presumed gcc was being used C 3 OS X You can build R using Apple s Command line Tools for Xcode and and suitable compilers You will also need readline or to configure with without readline That and other binary components are available from http r research att com libs You may also need to install an X sub system or you will need to configure using option without x X is part of the standard OS X distribution in versions prior to Moun tain Lion but not always installed For Mountain Lion and later see http xquartz macosforge org Note that XQuartz will likely need to be re installed after an OS upgrade In principle R can be built for 10 4 x 10 5 x and for PowerPC Macs but this has not been tested recently 10 6 Snow Leopard is the earliest version currently tested 32 bit Intel builds of R 3 0 0 were tested they would be needed for Snow Leopard running on very old machines with Core Solo or Core Duo CPUs The instructi
15. DESCRIPTION files of the packages separated by blank lines but only a few of the fields are needed The simplest way to set up such a file is to use function write PACKAGES in the tools package and its help explains which fields are needed Optionally there can also be a PACKAGES gz file a gzip compressed version of PACKAGES as this will be downloaded in preference to PACKAGES it should be included for large repositories If you have a mis configured server that does not report correctly non existent files you may need PACKAGES gz To add your repository to the list offered by setRepositories see the help file for that function Incomplete repositories are better specified via a contriburl argument than via being set as a repository A repository can contain subdirectories when the descriptions in the PACKAGES file of packages in subdirectories must include a line of the form Path path to subdirectory once again write_PACKAGES is the simplest way to set this up 6 7 Checking installed source packages It can be convenient to run R CMD check on an installed package particularly on a platform which uses sub architectures The outline of how to do this is with the source package in directory pkg or a tarball filename R CMD INSTALL 1 libdir pkg gt pkg log 2 gt amp 1 R CMD check 1 libdir install check pkg log pkg Chapter 6 Add on packages 29 Where sub architectures are in use the R CMD check line can be repeate
16. GNU Make e g via MAKE opt freeware bin make Further installation instructions to set up a proper R development environment can be found in the R on AIX project on R Forge http R Forge R project org projects aix C 6 FreeBSD There have been no reports for R 3 0 0 or later C 7 Cygwin The Cygwin emulation layer on Windows can be treated as a Unix alike OS This is unsup ported but experiments have been conducted and a few workarounds added Cygwin has not been tested for R 3 0 0 or later The 64 bit version is completely unsupported The 32 bit version has never worked well enough to pass R s make check R requires C99 complex type support which is available as from Cygwin 1 7 8 March 2011 However the then implementation of cacos gives incorrect results so we undefine HAVE CACOS in src main complex c on that platform It has been reported that some C99 long double mathematical functions are missing so configuring with disable long double was required Only building as a shared library can possibly work so use e g configure disable nls enable R shlib FLIBS lgfortran make Enabling NLS does work if required although adding with included gettext is prefer able You will see many warnings about the use of auto import Setting FLIBS explicitly seems needed currently as the auto detection gives an incorrect value You will need the tetex extra Cygwin package to build NEWS pdf and the
17. OptlonSua cios nna t Eben sa d egere Pee estes 10 2 8 Testing an Installation 00 cece eee eee 10 3 Installing R under Windows 12 3 1 Building from source 12 3 1 1 Getting the tools 12 3 1 2 Getting the source Des 12 3 1 3 Building the core les 13 3 1 4 Building the bitmap Des 14 3 1 5 Building the cairo devices 0 00 cece eee eee eee 14 3 1 5 1 Using ICU for collation esses 14 3 1 6 Checking the buld eee 15 3 1 7 Building the manual 15 3 1 8 Building the Inno Setup installer 00 16 3 1 9 Building the MSI mstaller 0 00 eee eee ee eee I7 3 1 10 64 bit Windows bilde 17 3 2 Testing an Installation ssseeeeeeeeee e 18 4 Installing R under OS X 19 4 31 Running R under OS 3 19 4 2 Uninstalling under OS 3 20 4 3 Multiple veraons 00 e cece ence ene e eee e ees 20 D R nning Lu uo irn Ripe d uda deir ganda 21 6 Add onpackages annarrar 22 6 1 Default packageg I 22 6 2 Managing libraries 0 0 cece cece eee eee eens 22 6 3 Installing packages 0 cece eee aee 23 6 3 1 Windows 24 0 3 2 OB IX feet fetches en TE dala dee RE AH ee 25 6 3 3 Customizing package compilation sssesesssusrrrsn 26 6 3 4 Multiple sub architectures 0 00 0 cece eee eens 26 6 3 5 Bvte compilation 0 0 cece eee e 27 6 4 Updating packages ssssssssseese eee eens Sr 6 5 Removing package
18. R version An alternative personal file can be specified via the environment variable R MAKEVARS USER Package developers are encouraged to use this mechanism to enable a reasonable amount of diagnostic messaging warnings when compiling such as e g Wall pedantic for tools from GCC the Gnu Compiler Collection Note that this mechanism can also be used when it necessary to change the optimization level for a particular package For example for C code CFLAGS g 0 mtune native for C code CXXFLAGS g O mtune native for Fortran code FFLAGS g O mtune native for Fortran 9x code FCFLAGS g 0 mtune native There is also provision for a site wide Makevars site file under R_HOME etc in a sub architecture specific directory if appropriate This is read immediately after Makeconf and an alternative file can be specified by environment variable RB MAKEVARS SITE 6 3 4 Multiple sub architectures When installing packages from their sources there are some extra considerations on in stallations which use sub architectures These are commonly used on Windows but can in principle be used on other platforms When a source package is installed by a build of R which supports multiple sub architectures the normal installation process installs the packages for all sub architectures The exceptions are Uniz alikes where there is an configure script or a file src Makef ile Windows where there is a non empt
19. a UTF 8 locale you will most likely find messages change to English Chapter 7 Internationalization and Localization 32 e Domain R pkg for the R stop warning and message messages in each package in cluding R base for the base package e Domain pkg for the C level messages in each package e Domain RGui for the menus etc of the R for Windows GUI front end 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 de_AT translation catalogue will be used in preference to a generic German one de for an Austrian user However if a specific translation catalogue exists but does not contain a translation the less specific catalogues are consulted For example R has catalogues for en GB that translate the Americanisms e g gray in the standard messages into English Two other examples there are catalogues for es which is Spanish as written in Spain and these will by default also be used in Spanish speaking Latin American countries and also for pt_BR which are used for B
20. add on packages is somewhat more forgiving but we recommend using the exact toolset at first and only substituting other tools once you are familiar with the process This appendix contains a lot of prescriptive comments They are here as a result of bitter experience Please do mot report problems to the R mailing lists unless you have followed all the prescriptions We have collected most of the necessary tools unfortunately not all due to license or size limitations into an executable installer named Rtoo1s31 exe available from http CRAN R project org bin windows Rtools You should download and run it choosing the default Package authoring installation to build add on packages or the full installa tion if you intend to build R You will need the following items to build R and packages See the subsections below for detailed descriptions e The command line tools in Rtools exe e The MinGW w64 32 64 bit toolchain to compile C Fortran and C For installing simple source packages containing data or R source but no compiled code none of these are needed Perl is no longer needed to build R nor to install nor develop source packages A complete build of R including PDF manuals and producing the installer will also need the following e DTEX e The Inno Setup installer e optional qpdf It is important to set your PATH properly The installer Rtools exe optionally sets the path to components that it installs
21. install binary packages from a suitable repos itory These OS X binary package files have the extension tgz The Rapp GUI provides menus for installation of either binary or source packages from CRAN or local files Note that most binary packages including compiled code are tied to a particular series e g R 3 0 x or 3 1 x of R Installing source packages which do not contain compiled code should work with no additional tools For others you will need the Command line Tools for Xcode and compilers which match those used to build R see Section C 3 OS X page 57 Note that the Fortran compilers differ for the Snow Leopard and Mavericks binary installations of R Package rJava and those which depend on it need a Java runtime installed and several packages need X11 installed including those using Tk For Mountain Lion and Mavericks see Section C 3 OS X page 57 and Section C 3 6 Java OS X page 61 Tcl Tk extensions BWidget and Tktable are part of the Tcl Tk contained in the R installer These are required by a number of CRAN and Bioconductor packages A few of the binary packages need other software to be installed on your system In particular packages using Gtk RGtk2 cairoDevice and those that depend on them need the GTK framework installed from http r research att com libs the appropriate version at the time of writing was http r research att com libs GTK 2 24 17 X11 pkg The default compilers s
22. refers to the process of enabling support for many human languages and localization to adapting to a specific country and language Current builds of R support all the character sets that the underlying OS can handle These are interpreted according to the current locale a sufficiently complicated topic to merit a separate section Note though that R has no built in support for right to left languages and bidirectional output relying on the OS services For example how character vectors in UTF 8 containing both English digits and Hebrew characters are printed is OS dependent and perhaps locale dependent The other aspect of the internationalization is support for the translation of messages This is enabled in almost all builds of R 7 1 Locales A locale is a description of the local environment of the user including the preferred lan guage the encoding of characters the currency used and its conventions and so on Aspects of the locale are accessed by the R functions Sys getlocale and Sys localeconv The system of naming locales is OS specific There is quite wide agreement on schemes but not on the details of their implementation A locale needs to specify e human language These are generally specified by a lower case two character abbre viation following ISO 639 see e g http en wikipedia org wiki ISO 639 1 e A territory used mainly to specify the currency These are generally specified by an upper case two
23. separated by spaces 1 2 Getting patched and development versions A patched version of the current release r patched and the current development version r devel are available as daily tarballs and via access to the R Subversion repository For the two weeks prior to the release of a minor 3 x 0 version r patched tarballs may refer to beta release candidates of the upcoming release the patched version of the current release being available via Subversion The tarballs are available from ftp ftp stat math ethz ch pub Software R Download R patched tar gz or R devel tar gz or the tar bz2 versions and unpack as described in the previous section They are built in exactly the same way as distributions of R releases 1 2 1 Using Subversion and rsync Sources are also available via https svn R project org R the R Subversion reposi tory If you have a Subversion client see http subversion apache org you can check out and update the current r devel from https svn r project org R trunk and the current r patched from https svn r project org R branches R x y branch l e g GNU tar version 1 15 or later or that from the libarchive as used on OS X versions 10 6 and later or Heirloom Toolchest distributions Chapter 1 Obtaining R 2 where x and y are the major and minor number of the current released version of R E g use svn checkout https svn r project org R
24. simplest way to ensure that all the packages on your system are up to date It downloads the list of available packages and their current versions compares it with those installed and offers to fetch and install any that have later versions on the repositories An alternative interface to keeping packages up to date is provided by the command packageStatus which returns an object with information on all installed packages and packages available at multiple repositories The print and summary methods give an over view of installed and available packages the upgrade method offers to fetch and install the latest versions of outdated packages One sometimes useful additional piece of information that packageStatus returns is the status of a package as ok upgrade or unavailable in the currently selected repositories For example gt inst lt packageStatus inst gt inst inst Status ok c Package Version Status Package Version Status Biobase Biobase 2 8 0 unavailable RCurl RCurl 1 4 2 upgrade Rgraphviz Rgraphviz 1 26 0 unavailable rgdal rgdal 0 6 27 upgrade 6 5 Removing packages Packages can be removed in a number of ways From a command prompt they can be removed by R CMD REMOVE 1 path to library pkg1 pkg2 From a running R process they can be removed by gt remove packages c pkgi pkg2 lib file path path to library Finally in most installations one can just remove the
25. the Free UCS Outline Fonts project http www gnu org software freefont which are OpenType TrueType fonts based on the URW fonts but with extended Unicode coverage See the R help on X11 on selecting such fonts The bitmapped graphics devices jpeg O pngO and tiff O need the appropriate headers and libraries installed jpeg version 6b or later or libjpeg turbo or libpng version 1 2 7 or later and zlib or libtiff any recent version 3 9 4567 and 4 0 23 have been tested respectively They also need support for either X11 or cairo see above Should support for these devices not be required or broken system libraries need to be avoided there are configure options without libpng without jpeglib and without libtiff For most system installations the TIFF libraries will require JPEG libraries to be present and perhaps linked explicitly so without jpeglib may also disable the tiff device The tiff devices only require a basic build of libtiff not even JPEG support is needed Recent versions allow several other libraries to be linked into libtiff such as lzma jbig and jpeg12 and these may need also to be present If you have them installed including the appropriate headers and of suitable versions system versions of zlib libbz2 and PCRE will be used if specified by with system zlib version 1 2 5 or later with system bzlib or with system pcre version 8 10 or later preferably 8 34 otherwise versions
26. the browserg 0c cece eee eee eee eens 49 B 3 8 Compilation Dags 49 B 3 4 Making manuals eee eee eens 49 B 4 Setting the sbell 0 0 c cece eee nee eens 49 B 5 Using make ueeec s eere RER EE dd E Read dps 49 B 6 Using FORIRAN e e 50 Dol Using ebortran n 50 B 7 Compile and load fa 51 B 8 Maintainer mode 52 Appendix C Platform notes 53 Cl XIl388068 2 eeeeu be EENS 53 E WEE OK 54 EN MER GIE EE 56 C 2 2 Intel compilerg 0 0 cece eee eee etatas 56 C 2 3 Oracle Solaris Studio compilers 00 0000 56 e MES PCM TT 57 C 3 1 Snow Leopard 59 E IMEEM 59 C 3 3 Mountain Lon 59 C 3 4 Mavericks osesssersrai eniste kE San Gs ee re 60 C 3 5 Tcl Tk headers and libraries i ecce 60 E EE 61 C 3 7 Frameworks sssssssseseesse eee e nee eens 62 C 3 8 Building Rapp 62 CLA EE 62 CALI USING PCC cec ketEEr t eeu se aie peered eww ees ceeds ob 65 Q D AVX cce sachin ake nba Cr ERRARE REG WA Ree C i ae ad pedi b deor ea ees 66 Cp FreeBSD a ossi bind Seeche e on Era ap be rd 68 Qo CYP Wits Ey EXE E e eeDei nex ade seven Sun TR OR ERRORS 68 C 8 New platioms es me 69 Appendix D The Windows toolset 70 DJ E euet PRG bere Sepe n FER weak nha 71 D 2 The Inno Setup installer 0 0 cece eee eee eee val D 3 The command line tools nil D 4 The MinGW w64 toolcham 72 D 5 Useful additional program 12 Function and variable index 73
27. to writable area is used If none do the final default is tmp on Unix alikes and the value of R USER on Windows The path should be an absolute path not containing spaces and it is best to avoid non alphanumeric characters such as Some Unix alike systems are set up to remove files and directories periodically from tmp for example by a cron job running tmpwatch Set TMPDIR to another directory before starting long running jobs on such a system Note that TMPDIR will be used to execute configure scripts when installing packages so if tmp has been mounted as noexec TMPDIR needs to be set to a directory from which execution is allowed Chapter 6 Add on packages 22 6 Add on packages It is helpful to use the correct terminology A package is loaded from a library by the function library O Thus a library is a directory containing installed packages the main library is R HOME library but others can be used for example by setting the environment variable R_LIBS or using the R function libPaths 6 1 Default packages The set of packages loaded on startup is by default gt get ption defaultPackages 1 datasets utils grDevices graphics stats methods plus of course base and this can be changed by setting the option in startup code e g in Rprofile It is initially set to the value of the environment variable RB DEFAULT PACKAGES if set as a comma separated list Setting R DEFAULT PACKAGE
28. which brought this to about 380MB or package texinfo and the collections collection fontsrecommended collection fontsextra and collection latexextra which will take this up to about 1GB TeX Live Utility available via the MacTeX front page provides a graphical means to manage TEX packages C 3 1 Snow Leopard A quirk on Snow Leopard is that the X11 libraries are not in the default linking path so something like LIBS L usr X11 lib may be required in config site or you can use the configure options x includes usr X11 include x libraries usr X11 lib The CRAN binaries are built using Xcode 4 2 a version available only to subscribing developers It is believed that 3 2 6 the last public free version for Snow Leopard will work C 3 2 Lion No tweaks are known to be needed on Lion See the notes on Mountain Lion if XQuartz is in use C 3 3 Mountain Lion The X11 system used with Mountain Lion is XQuartz see above To build the graphics devices depending on cairographics the XQuartz path for pkg config files needs to be known to pkg config when configure is run this usually means adding it to the DKG CONFIG PATH environment variable e g export PKG CONFIG PATH opt X11 lib pkgconfig usr local lib pkgconfig usr lib pkgconfig or putting 5 It is reported that for some non Apple toolchains CPPFLAGS needed to contain D__ACCELERATE__ Appendix C Platform notes 60 PKG_CONFIG_PATH opt X11 lib pkgconfig
29. 00 symbols if in doubt use the larger version To compile a profiling version of R one might for example want to use MAIN CFLAGS pg MAIN FFLAGS pg MAIN_LDFLAGS pg on platforms where pg cannot be used with position independent code Beware it may be necessary to set CFLAGS and FFLAGS in ways compatible with the libraries to be used one possible issue is the alignment of doubles another is the way structures are passed On some platforms configure will select additional flags for CFLAGS CPPFLAGS FFLAGS CXXFLAGS and LIBS in R_XTRA_CFLAGS and so on These are for options which are always required for example to force IEC 60559 compliance B 8 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 enable maintainer mode and then running make in the build directory This requires other tools to be installed discussed in the rest of this section File configure is created from configure ac and the files under m4 by autoconf and aclocal There is a formal version requirement on autoconf of 2 62 or later but it is unlikely that anything other than the most recent versions have been thoroughly tested File src include config h is created by autoheader Grammar files y are converted to C sources by an implementation of yacc usually bison y these are found in src main and src library tools src It is known that earlier ver
30. 2 Sources fOr EES i eu bereien cao ep ad andes needed anes 1 38 U User libraries seneiiee re 9 e pem rh EES 22 V KA EE 38 W KEE 14 Environment variable index Environment variable index B BLAS Lis 42 OO OE 50 CONFIG SIE 48 CPP MEME 50 COIN 72 D Damm 8 35 F BOC ee eS MU 50 EOOLIBS ES EEES ETE 50 FPICFLAGS eese ee 50 JAVA HOME esses eee 41 L EANG EE Ee 31 LANGUAGE 0 00 cece cece ees 31 32 BAP ACK LIBS orscncacssscua grace dme vr errtPPa EUR PE 46 EE EE El 31 DC COLLATE EE ii LC MESSAGE 31 LD_LIBRARY_PATH 35 43 50 52 65 LOCAL gr 24 75 O OBJECT ME 68 P PAPERSIZE esee 48 EES 38 50 67 70 R EE 9 R BROWSER sss eee 49 R DEFAULT PACKAGES sss 22 R DISABLE Bin 4 EE A0 R_INSTALL_TAR ee 24 R_JAVA_LD_LIBRARY_PATH 00 41 R LBS TEETH 22 RoE TBS SITE dni then eria GONE Rer ENS 22 RL LpauspR 0000 ee 22 R_PAPERSIZE eee 5 21 48 49 R_PDFVIEWER ise 49 KRIER E 6 49 71 ane 66 R USER eiretie cesera ie e e 21 T TAR Tm 38 TAR OPTIONS cese 1 13 TEMP RR 21 mp 21
31. 64 Linux Brian Ripley used version 9 0 of the compilers for x86_64 on Fedora Core 5 with CC icc CFLAGS g 03 wd188 ip mp F77 ifort FLAGS g 03 mp CXX icpc CXXFLAGS g 03 mp FC ifort FCFLAGS g 03 mp ICC_LIBS opt compilers intel cce 9 1 039 lib IFC_LIBS opt compilers intel fce 9 1 033 lib LDFLAGS L ICC_LIBS L IFC LIBS L usr local lib64 SHLIB CXXLD icpc configure will add c99 to CC for C99 compliance This causes warnings with icc 10 and later so use CC icc std c99 there The flag wd188 suppresses a large number of warnings about the enumeration type Rboolean Because the Intel C compiler sets __GNUC__ without complete emulation of gcc we suggest adding CPPFLAGS no gcc To maintain correct IEC 60559 arithmetic you most likely need add flags to CFLAGS FFLAGS and CXXFLAGS such as mp shown above or fp model precise fp model source depending on the compiler version Others have reported success with versions 10 x and 11 x C 2 3 Oracle Solaris Studio compilers Brian Ripley tested the Sun Studio 12 compilers since renamed to Oracle Solaris Studio http developers sun com sunstudio index jsp On x86 64 Linux with CC suncc CFLAGS x05 xc99 xlibmil nofstore CPICFLAGS Kpic Appendix C Platform notes 57 F77 sunf95 FFLAGS 05 libmil nofstore FPICFLAGS Kpic CXX sunCC library stlport4 CXXFLAGS x05 xlibmil nofstore features tmplrefstatic
32. 77 gfortran 4 2 arch x86_64 0BJC gcc arch x86_64 OBJCXX g arch x86_64 when installing on Mavericks See the comments under Mountain Lion about X11 and GTK C 3 5 Tcl Tk headers and libraries If you plan to use the tcltk package for R you need to install a distribution of Tcl Tk There are two alternatives If you use R APP you will want to use X11 based Tcl Tk as used on other Unix alikes which is installed as part of the CRAN binary for R This may need with tcltk usr local lib or with tcl config usr local lib tclConfig sh with tk config usr local lib tkConfig sh Appendix C Platform notes 61 Note that this expects a fully updated X11 installation There is also a native Aqua version of Tcl Tk which produces widgets in the native OS X style this will not work with R APP because of conflicting event loops but for those only using command line R this provides a much more intuitive interface to T k for experienced Mac users Most versions of OS X come with Aqua Tcl Tk libraries but these are not current versions of Tcl Tk 8 5 9 in Mountain Lion and Mavericks It is better to install Tcl Tk 8 6 x or 8 5 x from the sources or the binary distribution at http www activestate com activetcl downloads Configure R with with tcl config Library Frameworks Tcl framework tclConfig sh with tk config Library Frameworks Tk framework tkConfig sh for the versions bundled with OS X use paths starting with
33. ACK from http www netlib org clapack B 6 1 Using gfortran gfortran is the F95 compiler that is part of gcc 4 x y On Linux x86_64 systems there is an incompatibility in the return conventions for double complex functions between gfortran and g77 which results in the final example in example eigen hanging or segfaulting under external BLASs built under g77 and also some external LAPACKs The commonest cases will be detected by a configure test Although g77 is long obsolete this is still sometimes seen with C versions of external software using g77 conventions The default FFLAGS and FCFLAGS chosen by autoconf for a GNU FORTRAN compiler g 02 This has caused problems segfaults and infinite loops on x86_64 Linux in is On HP UX fort77 is the POSIX compliant FORTRAN compiler and comes after g77 3 as well as its equivalence to the Rcomplex structure defined in R_ext Complex h Appendix B Configuration on a Unix alike 51 the past but seems fine with gfortran 4 4 4 and later for gfortran 4 3 x set FFLAGS and FCFLAGS to use at most 0 B 7 Compile and load flags A wide range of flags can be set in the file config site or as configure variables on the command line We have already mentioned CPPFLAGS header file search directory I and any other miscellaneous options for the C and C preprocessors and compilers LDFLAGS path L stripping s and any other miscellaneous options for the
34. DERMAN_RAMAGE AHRENS_DIETER BOX_MULLER USER_NORM INVERSION KINDERMAN RAMAGE NOitype and USER_NORM is not available 9 1 Unix alikes If R has not already been made in the directory tree configure must be run as described in the main build instructions Then in src nmath standalone l eg Bessel beta and gamma functions Chapter 9 The standalone Rmath library 35 make will make standalone libraries 1ibRmath a and libRmath so libRmath dylib on OS X make static and make shared will create just one of them To use the routines in your own C or C programs include define MATHLIB STANDALONE include lt Rmath h gt and link against 1Rmath and 1m if needed on your OS The example file test c does nothing useful but is provided to test the process via make test Note that you will probably not be able to run it unless you add the directory containing libRmath so to the LD_LIBRARY_PATH environment variable libRmath dylib DYLD_LIBRARY_PATH on OS X The targets make install make uninstall will un install the header Rmath h and shared and static libraries if built Both prefix and DESTDIR are supported together with more precise control as described for the main build make install installs a file for pkg config to use by e g CC pkg config cflags libRmath c test c CC pkg config libs libRmath test o o test On some systems make install
35. FC F77 CPPFLAGS I opt csw include LDFLAGS L opt csw gcc4 lib sparcv9 L opt csw lib sparcv9 Note that paths such as opt csw gcc4 lib sparcv9 may need to be in the Un LIBRARY PATH during configuration The compilation can be tuned to a particular cpu the CRAN check system uses mtune niagara2 Compilation for an x86 target with gcc 4 9 0 needed CC opt csw gcc4 bin gcc m32 CPPFLAGS I opt csw include I usr local include F77 opt csw gcc4 bin gfortran m32 CXX opt csw gcc4 bin g m32 FC opt csw gcc4 bin gfortran m32 LDFLAGS L opt csw gcc4 lib L opt csw lib L usr local lib Appendix C Platform notes 66 L opt csw lib is needed since TeXLive was built using 32 bit gcc and we need opt csw lib in R LD LIBRARY PATH For an amd64 target with gcc 4 9 0 we used CC opt csw gcc4 bin gcc m64 CPPFLAGS I opt csw include I usr local include F77 opt csw gcc4 bin gfortran m64 FPICFLAGS fPIC CXX opt csw gcc4 bin g m64 FC F77 FCPICFLAGS FPICFLAGS LDFLAGS L opt csw gcc4 lib amd64 L opt csw lib amd64 C 5 AIX We no longer support AIX prior to 4 2 and configure will throw an error on such systems Ei ji Nakama was able to build under AIX 5 2 on powerpc with GCC 4 0 3 in sev eral configurations 32 bit versions could be configured with without iconv as well as enable R shlib For 64 bit versions he used OBJECT M DE 64 CC gcc maix64 CXX g mai
36. IS08859 2 75dpi xorg xli fonts Typel xorg xli fonts cyrillic for example X11 font at size 14 could not be loaded Appendix C Platform notes 54 and you need to ensure that the 100dpi versions are installed and on the X11 font path check via xset q The X11O 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 C locale The likely issues are a failure to find any fonts or glyphs being rendered incorrectly often as a pair of ASCII characters X11 works by being asked for a font specification and coming up with its idea of a close match For text as distinct from the symbols used by plotmath the specification is the first element of the option X11fonts which defaults to adobe helvetica As s Jd kk n If you are using a single byte encoding for example ISO 8859 2 in Eastern Europe or KOIS R in Russian use xlsfonts to find an appropriate family of fonts in your encoding the last field in the listing If you find none it is likely that you need to install further font packages such as xorg x11 fonts IS08859 2 75dpi and xorg x11 fonts cyrillic shown in the listing above Mu
37. R bin and 1ibR a without using position independent code However experiments showed that in many cases using a shared BLAS was as fast provided high levels of compiler optimization are used e It is easy to change the BLAS without needing to re install R and all the add on pack ages since all references to the BLAS go through 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 R HOME etc 1dpaths Another option to change the BLAS in use is to symlink a dynamic BLAS library such as ACML or Goto s to R_HOME 1ib 1ibRblas so For example just mv R HOME lib libRblas so R HOME lib libRblas so keep In s opt acm15 1 0 gfortran64 mp lib libacml mp so R HOME lib libRblas so will change the BLAS in use to multithreaded ACML A similar link works for some versions of the Goto BLAS and perhaps for MKL provided the appropriate lib directory is in the run time library path or 1d so cache A 3 2 LAPACK Provision is made for using an external LAPACK library principally to cope with BLAS libraries which contain a copy of LAPACK such as sunperf on Solaris Accelerate on OS X and ACML and MKL on ix86 x86_64 Linux At least LAPACK version 3 2 is required This can only be done if with blas has been used However the likely performance gains are thought to be small and may be negative and the d
38. R Installation and Administration Version 3 1 1 2014 07 10 R Core Team This manual is for R version 3 1 1 2014 07 10 Copyright 2001 2013 R Core Team Permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and this permission notice are preserved on all copies Permission is granted to copy and distribute modified versions of this manual under the conditions for verbatim copying provided that the entire resulting derived work is distributed under the terms of a permission notice identical to this one Permission is granted to copy and distribute translations of this manual into another language under the above conditions for modified versions except that this permission notice may be stated in a translation approved by the R Core Team Table of Contents MES conl T 1 1 1 Getting and unpacking the source 1 1 2 Getting patched and development vergaang 1 1 2 1 Using Subversion and ravmnc 2 cece eee eee 1 2 Installing R under Unix alikes 3 2 1 Simple compilation eens 3 2 2 Help Options ie Re Ee FERE EReXS les o s pan EELLERRERN uA 4 2 3 Making the manual 4 2 4 Installationcz uer ERE wets rt dae baba karen pa 6 2 5 UninstallatiOm zi eec casa gteee n er ERR MERECE pee 8 2 6 SBub architectures 0 ccc eee eee eee nent eee eeee 9 2 6 1 Mult libz ccce eere eto aed ee epe d aaa es 9 2 1 Other
39. S NULL ensures that only package base is loaded Changing the set of default packages is normally used to reduce the set for speed when scripting in particular not using methods will reduce the start up time by a factor of up to two and this is done by Rscript But it can also be used to customize R e g for class use 6 2 Managing libraries R packages are installed into libraries which are directories in the file system containing a subdirectory for each package installed there R comes with a single library R_HOME library which is the value of the R object Library containing the standard and recommended packages Both sites and users can create others and make use of them or not in an R session At the lowest level libPaths can be used to add paths to the collection of libraries or to report the cur rent collection R will automatically make use of a site specific library R_HOME site library if this exists it does not in a vanilla R installation This location can be overridden by setting Library site in R HOME etc Rprofile site or not recommended by setting the environment variable RB LIBS SITE Like Library the site libraries are always included by 1ibPaths Users can have one or more libraries normally specified by the environment variable R_ LIBS USER This has a default value to see it use Sys getenv R LIBS USER within an R session but that is only used if the corresponding directo
40. Y PATH For other compilers see the ACML documentation There is a multi threaded Linux version of ACML available for recent versions of gfortran To make use of this you will need something like with blas L opt acml15 1 0 gfortran64 mp lib lacml mp and you may need to arrange for the directory to be in 1d so cache See see Section A 3 1 5 Shared BLAS page 45 for an alternative and in many ways preferable way to use ACML The version last tested 5 1 0 failed the reg BLAS R test in its handling of NAs A 3 1 3 Goto and OpenBLAS Dr Kazushige Goto wrote another tuned BLAS which is available for several processors and OSes The final version is known as GotoBLAS2 and was re released under a much less restrictive licence Source code can be obtained from http www tacc utexas edu tacc projects gotoblas2 Once it is built and installed it can be used by configuring R with with blas lgoto2 See see Section A 3 1 5 Shared BLAS page 45 for an alternative and in many ways preferable way to use it Our understanding is that this project is now frozen and so will not be updated for CPUs released since mid 2010 However OpenBLAS http xianyi github com penBLAS is a descendant project with support for some current CPUs e g Intel Sandy Bridge and AMD Bulldozer A 3 1 4 Intel MKL For Intel processors and perhaps others and some distributions of Linux there is Intel s Math Kernel Library http www intel com so
41. Your PATH may include first then the bin directories of the tools the compiler toolchain and ATEX Do not use filepaths containing spaces you can always use the short forms found by dir x at the Windows command line Network shares with paths starting NX are not supported For example for a 32 bit build all on one line 1 For example the Cygwin version of make 3 81 fails to work correctly for R 3 0 0 and later Appendix D The Windows toolset 71 PATH c Rtools bin c Rtools gcc 4 6 3 bin c MikTeX miktex bin c R R 3 1 bin i386 c windows c windows system32 It is essential that the directory containing the command line tools comes first or second in the path there are typically like named tools in other directories and they will not work The ordering of the other directories is less important but if in doubt use the order above Our toolset contains copies of Cygwin DLLs that may conflict with other ones on your system if both are in the path at once The normal recommendation is to delete the older ones however at one time we found our tools did not work with a newer version of the Cygwin DLLs so it may be safest not to have any other version of the Cygwin DLLs in your path DI BIFX The MiKTeX http www miktex org distribution of IATEX includes a suitable port of pdftex This can be set up to install extra packages on the fly which is the simplest way to use it and the default The basic ve
42. age has an executable configure script or a src Makefile file In such cases you can install for extra builds by R arch name CMD INSTALL libs only pkg1 pkg2 If you want to mix sub architectures compiled on different platforms for example x86_64 Linux and i686 Linux it is wise to use explicit names for each and you may also need to set libdir to ensure that they install into the same place When sub architectures are used the version of Rscript in e g usr bin will be the last installed but architecture specific versions will be available in e g usr lib64 R bin exec R ARCH Normally all installed architectures will run on the platform so the architecture of Rscript itself does not matter The executable Rscript will run the R script and at that time the setting of the RB ARCH environment variable determines the architecture which is run When running post install tests with sub architectures use R arch name CMD make check devellall to select a sub architecture to check Sub architectures are also used on Windows but by selecting executables within the ap propriate bin directory R HOME bin i386 or R HOME bin x64 For backwards compatibil ity with R lt 2 12 0 there are executables R_HOME bin R exe or R H ME bin Rscript exe these will run an executable from one of the subdirectories which one being taken first from the R_ARCH environment variable then from the arch command line option and finally from
43. alty and has not been tested recently e You can run a parallel make by e g make j4 all make j4 recommended but this is only likely to be worthwhile on a multi core machine with ample memory and is not 10096 reliable e It is possible mainly for those working on R itself to set the make or environment variable BR NO BASE COMPILE to a non empty value which inhibits the byte compilation of the base and recommended packages 3 1 4 Building the bitmap files The file RLHOME library grDevices libs i386 x64 Rbitmap d11 is not built automat ically Running make in R HOME src gnuwin32 bitmap or make bitmapdll in R HOME src gnuwin32 should build Rbitmap dll and install it under RR HOME library grDevices libs 3 1 5 Building the cairo devices The devices based on cairographics svg cairo pdf cairo ps and the type cairo versions of png jpeg tiff and bmp are implemented in a separate DLL winCairo dll which is loaded when one of these devices is first used It is not built by default and needs to be built after Rbitmap dll by make cairodevices To enable the building of these devices you need to install the static cairographics libraries built by Simon Urbanek at http www rforge net Cairo files cairo current win tar gz Set the macro CAIRO_HOME in MkRules local Note that this tarball unpacks with a top level directory src CAIRO_HOME needs to include that directory in its path 3 1 5 1 Usin
44. an pdf or refman pdf The help files contain both ISO Latinl characters e g in text Rd and upright quotes neither of which are contained in the standard ATEX Computer Modern fonts We have provided four alternatives times The default Using standard PostScript fonts Times Roman Helvetica and Courier This works well both for on screen viewing and for printing One dis advantage is that the Usage and Examples sections may come out rather wide this can be overcome by using in addition either of the options inconsolata on a Unix alike only if found by configure or beramono which replace the Courier monospaced font by Inconsolata or Bera Sans mono respectively You will need a recent version of the appropriate IMTEX package inconsolata or bera installed inconsolata is likely to require upquote Note that in most IXTEX installations this will not actually use the standard fonts for PDF but rather embed the URW clones NimbusRom NimbusSans and for Courier if used NimbusMon This needs TFX packages times helvetic and if used courier installed 1m Using the Latin Modern fonts These are not often installed as part of a TEX distribution but can obtained from http www ctan org tex archive Instructions on how to install the latest version are at http www ctan org tex archive fonts inconsolata Chapter 2 Installing R under Unix alikes 6 fonts ps type1 1m and mirrors This uses fonts rather similar to Computer Mo
45. ater installed and if not some of the HTML manuals will be linked to CRAN To make PDF versions of the manuals you will also need file texinfo tex installed which is part of the GNU texinfo distribution but is often made part of the TEX package in re distributions as well as texi2dvi Further the versions of texi2dvi and texinfo tex need to be compatible we have seen problems with older TEX distributions TeXLive 2007 and MiK TeX 2 8 used with texinfo 4 13 It is possible to use texinfo version 5 x preferably 5 2 or later The PDF documentation including doc NEWS pdf and building vignettes needs pdftex and pdflatex We require ATX version 2005 12 01 or later for UTF 8 support Building PDF package manuals including the R reference manual and vignettes is sensitive to the version of the TFX package hyperref and we recommend that the TEX distribution used is kept up to date A number of standard LATEX packages are required including fancyvrb url and some of the font packages such as times helvetic ec and cm super and others such as hyperref and inconsolata are desirable and without them you may need to change R s defaults see Section 2 3 Making the manuals page 4 Note that most versions of inconsolata require package upquote and that hyperref currently requires packages kvoptions ltxcmds and refcount For distributions based on TeXLive the simplest approach may be to install collections collection latex collection fontsrecomm
46. ble of contents to be hyperlinked use ifthenelse boolean Rd use hyper hypersetup linktoc section or ifthenelse boolean RdG use hyper hypersetup linktoc all to hyperlink both text and page number Ebook versions in one or both of epub and mobi formats can be made by running in doc manual one of make ebooks make epub make mobi This requires ebook convert from Calibre http calibre ebook com download or from most Linux distributions If necessary the path to ebook convert can be set as make macro EBOOK to by editing doc manual Makefile which contains a commented value suitable for OS X 2 4 Installation To ensure that the installed tree is usable by the right group of users set umask appropriately perhaps to 022 before unpacking the sources and throughout the build process After 5 on a Unix alike inconsolata is omitted if not found by configure D The linktoc settings require hyperref version 6 78f or newer with older versions of hyperref use linktocpage false to hyperlink the text Chapter 2 Installing R under Unix alikes T configure make make check or when building outside the source TOP_SRCDIR configure etc have been completed successfully you can install the complete R tree to your system by typing make install A parallel make can be used but run make before make install This will install to the following directories prefix bin or bindir the front en
47. btain copies of the recommended packages from CRAN Put the tar gz files in R HOME src library Recommended and run make link recommended If you have an Internet connection you can do this automatically by running in R_HOME src gnuwin32 make rsync recommended The following additional items are normally installed by Rtools31 exe If instead you choose to do completely manual build you will also need e The Tcl Tk support files are contained in Rtools31 exe and available as zip files from http www stats ox ac uk pub Rtools Please make sure you install the right version there is a 32 bit version and a 64 bit version They should be installed to R HOME creating directory Tcl there e You need libpng jpeg and libtiff sources available e g from http www libpng org http www ijg org and http download osgeo org libtiff current versions are recommended and jpeg 7 or later is required It is also possible to use libjpeg turbo from http sourceforge net projects libjpeg turbo files Working in the directory R HOME src gnuwin32 bitmap install the libpng and jpeg sources in sub directories The jpeg sub directory for version 9 is named jpeg 9 if you use a different version e g jpeg 9a or libjpeg turbo copy file src gnuwin32 MkRules dist to src gnuwin32 MkRules local and edit the definition of JPEGDIR the names of the libpng and libtiff directories can also be set there Example gt tar zxf libpng 1 6
48. character abbreviation following ISO 3166 see e g http en wikipedia org wiki ISO_3166 e 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 e 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 Glatin cyrillic for Serbian iqtelif or language dialect e g saaho a dialect of Afar and bokmal and nynorsk dialects of Norwegian regarded by some OSes as separate languages no and nn R is principally concerned with the first for translations and third Note that the charset may be deducible from the language as some OSes offer only one charset per language 7 1 1 Locales under Unix alikes Modern Linux uses the XPG locale specifications which have the form en_GB en_GB UTF 8 aa_ER UTF 8 saaho de_AT iso885915 euro the components being in the order listed above See man locale and locale a for more details Similar schemes are used by most Unix alikes some including some distributions of Linux use utf8 rather than UTF 8 1 X Open Portability Guide which has had several versions Chapter 7 Internationalization and Localiza
49. ckages is available directly from the AIX Installation DVDs e g Java 6 X11 and Perl Additional open source software OSS is packaged for AIX in rpm files and available from both IBM s AIX Toolbox for Linux Applications http www 03 ibm com systems power software aix linux and http www oss4aix org download The latter website typically offers more recent versions of the available OSS All tools needed and libraries downloaded from these repositories e g GCC Make libreadline etc are typically installed to opt freeware hence corresponding executables are found in opt freeware bin which thus needs to be in PATH for using these tools As on other Unix systems one needs GNU libiconv as the AIX version of iconv is not sufficiently powerful Additionally for proper Unicode compatibility one should install the corresponding package from the ICU project http www icu project org download which offers pre compiled binaries for various platforms which in case of AIX can be installed via unpacking the tarball to the root file system For full IXTEX support one can install the TEX Live DVD distribution http www tug org texlive it is recommended to update the distribution using the tlmgr update manager For 64 bit R builds supporting Tcl Tk this needs to installed from the sources as available pre compiled binaries supply only 32 bit shared objects The recent WU testing was done using compilers from both the GNU Compile
50. ctions are essential and others will be used if available also known as IEEE 754 Note that C11 compilers need not be C99 compliant R requires support for double complex and variable length arrays which are optional in C11 but is mandatory in C99 HM e KI std c99 excludes POSIX functionality but config h will turn on all GNU extensions to include the POSIX functionality specifically the C99 functionality of headers wchar h and wctype h types wctans t and mbstate_t and functions mbrtowc mbstowcs wcrtomb wcscoll wcstombs wctrans wctype and iswctype A ao including the opendir readdir closedir popen stat glob access getcwd and chdir system calls and either putenv or setenv such as realpath symlink Appendix A Essential and useful other programs under a Unix alike 38 A tar program is needed to unpack the sources and packages including the recom mended packages A version that can automagically detect compressed archives is pre ferred for use with untar the configure script looks for gtar and gnutar before tar use environment variable TAR to override this There need to be suitable versions of the tools grep and sed the problems are usually with old AT amp T and BSD variants configure will try to find suitable versions including looking in usr xpg4 bin which is used on some commercial Unixes You will not be able to build most of the manuals unless you have makeinfo version 4 7 or l
51. d it is assumed to be UTF 8 7 2 Localization of messages The preferred language for messages is by default taken from the locale This can be overridden first by the setting of the environment variable LANGUAGE and then by the environment variables LC_ALL LC_MESSAGES and LANG The last three are normally used to set the locale and so should not be needed but the first is only used to select the language for messages The code tries hard to map locales to languages but on some systems notably Windows the locale names needed for the environment variable LC_ALL do not all correspond to XPG language names and so LANGUAGE may need to be set One example is LC_ALL es on Windows which sets the locale to Estonian and the language to Spanish It is usually possible to change the language once R is running via not Windows Sys setlocale LC MESSAGES new locale or by setting an environment variable such as LANGUAGE provided the language you are changing to can be output in the current character set But this is OS specific and has been known to stop working on an OS upgrade Messages are divided into domains and translations may be available for some or all messages in a domain R makes use of the following domains e Domain R for the C level error and warning messages from the R interpreter 2 On some systems setting LC ALL or LC MESSAGES to C disables LANGUAGE 3 If you try changing from French to Russian except in
52. d shell script and other scripts and executables prefix man mani or mandir mani the man page prefix LIBnn R or libdir R all the rest libraries on line help system Here LIBnn is usually lib but may be 1ib64 on some 64 bit Linux systems This is known as the R home directory where prefix is determined during configuration typically usr 1ocal and can be set by running configure with the option prefix as in configure prefix where you want R to go This causes make install to install the R script to where you want R to go bin and so on The prefix of the installation directories can be seen in the status message that is displayed at the end of configure You can install into another directory tree by using make prefix path to here install at least with GNU make and current Solaris and FreeBSD make but not some older Unix makes More precise control is available at configure time via options see configure help for details However most of the Fine tuning of the installation directories options are not used by R Configure options bindir and mandir are supported and govern where a copy of the R script and the man page are installed The configure option libdir controls where the main R files are installed the default is eprefix LIBnn where eprefix is the prefix used for installing architecture dependent files defaults to prefix and can be set via the configure option exec
53. d with additional architectures by R arch arch CMD check 1 libdir extra arch install check pkg log pkg where extra arch selects only those checks which depend on the installed code and not those which analyse the sources If multiple sub architectures fail only because they need different settings e g environment variables no multiarch may need to be added to the INSTALL lines On Unix alikes the architecture to run is selected by arch this can also be used on Windows with R_HOME bin R exe but it is more usual to select the path to the Rcmd exe of the desired architecture So on Windows to install check and package for distribution a source package from a tarball which has been tested on another platform one might use bin i386 Rcmd INSTALL 1 libdir tarball build gt pkg log 2 gt amp 1 bin i386 Rcmd check 1 libdir extra arch install check pkg log pkg bin x64 Rcemd check 1 libdir extra arch install check pkg log pkg where one might want to run the second and third lines in a different shell with different settings for environment variables and the path to find external software notably for Gtk R CMD INSTALL can do a i386 install and then add the x64 DLL from a single command by R CMD INSTALL merge multiarch 1 libdir tarball and build can be added to zip up the installation Chapter 7 Internationalization and Localization 30 7 Internationalization and Localization Internationalization
54. d zlib which might be linked against Fortunately these are normally built as shared libraries with the exception of the ATLAS BLAS libraries The default optimization settings chosen for CFLAGS etc are conservative It is likely that using mtune will result in significant performance improvements on recent CPUs especially for ix86 one possibility is to add mtune native for the best possible performance on the machine on which R is being installed if the compilation is for a site wide installation it may still be desirable to use something like mtume core2 It is also possible to increase the optimization levels to 03 however for many versions of the compilers this has caused problems in at least one CRAN package For platforms with both 64 and 32 bit support it is likely that LDFLAGS L usr local lib64 L usr local lib is appropriate since most but not all software installs its 64 bit libraries in usr local lib64 To build a 32 bit version of R on x86_64 with Fedora 18 we used CC gcc m32 CXX g m32 F77 gfortran m32 FC F77 OBJC CC LDFLAGS L usr local lib LIBnn lib Note the use of LIBnn x86_64 Fedora installs its 64 bit software in usr 1ib64 and 32 bit software in usr lib Linking will skip over inappropriate binaries but for example the 32 bit Tcl Tk configure scripts are in usr lib It may also be necessary to set the pkg config path e g by export PKG_CONFIG_PATH usr
55. dern but is not so good on screen as times cm super Using type 1 versions of the Computer Modern fonts by Vladimir Volovich This is a large installation obtainable from http www ctan org tex archive fonts ps typei cm super and its mirrors These type 1 fonts have poor hinting and so are nowhere near as readable on screen as the other three options ae A package to use composites of Computer Modern fonts This works well most of the time and its PDF is more readable on screen than the previous two op tions There are three fonts for which it will need to use bitmapped fonts tctt0900 600pk tctt1000 600pk and tcrmi1000 600pk Unfortunately if those files are not available Acrobat Reader will substitute completely incorrect glyphs so you need to examine the logs carefully The default can be overridden by setting the environment variable RLRD4PDF On Unix alikes this will be picked up at install time and stored in etc Renviron but can still be overridden when the manuals are built using make e The usual default value for R RDAPDF is times inconsolata hyper omit hyper if you do not want hyperlinks e g for printing the manual or do not have IATEX package hyperref and omit inconsolata if you do not have IXTEX package inconsolata installed Further options e g for hyperref can be included in a file Rd cfg somewhere on your IXTEX search path For example if you prefer the text and not the page number in the ta
56. dline and perhaps tiff pkg config is not provided by Apple and useful for many packages it will also be used if present when configuring the X110 device 4 This is a tarball which needs to be unpacked in the Terminal by e g sudo tar zxf gfortran 4 8 2 darwini3 tar bz2 C Appendix C Platform notes 59 The Accelerate library can be used via the configuration options with blas framework Accelerate with lapack to provide potentially higher performance versions of the BLAS and LAPACK routines Use of Accelerate with with lapack does not work on Snow Leopard it may work there without Looking at the top of Library Frameworks R framework Resources etc Makeconf will show the compilers and configuration options used for the CRAN binary package for R at the time of writing with system zlib enable memory profiling disable openmp was used for Snow Leopard and the first two for Mavericks Configure option with internal tzcode is the default as a 64 bit time t is available but the system implementation of time zones does not work correctly for times before 1902 or after 2037 The TEX implementation used by the developers is MacTeX http www tug org mactex the full installation is about 4GB but a smaller version is available at http www tug org mactex morepackages html you will need to add some packages e g for the 2014 version we needed to add cm super ec helvetic inconsolata and texinfo
57. e If you encounter any problem during the installation please check the Installer log by clicking on the Window menu and item Installer Log The full output select Show All Log is useful for tracking down problems If you update your OS X version you should re install R the installer tailors the instal lation to the current version of the OS For building R from source see Section C 3 OS X page 57 4 1 Running R under OS X There are two ways to run R on OS X from a CRAN binary distribution There is a GUI console normally installed with the R icon in Applications which you can run by double clicking e g from Launchpad or Finder This is usually referred to as R APP to distinguish it from command line R its user manual is currently part of the OS X FAQ at http cran r project org bin macosx RMacOSX FAQ html and can be viewed from R APP s Help menu You can run command line R from a Terminal like any other Unix alike see the next chapter of this manual There are some small differences which may surprise users of R on other platforms notably the default personal library directory under Library R e g Library R 3 1 library and that warnings messages and other output to stderr are highlighted in bold Users of R APP under Mavericks need to be aware of its App Nap feature https developer apple com library mac releasenotes MacO0SX WhatsNewInO0SX Articles MacOSX10_9 htm1 which can cause R ta
58. e MinGW w64 project http sourceforge net projects mingw w64 but commercial compilers such as those from Intel and PGI could be used and have been by R redistributors Support for MinGW w64 was developed in the R sources over the period 2008 10 and was first released as part of R 2 11 0 The assistance of Yu Gong at a crucial step in porting Chapter 3 Installing R under Windows 18 R to MinGW w64 is gratefully acknowledged as well as help from Kai Tietz the lead developer of the MinGW w64 project Windows 64 bit is now completely integrated into the R and package build systems 3 2 Testing an Installation The Windows installer contains a set of test files used when building R The Rtools are not needed to run these tests but more comprehensive analysis of errors will be given if diff is in the path and errorsAreFatal FALSE is then not needed below Launch either Rgui or Rterm preferably with vanilla Then run Sys setenv LC COLLATE C LANGUAGE en library tools testInstalledBasic both testInstalledPackages scope base errorsAreFatal FALSE testInstalledPackages scope recommended errorsAreFatal FALSE runs the basic tests and then all the tests on the standard and recommended packages These tests can be run from anywhere they write some of their results in the tests folder of the R home directory as given by R home O and hence may need to be run under the account used to install R
59. ectory in MkRules 1local You need to have the files for a complete R build including bitmap and Tcl Tk support and the manuals as well as the recommended packages There is no option in the installer to customize startup options so edit etc Rconsole and etc Rprofile site to set these as required Then cd installer make msi which will result in a file with a name like R 3 1 1 win32 msi This can be double clicked to be installed but those who need it will know what to do with it usually by running msiexec i with additional options Properties that users might want to set from the msiexec command line include ALLUSERS INSTALLDIR something like c Program Files R R 3 1 1 and RMENU the path to the R folder on the start menu and STARTDIR the starting directory for R shortcuts defaulting to something like c Users name Documents R The MSI installer can be built both from a 32 bit build of R R 3 1 1 win32 msi and from a 64 bit build of R R 3 1 1 win64 msi optionally including 32 bit files by setting the macro HOME32 when the name is R 3 1 1 win msi Unlike the main installer a 64 bit MSI installer can only be run on 64 bit Windows Thanks to David del Campo Dept of Statistics University of Oxford for suggesting WiX and building a prototype installer 3 1 10 64 bit Windows builds To build a 64 bit version of R you need a 64 bit toolchain the only one discussed here is based on the work of th
60. efault is not to search for a suitable LAPACK library and this is definitely not recommended You can specify a specific LAPACK library or a search for a generic library by the configuration option with lapack The default for with lapack is to check the BLAS library and then look for an external library 1lapack Sites searching for the fastest Appendix A Essential and useful other programs under a Unix alike 46 possible linear algebra may want to build a LAPACK library using the ATLAS optimized subset of LAPACK To do so specify something like with lapack L path to ATLAS libs llapack lcblas since the ATLAS subset of LAPACK depends on libcblas A value for with lapack can be set via the environment variable LAPACK_LIBS but this will only be used if with lapack is specified as the default value is no and the BLAS library does not contain LAPACK Since ACML contains a full LAPACK if selected as the BLAS it can be used as the LAPACK via with lapack If you do use with lapack be aware of potential problems with bugs in the LAPACK sources or in the posted corrections to those sources In particular bugs in DGEEV and DGESDD have resulted in error messages such as DGEBRD gave error code 10 Other potential problems are incomplete versions of the libraries seen several times in Linux distributions over the years Please do bear in mind that using with lapack is definitely not recommended it is provided o
61. en reported to be a problem on HP UX with the native cc In this case use a different compiler or a front end shell script which does the re ordering These flags can also be used to build a faster running version of R On most platforms using gcc having 03 in CFLAGS and FFLAGS produces worthwhile performance gains with gcc and gfortran but may result in a less reliable build both segfaults and incorrect numeric computations have been seen On systems using the GNU linker especially those using R as a shared library it is likely that including W1 01 in LDFLAGS is worthwhile and Bdirect hash style both W1 01 is recommended at http 1wn net Articles 192624 Tuning compilation to a specific CPU family e g mtune native for gcc can give worthwhile performance gains especially on older architectures such as 1x86 B 3 4 Making manuals The default settings for making the manuals are controlled by RB RDAPDF and R_PAPERSIZE B 4 Setting the shell By default the shell scripts such as R will be bin sh scripts or using the SHELL chosen by configure This is almost always satisfactory but on a few systems bin sh is not a Bourne shell or clone and the shell to be used can be changed by setting the configure variable R SHELL to a suitable value a full path to a shell e g usr local bin bash B 5 Using make To compile R you will most likely find it easiest to use GNU make although the Su
62. ended collection latexrecommended collection fontsextra and collection latexextra assuming they are not installed by default Fedora uses names like texlive collection fontsextra and Debian Ubuntu like texlive fonts extra If you want to build from the R Subversion repository you need both makeinfo and pdflatex The essential programs should be in your PATH at the time configure is run this will capture the full paths A 2 Useful libraries and programs The ability to use translated messages makes use of gettext and most likely needs GNU gettext you do need this to work with new translations but otherwise the version con tained in the R sources will be used if no suitable external gettext is found The modern version of the X110 jpegQ pngO and tiff graphics devices uses the cairo and optionally Pango libraries Cairo version 1 2 0 or later is required Pango needs T Such as GNU tar 1 15 or later bsdtar from http code google com p libarchive as used by FreeBSD and OS 10 6 and later or tar from the Heirloom Toolchest http heirloom sourceforge net tools html texi2dvi is normally a shell script Some versions e g that from texinfo 4 13a and 5 2 need to be run under bash rather than a Bourne shell as on say Solaris 8 Appendix A Essential and useful other programs under a Unix alike 39 to be at least version 1 10 and 1 12 is the earliest version we have tested For Fedora users we believe the pan
63. ents are met note that the installer will state that the contents are distributed under GPL 2 and this has a requirement for you to supply the complete sources including the R sources even if you started with a binary distribution of R and also the sources of any extra packages including their external software which are included The defaults for the startup parameters may also be customized For example Chapter 3 Installing R under Windows 17 make myR IMAGEDIR rootdir MDISDI 1 will create an installer that defaults to installing R to run in SDI mode See src gnuvin32 installer Makefile for the names and values that can be set The standard CRAN distribution of a 32 64 bit installer is made by first building 32 bit R just make 32 bit is needed and then building 64 bit R with the macro HOME32 set in file MkRules local to the top level directory of the 32 bit build Then the make rinstaller step copies the files that differ between architectures from the 32 bit build as it builds the installer image 3 1 9 Building the MSI installer It is also possible to build an installer for use with Microsoft Installer This is intended for use by sysadmins doing automated installs and is not recommended for casual use It makes use of the Windows Installer XML WiX toolkit version 3 5 or perhaps later untested available from http wix sourceforge net or http wixtoolset org Once WiX is installed set the path to its home dir
64. equisite links in src library Recommended A suitable incantation from the top level of the R sources using wget might be for the correct value of dir wget r 11 no parent A gz nd P src library Recommended http CRAN R project org src contrib dir tools link recommended for some Subversion clients http may appear to work but requires continual redirection Chapter 2 Installing R under Unix alikes 3 2 Installing R under Unix alikes R will configure and build under most common Unix and Unix alike platforms including cpu linux gnu for the alpha arm hppa 1x86 ia64 m68k mips mipsel powerpc s390 sparc and x86_64 CPUs x86_64 apple darwin i386 sun solaris and sparc sun solaris as well as perhaps it is tested less frequently on these platforms i386 apple darwin i386 freebsd x86_64 freebsd i386 netbsd i386 openbsd and powerpc ibm aix6 In addition binary distributions are available for some common Linux distributions and for OS X formerly Mac OS See the FAQ for current details These are installed in platform specific ways so for the rest of this chapter we consider only building from the sources 2 1 Simple compilation First review the essential and useful tools and libraries in Appendix A Essential and useful other programs under a Unix alike page 37 and ins
65. er you do need a 64 bit version of Windows to build 64 bit R as the build process runs R To select a 32 bit or 64 bit build of R set the options in MkRules local appropriately following the comments in the file Some external software libraries will need to be re compiled under the new toolchain especially those providing a C interface Many of those used by CRAN packages are available from http www stats ox ac uk pub Rtools multilib Users developing packages with Rcpp need to ensure that they use a version built with exactly the same toolchain as their package the recommendation is to build Rcpp from its sources yourself There is support for OpenMP and pthreads in this toolchain As the performance of OpenMP on Windows is poor for small tasks it is not used for R itself D 5 Useful additional programs The process of making the installer will make use of qpdf to compact some of the pack age vignettes if it is available Windows binaries of qpdf are available from http sourceforge net projects qpdf files Set the path to the qpdf installation in file MkRules local Developers of packages will find some of the goodies at http www stats ox ac uk pub Rtools goodies useful There is a version of the file command that identifies the type of files and is used by Rcmd check if available The binary distribution is included in Rtools30 exe The file xzutils zip contains the program xz which can be used to de compres
66. erge separate 32 and 64 bit installs This can only be applied to a tarball and will only succeed if both installs succeed If you have a package without compiled code and no Windows specific help you can zip up an installation on another OS and install from the that zip file on Windows However such a package can be installed from the sources on Windows without any additional tools There is provision to make use of a system wide library of installed external software by setting the make variable LOCAL SUFT to give an equivalent of usr local on a Unix alike for a small number of CRAN packages where this is known to be safe and is needed by the autobuilder this is the default Look at the source of too1s install packages for the list It can also be specified in the package s DESCRIPTION file Chapter 6 Add on packages 25 This can be set in src gnuwin MkRules local when R is built from sources see the com ments in src gnuwin MkRules dist or in file etc i386 Makeconf or etc x64 Makeconf for an installed version of R The version used by CRAN can be downloaded from http www stats ox ac uk pub Rtools libs html 6 3 2 OS X On OS X install packages works as it does on other Unix alike systems but there is an additional type mac binary the default in the CRAN distribution but not when compiling from source mac binary mavericks for a Mavericks only build which can be passed to install packages in order to download and
67. es in base packages only needed if building from an svn checkout manuals the PDF manuals rinstaller the install program crandir the CRAN distribution directory only for 64 bit builds The parts can be made individually if a full build is not needed but earlier parts must be built before later ones The Makefile doesn t enforce this dependency some build targets force a lot of computation even if all files are up to date The first four targets are the default build if just make or make a11 is run Parallel make is not supported and likely to fail If you want to customize the installation by adding extra packages replace make rinstaller by something like make rinstaller EXTRA PKGS pkgi1 pkg2 pkg3 An alternative way to customize the installer starting with a binary distribution is to first make an installation of R from the standard installer then add packages and make other customizations to that installation Then after having customized file MkRules possibly via MkRules local and having made R in the source tree in src gnuwin32 installer run make myR IMAGEDIR rootdir where rootdir is the path to the root of the customized installation in double quotes if it contains spaces or backslashes Both methods create an executable with a standard name such as R 3 1 1 win exe so please rename it to indicate that it is customized If you intend to distribute a customized installer please do check that license requirem
68. est results An installed shared static 1ibR can be uninstalled by make prefix path to here uninstall libR 7 This will be needed if more than one sub architecture is to be installed Chapter 2 Installing R under Unix alikes 9 2 6 Sub architectures Some platforms can support closely related builds of R which can share all but the executa bles and dynamic objects Examples include builds under Linux and Solaris for different CPUs or 32 and 64 bit builds R supports the idea of architecture specific builds specified by adding r_arch name to the configure line Here name can be anything non empty and is used to name subdi rectories of lib etc include and the package libs subdirectories Example names from other software are the use of sparcv9 on Sparc Solaris and 32 by gcc on x86_64 Linux If you have two or more such builds you can install them over each other and for 32 64 bit builds on one architecture one build can be done without r arch The space savings can be considerable on x86_64 Linux a basic install without debugging symbols took 63Mb and adding a 32 bit build added 6Mb If you have installed multiple builds you can select which build to run by R arch name and just running R will run the last build that was installed R CMD INSTALL will detect if more than one build is installed and try to install packages with the appropriate library objects for each This will not be done if the pack
69. f which need be installed You can use pkgutil unlink not supported by Lion or later to remove their files or pkgutil forget if you want the Apple Installer to forget about the package without deleting its files useful for the R framework when installing multiple R versions in parallel or after you have deleted the files Uninstalling the Tcl Tk component which is installed under usr 1ocal is not simple You can list the files it installed in a Terminal by pkgutil files org r project x86 64 tcltk x11 These are paths relative to the root of the file system 4 3 Multiple versions The installer will remove any previous version of the R framework which it finds installed This can be avoided by using pkgutil forget see the previous section However note that different versions are installed under Library Frameworks R framework Versions as 3 0 3 1 and so on so it is not possible to have different 3 x y versions installed for the same x A version of R can be run directly from the command line as e g Library Frameworks R framework Versions 3 1 Resources bin R However R APP will always run the current version that is the last installed version A small utility Rswitch app available at http r research att com Hother can be used to change the current version However this is of limited use as R APP is compiled against a particular version of R and will likely crash if switched to an earlier
70. ftware products mkl You are strongly encouraged to read the MKL User s Guide which is installed with the library before attempting to link to MKL There are also versions of MKL for OS X and Windows but they did not work with the standard compilers used for R on those platforms Appendix A Essential and useful other programs under a Unix alike 44 The MKL interface has changed several times and may change again the following notes apply exactly only to version 10 3 but have been used with version 11 1 Versions 10 and later of MKL support two linking models the default model which is backward compatible with version 9 see below and the layered model The layered model gives the user fine grained control over four different library layers interface threading computation and run time library support Some examples of linking to MKL using this layered model are given below These examples are for GCC compilers on x86_64 The choice of interface layer is important on x86_64 since the Intel Fortran compiler returns complex values in different registers from the GNU Fortran compiler You must therefore use the interface layer that matches your compiler mkl_intel or mkl_gf R can be linked to a sequential version of MKL by something like MKL LIB PATH opt intel mkl 10 311 339 lib intel64 export LD LIBRARY PATH MKL LIB PATH MKL L MKL LIB PATH 1mkl gf lp64 1mkl sequential lmkl core configure with blas
71. g ICU for collation It is possible and even recommended to build R to use ICU International Components for Unicode http site icu project org for collation as is commonly done on Unix alikes Chapter 3 Installing R under Windows 15 Two settings are needed in MkRules 1local set to use ICU USE_ICU YES path to parent of ICU headers ICU_PATH path to ICU The first should be uncommented and the second set to the top level directory of a suitably packaged binary build of ICU for example that at http www stats ox ac uk pub Rtools goodies ICU 531 zip Depending on the build it may be necessary to edit the macro ICU_LIBS 3 1 6 Checking the build You can test a build by running make check The recommended packages can be checked by make check recommended Other levels of checking are make check devel for a more thorough check of the R functionality and make check all for check devel and check recommended If a test fails there will almost always be a Rout fail file in the directory being checked often tests Examples or tests examine the file to help pinpoint the problem Parallel checking of package sources part of make check devel and make check recommended is possible see the environment variable TEST_MC_CORES to the maximum number of processes to be run in parallel 3 1 7 Building the manuals The PDF manuals can be made by make manuals If you want to make the info versions not including the Refe
72. go devel RPM and its dependencies suffice R checks for pkg config and uses that to check first that the pangocairo package is installed and if not cairo and if additional flags are needed for the cairo xlib package then if suitable code can be compiled These tests will fail if pkg config is not installed and are likely to fail if cairo was built statically unusual Most systems with Gtk 2 8 or later installed will have suitable libraries OS X comes with none of these libraries but XQuartz as used for 10 8 and later ships cairo but cairo support without Pango has been added to the binary distribution see http r research att com libs you need fontconfig freetype and pixman too pkg config is still needed when building R from source and can be installed from its sources For the best font experience with these devices you need suitable fonts installed Linux users will want the urw fonts package On platforms which have it available the msttcorefonts package provides TrueType versions of Monotype fonts such as Arial and Times New Roman Another useful set of fonts is the liberation TrueType fonts available at https fedorahosted org liberation fonts which cover the Latin Greek and Cyrillic alphabets plus a fair range of signs These share metrics with Arial Times New Roman and Courier New and contain fonts rather similar to the first two http en wWikipedia org wiki Liberation fonts Then there is
73. gtk org download windows 64bit html in the path it should work to have both 32 and 64 bit Gtk bin directories in the path on a 64 bit version of R R CMD INSTALL works in Windows to install source packages No addi tional tools are needed if the package does not contain compiled code and install packages type source will work for such packages and for those with compiled code if the tools see Appendix D The Windows toolset page 70 are in the path We have seen occasional permission problems after unpacking source packages on some Vista Windows 7 Server 2008 systems these have been circumvented by setting the environment variable BR INSTALL TAR to tar exe If you have only a source package that is known to work with current R and just want a binary Windows build of it you could make use of the building service offered at http win builder r project org For almost all packages R CMD INSTALL will attempt to install both 32 and 64 bit builds of a package if run from a 32 64 bit install of R It will report success if the installation of the architecture of the running R succeeded whether or not the other architecture was suc cessfully installed The exceptions are packages with a non empty configure win script or which make use of src Makefile win If configure win does something appropri ate to both architectures use option force biarch otherwise R CMD INSTALL merge multiarch can be applied to a source tarball to m
74. ibrary as above you will create a file Rmath def which can be used possibly after editing to create an import library for other systems such as Visual C If you make use of dynamic linking you should use define MATHLIB STANDALONE define RMATH DLL include Rmath h to ensure that the constants like NA REAL are linked correctly Auto import will probably work with MinGW but it is better to be sure This is likely to also work with VC Borland and similar compilers Appendix A Essential and useful other programs under a Unix alike 37 Appendix A Essential and useful other programs under a Unix alike This appendix gives details of programs you will need to build R on Unix like platforms or which will be used by R if found by configure Remember that some package management systems such as RPM and deb make a distinction between the user version of a package and the development version The latter usually has the same name but with the extension devel or dev you need both versions installed A 1 Essential programs and libraries You need a means of compiling C and FORTRAN 90 see Section B 6 Using FORTRAN page 50 Your C compiler should be ISO IEC 60059 POSIX 1003 1 and C99 compliant R tries to choose suitable flags for the C compilers it knows about but you may have to set CC or CFLAGS suitably For recent versions of gcc with glibc this means including std gnu99 If the compiler is detected as gcc
75. ight be under the X11 fonts directory or elsewhere for example usr share fonts default Typet usr share fonts ja TrueType C 2 Linux Linux is the main development platform for R so compilation from the sources is normally straightforward with the standard compilers Remember that some package management systems such as RPM and deb make a distinction between the user version of a package and the developer version The latter usually has the same name but with the extension devel or dev you need both versions installed So please check the configure output to see if the expected features are detected if for example readline is missing add the developer package On most Appendix C Platform notes 55 systems you will also need ncurses and its developer package although these should be dependencies of the readline package s When R has been installed from a binary distribution there are sometimes problems with missing components such as the FORTRAN compiler Searching the R help archives will normally reveal what is needed It seems that ix86 Linux accepts non PIC code in shared libraries but this is not necessarily so on other platforms in particular on 64 bit CPUs such as x86_64 So care can be needed with BLAS libraries and when building R as a shared library to ensure that position independent code is used in any static libraries such as the Tcl Tk libraries libpng libjpeg an
76. in the R sources will be compiled in As the latter suffice and are tested with R you should not need to change this Option with system tre is also available it needs a recent version of TRE The current sources are in the git repository at https github com laurikari tre but at the time of writing the resulting build will not pass its checks also known as ttf mscorefonts installer in the Debian Ubuntu world see also http en wikipedia org wiki Core fonts for the Web 10 ctf liberation in Debian Ubuntu 11 which is what is supplied with R PCRE must be built with UTF 8 support not the default and support for Unicode properties is assumed by some R packages Neither are tested by configure Appendix A Essential and useful other programs under a Unix alike 40 liblzma from xz utils version 5 0 3 or later will be used if installed the version in the R sources can be selected instead by configuring with with system xz no Systems differ in what they call the package including this e g on Fedora the library is in xz libs and the headers in xz devel An implementation of XDR is required and the R sources contain one which is likely to suffice although a system version may have higher performance XDR is part of RPC and historically has been part of libc on a Unix alike However some builds of glibc hide it with the intention that the TI RPC library be used instead in which case libtirpc and its developmen
77. ion prior to version 5 This is a version of gcc 4 2 1 with an LLVM backend e gfortran from http cran r project org bin macosx tools gfortran 4 2 3 pkg Note that this installs into usr local bin so make sure that is on your path Other compilers from http r research att com tools can also be used e clang from the Xcode distribution to compile the Objective C parts of the quartz device To use these have in config site something like CC llvm gcc 4 2 CXX 11lvm gt 4 2 F77 gfortran 4 2 arch x86_64 FC F77 OBJC clang Full names help to ensure that the intended compilers are used In particular gcc is a copy of llvm gcc 4 2 for Xcode lt 5 but of clang in Xcode 5 The recommended Fortran compiler defaults to 32 bit so arch x86_64 is needed For a 32 bit build use arch i386 for all compiler commands The OpenMP support in this version of gcc is problematic so the CRAN build is con figured with disable openmp The current CRAN Mavericks distribution of R is built using CC clang CXX clang F77 gfortran 4 8 FC F77 OBJC clang with clang and clang from Xcode 5 and the Fortran compiler from http r research att com libs gfortran 4 8 2 darwini3 tar bz2 Apple s build of clang has no OpenMP support Pre compiled versions of many of the Section A 2 Useful libraries and programs page 38 are available from http r research att com libs You will most likely want at least jpeg libpng and rea
78. jre directory of 32 bit Java gt setarch i686 R CMD javareconf to get a suitable setting When this mechanism is used the version of Rscript in e g usr bin will be the last installed but an architecture specific version will be available in e g usr 1ib64 R bin Normally all installed architectures will run on the platform so the architecture of Rscript does not matter 2 7 Other Options There are many other installation options most of which are listed by configure help Almost all of those not listed elsewhere in this manual are either standard autoconf options not relevant to R or intended for specialist uses by the R developers One that may be useful when working on R itself is the option disable byte compiled packages which ensures that the base and recommended packages are lazy loaded but not byte compiled Alternatively the make or environment variable R_NO_ BASE_COMPILE can be set to a non empty value for the duration of the build Option with internal tzcode makes use of R s own code and copy of the Olson database for managing timezones This will be preferred where there are issues with the system implementation usually involving times after 2037 or before 1916 An alternative time zone directory can be used pointed to by environment variable TZDIR this should contain files such as Europe London On all tested OSes the system timezone was deduced correctly but if necessary it can be set as the value of envir
79. lent to make sure that all libraries are on this path Note that only FORTRAN compilers which convert identifiers to lower case are sup ported You must set whatever compilation flags if any are needed to ensure that FORTRAN integer is equivalent to a C int pointer and FORTRAN double precision is equivalent to a C double pointer This is checked during the configuration process Some of the FORTRAN code makes use of COMPLEX 16 variables which is a Fortran 90 extension This is checked for at configure time but you may need to avoid compiler flags asserting FORTRAN 77 compliance Compiling the version of LAPACK in the R sources also requires some Fortran 90 ex tensions but these are not needed if an external LAPACK is used It might be possible to use 2c the FORTRAN to C converter http www netlib org f2c via a script An example script is given in scripts f77 f2c this can be customized by setting the environment variables F2C F2CLIBS CC and CPP You will need to ensure that the FORTRAN type integer is translated to the C type int Normally f2c h contains typedef long int integer which will work on a 32 bit platform but needs to be changed to typedef int integer on a 64 bit platform If your compiler is not gcc you will need to set FPICFLAGS appropriately Also the included LAPACK sources contain constructs that f2c is unlikely to be able to process so you would need to use an external LAPACK library such as CLAP
80. linker and others include CFLAGS debugging and optimization flags C MAIN_CFLAGS ditto for compiling the main program SHLIB_CFLAGS for shared objects FFLAGS debugging and optimization flags FORTRAN SAFE_FFLAGS ditto for source files which need exact floating point behaviour MAIN_FFLAGS ditto for compiling the main program SHLIB_FFLAGS for shared objects MAIN_LDFLAGS additional flags for the main link SHLIB_LDFLAGS additional flags for linking the shared objects LIBnn the primary library directory lib or 1ib64 CPICFLAGS special flags for compiling C code to be turned into a shared object FPICFLAGS special flags for compiling Fortran code to be turned into a shared object CXXPICFLAGS special flags for compiling C code to be turned into a shared object FCPICFLAGS special flags for compiling Fortran 95 code to be turned into a shared object DEFS defines to be used when compiling C code in R itself Appendix B Configuration on a Unix alike 52 Library paths specified as L lib path in LDFLAGS are collected together and prepended to LD_LIBRARY_PATH or your system s equivalent so there should be no need for R or rpath flags Variables such as CPICFLAGS are determined where possible by configure Some systems allows two types of PIC flags for example fpic and fPIC and if they differ the first allows only a limited number of symbols in a shared object Since R as a shared library has about 62
81. lly to a non standard location and utilities may not support it e g the pkg config file libR pc will be put somewhere unknown to pkg config C 3 8 Building R app Note that building the R APP GUI console is a separate project using Xcode Before compiling R APP make sure the current version of R is installed in Library Frameworks R framework and working at the command line this can be a binary install The current sources can be checked out by svn co https svn r project org R packages trunk Mac GUI This can be built by loading the R xcodeproj project select the R target and the SnowLeopard64 or Lion64 configuration or from the command line by e g xcodebuild target R configuration SnowLeopard64 See also the INSTALL file in the checkout or directly at https svn r project org R packages trunk Mac GUI INSTALL R APP does not need to be installed in any specific way Building R APP results in the R APP bundle which appears as one R icon This application bundle can be run anywhere and it is customary to place it in the Applications folder C 4 Solaris R has been built successfully on Solaris 10 both Sparc and x86 using the zero cost Oracle Solaris Studio compilers there has been some success with gcc 4 gfortran Recent Sun machines are AMD Opterons or Intel Xeons amd64 rather than x86 but 32 bit x86 executables are the default There have been few reports on Solaris 11 with no known extra i
82. local lib pkgconfig usr lib pkgconfig 64 bit versions of Linux are built with support for files gt 2Gb and 32 bit versions will be if possible unless disable largefile is specified To build a 64 bit version of R on ppc64 also known as powerpc64 with gcc 4 1 1 Ei ji Nakama used CC gcc m64 CXX gxx m64 F77 gfortran m64 FC gfortran m64 or mtune corei7 for Intel Core i3 15 17 with gcc gt 4 6 0 Appendix C Platform notes 56 CFLAGS mminimal toc fno optimize sibling calls g 02 FFLAGS mminimal toc fno optimize sibling calls g 02 the additional flags being needed to resolve problems linking against libnmath a and when linking R as a shared library C 2 1 Clang R has been built with Linux ix86 and x86_64 C and C compilers http clang llvm org based on the Clang front ends invoked by CC clang CXX clang together with gfortran These take very similar options to the corresponding GCC compilers This has to be used in conjunction with a Fortran compiler the configure code will remove 1gcc from FLIBS which is needed for some versions of gfortran The current default for clang is to use the C runtime from the installed g Using the runtime from the libct project http libcxx llvm org has also been tested for some R packages only the variant using libcxxabi was successful C 2 2 Intel compilers Intel compilers have been used under ix86 and x86_
83. lti byte encodings most commonly UTF 8 are even more complicated There are few fonts in iso10646 1 the Unicode encoding and they only contain a subset of the available glyphs and are often fixed width designed for use in terminals In such locales fontsets are used made up of fonts encoded in other encodings If the locale you are using has an entry in the XLC LOCALE directory typically usr share X11 locale it is likely that all you need to do is to pick a suitable font specification that has fonts in the encodings specified there If not you may have to get hold of a suitable locale entry for X11 This may mean that for example Japanese text can be displayed when running in ja_JP UTF 8 but not when running in en_GB UTF 8 on the same machine although on some systems many UTF 8 X11 locales are aliased to en_US UTF 8 which covers several character sets e g ISO 8859 1 Western European JISX0208 Kanji KSC5601 Korean GB2312 Chinese Han and JISX0201 Kana On some systems scalable fonts are available covering a wide range of glyphs One source is TrueType OpenType fonts and these can provide high coverage Another is Type 1 fonts the URW set of Type 1 fonts provides standard typefaces such as Helvetica with a larger coverage of Unicode glyphs than the standard X11 bitmaps including Cyrillic These are generally not part of the default install and the X server may need to be configured to use them They m
84. mask 0 and OSF1 required that computation be done with a ieee with inexact flag etc On a new platform you must find out the magic recipe and add some code to make it work This can often be done via the file config site which resides in the top level directory Beware of using high levels of optimization at least initially On many compilers these reduce the degree of compliance to the IEEE model For example using fast on the Solaris Studio compilers has caused R s NaN to be set incorrectly and gcc s ffast math has given incorrect results Shared Objects T here 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 GNU 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 xmkmf and then override this in situations where we know better for tools from the GNU Compiler Collection and or platforms we know about This typically works but you may have to manually override the results Scanning the manual entries for cc and 1d usually reveals the correct incantation Once you know the recipe you can modify the file config site following the instructions therein so that the build will use these options It seems that gcc 3 4 x and later on ix86 Linux defeat a
85. n Printed versions of the help pages for selected base packages over 1900 pages EA RFAQ R intro An Introduction to R R data R Data Import Export R admin R Installation and Administration this manual R exts Writing R Extensions R lang The R Language Definition To make these with fullrefman rather than refman use make pdf to create PDF versions make info to create info files not refman nor fullrefman You will not be able to build any of these unless you have makeinfo version 4 7 or later installed and for PDF you must have texi2dvi and texinfo tex installed which are part of the GNU texinfo distribution but are especially texinfo tex often made part of the TEX package in re distributions The PDF versions can be viewed using any recent PDF viewer they have hyperlinks that can be followed The info files are suitable for reading online with Emacs or the standalone GNU info program The PDF versions will be created using the paper size selected at configuration default ISO a4 this can be overridden by setting R_PAPERSIZE on the make command line or setting R_PAPERSIZE in the environment and using make e If re making the manuals for a different paper size you should first delete the file doc manual version texi The usual value for North America would be letter There are some issues with making the PDF reference manual fullrefm
86. n com or compiled from the sources You will also need zip and unzip from the Info ZIP project http www info zip org All of these tools are in Rtools exe 3 such as sort find and perhaps make Appendix D The Windows toolset 72 Beware Native ports of make are not suitable including those called MinGW make at the MinGW SourceForge site and mingw32 make in some MinGW w 64 distributions There were also problems with other versions of the Cygwin tools and DLLs To avoid frustration please use our tool set and make sure it is at the front of your path including before the Windows system directories If you are using a Windows shell type PATH at the prompt to find out You may need to set the environment variable CYGWIN to a value including nodosfilewarning to suppress messages about Windows style paths DA The MinGW w64 toolchain Technically you need more than just a compiler so the set of tools is referred to as a toolchain The preferred toolchain since R 2 14 2 is part of Rtools30 exe this uses a beta version of gcc 4 6 3 and version 2 0 1 of the MinGW w64 project s runtime This toolchain uses multilib that is there is a single front end such as gcc exe for each of the compilers and 32 bit the default and 64 bit compilation are selected by the flags m32 and m64 respectively The tools are all 32 bit Windows executables and should be able to run on any current version of Windows howev
87. n make works on Solaris as does the native FreeBSD make The native make has been reported to fail on SGI Irix 6 5 and Alpha OSF1 aka Tru64 To build in a separate directory you need a make that uses the VPATH variable for example GNU make or Sun make on Solaris 7 or later dmake has also been used e g on Solaris 10 If you want to use a make by another name for example if your GNU make is called gmake you need to set the variable MAKE at configure time for example configure MAKE gmake Appendix B Configuration on a Unix alike 50 B 6 Using FORTRAN To compile R you need a FORTRAN compiler The default is to search for 95 fort xlf95 ifort ifc efc pgf95 1f95 gfortran ftn g95 90 x1f90 pghpf pgf90 epcf90 g77 77 x1f frt pgf77 cf77 fort77 132 af77 in that order and use whichever is found first if none is found R cannot be compiled However if CC is gcc the matching FORTRAN compiler g77 for gcc 3 and gfortran for gcc 4 is used if available The search mechanism can be changed using the configure variable F77 which specifies the command that runs the FORTRAN 77 compiler If your FORTRAN compiler is in a non standard location you should set the environment variable PATH accordingly before running configure or use the configure variable F77 to specify its full path If your FORTRAN libraries are in slightly peculiar places you should also look at LD_ LIBRARY PATH or your system s equiva
88. nly because it is necessary on some platforms and because some users want to experiment with claimed performance improvements Reporting problems where it is used unnecessarily will simply irritate the R helpers Note too the comments about ISO IEC 60559 compliance in the section of external BLAS these apply equally to an external LAPACK and for example the Intel MKL documentation says LAPACK routines assume that input matrices do not contain IEEE 754 spe cial values such as INF or NaN values Using these special values may cause LAPACK to return unexpected results or become unstable We rely on limited support in LAPACK for matrices with 2 or more elements it is quite possible that an external LAPACK will not have that support If you have a pure FORTRAN 77 compiler which cannot compile LAPACK it may be possible to use CLAPACK from http www netlib org clapack by something like with lapack lclapack 1f2c provided these were built with position independent code and the calling conventions for double complex function return values match those in the BLAS used so it may be simpler to use CLAPACK built to use CBLAS and with lapack lclapack lcblas 1f2c A 3 3 Caveats As with all libraries you need to ensure that they and R were compiled with compatible compilers and flags For example this has meant that on Sun Sparc using the native compilers the flag dalign is needed so sunperf can be used On some systems it is necessa
89. ns of the Tcl Tk files you may need the configuration options with tcltk use Tcl Tk or specify its library directory with tcl config TCL CONFIG specify location of tclConfig sh with tk config TK CONFIG specify location of tkConfig sh or use the configure variables TCLTK_LIBS and TCLTK_CPPFLAGS to specify the flags needed for linking against the Tcl and Tk libraries and for finding the tc1 h and tk h headers respectively If you have both 32 and 64 bit versions of Tcl Tk installed specifying the paths to the correct config files may be necessary to avoid confusion between them Versions of Tcl Tk up to 8 5 12 and 8 6 0 have been tested including most versions of 8 4 x but not recently Appendix A Essential and useful other programs under a Unix alike 41 A 2 2 Java support The build process looks for Java support on the host system and if it finds it sets some settings which are useful for Java using packages JAVA HOME can be set to point to a specific JRE JDK Principal amongst these are setting some library paths to the Java libraries and JVM which are stored in environment variable R JAVA LD LIBRARY PATH in file R HOME etc ldpaths or a sub architecture specific version A typical setting for x86_64 Linux is JAVA HOME usr lib jvm java 1 7 0 openjdk 1 7 0 25 x86 64 jre HR JAVA LD LIBRARY PATH 1JAVA HOME 1lib amd64 server Note that this unfortunately depends on the exact version of the JRE JDK ins
90. o link against 1foo to find an external BLAS which needs to be found both at link time and run time The configure code checks that the external BLAS is complete it must include all double precision and double complex routines as well as LSAME and appears to be usable How ever an external BLAS has to be usable from a shared object so must contain position independent code and that is not checked Some enhanced BLASes are compiler system specific sunperf on Solaris libessl on IBM Accelerate on OS X The correct incantation for these is usually found via with blas with no value on the appropriate platforms Some of the external BLASes are multi threaded One issue is that R profiling which uses the SIGPROF signal may cause problems and you may want to disable profiling if you use a multi threaded BLAS Note that using a multi threaded BLAS can result in taking more CPU time and even more elapsed time occasionally dramatically so than using a similar single threaded BLAS Note that under Unix but not under Windows if R is compiled against a non default BLAS and enable BLAS shlib is not used then all BLAS using packages must also be So if R is re built to use an enhanced BLAS then packages such as quantreg will need to be re installed R relies on ISO IEC 60559 compliance of an external BLAS This can be broken if for example the code assumes that terms with a zero factor are always zero and do not need to be computed
91. on packages from CRAN to run on Windows XP or later on ix86 CPUs including AMD64 Intel64 cpus and Windows x64 Your file system must allow long file names as is likely except perhaps for some network mounted systems Installation is via the installer R 3 1 1 win exe Just double click on the icon and follow the instructions When installing on a 64 bit version of Windows the options will include 32 or 64 bit versions of R and the default is to install both You can uninstall R from the Control Panel Note that you will be asked to choose a language for installation and that choice applies to both installation and un installation but not to running R itself See the R Windows FAQ for more details on the binary installer 3 1 Building from source R can be built as either a 32 bit or 64 bit application on Windows to build the 64 bit application you need a 64 bit edition of Windows such an OS can also be used to build 32 bit R The standard installer combines 32 bit and 64 bit builds into a single executable which can then be installed into the same location and share all the files except the exe and d11 files and some configuration files in the etc directory Building is only tested in a 8 bit locale using a multi byte locale as used for CJK languages is unsupported and may not work the scripts do try to select a C locale Windows may not honour this 3 1 1 Getting the tools If you want to build R from the sources
92. onment variable TZ 2 8 Testing an Installation Full testing is possible only if the test files have been installed with make install tests which populates a 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 R home and run 10 How to prepare such a directory is described in file src extra tzone Notes in the R sources Chapter 2 Installing R under Unix alikes 11 cd tests followed by one of bin R CMD make check bin R CMD make check devel bin R CMD make check all and other useful targets are test BasePackages and test Recommended to the run tests of the standard and recommended packages if installed respectively This re runs all the tests relevant to the installed R including for example code in the package vignettes but not for example the ones checking the example code in the manuals nor making the standalone Rmath library This can occasionally be useful when the operating environment has been changed for example by OS updates or by substituting the BLAS see Section A 3 1 5 Shared BLAS page 45 Parallel checking of packages may be possible set the environment variable TEST MC CORES to the maximum number of processes to be run in parallel This affects both checking the package examples part of make check and package sources part of make check devel and make check recommended I
93. ons here are for x86 64 builds To use the quartz O graphics device you need to configure with with aqua which is the default quartz then becomes the default device when running R at the console and X11 would only be used for the data editor viewer This needs an Objective C compiler which can compile the code for quartz O Use without aqua if you want a standard Unix alike build apart from disabling quartz and the ability to use the build with R APP it also changes the default location of the personal library see 1ibPaths Also use disable R framework to install in the standard layout These days that is defined by Apple s implementation of clang so it is strongly recommended to use that Appendix C Platform notes 58 Command line Tools for Xcode used to be part of the Apple Developer Tools Xcode but nowadays need to be installed separately They can be downloaded from http developer apple com devcenter mac you will need to register there that allows you to download older versions available for your OS or some versions of Xcode from the App Store or from http developer apple com devcenter mac you can install the command line tools from within Xcode from the Downloads pane in the Preferences For Mavericks see the specific sub section below Various compilers can be used The current CRAN Snow Leopard distribution of R is built using e gcc from an Xcode distribut
94. pace and usually more time to manipulate So 64 bit builds of R will all other things being equal run slower than 32 bit builds On Sparc Solaris the difference was 15 20 e However other things may not be equal In the specific case of x86_64 vs ix86 the 64 bit CPU has features such as SSE2 instructions which are guaranteed to be present but are optional on the 32 bit CPU and also has more general purpose registers This means that on chips like a desktop Intel Core 2 Duo the vanilla 64 bit version of R has been around 10 faster on both Linux and OS X Laptop CPUs are usually relatively slower in 64 bit mode So for speed you may want to use a 32 bit build especially on a laptop but to handle large datasets and perhaps large files a 64 bit build You can often build both and install them in the same place See Section 2 6 Sub architectures page 9 This is done for the Windows binary distributions Even on 64 bit builds of R there are limits on the size of R objects see help Memory limits some of which stem from the use of 32 bit integers especially in FORTRAN code For example the dimensions of an array are limited to 2 1 1 also known as IEEE 754 at least when storing quantities the on FPU precision is allowed to vary Chapter 9 The standalone Rmath library 34 9 The standalone Rmath library The routines supporting the distribution and special functions in R and a few others are
95. package directory from the library Chapter 6 Add on packages 28 6 6 Setting up a package repository Utilities such as install packages can be pointed at any CRAN style repository and R users may want to set up their own The base of a repository is a URL such as http www omegahat org R this must be an URL scheme that download packages supports which also includes ftp and file but not on most systems https Under that base URL there should be directory trees for one or more of the following types of package distributions e source located at src contrib and containing tar gz files Other forms of com pression can be used e g tar bz2 or tar xz files Complete repositories contain the sources corresponding to any binary packages and in any case it is wise to have a src contrib area with a possibly empty PACKAGES file e win binary located at bin windows contrib x y for R versions x y z and con taining zip files for Windows e mac binary located at bin macosx contrib 3 y for R versions 3 y z and contain ing tgz files e mac binary mavericks located at bin macosx mavericks contrib 3 y for R versions 3 1 z to be run under OS X 10 9 Mavericks and containing tgz files e mac binary leopard located at bin macosx leopard contrib 2 y for R versions 2 y z and containing tgz files Each terminal directory must also contain a PACKAGES file This can be a concatena tion of the
96. path to the build directory Now rehash if necessary type R and read the R manuals and the R FAQ files FAQ or doc manual R FAQ html or http CRAN R project org doc FAQ R FAQ html which always has the version for the latest release of R 2 2 Help options By default HTML help pages are created when needed rather than being built at install time If you need to disable the server and want HTML help there is the option to build HTML pages when packages are installed including those installed with R This is enabled by the configure option enable prebuilt html Whether R CMD INSTALL and hence install packages pre builds HTML pages is determined by looking at the R installation and is reported by R CMD INSTALL help it can be overridden by specifying one of the INSTALL options html or no html The server is disabled by setting the environment variable R DISABLE HTTPD to a non empty value either before R is started or within the R session before HTML help including help start is used It is also possible that system security measures will prevent the server from being started for example if the loopback interface has been disabled See tools startDynamicHelp for more details 2 3 Making the manuals There is a set of manuals that can be built from the sources fullrefman Printed versions of all the help pages for base and recommended packages over 3300 pages Chapter 2 Installing R under Unix alikes 5 refma
97. pecified in Library Frameworks R framework Resources etc Makeconf depend on the version of OS X under which R was installed and are appropriate to the latest version of the Xcode command line tools for that version of OS X The settings can be changed either by editing that file or in a file such as R Makevars see the next section Entries which may need to be changed include CC CXX FC F77 FLIBS and the corresponding flags and perhaps CXXCPP DYLIB_LD MAIN_LD SHLIB_CXXLD SHLIB_FCLD and SHLIB_LD So for example you could select clang for both C and C with extensive checking by having in R Makevars CC clang CXX clangt CFLAGS mtune native g 02 Wall pedantic Wconversion CXXFLAGS mtune native g 02 Wall pedantic Wconversion and for another version of gfortran 4 2 we needed FLIBS lgfortran 5 or by adding it in a file such as etc i386 Makevars site which does not exist by default Chapter 6 Add on packages 26 6 3 3 Customizing package compilation The R system and package specific compilation flags can be overridden or added to by setting the appropriate Make variables in the personal file HOME R Makevars R PLATFORM but HOME R Makevars win or HOME R Makevars win64 on Windows or if that does not exist HOME R Makevars where R_PLATFORM is the platform for which R was built as available in the platform component of the R variable
98. pkg2 The part 1 path to library can be omitted in which case the first library of a normal R session is used that shown by 1ibPaths 1 There are a number of options available use R CMD INSTALL help to see the current list Alternatively packages can be downloaded and installed from within R First set the option CRAN to your nearest CRAN mirror using chooseCRANmirror Then download and install packages pkg1 and pkg2 by gt install packages c pkgi pkg2 The essential dependencies of the specified packages will also be fetched Unless the library is specified argument lib the first library in the library search path is used if this is not writable R will ask the user in an interactive session if the default personal library should be created and if allowed to will install the packages there If you want to fetch a package and all those it depends on in any way that are not already installed use e g gt install packages Rcmdr dependencies TRUE install packages can install a source package from a local tar gz file by setting argument repos to NULL this will be selected automatically if the name given is a single tar gz file install packages can look in several repositories specified as a character vector by the argument repos these can include a CRAN mirror Bioconductor Omegahat R forge rforge net local archives local files Function setRepositories can select amongst tho
99. prefix Each of bindir mandir and libdir can also be specified on the make install command line at least for GNU make The configure or make variables rdocdir and rsharedir can be used to install the system independent doc and share directories to somewhere other than libdir The C header files can be installed to the value of rincludedir note that as the headers are not installed into a subdirectory you probably want something like rincludedir usr local include R 3 1 1 If you want the R home to be something other than 1ibdir R use rhome for example Chapter 2 Installing R under Unix alikes 8 make install rhome usr local lib64 R 3 1 1 will use a version specific R home on a non Debian Linux 64 bit system If you have made R as a shared static library you can install it in your system s library directory by make prefix path to here install libR where prefix is optional and libdir will give more precise control However you should not install to a directory mentioned in LDPATHS e g usr 1ocal lib64 if you intend to work with multiple versions of R since that directory may be given precedence over the lib directory of other R installations make install strip will install stripped executables and on platforms where this is supported stripped libraries in directories lib and modules and in the standard packages Note that installing R into a directory whose path contains spaces is not supported and at least some aspec
100. r Collection version 4 2 4 which is available from one of the above OSS repositories and the IBM C C XL C C 10 01 as well as FORTRAN XL Fortran 12 01 compilers http www14 software ibm com webapp download byproduct jsp X To compile for a 64 bit powerpc Power6 CPU target one can use CC gcc maix64 pthread CXX g maix64 pthread FC gfortran maix64 pthread F77 gfortran maix64 pthread CFLAGS 02 g mcpu power6 FFLAGS 02 g mcpu power6 FCFLAGS 02 g mcpu power6 for the GCC and CC xlc CXX xlct FC x1f F77 x1f CFLAGS qarch auto qcache auto qtune auto 03 qstrict ma FFLAGS qarch auto qcache auto qtune auto 03 qstrict FCFLAGS qarch auto qcache auto qtune auto 03 qstrict CXXFLAGS qarch auto qcache auto qtune auto 03 qstrict Appendix C Platform notes 68 for the IBM XL compilers For the latter it is important to note that the decision for generating 32 bit or 64 bit code is done by setting the OBJECT MODE environment variable appropriately recommended or using an additional compiler flag q32 or q64 By default the IBM XL compilers produce 32 bit code Thus to build R with 64 bit support one needs to either export OBJECT MODE 64 in the environment or alternatively use the q64 compiler options It is strongly recommended to install Bash and use it as the configure shell e g via setting CONFIG SHELL usr bin bash in the environment and to use
101. razilian locales but not for locales specifying Portugal Iranslations in the right language but the wrong charset are made use of by on the fly re encoding The LANGUAGE variable only can be a colon separated list for example se de giving a set of languages in decreasing order of preference One special value is en quot which can be used in a UTF 8 locale to have American error messages with pairs of single quotes translated to Unicode directional quotes If no suitable translation catalogue is found or a particular message is not translated in any suitable catalogue English is used See http developer r project org Translations html for how to prepare and install translation catalogues 4 the language written in England some people living in the USA appropriate this name for their language D with Americanisms Chapter 8 Choosing between 32 and 64 bit builds 33 8 Choosing between 32 and 64 bit builds Almost all current CPUs have both 32 and 64 bit sets of instructions Most OSes running on such CPUs offer the choice of building a 32 bit or a 64 bit version of R and details are given below under specific OSes For most a 32 bit version is the default but for some e g x86_64 Linux and OS X gt 10 6 64 bit is All current versions of R use 32 bit integers and ISO IEC 60559 double precision reals and so compute to the same precision and with the same limits on the sizes of numerical quanti
102. rence Manual use cd doc manual make f Makefile win info all assuming you have pdftex pdflatex installed and in your path See the Section 2 3 Making the manuals page 4 section in the Unix alike section for setting options such as the paper size and the fonts used Version 4 x of makeinfo from Rtools is assumed by default If you have version 5 x of texinfo nakeinfo has been replaced by a Perl script texi2any file MkRules dist contains alternative macros to allow that to be used copy it to MkRules local before editing A package of texinfo 5 x for use on Windows is available at http www stats ox ac uk pub Rtools you will also need to install Perl Chapter 3 Installing R under Windows 16 3 1 8 Building the Inno Setup installer You need to have the files for a complete R build including bitmap and Tcl Tk support and the manuals as well as the recommended packages and Inno Setup see Section D 2 The Inno Setup installer page 71 Once everything is set up make distribution make check all will make all the pieces and the installer and put them in the gnuwin32 cran subdirectory then check the build This works by building all the parts in the sequence rbuild the executables the FAQ docs etc rpackages the base packages htmldocs the HTML documentation bitmapdll the bitmap support files cairodevices the cairo based graphics devices recommended the recommended packages vignettes the vignett
103. ries also needs to be Occasionally the option library stlport4 Crun has been needed Several CRAN packages using C need the more liberal interpretation given by adding CXXFLAGS features tmplrefstatic The performance library sunperf is available for use with the Solaris Studio compilers If selected as a BLAS it must also be selected as LAPACK via for Solaris Studio 12 2 configure with blas library sunperf with lapack This has often given test failures in the past in several different places At the time of writing it fails in tests reg BLAS R and on some builds including for amd64 it fails in example eigen Parsing very complex R expressions needs a lot of stack space when the Oracle compilers are used several packages require the stack increased to at least 20MB C 4 1 Using gcc If using gcc ensure that the compiler was compiled for the version of Solaris in use This can be ascertained from gcc v gcc makes modified versions of some header files and several reports of problems were due to using gcc compiled on one version of Solaris on a later version The notes here are for gcc set up to use the Solaris linker it can also be set up to use GNU 1d but that has not been tested Compilation for a 32 bit Sparc target with gcc 4 9 0 needed CPPFLAGS I opt csw include LDFLAGS L opt csw gcc4 lib L opt csw lib and for a 64 bit Sparc target CC gcc m64 F77 gfortran m64 CXX g m64
104. rsion of MiKTeX almost suffices when last tested packages epsf fancyvrb inconsolata listings mptopdf natbib upquote url needed to be added on the fly or via the MiKTeX Package Manager to install R In any case ensure that the inconsolata package is installed you can check with the MiKTeX Package Manager The Rtools exe installer does not include any version of ATEX It is also possible to use the TeXLive distribution from http www tug org texlive Please read Section 2 3 Making the manuals page 4 about how to make fullrefman pdf and set the environment variable R RDAPDF suitably ensure you have the required fonts installed or that MiKTeX is set up to install I3TEX packages on first use D 2 The Inno Setup installer To make the installer package R 3 1 1 win exe we currently require the Unicode version of Inno Setup 5 3 7 or later from http jrsoftware org This is not included in Rtools exe Copy file src gnuwin32 MkRules dist to src gnuwin32 MkRules 1local and edit it to set ISDIR to the location where Inno Setup was installed D 3 The command line tools This item is installed by the Rtools exe installer If you choose to install these yourself you will need suitable versions of at least basename cat cmp comm cp cut date diff du echo expr gzip 1s make makeinfo mkdir mv rm rsync sed sh sort tar texindex touch and uniq we use those from the Cygwin distribution http www cygwi
105. ry actually exists which by default it will not Both Rp LIBS USER and R_LIBS_SITE can specify multiple library paths separated by colons semicolons on Windows l unless they were excluded in the build its binding is locked once the startup files have been read so users cannot easily change it Chapter 6 Add on packages 23 6 3 Installing packages Packages may be distributed in source form or compiled binary form Installing source packages which contain C C Fortran code requires that compilers and related tools be installed Binary packages are platform specific and generally need no special tools to install but see the documentation for your platform for details Note that you may need to specify implicitly or explicitly the library to which the package is to be installed This is only an issue if you have more than one library of course Ensure that the environment variable TMPDIR is either unset and tmp exists and can be written in and executed from or is the absolute path to a valid temporary directory not containing spaces For most users it suffices to call install packages pkgname or its GUI equivalent if the intention is to install a CRAN package and internet access is available On most systems install packages will allow packages to be selected from a list box typically with several thousand items To install packages from source on a Unix alike use R CMD INSTALL 1 path to library pkgi
106. ry that an external BLAS LAPACK was built with the same FORTRAN compiler used to build R known problems are with R built with gfortran see Section B 6 1 Using gfortran page 50 Appendix B Configuration on a Unix alike 4T Appendix B Configuration on a Unix alike B 1 Configuration options configure has many options running configure help will give a list Probably the most important ones not covered elsewhere are defaults in brackets with x use the X Window System yes x includes DIR X include files are in DIR x libraries DIR X library files are in DIR with readline use readline library if available yes enable R profiling attempt to compile support for RprofO yes enable memory profiling attempt to compile support for Rprofmem and tracemem no enable R shlib build R as a shared dynamic library no enable BLAS shlib build the BLAS as a shared dynamic library yes except on AIX You can use without foo or disable foo for the negatives You will want to use disable R profiling if you are building a profiled executable of R e g with pg Flag enable R shlib causes the make process to build R as a dynamic shared library typically called libR so and link the main R executable 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 penalty So you probabl
107. s ssssessessee e 27 6 6 Setting up a package repository 00 cece cece eens 28 6 7 Checking installed source packages 0000s eee e eee 28 7 Internationalization and Localization 30 CE EE 30 7 1 1 Locales under Unix alikes 0 0 ccc cece eens 30 7 1 2 Locales under Windows 91 7 1 3 Locales under OS 3 31 7 2 Localization of messages 31 8 Choosing between 32 and 64 bit builds 33 9 The standalone Rmath library 34 9 1 Untzx abkes eee enn n erer eee eens 34 9 2 WindOWS sssiaockieteckeneer RtRR RE eee eed EE 35 Appendix A Essential and useful other programs under a Unix alike 37 A 1 Essential programs and libraries 000 eee ee eee 37 A 2 Useful libraries and programs cece eee sees 38 E We Ee NOE PIE TT ML 40 A 2 2 Jona support 41 A 2 3 Other compiled Language 41 A3 Linear algebra etuer ee be Ne E Sead AS ein at Al ABA BLAS iue eR AER ARA 42 AaLi UNE CET DEI 42 ABAZ ACM ET 43 A 3 1 3 Goto and Openb tAn 43 A 314 Intel MK eh ENNER ENEE 43 A3 15 Shared BLAS EEN ENEE Eeer EE 45 A 3 2 LAPAGCK ener RR Rh REESEN E EGO RU ecce or gos 45 A33 CAVGRIS ian dacs d esevet nei Re dixe ret ere uie dns 46 ii Appendix B Configuration on a Unix alike 47 B 1 Configuration option 4T B 2 Internationalization support 48 B 3 Configuration variable 48 B 3 1 Setting paper age 48 B 3 2 Setting
108. s files with that form of compression 4 these flags apply to the compilers some of the tools use different flags 32 bit builds are the default Function and variable index Function and variable index COnfigurei osssnvedeas eveenienes 3 4 6 7 48 49 I install pack geS 20 x b Sr dee ed 23 M EE 49 73 LN cui o XO Ee eS da Gene Y ae re ns 3 remove packages sss 27 update packages o sac d Pipe lie dag 24 Concept index Concept index F FORTRAN eed e y Ra E NEE 50 FreeBSD 2 2 2 000 cece eee eee esas na 68 I Installation 2225 esuitamer er acest pee ees 6 Installing under Unix alikes usnsnnnnnaa 3 Installing under Windows 12 Internationalization eese eese 30 L LAPACK library essssssss 45 58 65 Libraries oi opo tae eodein E DR cR eee 22 libraries Managing ENEE I EE 22 Libraries Site s i rcas esisti 9 ih ette en 22 Libraries gek EIERE EST SEELEN ERR 22 IDinbc Em 3 54 Locale ic Aces scan sneaeteateansnateeped ste E 30 Localization i e ciet mr ecd ga 30 74 Obtaining TEE Hi UE 3 19 57 P Packages eoi xb e prf ER Reed 22 Packages default 22 Packages installing 2000 23 Packages removing 020s ee 27 Packages updating 2 000008 27 R Rbitmap dll i 2 ica rm creases 14 Repositories tanecne niner cece eee eee eee tenes 28 Site lbrarie8 izenz2ssile ceder texeeeme de ire 22 DOLLS ee niece hs aw cee eee eee o EE ERE 6
109. se repositories that the R installation is aware of Naive users sometimes forget that as well as installing a package they have to use library to make its functionality available 3 Ifa proxy needs to be set see download file Chapter 6 Add on packages 24 6 3 1 Windows What install packages does by default is different on Unix alikes except OS X and Windows On Unix alikes it consults the list of available source packages on CRAN or other repository ies downloads the latest version of the package sources and installs them via R CMD INSTALL On Windows it looks by default at the list of binary versions of packages available for your version of R and downloads the latest versions if any although optionally it will also download and install a source package by setting the type argument On Windows install packages can also install a binary package from a local zip file by setting argument repos to NULL Rgui exe has a menu Packages with a GUI interface to install packages update packages and library Windows binary packages for R are distributed as a single binary containing either or both architectures A few of the binary packages need other software to be installed on your system see for example http CRAN R project org bin windows contrib 3 1 ReadMe For 64 bit builds packages using Gtk Cairo RGtk2 cairoDevice and those that depend on them need the bin directory of a bundled distribution from http www
110. sed by version 9 of MKL can be used by Appendix A Essential and useful other programs under a Unix alike 45 with blas lmkl lguide lpthread but this may not match your compiler on a 64 bit platform This is multi threaded but in version 9 the number of threads defaults to 1 It can be increased by setting OMP_NUM_ THREADS Thanks to Andy Liaw for the information A 3 1 5 Shared BLAS The 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 BLAS library as most of a static library will be compiled into the R executable and each BLAS using package R offers the option of compiling the BLAS into a dynamic library libRblas stored in R_HOME 1ib and linking both R itself and all the add on packages against that library This is the default on all platforms except AIX unless an external BLAS is specified and found for the latter it can be used by specifying the option enable BLAS shlib and it can always be disabled via disable BLAS shlib This has both advantages and disadvantages e t saves space by having only a single copy of the BLAS routines which is helpful if there is an external static BLAS such as used to be standard for ATLAS e There may be performance disadvantages in using a shared BLAS Probably the most likely is when R s internal BLAS is used and R is not built as a shared library when it is possible to build the BLAS into
111. sions of bison generate code which reads and in some cases writes outside array bounds bison 2 6 1 was found to be satisfactory The ultimate sources for package compiler are in its noweb directory To re create the sources from src library compiler noweb compiler nw the command notangle is re quired This is likely to need to be installed from the sources at http www cs tufts edu nr noweb and can also be found on CTAN The package sources are only re created even in maintainer mode if src library compiler noweb compiler nw has been updated It is likely that in future creating configure will need the GNU autoconf archive installed This can be found at http www gnu org software autoconf archive and as a package usually called autoconf archive in most packaged distributions for example Debian Fedora OpenCSW Homebrew and MacPorts Appendix C Platform notes 53 Appendix C 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 for R lt 2 10 0 contain notes on platforms such as HP UX IRIX and Alpha OSF1 for which we have had no recent reports
112. size One common variable to change is BR PAPERSIZE which defaults to a4 not letter Valid values are a4 letter legal and 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 a4 if R PAPERSIZE is unset If the Debian Linux program paperconf is found or the environment variable PAPERSIZE is set these are used to produce the default Appendix B Configuration on a Unix alike 49 B 3 2 Setting the browsers Another precious variable is R BROWSER the default HTML browser which should take a value of an executable in the user s path or specify a full path Its counterpart for PDF files is RLPDFVIEWER B 3 3 Compilation flags If you have libraries and header files e g for GNU readline in non system directories use the variables LDFLAGS for libraries using L flags to be passed to the linker and CPPFLAGS for header files using I flags to be passed to the C C preprocessors respectively to specify these locations These default to L usr local lib LDFLAGS L usr local lib64 on most 64 bit Linux OSes and I usr local include CPPFLAGS to catch the most common cases If libraries are still not found then maybe your compiler linker does not support re ordering of L and 1 flags this has be
113. sks to appear to run very slowly when not producing output in the console Here are three ways to avoid it e Ensure that the console is completely visible or at least the activity indicator at the top right corner is visible Chapter 4 Installing R under OS X 20 e Call Get Info on the application e g from Finder This will have two tick boxes in the General panel click the one named Prevent App Nap if it is not already ticked This only available for builds made prior to Mavericks e Ina Terminal run defaults write org R project R NSAppSleepDisabled bool YES see https developer apple com library mac releasenotes MacOSX WhatsNewInOSX Articles Mac0SX10 9 html 4 2 Uninstalling under OS X R for OS X consists of two parts the GUI R APP and the R framework The un installation is as simple as removing those folders e g by dragging them into the Trash The typical installation will install the GUI into the Applications R app folder and the R framework into the Library Frameworks R framework folder This does leave some links in usr bin If you want to get rid of R more completely using a Terminal simply run prepend sudo if needed rm rf Library Frameworks R framework Applications R app usr bin R usr bin Rscript The installation consisted of three Apple packages org r project R x86 64 fw pkg org r project R x86 64 GUI pkg and org r project x86 64 tcltk x11 not all o
114. ssues Solaris 9 and earlier are now so old that it is unlikely that R is still used with them and they will not be considered here The Solaris versions of several of the tools needed to build R e g make ar and 1d are in usr ccs bin so if using those tools ensure this is in your path A version of the Appendix C Platform notes 63 preferred GNU tar is if installed in usr sfw bin as sometimes are tools like makeinfo It may be necessary to avoid the tools in usr ucb POSIX compliant versions of some tools can be found in usr xpg4 bin and usr xpg6 bin A large selection of Open Source software can be installed from http www opencsw org by default installed under opt csw You will need GNU libiconv and readline the Solaris version of iconv is not suffi ciently powerful The native make suffices to build R but a small number of packages require GNU make some without good reason and without declaring it as SystemRequirements in the DESCRIPTION file Some people have reported that the Solaris libintl needs to be avoided for example by using disable nls or with included gettext or using libintl from OpenCSW The support for the C99 1ong double type on Sparc hardware uses quad precision arith metic and this is usually slow because it is done by software emulation On such systems configure option disable long double can be used for faster but less accurate com putations The Solaris time zone conversion ser
115. strip will install a stripped shared library 9 2 Windows You need to set up almost all the tools to make R and then run in a Unix like shell cd gnuwin32 make MkRules cd include make f Makefile win config h Rconfig h Rmath h make f Makefile win Alternatively in a cmd exe shell use cd include make f Makefile win config h Rconfig h Rmath h cd nmath standalone make f Makefile win This creates a static library libRmath a and a DLL Rmath dll If you want an import library libRmath dll a you don t need one use make f Makefile win shared implib To use the routines in your own C or C programs using MinGW include define MATHLIB STANDALONE include lt Rmath h gt and link against 1Rmath This will use the first found of libRmath dll a libRmath a and Rmath d11 in that order so the result depends on which files are present You should be able to force static or dynamic linking via including copying MkRules dist to MkRule local and selecting the architecture Chapter 9 The standalone Rmath library 36 Wl Bstatic lRmath Wl dynamic Wl Bdynamic l1Rmath or by linking to explicit files as in the test target in Makefile win this makes two exe cutables test ere which is dynamically linked and test static exe which is statically linked It is possible to link to Rmath d11 using other compilers either directly or via an import library if you make a MinGW import l
116. t does require a make command which supports the make j noption most do but on Solaris you need to select GNU make or dmake Where parallel checking of package sources is done a log file pngname 1log is left in the tests directory for inspection Alternatively the installed R can be run preferably with vanilla Then Sys setenv LC COLLATE C LC TIME C LANGUAGE en library tools testInstalledBasic both testInstalledPackages scope base testInstalledPackages scope recommended runs the basic tests and then all the tests on the standard and recommended packages These tests can be run from anywhere the basic tests write their results in the tests folder of the R home directory and run slightly fewer tests than the first approach in particular they do not test Internet access These tests work best if diff in Rtools exe for Windows users is in the path It is possible to test the installed packages but not the package specific tests by testInstalledPackages even if make install tests was not run Note that the results may depend on the language set for times and messages for maximal similarity to reference results you may want to try setting before starting the R session LANGUAGE en but use a UTF 8 or Latin 1 locale Chapter 3 Installing R under Windows 12 3 Installing R under Windows The bin windows directory of a CRAN site contains binaries for a base distribution and a large number of add
117. t version needs to be installed and its headers need to be on the C include path or in usr include tirpc Use of the X11 clipboard selection requires the Xmu headers and libraries These are normally part of an X11 installation e g the Debian meta package xorg dev but some distributions have split this into smaller parts so for example recent versions of Fedora require the libXmu and libXmu devel RPMs Some systems notably OS X and at least some FreeBSD systems have inadequate support for collation in multibyte locales It is possible to replace the OS s collation support by that from ICU International Components for Unicode http site icu project org and this provides much more precise control over collation on all systems ICU is available as sources and as binary distributions for at least most Linux distributions Solaris FreeBSD and AIX usually as libicu or icu4c It will be used by default where available including on OS X 10 4 should a very old or broken version of ICU be found this can be suppressed by without ICU The bitmap and dev2bitmap devices and function embedFonts use ghostscript http www ghostscript com This should either be in your path when the command is run or its full path specified by the environment variable R_GSCMD at that time A 2 1 Tcl Tk The tcltk package needs Tcl Tk gt 8 4 installed the sources are available at http www tcl tk To specify the locatio
118. tall those you want or need Ensure that the environment variable TMPDIR is either unset and tmp exists and can be written in and scripts can be executed from or points to the absolute path to a valid temporary directory one from which execution of scripts is allowed which does not contain spaces Choose a directory to install the R tree R is not just a binary but has additional data sets help files font metrics etc Let us call this place R HOME Untar the source code This should create directories src doc and several more under a top level directory change to that top level directory At this point North American readers should consult Section B 3 1 Setting paper size page 48 Issue the following commands configure make See Section B 5 Using make page 49 if your make is not called make Users of Debian based 64 bit systems may need configure LIBnn lib make Then check the built system works correctly by make check Failures are not necessarily problems as they might be caused by missing functionality but you should look carefully at any reported discrepancies Some non fatal errors are expected in locales that do not support Latin 1 in particular in true C locales and non UTF 8 non Western European locales A failure in tests ok errors R may indicate inadequate resource limits see Chapter 5 Running R page 21 More comprehensive testing can be done by make check devel or Most aspects will work wi
119. talled and so may need updating if the Java installation is updated This can be done by running R CMD javareconf which updates settings in both etc Makeconf and R_HOME etc ldpaths See R CMD javareconf help for details Another way of overriding those settings is to set the environment variable RB JAVA LD_LIBRARY_PATH before R is started hence not in Renviron which suffices to run already installed Java using packages For example R JAVA LD LIBRARY PATH usr lib jvm java 1 7 0 jre lib amd64 server It may be possible to avoid this by specifying an invariant link as the path For example on that system either of JAVA HOME usr lib jvm java 1 7 0 JAVA HOME usr lib jvm java 1 7 0 jre worked A 2 3 Other compiled languages Some add on packages need a C compiler This is specified by the configure variables CXX CXXFLAGS and similar configure will normally find a suitable compiler However in most cases this will be a C 98 compiler and as from R 3 1 0 it is possible to specify an alternative compiler for use with C 11 by the configure variables CXX1X CXX1XSTD CXX1XFLAGS and similar Again configure will normally find a suitable value for CXX1XSTD if the compiler given by CXX is capable of compiling C 11 code but it is possible that a completely different compiler will be needed it is for OS X 10 9 and Solaris for example Other packages need full Fortran 90 or later support For source files with extension
120. th paths containing spaces but external software used by R e g texi2dvi version 4 8 may not which use lib rather than lib64 for their primary 64 bit library directories for example if you configured R with without recommended Chapter 2 Installing R under Unix alikes 4 make check all see file tests README and Section 2 8 Testing a Unix alike Installation page 10 for the possibilities of doing this in parallel Note that these checks need the recommended packages to be installed If the command configure and make commands execute successfully a shell script front end called R will be created and copied to R_HOME bin You can link or copy this script to a place where users can invoke it for example to usr local bin R You could also copy the man page R 1 to a place where your man reader finds it such as usr local man man1 If you want to install the complete R tree to e g usr local lib R see Section 2 4 Installation page 6 Note you do not need to install R you can run it from where it was built You do not necessarily have to build R in the top level source directory say TOP SRCDIR To build in BUILDDIR run cd BUILDDIR TOP SRCDIR configure make and so on as described further below This has the advantage of always keeping your source tree clean and is particularly recommended when you work with a version of R from Subversion You may need GNU make to allow this and you will need no spaces in the
121. the installation default which is 32 bit for a combined 32 64 bit R installation 2 6 1 Multilib On Linux there is an alternative mechanism for mixing 32 bit and 64 bit libraries known as multilib If a Linux distribution supports multilib then parallel builds of R may be 8 with possible values 1386 x64 32 and 64 mainly on RedHat and Fedora whose layout is described here Chapter 2 Installing R under Unix alikes 10 installed in the sub directories lib 32 bit and lib64 64 bit The build to be run may then be selected using the setarch command For example a 32 bit build may be run by setarch i686 R The setarch command is only operational if both 32 bit and 64 bit builds are installed If there is only one installation of R then this will always be run regardless of the architec ture specified by the setarch command There can be problems with installing packages on the non native architecture It is a good idea to run e g setarch i686 R for sessions in which packages are to be installed even if that is the only version of R installed since this tells the package installation code the architecture needed At present there is a potential problem with packages using Java as the post install for a i686 RPM on x86_64 Linux reconfigures Java and will find the x86_64 Java If you know where a 32 bit Java is installed you may be able to run as root export JAVA_HOME lt path to
122. ties The principal difference is in the size of the pointers 64 bit builds have both advantages and disadvantages e The total virtual memory space made available to a 32 bit process is limited by the pointer size to 4GB and on most OSes to 3GB or even 2GB The limits for 64 bit processes are much larger e g 8 128TB R allocates memory for large objects as needed and removes any unused ones at garbage collection When the sizes of objects become an appreciable fraction of the address limit fragmentation of the address space becomes an issue and there may be no hole available that is the size requested This can cause more frequent garbage collection or the inability to allocate large objects As a guide this will become an issue with objects more than 10 of the size of the address space around 300Mb or when the total size of objects in use is around one third around 1Gb e Only 64 bit builds support long vectors those with 2 or more elements each of which needs at least 8GB of storage 16GB for a numeric vector e Most 32 bit OSes by default limit file sizes to 2GB and this may also apply to 32 bit builds on 64 bit OSes This can often be worked around and configure selects suitable defines if this is possible We have also largely worked around that limit on 32 bit Windows 64 bit builds have much larger limits e Because the pointers are larger R s basic structures are larger This means that R objects take more s
123. tion 31 Note that whereas UTF 8 locales are nowadays almost universally used locales such as en_GB use 8 bit encodings for backwards compatibility 7 1 2 Locales under Windows Windows also uses locales but specified in a rather less concise way Most users will encounter locales only via drop down menus but more information and lists can be found at http msdn microsoft com en us library hzz3tw78 v vs 80 or if Microsoft moves it yet again search for Windows language country strings It offers only one encoding per language Some care is needed with Windows locale names For example chinese is Traditional Chinese and not Simplified Chinese as used in most of the Chinese speaking world 7 1 3 Locales under OS X OS X supports locales in its own particular way but the R GUI tries to make this easier for users See http developer apple com documentation MacOSX Conceptual BPInternational for how users can set their locales As with Windows end users will generally only see lists of languages territories Users of R in a terminal may need to set the locale to something like en_GB UTF 8 if it defaults to C as it sometimes does when logging it remotely and in batch jobs note whether Terminal sets the LANG environment variable is an advanced option but the default Internally OS X uses a form similar to Linux the main difference from other Unix alikes is that where a character set is not specifie
124. to specify a 64 bit Java VM by e g JAVA_CPPFLAGS I JAVA_HOME include I JAVA_HOME include solaris JAVA_LD_LIBRARY_PATH JAVA_HOME 1ib amd64 server JAVA_LIBS L JAVA_HOME 1lib amd64 server R JAVA_HOME 1lib amd64 server 1jvm With Solaris Studio 12 23 on Sparc FCLIBS needs to be FCLIBS 1fai lfai2 lfsu and possibly other Fortran libraries but this suffices for the packages currently on CRAN Currently amd64 and sparcv9 builds work out of the box with Sun Studio 12ul but not Solaris Studio 12 2 and 12 3 libRblas so and lapack so are generated with code that causes relocation errors which is being linked in from the Fortran libraries This means that building 64 bit R as a shared library may be impossible with Solaris Studio gt 12 2 For a standard build the trick seems to be to manually set FLIBS to avoid the troublesome libraries For example on amd64 set in config site something like FLIBS_IN_SO R opt solarisstudio12 3 lib amd64 opt solarisstudio12 3 lib amd64 libfui so opt solarisstudio12 3 lib amd64 libfsu so For 64 bit Sparc set in config site something like FLIBS R opt solarisstudio12 3 prod lib sparc 64 lifai lsunimath lfai lfai2 lfsumai lfprodai lfminlai lfmaxlai lfminvai lfmaxvai lfui lsunmath lmtsk opt solarisstudio12 3 prod lib sparc 64 libfsu so 1 By default the Solaris Studio compilers do not by default conform to the C99 standard appendix F 8 9
125. trunk path to check out r devel into directory path which will be created if necessary The alpha beta and RC versions of an upcoming x y release are available from https svn r project org R branches R x y branch in the four week period prior to the release Note that https is required and that the SSL certificate for the Subversion server of the R project should be recognized as from a trusted source Note that retrieving the sources by e g wget r or svn export from that URL will not work and will give a error early in the make process the Subversion information is needed to build R The Subversion repository does not contain the current sources for the recom mended packages which can be obtained by rsync or downloaded from CRAN To use rsync to install the appropriate sources for the recommended packages run tools rsync recommended from the top level directory of the R sources If downloading manually from CRAN do ensure that you have the correct versions of the recommended packages if the number in the file VERSION is x y z you need to download the contents of http CRAN R project org src contrib dir where dir is x y z Recommended for r devel or x y patched Recommended for r patched respectively to directory src library Recommended in the sources you have unpacked After down loading manually you need to execute tools link recommended from the top level of the sources to make the r
126. ts such as installing source packages will not work To install info and PDF versions of the manuals use one or both of make install info make install pdf Once again it is optional to specify prefix libdir or rhome the PDF manuals are in stalled under the R home directory make install info needs Perl installed if there is no command install info on the system More precise control is possible For info the setting used is that of infodir default prefix info set by configure option infodir The PDF files are installed into the R doc tree set by the make variable rdocdir A staged installation is possible that it is installing R into a temporary directory in order to move the installed tree to its final destination In this case prefix and so on should reflect the final destination and DESTDIR should be used see http www gnu org prep standards html node DESTDIR html You can optionally install the run time tests that are part of make check all by make install tests which populates a tests directory in the installation 2 5 Uninstallation You can uninstall R by make uninstall optionally specifying prefix etc in the same way as specified for installation This will also uninstall any installed manuals There are specific targets to uninstall info and PDF manuals in file doc manual Makefile Target uninstall tests will uninstall any installed tests as well as removing the di rectory tests containing the t
127. ttempts by the LAPACK code to avoid computations entirely in extended precision registers so file src modules lapack dlamc f may need to be compiled without optimization Set the configure variable SAFE FFLAGS to the flags to be used for this file If configure detects GNU FORTRAN it adds flag float store to FFLAGS Other settings are needed when using icc on ix86 Linux for example Using mpc64 is preferable on more recent GCC compilers If you do manage to get R running on a new platform please let us know about it so we can modify the configuration procedures to include that platform If you are having trouble getting R to work on your platform please feel free to use the R devel mailing list to ask questions We have had a fair amount of practice at porting R to new platforms Appendix D The Windows toolset TO Appendix D The Windows toolset If you want to build R or add on packages from source in Windows you will need to collect install and test an extensive set of tools See http CRAN R project org bin windows Rtools for the current locations and other updates to these instructions Most Windows users will not need to build add on packages from source see Chapter 6 Add on packages page 22 for details We have found that the build process for R is quite sensitive to the choice of tools please follow our instructions exactly even to the choice of particular versions of the tools The build process for
128. uilding in a directory different from the sources there can be copies of config site in the source and the build directories and both will be read in that order In addition if there is a file R config it is read between the config site files in the source and the build directories There is also a general autoconf mechanism for config site files which are read before any of those mentioned in the previous paragraph This looks first at a file specified by the environment variable CONFIG SITE and if not is set at files such as usr local share config site and usr local etc config site in the area exemplified by usr 1ocal where R would be installed These variables are 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 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 config cache and it is a good idea to remove that file if it exists before re configuring Note that caching is turned off by default use the command line option config cache or C to enable caching B 3 1 Setting paper
129. vaVM framework Headers JAVA_LD_LIBRARY_PATH JAVA LIBS framework JavaVM The Apple developer versions of the JDK install somewhere like JAVA HOME Library Java JavaVirtualMachines 1 6 0 43 b01 447 jdk Contents Home The Oracle JDK can be specified explicitly by something like JAVA HOME Library Java JavaVirtualMachines jdk1 7 0 45 jdk Contents Home JAVA_CPPFLAGS I JAVA_HOME include I JAVA_HOME include darwin JAVA_LD_LIBRARY_PATH JAVA_HOME jre lib server JAVA_LIBS L JAVA_HOME jre lib server 1jvn in config site Appendix C Platform notes 62 Note that it is necessary to set the environment variable NOAWT to 1 to install many of the Java using packages C 3 7 Frameworks The CRAN build of R is installed as a framework which is selected by the default option configure enable R framework This is intended to be used with an Apple toolchain other compilers may not support frameworks correctly It is only needed if you want to build R for use with the R APP console and implies enable R shlib to build R as a dynamic library This option configures R to be built and installed as a framework called R framework The default installation path for R framework is Library Frameworks but this can be changed at configure time by specifying the flag enable R framework DIR or at install time as make prefix where you want R framework to go install Note that installation as a framework is non standard especia
130. version This may allow you to install a development version of R de selecting R APP and then switch back to the release version Chapter 5 Running R 21 5 Running R How to start R and what command line options are available is discussed in Section In voking R in An Introduction to R You should ensure that the shell has set adequate resource limits R expects a stack size of at least 8MB and to be able to open at least 256 file descriptors Any modern OS will have default limits at least as large as these but apparently NetBSD does not Use the shell command ulimit sh bash or limit csh tcsh to check R makes use of a number of environment variables the default values of many of which are set in file R HOME etc Renviron there are none set by default on Windows and hence no such file These are set at configure time and you would not normally want to change them a possible exception is RLPAPERSIZE see Section B 3 1 Setting paper size page 48 The paper size will be deduced from the LC_PAPER locale category if it exists and R_PAPERSIZE is unset and this will normally produce the right choice from a4 and letter on modern Unix alikes but can always be overridden by setting R PAPERSIZE Various environment variables can be set to determine where R creates its per session temporary directory The environment variables TMPDIR TMP and TEMP are searched in turn and the first one which is set and points
131. vices seem to be unreliable pre 1916 in Europe when daylight savings time was first introduced most often reporting in the non existent DST variant Using configure option with internal tzcode is recommended and required if you find time zone abbreviations being given odd values as has been seen on 64 bit builds without it When using the Oracle compilers do not specify fast as this disables IEEE arithmetic and make check will fail It has been reported that some Solaris installations need INTERNET LIBS 1socket lns1 on the configure command line or in file config site however there have been many successful installs without this A little juggling of paths was needed to ensure GNU libiconv in usr local was used rather than the Solaris iconv CC cc xc99 CFLAGS 0 xlibmieee F77 95 FFLAGS 0 CXX CC library stlport4 CXXFLAGS 0 FC f95 FCFLAGS FFLAGS FCLIBS 1fai lfsu R LD LIBRARY PATH usr local lib opt csw gcc4 lib opt csw lib For a 64 bit target add m64 to the compiler macros and use something like LDFLAGS L usr local lib sparcv9 Or LDFLAGS L usr local lib amd64 as appropriate It will also be necessary to point pkg config at the 64 bit directories e g one of D including gcc for Sparc from Oracle Appendix C Platform notes 64 PKG_CONFIG_PATH opt csw lib amd64 pkgconfig usr lib amd64 pkgconfig PKG_CONFIG_PATH opt csw lib sparcv9 pkgconfig usr lib sparcv9 pkgconfig and
132. vignettes Note that this gives you a command line application using readline for command editing The X11 graphics device will work if a suitable X server is running and the standard Unix alike ways of installing source packages work There was a bug in the usr lib tkConfig sh script in the version we looked at which needs to have TK LIB SPEC 1tk84 The overhead of using shell scripts makes this noticeably slower than a native build of R on Windows T Windows DLLs need to have all links resolved at build time and so cannot resolve against R bin Appendix C Platform notes 69 Even when R could be built not all the tests passed there were incorrect results from wide character regular expressions code and from sourcing CR delimited files Do not use Cygwin s BLAS library it is known to give incorrect results C 8 New platforms There are a number of sources of problems when installing R on a new hardware OS plat form These include Floating Point Arithmetic R requires arithmetic compliant with IEC 60559 also known as IEEE 754 This mandates the use of plus and minus infinity and NaN not a number as well as specific details of rounding Although almost all current FPUs 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 Sun Sparc SGI IRIX and ix86 Linux require no special action FreeBSD requires a call to the macro fpset
133. x64 F77 gfortran maix64 FC gfortran maix64 and was also able to build with the IBM x1c and Hitachi 90 compilers by OBJECT_MODE 64 CC xlc q64 CXX g maix64 F77 90 cpu pwr4 hf77 parallel 0 i L 03 64 FC f90 cpu pwr4 hf77 parallel 0 i L 03 64 FLIBS L opt ofort90 lib lhf90vecmath 1hf90math 1f90 Some systems have 95 as an IBM compiler that does not by default accept FORTRAN 77 It needs the flag qfixed 72 or to be invoked as xlf_r The AIX native iconv does not support encodings latin1 nor and so cannot be used As far as we know GNU libiconv could be installed Fan Long reports success on AIX 5 3 using OBJECT MODE 64 LIBICONV where libiconv installed CC xlc r q64 CFLAGS 0 qstrict CXX xlC r q64 CXXFLAGS 0 qstrict F77 xlf_r q64 AR ar X64 CPPFLAGS I LIBICONV include I usr lpp X11 include X11 LDFLAGS L LIBICONV lib L usr lib L usr X11R6 lib Appendix C Platform notes 67 On one AIX 6 x system it was necessary to use Rb SHELL to set the default shell to be Bash rather than Zsh Kurt Hornik and Stefan Theussl at WU Wirtschaftsuniversitat Wien successfully built R on a powerpc 8 CPU Power6 system running AIX 6 1 configuring with or without enable R shlib Ei ji Nakama s support is gratefully acknowledged It helps to describe the WU build environment first A small part of the software needed to build R and or install pa
134. y configure win script or a file src Makefile win with some exceptions where the package is known to have an architecture independent configure win or if force biarch or a field in the DESCRIPTION file is used to assert so In those cases only the current architecture is installed Further sub architectures can be installed by R CMD INSTALL libs only pkg using the path to R or R arch to select the additional sub architecture There is also R CMD INSTALL merge multiarch to build and merge the two architectures starting with a source tarball Chapter 6 Add on packages 27 6 3 5 Byte compilation The base and recommended packages are byte compiled by default Other packages can be byte compiled on installation by using R CMD INSTALLwith option byte compile or by install packages type source INSTALL opts byte compile Not all contributed packages work correctly when byte compiled for example because they interfere with the sealing of namespaces For most packages especially those which make extensive use of compiled code the speed up is small Unless a package is used frequently the time spent in byte compilation can outweigh the time saved in execution also byte compilation can add substantially to the installed size of the package Byte compilation can be controlled on a per package basis by the ByteCompile field in the DESCRIPTION file 6 4 Updating packages The command update packages is the
135. y 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 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 If you need to re configure R with different options you may need to run make clean or even make distclean before doing so 1 We have measured 15 2096 on i686 Linux and around 10 on x86_64 Linux Appendix B Configuration on a Unix alike 48 B 2 Internationalization support Translation of messages is supported via GNU gettext unless disabled by the configure option disable nls The configure report will show NLS as one of the Additional capabilities if support has been compiled in and running in an English locale but not the C locale will include Natural language support but running in an English locale in the greeting on starting R B 3 Configuration variables If you need or want to set certain configure variables to something other than their default you can do that by either editing the file config site which documents many of the variables you might want to set others can be seen in file etc Renviron in or on the command line as configure VAR value If you are b

Section “Installing packages” in R Installation and Administration

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Section &ldquo;Installing packages&rdquo; in R Installation and Administration

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Section “Installing packages” in R Installation and Administration