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Section “Installing packages” in R Installation and Administration

1. 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 1ib64 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 F77 sunf95 Appendix C Platform notes 56 FFLAGS 05 libmil nofstore FPICFLAGS Kpic CXX sunCC library stlport4 CXXFLAGS x05 xlibmil nofstore features
2. 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 llvm gr 4 2 F77 gfortran 4 2 arch x86 64 FC F77 OBJC clang Full names are not needed but help to ensure that the intended compilers are used The recommended Fortran compiler defaults to 32 bit so arch x86_64 is needed For a 32 bit build add arch i386 to all compiler commands 4 Apple s clang should be able to some builds of gcc can but not all built with Objective C support work Appendix C Platform notes 58 The OpenMP support in this version of gcc is problematic so the CRAN build is con figured with disable openmp Pre compiled versions of many of the Section A 2 Useful libraries and programs page 37 are available from http r research att com libs You will most likely want at least jpeg libpng and readline and perhaps tiff The Accelerate library can be used via the configuration options with blas framework Accelerate with lapack to provide 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 option
3. 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 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 3 such as sort find and perhaps make Appendix D The Windows toolset TO You may need to set the environment variable CYGWIN to a value including nodosfilewarning to suppress messages about Windows style paths D 4 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 Wi
4. 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 locations of the Tcl Tk files you may need the configuration options with tcltk use Tcl Tk or specify its library directory with tcl config TCL_CONFIG specify location of tclConfig sh with tk config TK_CONFIG specify location of tkConfig sh or use the configure variables TCLTK_LIBS and TCLTK_CPPFLAGS to specify the flags needed for linking against the Tcl and Tk libraries and for finding the tcl h and tk h headers respectively If you have both 32 and 64 bit versions of Tcl Tk installed specifying the paths to the correct config files may be necessary to avoid confusion between them Versions of Tcl Tk up to 8 5 12 and 8 6 0 have been tested including most versions of 8 4 x but not recently 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 HUME etc ldpaths or a sub archi
5. 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 Chapter 2 Installing R under Unix alikes 9 usr 1ib64 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 R 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 appropriate bin directory R HOME bin i386 or R HOME bin x64 For backwards compatibility with R lt 2 12 0 there are executables R_HOME bin R exe or R_HOME 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 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
6. 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 eas ier 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 specified 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
7. TK XINCLUDES I opt X11 include usr lib pkgcon Appendix C Platform notes 59 There is also a native Aqua version of Tcl Tk which produces widgets in the native OS X style this wil 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 Tk 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 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 System Library C 4 5 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 runtime JRE Mountain Lion does not come with an installed JRE and an upgrade to Mountain Lion 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 for security reasons you may want need to ins
8. The option with lapack is used since MKL contains a tuned copy of 1 and perhaps others Appendix A Essential and useful other programs under a Unix alike 43 LAPACK as well as BLAS see Section A 3 2 LAPACK page 44 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 lmkl gf l1p64 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 MKL NUM THREADS and in recent versions seems to produce 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 gnu thread a MKL LIB PATH libmkl core a Wl end group lgomp lpthread Thanks to Ei ji Nakama The MKL documentation includes a link line advisor which will suggest appropri ate incantations an on line version was available at http software intel com en us articles intel mkl link line advisor PUE a d uat E The default linking model which was also used by version 9 of MKL can be used by with blas lmkl lguide lpthread but this may
9. 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 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 Rtools30 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 installation 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 als
10. Window menu and item Installer Log The full output select Show All Log is useful for tracking down problems For building R from source see Section C 4 OS X page 57 4 1 Running R under OS X There are two ways to run R on OS X from the 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 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 0 library and that warnings messages and other output to stderr are highlighted in bold 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 frameweork folder This does leave some links in usr bin If you want to get rid of R more completely using a
11. development version needs to be installed and its headers need to be on the C include path and configure tries usr include tirpc if the headers are not found on the standard include path The R sources contain a fall back implementation of XDR which is likely to suffice on both 32 and 64 bit platforms l also known as IEEE 754 Note that C11 compilers when they appear need not be C99 compliant R requires support for double complex which is optional in C11 but is mandatory in C99 w std c99 excludes POSIX functionality but config h will turn on all GNU extensions to include the POSIX functionality apparently when built by default but not for example as built for Fedora 15 IS Appendix A Essential and useful other programs under a Unix alike 37 The OS needs to have enough support for wide character types this is checked at configuration 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 O 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
12. 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 fullrefman 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 IATEX 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 which is part of the current default
13. not recommended by setting the environment variable R 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 use Sys getenv R_LIBS_USER within an R session to see what it is but only is used if the corresponding directory actually exists which by default it will not Both R_LIBS_USER and R_LIBS_SITE can specify multiple library paths separated by colons semicolons on Windows 1 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 22 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 If installing packages on a Unix alike to be used by other users ensure that the system umask is set to give sufficient permissions see also Sys umask in R To a large extent this is unnecessary i
14. 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 the appropriate ATEX package incon solata or bera installed 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 1m Using the Latin Modern fonts These are not often installed as part of a TEX dis tribution but can obtained from http www ctan org tex archive fonts ps typei 1m and mirrors This uses fonts rather similar to Computer Modern but is not so good on screen as times 3 Many Debian Ubuntu systems use a rather old version of TeXLive and so need Debian package texlive fonts extra installed Fedora prior to 18 used an even older ver sion of TeXLive the best option is to update to TeXLive 2012 from the sources or see http fedoraproject org wiki Features TeXLive Chapter 2 Installing R under Unix alikes 6 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 type1 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 re
15. 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 8 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 33 9 The standalone Rmath library The routines supporting the distribution and special functions in R and a few others are 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
16. GU ERE Oc TEM 57 CAD Snow Leopard i erwm bee bere EE ER ORE TIERE 58 CA2 Mi Otis sare petits ch aa ese neath eae te MID LATE 58 C 43 Mountain Lion ec eed ndedeeeteaaddasde niece 58 CAA Tcl Tk headers aud librari s ise eie rna 58 CAS Maver FREE ERIT 59 CA6 Brameworks 2 e e E ECCLE ea eesaad kaw 60 CAT Building Rapp acces re reri eme Ere ta dee 60 7 5 SO BPISL isl epube t a ERR RCaTeUMDU eEEERPENRMS eed 60 55 1 Using goQuoussestesfecie ARR X RERR ARIS DPE S eeS REP 63 CO AIX S Lect tinea eee deter didt aetna ang oes 64 Clk CY IRR 66 7 8 New platforms sinc eeeeenss nini onia in acte a os A RR A 66 Appendix D The Windows toolset 68 DA 11 LT 69 D 2 The Inno Setup installer seeeesseeeeeeeeseeee 69 D 3 The command line tools 0 cece eee eee eens 69 D 4 The MinGW w64 toolchain 0 0 0 cece eee eee eee 70 D 5 Useful additional programs 0 00 cece eee eee eee 70 Function and variable index 71 Concept INGEN is esq soe sac dace dc dod Roa Oa qx T2 Environment variable index 73 iii 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 t
17. 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 2 ie you try changing from French to Russian except in a UTF 8 locale you will most likely find messages change to English Chapter 7 Internationalization and Localization 31 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 f
18. 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 two Apple packages org r project R Leopard fw pkg and org r project R Leopard GUI pkg You can use pkgutil unlink not supported by Lion or later to remove their files or pkgutil forget if you want the Apple Installer Chapter 4 Installing R under OS X 19 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 Chapter 5 Running R 20 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 R PAPERSIZE see Section B 3 1 Setting paper size page 47 The
19. 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 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 51 Library paths specified as L 1ib 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 Variabl
20. a 32 bit build of R R devel win32 msi and from a 64 bit build of R R devel win64 msi optionally including 32 bit files by setting the macro HOME32 when the name is R devel 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 the 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 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 l
21. allocations You can opt out of this by setting LEA MALLOC NO in MkRules dist in which case the malloc in msvcrt d11 is used This does impose a considerable performance penalty 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 100 reliable e It is possible mainly for those working on R itself to set the make or environment variable R NO BASE COMPILE to a non empty value which inhibits the byte compilation of the base and recommended packages 3 1 4 Building the bitmap files The file R_HOME library grDevices libs i386 x64 Rbitmap d1l is not built auto matically Running make in R_HOME src gnuwin32 bitmap or make bitmapdll in R HUME src gnuwin32 should build Rbitmap dll and install it under R_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 li braries built by Simon Urbanek at http www rforge net Cairo files cairo curren
22. 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 pkg Chapter 6 Add on packages 28 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 Rcmd 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 29 7 Internationalization and Localization Internationalization 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 m
23. 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 mani If you want to install the complete R tree to e g usr local lib R see Section 2 4 Installation page 6 Note you do not need to install R you can run it from where it was built You do not necessarily have to build R in the top level source directory say TOP_SRCDIR To build in BUILDDIR run cd BUILDDIR TOP SRCDIR configure make and so on as described further below This has the advantage of always keeping your source tree clean and is particularly recommended when you work with a version of R from Subversion You may need GNU make to allow this and you will need no spaces in the path to the build directory 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 an
24. bit and 64 bit libraries known as multilib If a Linux distribution supports multilib then parallel builds of R may be installed in the sub directories lib 32 bit and 1ib64 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 1386 RPM on x86_64 Linux reconfigures Java and will find the x86_64 Java If you know where a 32 bit Java is installed you may be able to run as root export JAVA HOME path to jre directory of 32 bit Java setarch i686 R CMD javareconf to get a suitable setting When this mechanism is used the version of Rscript in e g usr bin will be the last installed but an architecture specific version will be available in e g usr 1ib64 R bin Normally all installed architectures will run on the pla
25. 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 47 Issue the following commands configure make See Section B 5 Using make page 48 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 20 More comprehensive testing can be done by make check devel or 1 which use lib rather than 1ib64 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 If the command configure and make commands execute successfully a shell script front end called R will be created and copied to R_HOME
26. 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 directory in MkRules local 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 devel 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 devel 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 Chapter 3 Installing R under Windows 17 The MSI installer can be built both from
27. like Fedora s xorg x11 fonts 75dpi xorg x11 fonts 100dpi xorg xli fonts I1508859 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 53 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 d X k X x 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 IS
28. 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 7 2 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 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 LD 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 7 2 needed CC opt csw gcc4 bin gcc m32 CPPFLAGS I opt csw include I usr local include F77 2 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 L opt csw lib is needed since TexLive 2011 was built using 32 bit gcc and we need opt csw lib in R LD LIBRARY PATH For an amd64 target with gcc 4 7 2 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 li
29. part of the default install and the X server may need to be configured to use them They might be under the X11 fonts directory or elsewhere for example usr share fonts default 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 54 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
30. project should be recognized as from a trusted source Note that retrieving the sources by e g wget r or svn export from that URL will not work and will give a error early in the make process the Subversion information is needed to build R The Subversion repository does not contain the current sources for the recommended 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 respec tively to directory src library Recommended in the sources you have unpacked After downloading manually you need to execute tools link recommended from the top level of the sources to make the requisite links in src library Recommended A suitable in cantation 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
31. 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 ix86 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 36 and install 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 a valid temporary directory one from which execution of scripts is allowed Choose a directory to install the R tree R is not just a binary but has additional data sets
32. set in config site something like FLIBS R opt solarisstudio12 3 prod lib sparc 64 lifai lsunimath lfai lfai2 lfsumai lfprodai lfminlai lfmaxlai lfminvai lfmaxvai lfui lsunmath lmtsk opt solarisstudio12 3 prod lib sparc 64 libfsu so 1 By default the Solaris Studio compilers do not by default conform to the C99 standard appendix F 8 9 on the return values of functions such as log use xlibmieee to ensure this You can target specific Spare 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 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
33. tmplrefstatic 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 FreeBSD Rainer Hurling has reported success on amd64 FreeBSD 9 0 and on earlier versions in the past and Brian Ripley tested amd64 FreeBSD 8 2 Since Darwin the base OS of OS X is based on FreeBSD we find testing on Darwin tends to pick up most potential problems on FreeBSD However FreeBSD lacks adequate character type e g which are alphabetic and collation support for multi byte locales but a port of ICU is available and does not yet implement C99 complex math functions for which R s substitutes are used The native BSD make suffices to build R but a number of packages require GNU make despite the recommendations of the Writing R Extensions manual The simplest way to get the additional software needed to build R is to install a pre compiled version first e g by pkg add r R on the system this was tested on this installed Tcl Tk blas lapack and
34. 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 1f77blas latlas if the libraries are in the library path otherwise by 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 at least on version 3 8 0 and later 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 acm15 1 0 gfortran64 1ib is in the LD LIBRARY PATH For other compilers see the ACML documentation There is a multi threaded Linux versi
35. 08859 2 75dpi and xorg x11 fonts cyrillic shown in the listing above Multi byte encodings most commonly UTF 8 are even more complicated There are few fonts in iso10646 1 the Unicode encoding and they only contain a subset of the available glyphs and are often fixed width designed for use in terminals In such locales fontsets are used made up of fonts encoded in other encodings If the locale you are using has an entry in the XLC_LOCALE directory typically usr share X11 locale it is likely that all you need to do is to pick a suitable font specification that has fonts in the encodings specified there If not you may have to get hold of a suitable locale entry for X11 This may mean that for example Japanese text can be displayed when running in ja_JP UTF 8 but not when running in en_GB UTF 8 on the same machine although on some systems many UTF 8 X11 locales are aliased to en_US UTF 8 which covers several character sets e g ISO 8859 1 Western 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
36. 6 Linux require no special action FreeBSD requires a call to the macro fpsetmask 0 and OSF1 requires that computation be done with a ieee_with_inexact flag etc On a new platform you must find out the magic recipe and add some code to make it work This can often be done via the file config site which resides in the top level directory Beware of using high levels of optimization at least initially On many compilers these reduce the degree of compliance to the IEEE model For example using fast on the Solaris Studio compilers has caused R s NaN to be set incorrectly 6 Windows DLLs need to have all links resolved at build time and so cannot resolve against R bin Appendix C Platform notes 67 Shared Objects There seems to be very little agreement across platforms on what needs to be done to build shared objects there are many different combinations of flags for the compilers and loaders 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 xmkm 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
37. 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 X11 jpegQ pngO and tiff graphics devices uses the cairo and optionally Pango libraries Cairo version 1 2 0 or later is required Pango needs to be at least version 1 10 and 1 12 is the earliest version we have tested For Fedora users we believe the pango devel RPM and its dependencies suffice R checks for 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 9 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 T texi2dvi is normally a shell script Some versions e g that from texinfo 4 13a need to be run under bash rather than a Bourne shell as on say Solaris Appendix A Essential and useful other programs under a Unix alike 38 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
38. ARY PATH 39 40 RDI BS MNT T E N 21 R LIBS SITE 0 0000 eee 21 R LIBS USER teree dag URNA E Deni Od 21 R_PAPERSIZE 00 00s 5 20 47 48 R_PDFVIEWER 00000 000 c cece eeeeeeeeeeeeeees 48 R_RD4PDF 2 eee 6 48 69 ROSHELL esee eee 64 RUUSER eene A E TE 20 T N O 37 TAR OPTIONS esse 1 32 TEMP 0 0 oo cece eee eeeeeeeeeeeeeeeeeeeeeeeeees 20 n 20
39. D qc 24 6 3 3 Customizing package compilation 000 24 6 3 4 Multiple sub architectures 00 0000 ccc eee eee ees 25 6 3 5 Byte compilation s444 22642 peeecdegedie santana riksini aas 25 6 4 Updating packages 0 cece eee eee re 26 6 5 Removing packages 0 cece cence e ne 26 6 6 Setting up a package repository 0 cece eee 26 6 7 Checking installed source packages 0000 ence e eee 2T 7 Internationalization and Localization 29 T NEN ERTEILEN 29 7 1 1 Locales under Unix alikes 0 00 c cece eee eee 29 7 1 2 Locales under Windows cc cece cence eee eeees 30 7 1 3 Locales under OS X ccc EREET ERER E 30 7 2 Localization of messages 0 e eee ee 30 8 Choosing between 32 and 64 bit builds 32 9 The standalone Rmath library 33 91 Unix Alikes iux cag aide bsp eee e dct eR M ee ates 33 9 2 WindOWSeassostieic e t Un RPG EP dened ECL TER Aq quee tees 34 Appendix A Essential and useful other programs under a Unix alike 36 A 1 Essential programs and libraries lssssselseelseessse 36 A 2 Useful libraries and programs sssssssssees esee 37 EM so MNA ROREM 39 A22 Java Support cxi eser ERPRPR EROS E CENAMERRIM PRESA 39 AS Linear algebras t re erre LAU eere hene 40 A9 T BISASaezoceii is ek ER Sen Om ELNTORREPE REOR dditan ueri 40 ACS GATLADSGS eR t idan oe Hh t
40. GS 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 been reported to be a problem on HP UX with the native cc In this case use a different compiler or a front end shell script which does the re ordering These flags can also be used to build a faster running version of R On most plat forms 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 lwn net Articles 192624 Tuning compilation to a specific CPU family e g mtune native for gcc can give worthwhile performance gains especially on older archi tectures such as ix86 B 3 4 Making manuals The default settings for making the manuals are controlled by R_RD4PDF 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 th
41. R Installation and Administration Version 3 1 0 Under development 2013 03 29 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 con ditions 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 lan guage under the above conditions for modified versions except that this permission notice may be stated in a translation approved by the R Core Team Copyright 2001 2013 R Core Team Table of Contents LA o Pm 1 1 1 Getting and unpacking the sources slessseeeeeeseeeeee 1 1 2 Getting patched and development versions 00 1 1 2 1 Using Subversion and rsync cece eee eee 1 2 Installing R under Unix alikes 3 2 1 Simple compilation sesser ee rhe EI rra Rr tee eed 3 2 2 Help Options so 2ececvs coisa esse EREN e Red bre o RR eek 4 2 3 Making the manuals 00 00 e cece ene e 4 2 4 Installaatio escret erret Eom xc deep ERR RS ERERE EE es 6 2 5 Unmstallatiotisssiss sete bee RAm eI prete ew Ri DE Rana 8 2 6 Sub architecturessuuisese sere nee Ap RR Rue eee hells 8 2 6 1 Multilib cr i
42. adable on screen than the previous two options There are three fonts for which it will need to use bitmapped fonts tctt0900 600pk tctt1000 600pk and tcrm1000 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 R_RD4PDF 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 The usual default value for R_RD4PDF is times inconsolata hyper omit hyper if you do not want hyperlinks e g for printing the manual or do not have I3TEX package hyperref and omit inconsolata if you do not have TFX package inconsolata installed 2 4 Installation To ensure that the installed tree is usable by the right group of users set umask appropriately perhaps to 022 before unpacking the sources and throughout the build process After configure make make check or when building outside the source TOP_SRCDIR configure etc have been completed 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 end shell script and other scripts and executables prefix man ma
43. ake 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 Chapter 2 Installing R under Unix alikes 8 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 test results 2 6 Sub architectures Some platforms can support c
44. akefile 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 1ibRmath a and a DLL Rmath d11 If you want an import library 1ibRmath 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 1ibRmath d11 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 35 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 executables test exe which is dynamically linked and test static exe which is stat ically 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 library as above you will create a file Rmath def which can be used possibly after editing to create an import library for other systems such as Visual C If you make use of dynamic linking you should us
45. ant 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 OO can select amongst those 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 23 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 packag
46. ar 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 6 and perhaps also include the option no same permissions These options can also be set in the TAR OPTIONS environment variable if more than one option is included they should be 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 t
47. ard64 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 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 5 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 issues Solaris 9 and earlier are now so old that it is unlikely that R is still used with them and they will not be considered here The Solaris versions of several of the tools needed to build R e g make ar and 1d are in usr ccs bin so if using those tools ensure this is in your path A version of the preferred GNU tar is if installed in usr sfw bin 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 Appendix C Platform notes 61 A large selec
48. arnings about the use of auto import Setting FLIBS explicitly seems needed currently as the auto detection gives an incorrect value You will need the tetex extra Cygwin package to build NEWS pdf and the vignettes Note that this gives you a command line application using readline for command editing The X11 graphics device will work if a suitable X server is running and the standard Unix alike ways of installing source packages work There was a bug in the usr lib tkConfig sh script in the version we looked at which needs to have TK LIB SPEC 1tk84 The overhead of using shell scripts makes this noticeably slower than a native build of R on Windows Even when R can 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 ix8
49. b amd64 Appendix C Platform notes 64 C 6 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 MO DE 64 CC gcc maix64 CXX g maix64 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 O i L 03 64 FLIBS L opt ofort90 lib lhf90vecmath lhf90math 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 On one AIX 6 x system it was necessary to use R SHELL to set the default
50. be able to build most of the manuals unless you have makeinfo version 4 7 or later 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 should be possible to use makeinfo version 5 0 but e g 4 13 produces better formatted output The PDF documentation including doc NEWS pdf and building vignettes needs pdftex and pdflatex We require IATEX 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 IXTEX package hyperref and we recommend that the TEX distribution used is kept up to date A number of IATEX packages are required including urlsty and listings sty 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 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
51. be compiled into a dynamic library and there may be a performance penalty So you probably only want this if you will be using an application which embeds R Note that C code in packages installed on an R system linked with 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 20 on i686 Linux and around 10 on x86_64 Linux Appendix B Configuration on a Unix alike 4T 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 othe
52. cheme 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 Chapter 6 Add on packages 27 e source located at src contrib and containing tar gz files Other forms of compression 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 snowleopard contrib 3 y for R versions 3 y z and containing tgz files e mac binary leopard located at bin macosx leopard contrib 2 y for R ver sions 2 y z and containing tgz files Each terminal directory must also contain a PACKAGES file This can be a concatenation of the 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 downl
53. d 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 refman Printed versions of the help pages for selected base packages over 1900 pages Chapter 2 Installing R under Unix alikes 5 R FAQ 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
54. e exe and d1l files and some configuration files in the etc directory 3 1 1 Getting the tools If you want to build R from the sources you will first need to collect install and test an extensive set of tools See Appendix D The Windows toolset page 68 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 68 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 0 tar gz from CRAN Open a command window or another shell at directory R HOME and run tar xf R 3 1 0 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 tar no same owner xf R 3 1 0 tar gz or perhaps better set the environment variable TAR OPTIONS to the value no same owner no same permissions Chapter 3 Installing R und
55. e define MATHLIB_STANDALONE define RMATH DLL include lt Rmath h gt 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 36 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 49 Some add on packages also need a C compiler 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 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
56. e 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 Sun 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 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 49 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 according
57. ecify 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 and most OSes have only one charset each for most languages 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 Localization 30 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
58. enigedd aonere eae dkes 41 ASLA ACM erroreen nre per irre epe oiu 41 A 3 1 3 Goto and OpenBLAS sssssssssssssssss 42 A 3 1 4 Intel MK oss fates sere etm reme Een ees 42 A 3 1 5 Shared BLAS is ccierehr et eee ee UE EE 43 A 3 2 IGAPACK cerere neces e aint Retna PR ERO IRURE 44 A33 Caveats isses xk iow tee ase ira Sun teow eed dee ube doe ccs apenas RR 45 i Appendix B Configuration on a Unix alike 46 B 1 Configuration options sssseesesee aee 46 B 2 Internationalization support sssesseee eee eee 47 B 3 Configuration variables 0000 eee eee eens 4T B 3 1 Setting paper SiZe nec iecur de Alen abe ara idee dela 4T B 3 2 Setting the browsers esses 48 B 3 3 Compilation flags 2 etrRR eet Ra ERR evden needs 48 B 3 4 Makimng manual8 ect atebese rade UE EEE E 48 BA Setting the shell secet rr bI 48 Bb Using make eseceso ep exter x cec tide tae maaan 48 B 6 Using FORTRAN 52 rer ebRE RYDER EDR r FE 49 B 6 l Using gfortran 2 ge ER rU EORR DRE REUS 49 B 7 Compile and load flags 0 0 50 Appendix C Platform notes 52 C L XLIJ88U6S i 4 serre POP ERR u esrb EA E LIPS 52 C2 Eh a ob cO EPI PPM 53 C2 I Clan cesi orietan eR CAE IIR RE RE E Ed 55 7 2 2 Intel compilers exierit ettet ERES pese e 55 C 2 3 Oracle Solaris Studio compilers 000 200 55 Ci FreeBSD 1 5 2c ce ree REX e epe EH C ER a PIE Tees 56
59. er Windows 13 It is also possible to obtain the source code using Subversion see Chapter 1 Obtaining R page 1 for details If you are not using a tarball you need to obtain copies of the recommended pack ages 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 Rtool1s30 exe If instead you choose to do completely manual build you will also need The Tcl Tk support files are contained in Rtools30 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 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 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 8d or libjpeg turbo copy file src gnuwin32 MkRules dist to src gnuwin32 MkRules local and edit
60. erit 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 A 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 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 sp
61. es 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 0 0ReadMe 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 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 68 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 R INSTALL TAR to tar exe If you have only a source package that is known to work with current R and just want a binary Windows build of it you could make use of the buildin
62. es such as CPICFLAGS are determined where possible by configure Some systems allows two types of PIC flags for example fpic and fPIC and if they differ the first allows only a limited number of symbols in a shared object Since R as a shared library has about 6200 symbols if in doubt use the larger version To compile a profiling version of R one might for example want to use MAIN CFLAGS pg MAIN FFLAGS pg MAIN_LDFLAGS pg on platforms where pg cannot be used with position independent code Beware it may be necessary to set CFLAGS and FFLAGS in ways compatible with the libraries to be used one possible issue is the alignment of doubles another is the way structures are passed On some platforms configure will select additional flags for CFLAGS CPPFLAGS FFLAGS CXXFLAGS and LIBS in R_XTRA_CFLAGS and so on These are for options which are always required for example to force IEC 60559 compliance Appendix C Platform notes 52 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
63. ests 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 43 Alternatively the installed R can be run preferably with vanilla Then 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 and on some systems need the collation locale set manually the R code tries to do so but it may not be possible to reset it so if needed try setting the environment variable LC_COLLATE to C before starting R 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 resu
64. g 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 appropriate to both architectures use option force biarch otherwise R CMD INSTALL merge multiarch can be applied to a source tarball to merge separate 32 and 64 bit installs This can only be applied to a tarball and will only succeed if both installs succeed If you have a package without compiled code and no Windows specific help you can zip up an installation on another OS and install from the that zip file on Windows However such a package can be installed from the sources on Windows without any additional tools for a small number of CRAN packages where this is known to be safe and is needed by the autobuilder this is the default Look at the source of tools install_packages for the list It can also be specified in the package s DESCRIPTON file Chapter 6 Add on packages 24 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 defa
65. gcc 4 6 2 which includes gfortran46 A listing of dependencies not necessarily for current R can be found at http www freebsd org ports lang html you will however also need a TEX system to build the manuals Then R itself can be built by something like configure CC gcc46 F77 gfortran46 CXX g 46 FC gfortran46 There are also FreeBSD packages for a small eclectic collection of CRAN packages Beware that the lack of adequate support for non ASCII characters in UTF 8 locales has many consequences in R for example names will not be recognized as alphabetic by make names TeXLive is recommended Appendix C Platform notes 57 C 4 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 You may also need to install an X sub system or you will need to configure with without x X is part of the standard OS X distribution in versions prior to Mountain Lion but not always installed For Mountain Lion see http xquartz macosforge org some people prefer to use XQuartz on earlier versions of OS X instead of the Apple version 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 Co
66. he MiKTeX http www miktex org distribution of IXTEX includes a suitable port of pdftex The basic version of MiKTeX almost suffices the grid vignettes need fancyvrb sty but it will install the 15Mb 1m package if allowed to although that is not actually used The Rtools exe installer does not include any version of I3TEX It is also possible to use the TeXLive distribution from http www tug org texlive Please read Section 2 3 Making the manuals page 4 about how to make fullrefman pdf and set the environment variable R_RD4PDF suitably ensure you have the required fonts installed or that MiKTeX is set up to install IATEX on first use D 2 The Inno Setup installer To make the installer package R devel win exe we currently require the Unicode ver sion 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 local 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 cygwin com
67. he 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 eg GNU tar version 1 15 or later or that from the libarchive as used on OS 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 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 0 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
68. ibrary 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 their results in the tests folder of the R home directory as given by R home and hence may need to be run under the account used to install R Chapter 4 Installing R under OS X 18 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 0 pkg and install it This runs on OS X 10 6 and later Snow Leopard Lion Mountain Lion 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 To install just double click on the icon of the file you downloaded Note that Xll based Tcl Tk needs to be installed separately if needed from http cran r project org bin macosx tools and for Mountain Lion or later XQuartz will also need to be installed to use Tk On Mountain Lion with GateKeeper active you may need to right control click on some of the packages and select Open This is an Apple Installer package If you encounter any problem during the installation please check the Installer log by clicking on the
69. ich can be used to de compress 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 COhflgure lesser irigis menies 3 4 6 47 48 I install packages 2 bv RR ER RP E PERMOS 22 M MAKE cen deities i teates vee eb eek ea ER RETO 48 71 R H ME IMs RE E eee G80 Rade Aff ee 3 remove packageS eene 26 upda te packages lo ca e a UR REG 26 Concept index Concept index F FORIRAN ZoiGIeeeiGc e er E UEPePERERAECPLE 49 EreeB91 id ihenzerkenest eek ur M E EG 56 I Installation 2 c2 caugies taeda cktaasnsetaelt sans 6 Installing under Unix alikes 3 Installing under Windows 5 12 Internationalization eese 29 L LAPACK library iiim Ree 44 58 62 TJbYaeSu is lZoresi6LeswesriFbeRS NAR p 21 Libraries managing ssseeeeeese 21 Libraries S106 re RYE P added SERE WR 21 Libraries USP resis o te ree RD E ree pO exe 21 DInibb iickeneereisuRERRee n EESUU RUEDA 3 53 ocal seu RR RUFEN REQUE 29 Localization 2i2 2 20 bl f ee Yer iceren 29 M Manuals ES EREVERIPEDIMRI ERE APER 4 Manuals installing err RI UtRRHPRS 7 72 Otaning Rss senres kemis ne nang poni ieaiai as 1 OS X etiaseeat ecw ei deena ac RE hom 3 18 57 P Packages i i epe ien iron EPI enn IHRE 2l Pack ge
70. ics 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 including 1 4 x and 1 5 x 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 requires 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 32 which is what is supplied with R otherwise versions in the R sources will be compiled in As the latter suffice and are tested with R you should not need to change this liblzma from xz utils version 4 999 or
71. 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 R VERSION STRING which is a character string containing the cur rent R version for example 3 0 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 will 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 NO1 kind This takes values from the enumeration type typedef enum BUGGY_KINDERMAN_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 be made in the directory tree configure must be run as described in
72. independent code is used in any static libraries such as the Tcl Tk libraries libpng libjpeg and zlib which might be linked against Fortunately these are normally built as shared libraries with the exception of the ATLAS BLAS libraries The default optimization settings chosen for CFLAGS etc are conservative It is likely that using mtune will result in significant performance improvements on recent CPUs especially for ix86 one possibility is to add mtune native for the best possible performance on the machine on which R is being installed if the compilation is for a site wide installation it may still be desirable to use something like mtume core2 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 1ib64 To build a 32 bit version of R on x86_64 with Fedora 16 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 bi
73. ing 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 0 mtune native for Fortran code FFLAGS g 0 mtune native for Fortran 95 code FCFLAGS g O 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 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 Makefile Windows where there is a non empty 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 archi
74. installing architecture dependent files defaults to prefix and can be set via the configure option exec prefix Each of bindir mandir and libdir can also be specified on the make install command line at least for GNU make The configure or make variables rdocdir and rsharedir can be used to install the system independent doc and share directories to somewhere other than libdir The C header files can be installed to the value of rincludedir note that as the headers are not installed into a subdirectory you probably want something like rincludedir usr local include R 3 1 0 If you want the R home to be something other than libdir R use rhome for example make install rhome usr local lib64 R 3 1 0 will use a version specific R home on a non Debian Linux 64 bit system If you have made R as a shared dynamic 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 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 aspects 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 m
75. later preferably 5 0 0 or later will be used if installed the version in the R sources can be selected instead by configuring with with system xz no 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 5 also known as ttf mscorefonts installer in the Debian Ubuntu world see also http en wikipedia org wiki Core fonts for the Web ttf liberation in Debian Ubuntu Appendix A Essential and useful other programs under a Unix alike 39 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 sup port 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 avail able 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 gt 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 also embedFonts use ghostscript http
76. les 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 devel win exe so please rename it to indicate that it is customized If you intend to distribute a customized installer please do check that license requirements are met note that the installer will state that the contents are distributed under GPL 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 make myR IMAGEDIR rootdir MDISDI 1 will create an installer that defaults to installing R to run in SDI mode See src gnuwin32 installer Makefile for the names and values that can be set The standard CRAN distribution of a 32 64 bit installer is made by first building 32 bit R just make 32 bit is needed and then 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
77. library and this is definitely not recommended You can specify a specific LAPACK library or a search for a generic library by the configuration option with lapack The default for with lapack is to check the BLAS library and then look for an external library llapack Sites searching for the fastest possible linear algebra may want to build a LAPACK library using the ATLAS optimized subset of LAPACK To do so specify something like with lapack 2 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 only because it is necessary on some platforms and because some users want to Ap
78. ll make all the pieces and the installers 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 vignettes 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 pkgi 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 Chapter 3 Installing R under Windows 16 customizations to that installation Then after having customized file MkRu
79. loaded not just for the Java libraries and JVM This can cause problems with conflicts between libraries supplied for use with Java and system libraries and JAVA LD LIBRARY PATH may need to be adjusted Where the OS supports it it is better to set a run time path e g by R or rpath as part of JAVA LIBS A 3 Linear algebra 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 to 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 c
80. local lib amd64 as appropriate It will also be necessary to point pkg config at the 64 bit directories e g one of PKG_CONFIG_PATH opt csw lib amd64 pkgconfig usr lib amd64 pkgconfig PKG_CONFIG_PATH opt csw lib sparcv9 pkgconfig usr lib sparcv9 pkgconfig and to specify a 64 bit Java VM by e g JAVA_CPPFLAGS I JAVA_HOME include I JAVA_HOME include solaris JAVA LD LIBRARY PATH 1JAVA HOME lib amd64 server JAVA LIBS L JAVA HOME 1ib amd64 server R JAVA_HOME 1lib amd64 server ljvm 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 later libRblas so and lapack so are generated with code 5 including gcc for Sparc from Oracle Appendix C Platform notes 62 that causes relocation errors which is being linked in from the Fortran libraries This means that building R as a shared library may be impossible with Solaris Studio 12 2 For a standard build the trick seems to be to manually set FLIBS to avoid the troublesome libraries For example on amd64 set in config site something like FLIBS_IN_SO R opt solarisstudio12 3 lib amd64 opt solarisstudio12 3 lib amd64 libfui so opt solarisstudio12 3 lib amd64 libfsu so For 64 bit Sparc
81. losely 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 package 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
82. lts you may want to try setting Chapter 2 Installing R under Unix alikes LANGUAGE en LC TIME C LC COLLATE C but use a UTF 8 or Latin 1 locale 11 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 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 devel 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 th
83. ly before running configure or use the configure variable F77 to specify its full path If your FORTRAN libraries are in slightly peculiar places you should also look at LD_ LIBRARY PATH or your system s equivalent to make sure that all libraries are on this path Note that only FORTRAN compilers which convert identifiers to lower case are 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 co
84. mpiler is not gcc you will need to set FPICFLAGS appropriately Also the included LAPACK sources contain constructs that 2c is unlikely to be able to process so you would need to use an external LAPACK library such as CLAPACK from http www netlib org clapack 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 as well as its equivalence to the Rcomplex structure defined in R_ext Complex h Appendix B Configuration on a Unix alike 50 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
85. n 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 16GB of storage 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 space 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
86. n recent versions of R which install packages as if umask 022 For most users it suffices to call nstall 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 l path to library pkgi 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 Ensure that the environment variable TMPDIR is either unset and tmp exists and can be written in and executed from or points to a valid temporary directory 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 w
87. n1 or mandir man1 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 local and can be set by running configure with the option prefix as in on a Unix alike incosolata is omitted if not found by configure Chapter 2 Installing R under Unix alikes 7 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
88. ndows however you do need a 64 bit version of Windows to build 64 bit R as the build process runs R To select a 32 bit or 64 bit build of R set the options in MkRules local appropriately following the comments in the file Some external software libraries will need to be re compiled under the new toolchain 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 Repp need to ensure that they use a version built with exactly the same toolchain as their package the recommendation is to build Repp 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 wil make use of qpdf to compact some of the package 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 wh
89. 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 Appendix A Essential and useful other programs under a Unix alike 44 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 R bin and libR a without using position independent code Howe
90. o need the following e IATEX 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 Your PATH may include first then the bin directories of the tools the compiler toolchain and IATEX 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 For example the Cygwin version of make 3 81 fails to work correctly for R 2 15 3 and later Appendix D The Windows toolset 69 PATH c Rtools bin c Rtools gcc 4 6 3 bin c MikTeX miktex bin c R R 3 0 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 D 1 BTgX T
91. o use other compilers with the CRAN distribution of R but the settings in the file Library Frameworks R framework Resources etc Makeconf will need to be changed either by editing that file or in a file such as R Makevars see the next section Entries which may need to be changed include CC CXX FC F77 FLIBS and the corresponding flags and perhaps CXXCPP DYLIB_LD MAIN LD SHLIB CXXLD SHLIB_FCLD and SHLIB_LD So for example you could select clang for both C and C with extensive checking by having in R Makevars CC clang CXX clang CFLAGS mtune native g 02 Wall pedantic Wconversion CXXFLAGS mtune native g 02 Wall pedantic Wconversion and for at least one version of gfortran 4 2 we needed FLIBS lgfortran 6 3 3 Customizing package compilation The R system and package specific compilation flags can be overridden or added to by set ting 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 R version Chapter 6 Add on packages 25 Package developers are encouraged to use this mechanism to enable a reasonable amount of diagnostic messaging warnings when compil
92. oaded 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 l libdir pkg gt pkg log 2 gt amp 1 R CMD check 1 libdir install check pkg log pkg Where sub architectures are in use the R CMD check line can be repeated with additional architectures by R arch arch CMD check 1 libdir extra arch install check pkg log 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
93. oducts mkl You are strongly encour aged 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 The MKL interface has changed several times and may change again the following notes apply exactly only to version 10 3 Version 10 of MKL supports two linking models the default model which is backward compatible with version 9 see below and the pure 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 1lib inte164 export LD LIBRARY PATH MKL LIB PATH MKL L MKL LIB PATH 1mkl gf l1p64 1mkl sequential lmkl core configure with blas MKL with lapack where some versions may need 1mkl lapack before 1mkl core The order of the libraries is important
94. omplex 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 10 on e g Linux and Solaris is prepended to the library path as from R 3 0 0 it is effectively appended on OS X Appendix A Essential and useful other programs under a Unix alike Al 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 v a 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 whereas x
95. on of ACML available for recent versions of gfortran To make use of this you will need something like H Using the Oracle Solaris Studio cc and 95 compilers Appendix A Essential and useful other programs under a Unix alike 42 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 43 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 current version is known as GotoBLAS2 and has in November 2010 been 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 43 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 OpenBLAS is a descendant project with support for some current CPUs A 3 1 4 Intel MKL For Intel processors under Linux there is Intel s Math Kernel Library http www intel com software pr
96. or 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 Brazilian locales but not for locales specifying Portugal Translations in the right language but the wrong charset are made use of by on the fly re encoding The LANGUAGE variable only can be a colon separated list for example se de giving a se
97. 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 M0DE 64 in the environment or alternatively use the q64 compiler options It is strongly recommended to install Bash and use it as the configure shell e g via setting CONFIG_SHELL usr bin bash in the environment and to use GNU Make e g via MAKE opt freeware bin make Further installation instructions to set up a proper R development environment can be found in the R on AIX project on R Forge http R Forge R project org projects aix Appendix C Platform notes 66 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 R requires C99 complex type support which is available as from Cygwin 1 7 8 March 2011 However the new implementation of cacos gives incorrect results so we undefine HAVE CACOS in src main complex c on that platform Many versions of Cygwin during 2011 were unable to build R 1 7 9 1 with GCC 4 5 3 3 in November 2011 was able to do so 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 w
98. osce ett eR eRRRPOPES UN bey ac Eg up d 9 20 Other Options lt i cedere vie ob sos bh E DEP 10 2 8 Testing an Installation ies e eim tet eRERR E Rd dn need 10 3 Installing R under Windows 12 3 1 Building from source eei ner S ka eem ds 12 3 Ll Getting the tools oss cesseecesie rem erp RE epa 12 3 1 2 Getting the source files 00 cece eee eee eee 12 3 1 8 Building the core files 0 00 cece eee eens 13 3 1 4 Building the bitmap files 0 e eee eee 14 3 1 5 Building the cairo devices 0 00 cece eee eee eee 14 3 1 6 Checking the build 00 eee 14 3 L 7 Building the manuals cere eere Rega 15 3 1 8 Building the Inno Setup installer 00 15 3 1 9 Building the MSI installer 0 00 eee eee eee ee 16 3 1 10 64 bit Windows builds 0 Lr 3 2 Testing an Installation coe ERR Rer 17 4 Installing R under OS X 18 4 Running R under OS X ssssskecteeetbs ree hsePEREE EIER 18 4 2 Uninstalling under OS X sccis cece cee eee eens 18 5 Running TE oasis ce eheacledaiee Sere ea Rb nw d 20 6 Add on packages uuuuussuss 21 6 1 Default packages usas tie stb RR oae Posted ees 21 6 2 Managing libraries caecitate sed wer rua es 21 6 9 Installing packages esos coe ee eek un sigs rem Ri peu 22 5 915 M ndOWSussaeRNP cue sete RR E EEE eae ete a 23 um AMEN
99. packing 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 Compiler Col lection 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 wwwi4 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 x1lf FTT xlf 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 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
100. 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 to a writable area is used If none do the final default is tmp on Unix alikes and the value of R USER on Windows Some Unix alike systems are set up to remove files and directories periodically from tmp for example by a cron job running tmpwatch Set TMPDIR to another directory before starting long running jobs on such a system Note that TMPDIR will be used to execute configure scripts when installing packages so if tmp has been mounted as noexec TMPDIR needs to be set to a directory from which execution is allowed Chapter 6 Add on packages 21 6 Add on packages It is helpful to use the correct terminology A package is loaded from a library by the function library 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 star
101. pendix A Essential and useful other programs under a Unix alike 45 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 As from R 3 0 0 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 system
102. platforms such as HP UX IRIX and Alpha OSF1 for which we have had no recent reports C macros to select particular platforms can be tricky to track down there is a fair amount of misinformation on the Web The Wiki currently at 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
103. re Solo or Core Duo CPUs The instructions here concentrate on x86_64 builds To use the quartz graphics device you need to configure with with aqua which is the default quartz then becomes the default device when running R at the console and X11 would only be used for the 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 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 download you will need to reg ister there or if you have a recent Xcode installed from the App Store or from https developer apple com devcenter mac you can install the command line tools from within Xcode from the Downloads pane in the Preferences Various compilers can be used The CRAN distribution of R is built using e gcc from the Xcode distribution This is a version of gcc 4 2 1 with an LLVM backend e gfortran rom 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
104. re 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 size One common variable to change is R 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 RLPAPERSIZE 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 48 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 1ib64 on most 64 bit Linux OSes and I usr local include CPPFLA
105. recipe you can modify the file config site following the instructions therein so that the build will use these options It seems that gcc 3 4 x and later on ix86 Linux defeat attempts by the 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 ffloat store to FFLAGS Other settings are needed when using icc on ix86 Linux for example Using mpc64 is preferable on more recent GCC compilers If you do manage to get R running on a new platform please let us know about it so we can modify the configuration procedures to include that platform If you are having trouble getting R to work on your platform please feel free to use the R devel mailing list to ask questions We have had a fair amount of practice at porting R to new platforms Appendix D The Windows toolset 68 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 21 for details
106. rface 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 package directory from the library 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 s
107. rs can be seen in file etc Renviron in or on the command line as configure VAR value If you are building 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 local 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 befo
108. s default ete etes 21 Packages installing 0 cece eee ee 22 Packages removing e sees eee 26 Packages updating em tonii e RR e 26 R Ebitmap dll oi ad ertet bL RR E PEE 14 Repositories 2o stqe awe ree ph Une 26 Site libraries i24s eissecche x br ER RT IIS 21 SOlBaFIS iebIre ISPRSeTesrebruek o rePexrHebeera 60 Sources for Re icu eese em Rid dake ge RS 1 SUDYVeFSIOR ceret rime E EE Rd Ree DER ALS 1 37 U User hbrares e e bee RRESEPRPPRESDPeR RES 21 V Vighettess oo isos tis Maaenvdeaie tan REPE 37 W syiuCairo dll 21isiisieizckR e a E 14 Environment variable index Environment variable index B BLAS LIBS isses eee 40 CS eM E M 49 CONFIG SITE ee 4T nj PREX 49 CYGWIN S eise ieu Rar 69 D DESTDIR eese een 8 34 F A E E Sn eee ee 49 FOCI IRS SERRE E A a ea 49 FPIGFLAGS oie tai oes safer E E Mas 49 JAVA HOME e eee 39 L TANG 30 LANGUAGE uaou unini eie e eee 30 31 LAP CK LIBS eere neser a E 44 ION IDEE E E EE RESE 30 EC COLLATE oem a e TS 10 LC MESSAGES n see 30 LD LIBRARY PATH 34 41 49 51 63 T3 O OBJECT MODE ee 65 P PAPERSIZE sss eee 47 PATH sees see 37 49 65 68 R REARCH c Mu LU aden ee 9 R BROWSER sss ees 48 R DEFAULT PACKAGES sss 21 R DISABLE HTTPD isses 4 R GSCMD sesssssssssssee ee eee 39 R_INSTALL_TAR 000 0c eee 23 R JAVA LD LIBR
109. s it is necessary that an external BLAS LAPACK was built with the same FORTRAN compiler used to build R known problems are with R built with gfortran see Section B 6 1 Using gfortran page 49 Appendix B Configuration on a Unix alike 46 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 Rprof 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 1ibR 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
110. s part of DYLD FALLBACK LIBRARY PATH and so is less likely to cause conflicts but Appendix C Platform notes 60 JAVA_HOME jre 1ib is still best avoided as in some JDKs it contains libraries which conflict with system libraries Note that it is necessary to set the environment variable NOAWT e g to 1 to install some Java using packages such as iplots C 4 6 Frameworks The CRAN build of R is installed as a framework which is selected by the default option configure enable R framework This is 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 C 4 7 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 R xcodeproj project select the R target and the SnowLeop
111. s used for the CRAN binary package for R at the time of writing with system zlib enable memory profiling disable openmp was used C 4 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 C 4 2 Lion No tweaks are known to be needed on Lion See the notes on Mountain Lion if XQuartz is in use C 4 3 Mountain Lion The X11 system used with Mountain Lion will be XQuartz 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 PKG CONFIG PATH environment variable e g export PKG_CONFIG_PATH opt X11 lib pkgconfig usr local lib pkgconfig C 4 4 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 install http cran r project org bin macosx tools tcltk 8 5 5 x11 pkg which is a binary package for the X11 based Tcl Tk as used on other Unix alikes This may need with tcl config usr local lib tclConfig sh with tk config usr local lib tkConfig sh and on a system with XQuartz usr local lib tkConfig sh needed to be edited to have
112. shell to be Bash rather than Zsh Kurt Hornik and Stefan Theussl at WU Wirtschaftsuniversit t Wien successfully built R on a powerpc 8 CPU Power6 system running AIX 6 1 configuring with or without enable R shlib Ei ji Nakama s support is gratefully acknowledged It helps to describe the WU build environment first A small part of the software needed to build R and or install packages is available directly from the AIX Installation DVDs e g Java 6 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 Appendix C Platform notes 65 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 un
113. 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 An implementation of XDR is required This is part of RPC and historically has been part of libc on a Unix alike however some builds of glibc 2 14 hide it The intention seems to be that the TI RPC library be used instead in which case libtirpc and its
114. t Tcl Tk configure scripts are in usr lib It may also be necessary to set the pkg config path e g by export PKG_CONFIG_PATH usr local lib pkgconfig usr lib pkgconfig 64 bit versions of Linux are built with support for files 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 55 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 versions 3 0 and 3 2 2 based on the Clang front ends invoked by CC clang CXX clangt 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 Note that clang 3 0 is rather broken when used with g C headers C 2 2 Intel compilers Intel compilers have been used under ix86 and x86_64
115. t 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 the language written in England some people living in the USA appropriate this name for their language 5 with Americanisms Chapter 8 Choosing between 32 and 64 bit builds 32 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 quantities 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 eve
116. t 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 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 Chapter 3 Installing R under Windows 15 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 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 Reference 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 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 69 Once everything is set up make distribution make check all wi
117. tall 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 later 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 JavaVM framework Headers JAVA LD LIBRARY PATH JAVA LIBS framework JavaVM The Apple developer versions of the JDK install somewhere like JAVA HOME Library Java JavaVirtualMachines 1 6 0 43 b01 447 jdk Contents Home The Oracle JDK can be specified explicitly by something like JAVA HOME Library Java JavaVirtualMachines jdk1 7 0 17 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 1jvm in config site As from R 3 0 0 JAVA LD LIBRARY PATH is used a
118. tecture 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 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 the option byte compile with R CMD INSTALL or with install packages type source 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 Chapter 6 Add on packages 26 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 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 inte
119. tecture specific version A typical setting for x86_64 Linux is JAVA HOME usr lib jvm java 1 7 0 openjdk 1 7 0 9 x86 64 jre R JAVA LD LIBRARY PATH JAVA HOME lib amd64 server Note that this unfortunately depends on the exact version of the JRE JDK installed and so may need updating if the Java installation is updated This can be done by running R CMD Appendix A Essential and useful other programs under a Unix alike 40 javareconf which updates settings in both etc Makeconf and R_HOME etc ldpaths See R CMD javareconf help for details Alternatively a less specific version of JAVA HOME can be supplied at configuration in the example above this would be JAVA HOME usr lib jvm java 1 7 0 jre Another way of overriding those setting is to set R JAVA LD LIBRARY PATH e g in Renviron or use etc ld so conf to specify the Java runtime library paths to the system Other settings are recorded in etc Makeconf or a sub architecture specific version e g JAVA usr bin java JAVAC usr bin javac JAVA_HOME usr java jdk1 7 0_17 jre JAVA LD LIBRARY PATH JAVA HOME lib amd64 server JAVA LIBS L JAVA HOME lib amd64 server 1jvm where JAVA_LIBS contains flags necessary to link JNI programs Some of the above vari ables can be queried using R CMD config Beware that on most OSes setting R JAVA LD LIBRARY PATH changes the library path when R and all its packages are
120. tform so the architecture of Rscript does not matter 5 with possible values i386 x64 32 and 64 5 mainly on RedHat and Fedora whose layout is described here Chapter 2 Installing R under Unix alikes 10 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 lazyloaded 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 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 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 t
121. the definition of JPEGDIR the names of the libpng and libtiff directories can also be set there Example gt tar zxf libpng 1 5 14 tar gz mv libpng 1 5 14 libpng tar zxf jpegsrc v9 tar gz tar zxf tiff 4 0 3 tar gz mv tiff 4 0 3 libtiff rm rf tiff 4 0 3 and see the comment above about no same owner V VM M M 3 1 3 Building the core files Set the environment variable TMPDIR to point 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 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 Chapter 3 Installing R under Windows 14 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
122. the main build instructions Then in src nmath standalone l eg Bessel beta and gamma functions Chapter 9 The standalone Rmath library 34 make will make standalone libraries libRmath a and libRmath so libRmath dylib on OS X make static and make shared will create just one of them To use the routines in your own C or C programs include 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 The targets make install make uninstall will un install the header Rmath h and shared and static libraries if built Both prefix and DESTDIR are supported together with more precise control as described for the main build make install installs a file for pkg config to use by e g CC pkg config cflags libRmath c test c CC pkg config libs libRmath test o o test On some systems make install strip will install a stripped shared library 9 2 Windows You need to set 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 M
123. 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 wikipedia org wiki Liberation fonts Then there is 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 graph
124. tion 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 libint1 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 When using the Oracle compilers do not specify fast as this disables IEEE arithmetic and make check will fail 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 1
125. tup is by default gt getOption defaultPackages 1 datasets utils erDevices 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 R_DEFAULT_ PACKAGES if set as a comma separated list Setting R DEFAULT PACKAGES 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 O can be used to add paths to the collection of libraries or to report the current 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
126. ult in the CRAN distribution but not when compiling from source that can be passed to install packages in order to download and install binary packages from a suitable repository These OS X binary package files have the extension tgz The R APP GUI provides menus for installation of either binary or source packages from CRAN or local files Note that many 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 4 OS X page 57 Package rJava and those which depend on it need a Java runtime installed for Mountain Lion see Section C 4 3 Mountain Lion page 58 Several packages need X11 installed including those using Tk for Mountain Lion see Section C 4 3 Mountain Lion page 58 The version of Tcl Tk available for download from CRAN comes with the Tktable extension but not with BWidget which quite a few packages require without declaring it maybe because it is shipped as part of R for Windows It is easy to install e Download the sources from http sourceforge net projects tcllib files BWidget e Ina Terminal run something like depending on the version you downloaded tar xf bwidget 1 9 6 tar gz sudo mv bwidget 1 9 6 usr local lib It may be possible t
127. use stlport4 currently the most modern of the options the default but still needed to be specified as it is needed for linking is Cstd see http developers sun 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 libraries also needs to be Occasionally the flag 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 Appendix C Platform notes 63 As from R 3 0 0 parsing very complex expressions needs a lot of stack space when the Oracle compilers are used several packages require the stack increased to say 20MB C 5 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
128. ver experiments showed that in many cases using a shared BLAS was as fast provided high levels of compiler optimization are used e t 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 ldpaths 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 ln 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 default is not to search for a suitable LAPACK

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