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R Installation and Administration Version 2.7.1 (2008-06-23)

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R Installation and Administration Version 2.7.1 (2008-06-23) R Installation and Administration Version 2.7.1 (2008-06-23) R Development Core Team Permission is granted to make and distribute verbatim copies of this manual provided the copy- right notice and this permission notice are preserved on all copies. Permission is granted to copy and distribute modified versions of this manual under the condi- tions for verbatim copying, provided that the entire resulting derived work is distributed under the terms of a permission notice identical to this one. Permission is granted to copy and distribute translations of this manual into another language, under the above conditions for modified versions, except that this permission notice maybe stated in a translation approved by the R Development Core Team. Copyright c 2001{2006 R Development Core Team ISBN 3-900051-09-7 i Table of Contents 1 Obtaining R:::::::::::::::::::::::::::::::::::::::::::::::::::: 1 1.1 Getting and unpacking the sources::::::::::::::::::::::::::::::::::::::::::::::::: 1 1.2 Getting patched and development versions ::::::::::::::::::::::::::::::::::::::::: 1 1.2.1 Using Subversion and rsync ::::::::::::::::::::::::::::::::::::::::::::::::::: 1 2 Installing R under Unix-alikes:::::::::::::::::::::::::::::::: 3 2.1 Simple compilation :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 3 2.2 Making the manuals ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 4 2.3 Installation :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 5 2.4 Uninstallation ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 6 2.5 Sub-architectures :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 7 3 Installing R under Windows :::::::::::::::::::::::::::::::::: 8 3.1 Building from source :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 8 3.1.1 Getting the tools ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 8 3.1.2 Getting the source files ::::::::::::::::::::::::::::::::::::::::::::::::::::::: 8 3.1.3 Building the core files::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 9 3.1.4 Building the bitmap files::::::::::::::::::::::::::::::::::::::::::::::::::::: 10 3.1.5 Checking the build :::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 10 3.1.6 Building the manuals :::::::::::::::::::::::::::::::::::::::::::::::::::::::: 10 3.1.7 Building the Inno Setup installer::::::::::::::::::::::::::::::::::::::::::::: 10 3.1.8 Building the MSI installer ::::::::::::::::::::::::::::::::::::::::::::::::::: 11 3.1.9 Cross-building on Linux ::::::::::::::::::::::::::::::::::::::::::::::::::::: 11 4 Installing R under Mac OS X ::::::::::::::::::::::::::::::: 13 4.1 Building from source on Mac OS X ::::::::::::::::::::::::::::::::::::::::::::::: 13 5 Running R :::::::::::::::::::::::::::::::::::::::::::::::::::: 14 6 Add-on packages ::::::::::::::::::::::::::::::::::::::::::::: 15 6.1 Default packages ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 15 6.2 Managing libraries ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 15 6.3 Installing packages ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 15 6.3.1 Windows :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 16 6.3.2 Mac OS X::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 17 6.3.3 Customizing package compilation under Unix :::::::::::::::::::::::::::::::: 17 6.3.4 Customizing package compilation under Windows :::::::::::::::::::::::::::: 17 6.4 Updating packages ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 18 6.5 Removing packages ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 18 6.6 Setting up a package repository::::::::::::::::::::::::::::::::::::::::::::::::::: 19 7 Internationalization and Localization ::::::::::::::::::::::: 20 7.1 Locales::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 20 7.1.1 Locales under Linux ::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 20 7.1.2 Locales under Windows:::::::::::::::::::::::::::::::::::::::::::::::::::::: 21 7.1.3 Locales under Mac OS X :::::::::::::::::::::::::::::::::::::::::::::::::::: 21 7.2 Localization of messages :::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 21 ii 8 Choosing between 32- and 64-bit builds :::::::::::::::::::: 23 8.1 Windows ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 23 9 The standalone Rmath library :::::::::::::::::::::::::::::: 25 9.1 Unix ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 25 9.2 Windows ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 26 Appendix A Essential and useful other programs under Unix ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 28 A.1 Essential programs::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 28 A.2 Useful libraries and programs :::::::::::::::::::::::::::::::::::::::::::::::::::: 29 A.2.1 Tcl/Tk ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 29 A.2.2 Java support:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 30 A.3 Linear algebra ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 30 A.3.1 BLAS::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 30 A.3.1.1 ATLAS :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 31 A.3.1.2 ACML ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 31 A.3.1.3 Goto BLAS :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 32 A.3.1.4 Intel MKL ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 32 A.3.1.5 Shared BLAS :::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 32 A.3.2 LAPACK ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 33 A.3.3 Caveats ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 34 Appendix B Configuration on Unix :::::::::::::::::::::::::: 35 B.1 Configuration options :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 35 B.2 Internationalization support:::::::::::::::::::::::::::::::::::::::::::::::::::::: 35 B.3 Configuration variables::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 36 B.3.1 Setting paper size ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 36 B.3.2 Setting the browser ::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 36 B.3.3 Compilation flags ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 37 B.3.4 Making manuals :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 37 B.4 Using make :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 37 B.5 Using FORTRAN :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 37 B.5.1 Using gfortran :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 38 B.6 Compile and load flags ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 38 Appendix C Platform notes::::::::::::::::::::::::::::::::::: 40 C.1 X11 issues ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 40 C.2 Linux:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 41 C.2.1 Intel compilers :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 42 C.2.2 PGI compilers :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 43 C.2.3 SunPro compilers ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 43 C.3 Mac OS X ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 43 C.3.1 64-bit builds :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 44 C.4 Solaris ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 44 C.4.1 Solaris 10 and Open Solaris ::::::::::::::::::::::::::::::::::::::::::::::::: 44 C.4.2 Sparc Solaris 9 and earlier::::::::::::::::::::::::::::::::::::::::::::::::::: 45 C.5 HP-UX :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 47 C.6 IRIX :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 48 C.7 Alpha/OSF1::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 49 C.8 Alpha/FreeBSD:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 49 C.9 AIX ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 49 iii C.10 Cygwin ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 50 C.11 New platforms :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 50 Appendix D Enabling search in HTML help ::::::::::::::::: 52 D.1 Java Virtual Machines on Linux:::::::::::::::::::::::::::::::::::::::::::::::::: 52 D.2 Java Virtual Machines on Unix::::::::::::::::::::::::::::::::::::::::::::::::::: 52 D.3 Java Virtual Machines on Windows :::::::::::::::::::::::::::::::::::::::::::::: 52 D.4 Java Virtual Machines on Mac OS X ::::::::::::::::::::::::::::::::::::::::::::: 53 Appendix E The Windows toolset ::::::::::::::::::::::::::: 54 E.1 Perl ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 55 E.2 The Microsoft HTML Help Workshop::::::::::::::::::::::::::::::::::::::::::::: 55 E.3 LATEX:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 55 E.4 The Inno Setup installer ::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 55 E.5 The command line tools:::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 55 E.6 The MinGW compilers ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 56 Function and variable index :::::::::::::::::::::::::::::::::::::
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