Several days ago I posted a query as to how to get R-2.6.0 installed on Ubuntu Gutsy AMD64 build. With helpful suggestions from others on the list, I have come up with the following script which may be helpful to those who have some experience with R and BioConductor but, like me, are novices with Debian/Ubuntu. Development of the script was not a linear process, and it is possible that something is missing, so please let me know via the list if you encounter problems.
Mark ######################################################### #Making R and BioC on Ubuntu Gutsy with AMD64-bit OS #Add this to /etc/apt/sources.list and update apt deb-src http://cran.r-project.org/bin/linux/debian etch/ apt-get update #make a directory for deb source files mkdir /home/USER/r-2.6.0-deb cd /home/USER/r-2.6.0-deb #get the source files and unpack them sudo apt-get source r-base sudo dpkg-source -x r-base_2.6.0-1~etchcran.1.dsc #cd into r-base-VERSION cd r-base-2.6.0 #compile the package, this may be un-necessary, but I did it sudo dpkg-buildpackage -rfakeroot -b -us -uc -tc #get some libraries need for building R apt-get install build-essential # fail and will produce a suggestion to do the following command, DO IT # Dirk says this represents a possible bug, the following did work for me, but may be dangerous apt-get -f install #install the package from .deb sudo dpkg -i ../r-base-core_2.6.0-1~etchcran.1_amd64.deb #install some development libraries for building packages sudo apt-get install r-base-dev ## to get rgl to install into R with Ubuntu Gutsy AMD64 apt-get install freeglut3 freeglut3-dev libgl1-mesa-dev libglu1-mesa-dev libice-dev libsm-dev libx11-dev libxau-dev libxdmcp-dev libxext-dev libxt-dev mesa-common-dev x11proto-core-dev x11proto-input-dev x11proto-kb-dev x11proto-xext-dev xlibmesa-gl-dev xtrans-dev ##OR, after R is installed, do sudo apt-get build-dep r-cran-rgl ([EMAIL PROTECTED]) ## to get Rgraphviz to install apt-get install graphviz graphviz-dev ##NO sudo apt-get build-dep r-cran-rgraphviz available ## to get XML to install apt-get install xml2 libxml2-dev libxml2-utils libxml2 libxml++2.6-dev libxml++2.6c2a ##OR, after R is installed, do sudo apt-get build-dep r-cran-xml ([EMAIL PROTECTED]) ## to get RCurl to install apt-get install libcurl4-gnutls-dev libcurl3-gnutls libcurl3 ##No sudo apt-get build-dep r-cran-rcurl available #Now, if you are upgrading from an X_86 architecture to AMD64, replace site-library with an empty one for new packages cd R_HOME #if not made, make it mv site-library site-library-X_86 #if you have an old site-library you want to save mkdir site-library #if have packages in old library that you want installed in new one cd site-library-X_86 ls > ../my.packages.txt #to .Rprofile add at beginning: .libPaths(new= "~/R_HOME/site-library") #tell R where site-library is export PATH:$PATH:/usr #Start R #install.packages from appropriate repositories, may read in old package names from old library using: packages.to.install <- read.delim("~/R_HOME/my.packages.txt", as.is = TRUE)[,1] source("http://bioconductor.org/biocLite.R") biocLite(packages.to.install) my.new.packages <- c( dir("~/R_HOME/site-library"), dir("/usr/lib/R/library")) yet.to.install <- setdiff(packages.to.install, my.new.packages) biocLite(yet.to.install, dependencies = TRUE) #After everything else installs, this works install.packages("RSPerl", repos="http://www.omegahat.org/R", dependencies = TRUE) install.packages("RSPython", repos="http://www.omegahat.org/R", dependencies = TRUE) # "TMat" not available in any repos, dc/d? These all installed without problems with R-2.6.0 on 11.1.2007 my.new.packages [1] "acepack" "affxparser" "affy" [4] "affycomp" "affycoretools" "affydata" [7] "affyio" "affypdnn" "affyPLM" [10] "affyQCReport" "akima" "ALL" [13] "altcdfenvs" "amap" "annaffy" [16] "AnnBuilder" "annotate" "AnnotationDbi" [19] "annotationTools" "aroma.light" "arrayMagic" [22] "aws" "Biobase" "biocViews" [25] "bioDist" "biomaRt" "Biostrings" [28] "boot" "BSgenome" "BufferedMatrix" [31] "BufferedMatrixMethods" "CALIB" "car" [34] "Category" "cellHTS" "ChromoViz" [37] "chron" "class" "cluster" [40] "clusterStab" "CoCiteStats" "coda" [43] "codelink" "codetools" "colorspace" [46] "combinat" "convert" "copa" [49] "corpcor" "cosmo" "cosmoGUI" [52] "DAAG" "DBI" "DEDS" [55] "Design" "diffGeneAnalysis" "digest" [58] "DynDoc" "dynlm" "e1071" [61] "EBarrays" "Ecdat" "edd" [64] "EMV" "factDesign" "fBasics" [67] "fCalendar" "fdrtool" "fEcofin" [70] "fibroEset" "fields" "fImport" [73] "foreign" "fSeries" "fUtilities" [76] "gam" "gcrma" "gdata" [79] "GeneCycle" "genefilter" "GeneMeta" [82] "GeneNet" "geneplotter" "GeneR" [85] "geneRecommender" "GeneTS" "GEOquery" [88] "GLAD" "GlobalAncova" "globaltest" [91] "gmodels" "GO" "GO.db" [94] "golubEsets" "GOstats" "goTools" [97] "gplots" "gpls" "graph" [100] "GraphAT" "gregmisc" "gridBase" [103] "GSEABase" "gtools" "Harshlight" [106] "Heatplus" "hexbin" "hgfocus" [109] "hgfocuscdf" "hgu133a" "hgu133acdf" [112] "hgu133aprobe" "hgu133plus2" "hgu95acdf" [115] "hgu95av2" "hgu95av2cdf" "hgu95av2.db" [118] "hgu95av2probe" "Hmisc" "hopach" [121] "hsahomology" "hu6800" "hu6800cdf" [124] "hu6800probe" "humanLLMappings" "hypergraph" [127] "Icens" "idiogram" "impute" [130] "ipred" "its" "KEGG" [133] "KEGG.db" "keggorth" "KernSmooth" [136] "lapmix" "lattice" "LBE" [139] "leaps" "limma" "lme4" [142] "LMGene" "lmtest" "locfdr" [145] "locfit" "lodplot" "longitudinal" [148] "LPE" "maanova" "macat" [151] "maCorrPlot" "makecdfenv" "makePlatformDesign" [154] "MantelCorr" "mapproj" "maps" [157] "marray" "maSigPro" "MASS" [160] "matchprobes" "Matrix" "mclust" [163] "MCMCpack" "mda" "MergeMaid" [166] "metaArray" "Mfuzz" "mgcv" [169] "mgu74av2" "minpack.lm" "MiPP" [172] "mlbench" "MLInterfaces" "mlmRev" [175] "multtest" "MVCClass" "mvtnorm" [178] "nlme" "nnet" "nnNorm" [181] "odesolve" "odfWeave" "oligo" [184] "oligoClasses" "ontoTools" "OrderedList" [187] "oz" "pamr" "panp" [190] "pcaMethods" "pcot2" "pdInfoBuilder" [193] "pdmclass" "pickgene" "pixmap" [196] "pkgDepTools" "plier" "plotrix" [199] "pls" "prada" "preprocessCore" [202] "PROcess" "qtl" "quadprog" [205] "quantreg" "quantsmooth" "qvalue" [208] "R2HTML" "rae230a" "rae230aprobe" [211] "rama" "randomForest" "RankProd" [214] "rat2302" "rat2302cdf" "RbcBook1" [217] "RBGL" "RColorBrewer" "rcompgen" [220] "R.css" "RCurl" "rda" [223] "Rdbi" "reb" "RefPlus" [226] "Resourcerer" "rgl" "Rgraphviz" [229] "rgu34a" "rgu34acdf" "rlecuyer" [232] "RLMM" "RMAPPER" "robustbase" [235] "ROC" "R.oo" "rpart" [238] "rrcov" "RSNPper" "RSPerl" [241] "RSPython" "RSQLite" "RSvgDevice" [244] "RUnit" "R.utils" "Ruuid" [247] "safe" "SAGx" "sandwich" [250] "SBMLR" "scatterplot3d" "sem" [253] "SemSim" "seqLogo" "sgeostat" [256] "siggenes" "sigPathway" "simpleaffy" [259] "sizepower" "sma" "snow" [262] "SparseM" "spatial" "splots" [265] "ssize" "statmod" "stepNorm" [268] "strucchange" "survival" "systemfit" [271] "TeachingDemos" "time" "tkrplot" [274] "tkWidgets" "topGO" "tripack" [277] "tseries" "tweedie" "twilight" [280] "TypeInfo" "vsn" "weaver" [283] "widgetTools" "xgobi" "XML" [286] "xtable" "zoo" "base" [289] "boot" "class" "cluster" [292] "codetools" "datasets" "foreign" [295] "graphics" "grDevices" "grid" [298] "KernSmooth" "lattice" "MASS" [301] "methods" "mgcv" "nlme" [304] "nnet" "rcompgen" "R.css" [307] "rpart" "spatial" "splines" [310] "stats" "stats4" "survival" [313] "tcltk" "tools" "utils" Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 204-4202 Home (no voice mail please) mwkimpel<at>gmail<dot>com _______________________________________________ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian