[R-sig-Debian] trouble installing building packages from source using R 2.6.0 on Ubuntu Gutsy AMD64
Mark W Kimpel
mwkimpel at gmail.com
Sat Nov 3 03:07:05 CET 2007
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
(edd at debian.org)
## 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
(edd at debian.org)
## 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
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