[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
Fri Nov 2 21:01:35 CET 2007

First off, if this is a duplicate post, I apologize as I am reposting 
after getting a kick-back from the mail-server after changing email 

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.


#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
##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 =
my.new.packages <- c( dir("~/R_HOME/site-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

  [1] "acepack"               "affxparser"
  [4] "affycomp"              "affycoretools"
  [7] "affyio"                "affypdnn"
[10] "affyQCReport"          "akima"
[13] "altcdfenvs"            "amap"
[16] "AnnBuilder"            "annotate"
[19] "annotationTools"       "aroma.light"
[22] "aws"                   "Biobase"
[25] "bioDist"               "biomaRt"
[28] "boot"                  "BSgenome"
[31] "BufferedMatrixMethods" "CALIB"
[34] "Category"              "cellHTS"
[37] "chron"                 "class"
[40] "clusterStab"           "CoCiteStats"
[43] "codelink"              "codetools"
[46] "combinat"              "convert"
[49] "corpcor"               "cosmo"
[52] "DAAG"                  "DBI"
[55] "Design"                "diffGeneAnalysis"
[58] "DynDoc"                "dynlm"
[61] "EBarrays"              "Ecdat"
[64] "EMV"                   "factDesign"
[67] "fCalendar"             "fdrtool"
[70] "fibroEset"             "fields"
[73] "foreign"               "fSeries"
[76] "gam"                   "gcrma"
[79] "GeneCycle"             "genefilter"
[82] "GeneNet"               "geneplotter"
[85] "geneRecommender"       "GeneTS"
[88] "GLAD"                  "GlobalAncova"
[91] "gmodels"               "GO"
[94] "golubEsets"            "GOstats"
[97] "gplots"                "gpls"
[100] "GraphAT"               "gregmisc"
[103] "GSEABase"              "gtools"
[106] "Heatplus"              "hexbin"
[109] "hgfocuscdf"            "hgu133a"
[112] "hgu133aprobe"          "hgu133plus2"
[115] "hgu95av2"              "hgu95av2cdf"
[118] "hgu95av2probe"         "Hmisc"
[121] "hsahomology"           "hu6800"
[124] "hu6800probe"           "humanLLMappings"
[127] "Icens"                 "idiogram"
[130] "ipred"                 "its"
[133] "KEGG.db"               "keggorth"
[136] "lapmix"                "lattice"
[139] "leaps"                 "limma"
[142] "LMGene"                "lmtest"
[145] "locfit"                "lodplot"
[148] "LPE"                   "maanova"
[151] "maCorrPlot"            "makecdfenv"
[154] "MantelCorr"            "mapproj"
[157] "marray"                "maSigPro"
[160] "matchprobes"           "Matrix"
[163] "MCMCpack"              "mda"
[166] "metaArray"             "Mfuzz"
[169] "mgu74av2"              "minpack.lm"
[172] "mlbench"               "MLInterfaces"
[175] "multtest"              "MVCClass"
[178] "nlme"                  "nnet"
[181] "odesolve"              "odfWeave"
[184] "oligoClasses"          "ontoTools"
[187] "oz"                    "pamr"
[190] "pcaMethods"            "pcot2"
[193] "pdmclass"              "pickgene"
[196] "pkgDepTools"           "plier"
[199] "pls"                   "prada"
[202] "PROcess"               "qtl"
[205] "quantreg"              "quantsmooth"
[208] "R2HTML"                "rae230a"
[211] "rama"                  "randomForest"
[214] "rat2302"               "rat2302cdf"
[217] "RBGL"                  "RColorBrewer"
[220] "R.css"                 "RCurl"
[223] "Rdbi"                  "reb"
[226] "Resourcerer"           "rgl"
[229] "rgu34a"                "rgu34acdf"
[232] "RLMM"                  "RMAPPER"
[235] "ROC"                   "R.oo"
[238] "rrcov"                 "RSNPper"
[241] "RSPython"              "RSQLite"
[244] "RUnit"                 "R.utils"
[247] "safe"                  "SAGx"
[250] "SBMLR"                 "scatterplot3d"
[253] "SemSim"                "seqLogo"
[256] "siggenes"              "sigPathway"
[259] "sizepower"             "sma"
[262] "SparseM"               "spatial"
[265] "ssize"                 "statmod"
[268] "strucchange"           "survival"
[271] "TeachingDemos"         "time"
[274] "tkWidgets"             "topGO"
[277] "tseries"               "tweedie"
[280] "TypeInfo"              "vsn"
[283] "widgetTools"           "xgobi"
[286] "xtable"                "zoo"
[289] "boot"                  "class"
[292] "codetools"             "datasets"
[295] "graphics"              "grDevices"
[298] "KernSmooth"            "lattice"
[301] "methods"               "mgcv"
[304] "nnet"                  "rcompgen"
[307] "rpart"                 "spatial"
[310] "stats"                 "stats4"
[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)


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