R SIG Debian - Oct 2007 - trouble installing building packages from source using R 2.6.0 on Ubuntu Gutsy AMD64

I have recently upgraded to Ubuntu Gutsy and, for the first time, am 
using a 64-bit installation. After failing miserably to install R from 
source, not a problem for me in the past with a 32-bit install, I went 
the route of using the Debian Etch build. This went smoothly, but I am 
unable to update my numerous R and BioConductor packages, getting 
non-zero exit status errors on each package. Is there a repository of 
pre-built packages for Debian Etch 64 besides the r-base and 
r-recommended? If not, could someone suggest how I might get things 
working installing from source?

I have installed the ia32 library, which did help me build VMWare, but 
did not help with R. Reading the R-admin manual, there are some 
suggested compiler flags, but I don't know how to enter them as I am a 
relative new-comer to Linux.

Thanks so much,
Mark

---

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) 663-0513 Home (no voice mail please)

On 30 October 2007 at 11:26, Mark W Kimpel wrote:
| I have recently upgraded to Ubuntu Gutsy and, for the first time, am 
| using a 64-bit installation. After failing miserably to install R from 
| source, not a problem for me in the past with a 32-bit install, I went 
| the route of using the Debian Etch build. This went smoothly, but I am 

You mean you installed the .deb file from Debian onto Ubuntu?  Not something
I'd recommend....

IIRC we have backports for 64 bit, and we have backports for Ubuntu.  We just
don't have them for 64 Bit Ubuntu ...   

| unable to update my numerous R and BioConductor packages, getting 
| non-zero exit status errors on each package. Is there a repository of 
| pre-built packages for Debian Etch 64 besides the r-base and 
| r-recommended? If not, could someone suggest how I might get things 
| working installing from source?

At work, I use Ubuntu 32bit.  I simply have and entry for Debian _sources_:

foo:~> grep debian /etc/apt/sources.list
deb-src http://localhost:9999/ftp.debian.org/debian/ unstable main contrib
non-free

(and please ignore the localhost bit, just my apt-proxy ...)   

Then it is just a matter of apt-get update; apt-get source r-base to fetch
the sources for a local rebuild / backport.  For Feisty, I need to modidy
debian/rules and debian/control to un-hardwire the choice of gcc 4.2 to just
gcc (and g++, gfortran).  We can help you with that; and the exisiting
backports have the _exact_ patch required.

After that, everything just works. I tend to install CRAN and BioC directly
into /usr/local which I then share over NFS.  No problems whatsoever. [ A
while back I needed a more recent graphviz from Debian but Gutsy may already
have that for you. ]

If all this is too much sys-admining for you, then you should consider
getting some local help.  We'll try to coach you from here but you do need
to
some of the heavy lifting too.

Hth, Dirk

-- 
Three out of two people have difficulties with fractions.

Hi Mark,

Did you try what is written at the very end of the READMEs

	http://cran.r-project.org/bin/linux/ubuntu/

and

	http://cran.r-project.org/bin/linux/debian/

i.e. install r-base-dev and then update the packages from within R?

Johannes

* Mark W Kimpel <mwkimpel at gmail.com> [071030
16:40]:
> I have recently upgraded to Ubuntu Gutsy and, for the first time, am 
> using a 64-bit installation. After failing miserably to install R from 
> source, not a problem for me in the past with a 32-bit install, I went 
> the route of using the Debian Etch build. This went smoothly, but I am 
> unable to update my numerous R and BioConductor packages, getting 
> non-zero exit status errors on each package. Is there a repository of 
> pre-built packages for Debian Etch 64 besides the r-base and 
> r-recommended? If not, could someone suggest how I might get things 
> working installing from source?
> 
> I have installed the ia32 library, which did help me build VMWare, but 
> did not help with R. Reading the R-admin manual, there are some 
> suggested compiler flags, but I don't know how to enter them as I am a 
> relative new-comer to Linux.
> 
> Thanks so much,
> Mark
> 
> ---
> 
> 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) 663-0513 Home (no voice mail please)
> 
> _______________________________________________
> R-SIG-Debian mailing list
> R-SIG-Debian at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-debian
-- 
Dr. Johannes Ranke                 jranke at uni-bremen.de     Key ID: F649AF90
UFT Bremen, Leobenerstr. 1         +49 421 218 63373
D-28359 Bremen                     http://www.uft.uni-bremen.de/chemie/ranke

Le mar. 30 oct. ? 11:26, Mark W Kimpel a ?crit :
> I have recently upgraded to Ubuntu Gutsy and, for the first time, am
> using a 64-bit installation. After failing miserably to install R from
> source, not a problem for me in the past with a 32-bit install, I went
> the route of using the Debian Etch build. This went smoothly, but I am
> unable to update my numerous R and BioConductor packages, getting
> non-zero exit status errors on each package. Is there a repository of
> pre-built packages for Debian Etch 64 besides the r-base and
> r-recommended? If not, could someone suggest how I might get things
> working installing from source?
As Dirk mentioned, there aren't any binary packages of R for 64-bit  
Ubuntu. If you look up the archives of the list, you'll see that this  
subject has been discussed a few times already, but so far nobody has  
volunteered to maintain packages.

I cannot help you to build from source any further than pointing to  
the build scripts I use for the i386 packages. There you will see the  
changes (referred to by Dirk) I make to the Debian source packages so  
that they build on Ubuntu. See the Ubuntu README for details.

Vincent
>
> I have installed the ia32 library, which did help me build VMWare, but
> did not help with R. Reading the R-admin manual, there are some
> suggested compiler flags, but I don't know how to enter them as I am a
> relative new-comer to Linux.
>
> Thanks so much,
> Mark
>
> ---
>
> 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) 663-0513 Home (no voice mail please)
>
> _______________________________________________
> R-SIG-Debian mailing list
> R-SIG-Debian at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-debian

Hugh,

Thanks for the advice. I decided to go the route of using source debian 
packages this time around. Below is the basic script I used, adapted 
from the other replies I received. This was successful in getting the 
base R installed as well as an addition ~275 packages from CRAN, 
Omegahat, and BioConductor.

Unfortunately, I have not yet had luck with the following packages:
  [1] "affycoretools" "AnnBuilder"    "biocViews" 
"biomaRt"
  [5] "GSEABase"      "odfWeave"      "RCurl"     
"Resourcerer"
  [9] "Rgraphviz"     "RSPerl"        "RSPython"  
"SBMLR"
[13] "TMat"          "XML"
Some of which may depend on one another. In particular, I get errors 
from both curl and graphviz, I suspect a version problem as they are 
both on my PATH. I am going to work on them some more tomorrow and may 
be posting more specific error messages if I cannot get the problems 
fixed myself.

The script below is what I believe I did, but this was not done on a 
virgin Ubuntu install as I have been futzing with this for a day or so. 
I am also not absolutely sure I have included every necessary step nor 
perhaps included some un-necessary ones. I am brand new to Debian/Ubuntu 
and just learning about the apt/synaptic system.

If Johannes, Vincent, or Dirk could comment on what I did below, it 
would be helpful to me and perhaps other Debian newbies.

Thanks again to all,
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

#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
apt-get -f install

#install the package from .deb
sudo dpkg -i ../r-base-core_2.6.0-1~etchcran.1_amd64.deb

## 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

#Now replace i686 site-library with an empty one for new packages
cd R_HOME #if not made, make it
mv site-library site-library-i686 #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-i686
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,my.new.packages)
biocLite(yet.to.install, dependencies = TRUE)






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

******************************************************************


hugh wrote:
> Mark,
> 
> I am also a relatively new user of Linux, so am not an expert and thus
> am not responding to the whole R-sig-Debian group.  I am running the
> 64-bit version (intel Q6700 CPU) of Gutsy and was able to compile from
> source file on CRAN.  I am able to use 'install.packages(FOO)'
within my
> compiled R to successfully add packages.  If building a shared library
> is important to you, I was NOT successful in doing that (a shared
> library appears to be important if you want to use GUI's like JGR).
> 
> The only change/flag I used was LDFLAGS="-L/usr/local/lib64
> -L/usr/local/lib".  You can edit your config.site file (e.g., sudo
gedit
> config.site) and search for LDFLAGS....uncomment it and use the line I
> used.  Alternately, you can just type sudo ./configure
> LDFLAGS="-L/usr/local/lib64 -L/usr/local/lib"  (that is how you
can set
> flags).
> 
> My experience was that the "standard" Gutsy install was missing a
number
> of programs/librarys to compile R, so I had to add a lot of them.  If
> you are having compile problems, my guess is that you are missing some
> of these libraries which you can install using the Synaptic Package
> Manager.  If you are still having problems, I can try to figure out how
> to send a list of the packages/libraries I have installed if that is
> helpful.
> 
> I also found this site helpful:
>  http://idecide.mskcc.org/yl_home/linux.html
> 
> 
> Best,
> Hugh Whelan
> 
> 
> 
> 
> 
> On Tue, 2007-10-30 at 11:26 -0400, Mark W Kimpel wrote:
>> I have recently upgraded to Ubuntu Gutsy and, for the first time, am
>> using a 64-bit installation. After failing miserably to install R from
>> source, not a problem for me in the past with a 32-bit install, I went
>> the route of using the Debian Etch build. This went smoothly, but I am
>> unable to update my numerous R and BioConductor packages, getting
>> non-zero exit status errors on each package. Is there a repository of
>> pre-built packages for Debian Etch 64 besides the r-base and
>> r-recommended? If not, could someone suggest how I might get things
>> working installing from source?
>>
>> I have installed the ia32 library, which did help me build VMWare, but
>> did not help with R. Reading the R-admin manual, there are some
>> suggested compiler flags, but I don't know how to enter them as I
am a
>> relative new-comer to Linux.
>>
>> Thanks so much,
>> Mark
>>
>> ---
>>
>> 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) 663-0513 Home (no voice mail please)
>>
>> _______________________________________________
>> R-SIG-Debian mailing list
>> R-SIG-Debian at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-debian
> 
>

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 
addresses.

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

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