[R-sig-Debian] trouble installing building packages from source using R 2.6.0 on Ubuntu Gutsy AMD64

[Mark W Kimpel]

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
> 
>