[BioC] Problems installing bioconductor on ubuntu

[Wolfgang Huber]

Dear Rebecca,


please see below


> I have been trying to install bioconductor on ubuntu 7.10 gutsy using R
> version 2.5.1, and getting a lot of error messages:
> 
>  
> 
>  Here are a few:
> 
> 1: package âxtableâ is not available in: install.packages(pkgs = pkgs, repos
> = repos, dependencies = dependencies,   ...
> 
> 2: dependency âsurvivalâ is not available in: install.packages(pkgs = pkgs,
> repos = repos, dependencies = dependencies,   ...
> 
> 3: installation of package 'affyio' had non-zero exit status in:
> install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,
> ...
> 
> 4: installation of package 'lattice' had non-zero exit status in:
> install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,
> ...
> 
> 5: installation of package 'KernSmooth' had non-zero exit status in:
> install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,
> ...
> 
>  
> 
> I have installed r-base-core, build-essential, g77, reflas3, reflas3-dev,
> r-base-dev, and r-recommended.
> 
>  
> 
> When I tried to install affyio by itself, I got the following error message:
> 
>> biocLite(c("affyio"))
> 
> Running biocinstall version 2.0.8 with R version 2.5.1
> 
> Your version of R requires version 2.0 of Bioconductor.
> 
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
> 
>          argument 'lib' is missing: using '/usr/local/lib/R/site-library'
> 
> trying URL
> 'http://bioconductor.org/packages/2.0/bioc/src/contrib/affyio_1.4.1.tar.gz'
> 
> Content type 'application/x-gzip' length 59104 bytes
> 
> opened URL
> 
> ==================================================
> 
> downloaded 57Kb
> 
>  
> 
> * Installing *source* package 'affyio' ...
> 
> creating cache ./config.cache
> 
> checking how to run the C preprocessor... cc -E
> 
> checking for main in -lz... no
> 
> updating cache ./config.cache
> 
> creating ./config.status
> 
> creating src/Makevars
> 
> ** libs
> 
> gcc-4.2 -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic
> -g -O2 -c read_abatch.c -o read_abatch.o
> 
> /bin/bash: gcc-4.2: command not found
> 


^^^^^^^^^^ This is the first problem. To install packages from source 
(which is the common thing to do in Linux) you will need to install 
various compilers and software development tools into your Ubuntu. Note 
that this is not a Bioconductor "problem" but a general property of R.

MacOSX and Windows versions of R and Bioconductor make it a bit easier 
by offering "precompiled" packages, but in Linux you (and your computer) 
are expected to build "from source code".

I am afraid that this will require some iterations and careful reading 
of the output of attempts at installation, in order to see which Ubuntu 
packages you need to add.

As Steve pointed out, it is also recommendable that you install R 2.7 
rather than 2.5.1, and you can do this on your "old" Ubuntu, just not 
with the Ubuntu package manager, but rather by also building R 2.7 "from 
source". Some general help can be found here:
http://cran.r-project.org/doc/manuals/R-admin.html

  Hope this helps
  Wolfgang

> make: *** [read_abatch.o] Error 127
> 
> chmod: cannot access `/usr/local/lib/R/site-library/affyio/libs/*': No such
> file or directory
> 
> ERROR: compilation failed for package 'affyio'
> 
> ** Removing '/usr/local/lib/R/site-library/affyio'
> 
>  
> 
> The downloaded packages are in
> 
>         /tmp/RtmpowXclV/downloaded_packages
> 
> Warning message:
> 
> installation of package 'affyio' had non-zero exit status in:
> install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,
> 
>  
> 
>  
> 
> If anyone can offer suggestions or help, it would be appreciated.
> 
>  
> 
> Thanks,
> 
> R
> 
> 
> 	[[alternative HTML version deleted]]
> 
> 
> 
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> 
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-- 
----------------------------------------------------
Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber