[BioC] Problems installing bioconductor on ubuntu

[Steve Lianoglou]

Hi again,

On Jul 10, 2008, at 6:22 PM, Wolfgang Huber wrote:

> 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


Ah! Sorry! I didn't look through the entire error dump and just tried  
to pick at the "low hanging fruit" first. Maybe I can be more helpful  
this time.

Typically to get the development tools in ubuntu, you'll just have to  
install the "build-essential" package. From the terminal, you'd do it  
like so:

sudo apt-get install build-essential

That should get you gcc, make and other stuff (listed here: http://packages.ubuntu.com/gutsy/devel/build-essential)

Hope that helps,
-steve

--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Cornell Medical College

http://cbio.mskcc.org/~lianos