[R] Install bioconductor

[Prof Brian D Ripley]

You are missing both the library and headers for what would be called 
either zlib or libz.  (On an RPM-based system it would be zlib-devel that 
is missing.)

However, this is the wrong list for questions anout installing BioC 
packages: please see the R posting guide.  (And probably the packages 
should check for the headers like zlib.h as well as for -lz, something 
which is best discussed on the BioC list.)

On Sat, 11 Nov 2006, David Hajage wrote:

> Hello useRs,
>
> I'm trying to install bioconductor on ubuntu edgy eft and R 2.4.0.
>
> I have some error messages during installation, in particular for the
> package "affy" :
>
> "Error: package 'affy' required by 'makecdfenv' could not be found"
>
> I have tryed to install 'makecdfenv' with the command :
>
> getBioC("makecdfenv")
>
> But I have this message :
>
> Running getBioC version 0.1.8 with R version 2.4.0
> Running biocinstall version 1.9.9 with R version 2.4.0
> Your version of R requires version 1.9 of Bioconductor.
> Avis dans install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>        argument 'lib' is missing: using /usr/local/lib/R/site-library
> also installing the dependencies 'affy', 'affyio'
>
> essai de l'URL '
> http://bioconductor.org/packages/1.9/bioc/src/contrib/affy_1.12.1.tar.gz'
> Content type 'application/x-gzip' length 1370295 bytes
> URL ouverte
> ==================================================
> downloaded 1338Kb
>
> essai de l'URL '
> http://bioconductor.org/packages/1.9/bioc/src/contrib/affyio_1.2.0.tar.gz'
> Content type 'application/x-gzip' length 57410 bytes
> URL ouverte
> ==================================================
> downloaded 56Kb
>
> essai de l'URL '
> http://bioconductor.org/packages/1.9/bioc/src/contrib/makecdfenv_1.12.0.tar.gz
> '
> Content type 'application/x-gzip' length 3222836 bytes
> URL ouverte
> ==================================================
> downloaded 3147Kb
>
> * Installing *source* package 'affyio' ...
> creating cache ./config.cache
> checking how to run the C preprocessor... cc -E
> checking for main in -lz... no

[etc]


-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595