Install problems with BioC (was Re: [BioC] Bioconductor on Unix: cannot load the library affy)

[Ramon Diaz]

Dear Johanne,

What error message are you getting? I think you are running Linux; could you 
give more details?

Do you get the same error with another version of R? I just tried, and I do 
not get any errors with R-1.6.2. Could this be a problem with R-1.7.0? If so, 
then maybe we sould post a summary of this problem to R-help. What seems 
strange, though, is that not many people seem to be experiencing this 
problem.

Ramón



On Friday 09 May 2003 15:17, Duhaime Johanne wrote:
> Hellp
>
> I have installed the affy package alone. De-install it and Reinstall it
> without success. I used R CMD INSTALL affyXXX. In the lib directory created
> by the installation I do have the DESCRIPTION file installed.
>
> Thank you
>
>
> -----Message d'origine-----
> De : Ramon Diaz [mailto:rdiaz at cnio.es]
> Envoyé : 09-mai-2003 07:30
> À : Jeff Gentry; Duhaime Johanne
> Cc : bioconductor at stat.math.ethz.ch
> Objet : Re: [BioC] Bioconductor on Unix: cannot load the library affy
>
>
> Actually, I get an identical error which seems to be caused by the
> installation process not installing the DESCRIPTION file.
>
> If I install by downloading Bioconductor_1.1.tar.gz  and then doing the
> usual "R CMD INSTALL Bioconductor_1.1.tar.gz", then there are no
> DESCRIPTION files in the directories. (The same thing happens if I use the
> getBioC() function).
>
> However, if I download the individual tar.gz file for each package, and
> install each of them individually, then everything works fine.
>
>
> The strange thing is that this did not happen to me about two days after
> the release of R 1.7.0, when I installed the deb package. A few weeks later
> I built R from sources, and I just noticed this problem with bioconductor
> last night.
> If I now use the original installed package, I get the same error. Note
> that I have been able to install other packages from CRAN, such as car,
> gregmisc or e1071, without trouble.
>
> Maybe this is a problem with my setup (and with Johanne's set up), but I
> don't see it, specially since everything works OK when I install the
> individual Bioc. packages one by one.
>
> > version
>
>          _
> platform i686-pc-linux-gnu
> arch     i686
> os       linux-gnu
> system   i686, linux-gnu
> status
> major    1
> minor    7.0
> year     2003
> month    04
> day      16
> language R
>
>
> Ramón
>
> On Thursday 08 May 2003 22:37, Jeff Gentry wrote:
> > > > library(affy)
> > >
> > > Error in library(package, character.only = TRUE, logical = TRUE,
> > > warn.conflicts = warn.conflicts,  : This is not a valid package -- no
> > > DESCRIPTION exists
> > > Error in library(affy) : .First.lib failed
> > >
> > > > q()
> >
> > It would seem that somehow your installation of the affy package is
> > broken.
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

-- 
Ramón Díaz-Uriarte
Bioinformatics Unit
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

http://bioinfo.cnio.es/~rdiaz