[BioC] Bioconductor on Unix: cannot load the library affy

[Duhaime Johanne]

Hello

I succeded in installing BioC with getBioC instead of using the bundle.

Thank you for your help



-----Message d'origine-----
De : Duhaime Johanne 
Envoyé : 09-mai-2003 09:17
À : Ramon Diaz; Jeff Gentry
Cc : bioconductor at stat.math.ethz.ch
Objet : RE: [BioC] Bioconductor on Unix: cannot load the library affy


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

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