[Bioc-devel] biocLite - can it produce better error messages?

[Herve Pages]

Hi Wolfgang,

Not sure the problem was a transient outage of the bioconductor repository:

  > install.packages('limma', repos="http://toto.fr/")
  Warning: unable to access index for repository http://toto.fr/src/contrib
  Warning in download.packages(unique(pkgs), destdir = tmpd, available = available,  :
           no package 'limma' at the repositories

biocLite is just a wrapper to install.packages, hence those errors you see
are those raised by install.packages, not biocLite.
Your collaborator got this:

  dependency '‘cellHTS’' is not available

but no warning message like in my previous example, so it seems that install.packages
was able to access the repository indexes but that there was indeed no cellHTS package
available for _him_ (I would not be surprised he tried this on a Mac ;-) )

Cheers,
H.


Wolfgang Huber wrote:
> Hi all,
> 
> a collaborator of mine tried to install a package from the 1.9 release 
> earlier this morning, getting the error messages below. Now I am not 
> getting these, apparently this may have been a transient outage of the 
> bioconductor repository.
> 
> My suggestion is that the "getBioC" function would produce a more 
> helpful error message. While it is true that dependency '‘pkgname’' is 
> not available, if the deeper problem is that no connection can be 
> established with the repository server, many users might be less 
> confused if this were what they'd be told...
> 
>   Best wishes
>    Wolfgang
> 
> -------- Original Message --------
> Subject: quick question - BioC install
> Date: Sun, 28 Jan 2007 09:30:35 +0100
> From:
> To: huber at ebi.ac.uk
> 
> 
>> source('http://www.bioconductor.org/biocLite.R')
>> biocLite('cellHTS')
> Running getBioC version 0.1.8 with R version 2.4.1
> Running biocinstall version 1.9.9 with R version 2.4.1
> Your version of R requires version 1.9 of Bioconductor.
> dependency '‘cellHTS’' is not available
> 
>> biocLite('prada')
> Running getBioC version 0.1.8 with R version 2.4.1
> Running biocinstall version 1.9.9 with R version 2.4.1
> Your version of R requires version 1.9 of Bioconductor.
> dependency '‘prada’' is not available
> 
> ------------------------------------------------------------------
> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
> 
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