[BioC] BioC 2.2 release update.packages error

[Patrick Aboyoun]

Elliot,
My best guess at this time is that the bioconductor.org mirroring  
didn't properly capture the newly updated XML package. Interestingly,  
the XML packaged page at http://cran.fhcrc.org has a link to version  
2.1-0 of XML and the PACKAGES file mentions version 2.1-0, but the  
CRAN repository at fhcrc.org still had version 1.99-0 of the XML  
source package.

I just hand downloaded version 2.1-0 of the source package for XML to  
the CRAN mirror at fhcrc.org and tested downloading XML via biocLite  
and all looks well now. Give it a try.


Patrick


Quoting Elliot Kleiman <kleiman at rohan.sdsu.edu>:

> Hi BioC,
>
> When trying to update my R-2.7.2/BioC-2.2
> release, the update script errs out,
>
> # source the update file
>> source("http://bioconductor.org/biocLite.R")
> Warning messages:
> 1: In safeSource() : Redefining 'biocinstall'
> 2: In safeSource() : Redefining 'biocinstallPkgGroups'
> 3: In safeSource() : Redefining 'biocinstallRepos'
>
> # update packages
>> update.packages(repos=biocinstallRepos(), ask=FALSE)
> trying URL 'http://cran.fhcrc.org/src/contrib/XML_2.1-0.tar.gz'
> Error in download.file(url, destfile, method, mode = "wb", ...) :
>  cannot open URL 'http://cran.fhcrc.org/src/contrib/XML_2.1-0.tar.gz'
> In addition: Warning message:
> In download.file(url, destfile, method, mode = "wb", ...) :
>  cannot open: HTTP status was '404 Not Found'
> Warning in download.packages(p0, destdir = tmpd,
> available = available,  : download of package 'XML' failed
>
> [:Question:]
> * What am I doing wrong here?
> i.e., it used to work fine ...
>
> # print sessionInfo()
>> sessionInfo()
> R version 2.7.2 (2008-08-25)
> i686-pc-linux-gnu
>
> locale:
> LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;
> LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=en_US;
> LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;
> LC_TELEPHONE=C;LC_MEASUREMENT=en_US;
> LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] tools_2.7.2
>
> Thank you,
>
> ... Elliot
>
> -- 
> MS graduate student Computational Science Program San Diego State University
> http://www.csrc.sdsu.edu/ http://www.sdsu.edu/
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor