[BioC] modules incompatible with R 2.15.1

Marcus Moeller marcus.moeller at gmx.ch
Thu Aug 30 10:37:47 CEST 2012

Hi all.

>     we have noticed that the following modules from the bioc archive are
>     no longer compatible with R version 2.15.1:
>     GOstats
>     GlobalAncova
>     globaltest
>     hgu133a
>     GeneR
>     I would like to ask what is the official way to get them updated? Do
>     I have to contact the authors directly or is there something like a
>     Bugzilla available?
> Hi, Marcus.
> You can look here for build reports:
> http://bioconductor.org/checkResults/release/bioc-LATEST/
> And here for software releases:
> http://www.bioconductor.org/packages/release/BiocViews.html#___Software
> It looks at first glance like all the bioconductor packages except
> GlobalAncova are building fine right now and are available.  GeneR is a
> special case since it is not a bioconductor package.
> Could you let us know what you mean by "no longer compatible with R
> version 2.15.1"?  What did you try to do that suggested that was the
> case?  Be sure to include the code you are trying and the output of
> sessionInfo().

I have re-checked was able to build most of the packages now, but 
hgu133a and GeneR where I got an error message like:

Warning message:
package ‘hgu133a’ is not available (for R version 2.15.1)

when trying to install it using:

/usr/bin/R --no-save --no-restore 
<<<'source("http://bioconductor.org/biocLite.R"); biocLite("hgu133a")'

Maybe hgu133a has been removed from the repository? Concerning GeneR, I 
am sure that I have installed it from the bioc repository in the past.



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