[Bioc-devel] r+w permissions in release branches

[Andrzej Oleś]

Dear Kasper,

regarding your issue with R-2.15: I was wondering whether using an
older version of Rcpp from
http://cran.r-project.org/src/contrib/Archive/Rcpp/ would help?

Cheers,
Andrzej

On Tue, Apr 22, 2014 at 2:46 PM, Kasper Daniel Hansen
<kasperdanielhansen at gmail.com> wrote:
> This is because commits to this branch of Bioconductor has been disabled
> and it is intentional.
>
> But it raises the larger question, recently touched upon in a lengthy
> thread on R-devel, on whether this is a good state of affairs for
> Bioconductor.  Specifically the issue has to do with dependency of a
> Bioconductor package on a CRAN package and what happens when CRAN packages
> gets updated in a way that breaks backwards compability.  Right now, we
> (Bioconductor) might get hosed.
>
> For example, we recently deployed a new computing cluster here at Hopkins.
>  I maintain our R installation and some users have asked for an install of
> Bioconductor using the latest version of R-2.15, for reproducibility
> reasons.  I have a number of scripts which installs a standard suite of
> packages we use here.  The issue I am facing is that Rcpp has been updated
> and does not seem to be available for this version of R.  This indirectly
> breaks crlmm, lumi, minfi, charm, methylumi, bead array,
> arrayQualityMetrics to mention but a few we use on our end.  This seems
> somewhat undesirable from a reproducibility perspective - I cannot even
> install the packages!
>
> Best,
> Kasper
>
>
>
>
>
> On Tue, Apr 22, 2014 at 2:19 PM, Alejandro Reyes <alejandro.reyes at embl.de>wrote:
>
>> Dear Dan, Dear developers list,
>>
>> Due a recent change in one cran package, DEXSeq 1.8.0 (for the R version
>> 3.0.*) stop working. I fixed this conflict in the release branch of
>> bioconductor and tried to commit my changes. But I don't seem to have write
>> access, e.g:
>>
>> $ svn ci --username a.reyes -m "fixed conflicts with newest version of
>> cran package"
>> Sending        DESCRIPTION
>> svn: Commit failed (details follow):
>> svn: access to '/bioconductor/!svn/ver/81643/branches/RELEASE_2_13/madman/Rpacks/DEXSeq/DESCRIPTION'
>> forbidden
>>
>> I  also noticed that I also don't have read access...
>>
>> svn co --username a.reyes https://hedgehog.fhcrc.org/
>> bioconductor/branches/RELEASE_2_13/madman/Rpacks/DEXSeq
>> svn: access to 'https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_
>> 2_13/madman/Rpacks/DEXSeq' forbidden
>>
>> I was wondering if this intentional? If so, what would be the way to solve
>> this kind of problems (e.g. a dependency changing outside bioconductor that
>> breaks previous versions of a bioconductor package)?
>>
>> Best regards,
>> Alejandro
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
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