Hi Andrej,
Yes, that would help, that would be also a solution for my case,
installing an old version of the cran package (stamod in my case)
However, I don't know if this could be a "general solution for all
users" since when installing a package via
biocLite, the latest version of the cran package is installed
regardless the R/BiocInstaller version you are using. Users
would need to download the versions of the dependencies that they need
and install them manually.
Alejandro
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
<kasperdanielhan...@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.re...@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
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