Let me add my opinion: we do not have perfect (easy) reproducibility with
Bioc because we can only (easily) download the tar ball corresponding to
the latest commit in a given branch. I am ok with that. What I (and
Alejandro) is concerned about is the inability to install even that.
There is a
On 04/30/2014 05:30 PM, Kasper Daniel Hansen wrote:
Let me add my opinion: we do not have perfect (easy) reproducibility with
Bioc because we can only (easily) download the tar ball corresponding to
the latest commit in a given branch. I am ok with that. What I (and
Alejandro) is concerned
Hi,
See the latest software builds for BioC 2.13:
http://bioconductor.org/checkResults/2.13/bioc-20140405/
The number of packages that needed to be installed on the build
system in order to build and check the 750 BioC software packages
is displayed in the right-most column of the top table:
Hi Martin
to come back to the original trigger for this thread: it was not concerns for
reproducibility, but the fact that a Bioc package in the current release
stopped working because a CRAN package has changed in the meanwhile.
What’s the most practical solution to this specific problem?
Wolfgang,
Alejandro did not have a problem with the current release, but with the
most recent prior release. His issue is precisely because it is no longer
the current (stable) release.
Kasper
On Thu, Apr 24, 2014 at 3:05 PM, Wolfgang Huber whu...@embl.de wrote:
Hi Martin
to come back to
Hi all,
Just saw this tangentially related link to packrat which seems something
analogous to a virtualenv (of sorts) for R by the Rstudio folks, which I
thought might be useful
It actually doesn't solve anybody's problem here, but as I said ...
tangential :-)
http://rstudio.github.io/packrat/
On 04/22/2014 09:47 AM, Kasper Daniel Hansen wrote:
I think we should have a CRAN snapshot (or a subset of CRAN used in Bioc)
inside each Bioc release; I don't know how hard that is to manage from a
technical point of view.
I followed this thread with some interest.
It would be surprisingly
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
I think we should have a CRAN snapshot (or a subset of CRAN used in Bioc)
inside each Bioc release; I don't know how hard that is to manage from a
technical point of view.
Best,
Kasper
On Tue, Apr 22, 2014 at 6:06 PM, Julian Gehring julian.gehr...@embl.dewrote:
Hi,
For most problems
