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 about is the inability to install even that.
There is a clear candidate for which version of the CRAN package we should store: the version we use when we run R CMD check. This is the version we implicitly say things are working with.
We discussed this internally and are likely to create snapshots at the end of each release cycle of all Bioc packages and their CRAN dependencies. Perhaps these will be available too as an AMI. A snapshot facilitates (though hardly guarantees) reproducibility without too much cost, and is consistent with project objectives.
Martin
Best, Kasper On Fri, Apr 25, 2014 at 7:41 AM, Hervé Pagès <hpa...@fhcrc.org> wrote: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: 1510 on zin1 (Linux) 1486 on moscato1 (Windows) 1500 on perceval (Mac) If you click on these numbers, you get the full list of packages plus their version. Once you've subtracted the 750 software packages + the number of data annotation and data experiment packages (a few more hundreds) from these numbers, that gives you the number of CRAN packages that BioC 2.13 depends on. Not that many really (only a very small fraction of the 5400 CRAN packages). If we hosted only this small subset of CRAN packages under http://bioconductor.org/packages/2.13/cran next to the other 4 frozen repos http://bioconductor.org/packages/2.13/bioc http://bioconductor.org/packages/2.13/data/annotation http://bioconductor.org/packages/2.13/experiment http://bioconductor.org/packages/2.13/extra and have biocLite() modified to point to http://bioconductor.org/packages/2.13/cran instead of http://cran.fhcrc.org then anybody that has R 3.0.3 could *easily* install and run BioC 2.13 now or in 5 years from now. Cheers, H. On 04/24/2014 08:09 AM, Steve Lianoglou wrote: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 Thursday, April 24, 2014, Wolfgang Huber <whu...@embl.de> wrote: Hi Kasperyou are right, I had misunderstood the problem. In that case I agree with Martin that the problem resolves into components that are either intractable, already addressed by deprecation policies, or not very important. Sorry for the noise. Wolfgang On 24 Apr 2014, at 15:18, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: Wolfgang,Alejandro did not have a problem with the current release, but with themost 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 the original trigger for this thread: it was notconcerns 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? Best wishes Wolfgang On 23 Apr 2014, at 19:41, Martin Morgan <mtmor...@fhcrc.org> wrote: 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 inBioc)inside each Bioc release; I don't know how hard that is to managefrom atechnical point of view.I followed this thread with some interest. It would be surprisingly challenging to update even a 2.13 package --the build machines have moved on to other tasks, unconstrained by theunique system dependencies needed for 2.13 builds.The idea of a 'forever' repository snapshot seems possible, but wouldthe snapshot be at the beginning of the release and hence miss the fewbut important bug fixes introduced during the release, or at the end of the release, which might be after the time required for the purposes of replication? Either way it is certain that the peanut butter would land face down for one's particular need. Also, the need for the user to satisfy system dependencies becomes increasingly challenging, even with a binary repository. I don't think a central 'Bioc' solution would really address the problem of reproducibility.It is not that 'hard' for an individual group to create a snapshot ofBioc and CRAN, using rsynchttp://www.bioconductor.org/about/mirrors/mirror-how-to/ http://cran.r-project.org/mirror-howto.html and to use install.packages() or even biocLite to access these (see?setRepositories). This would again require that the system dependenciesfor these packages are satisfied in some kind of frozen fashion.A more robust possibility is of course a virtual machine, such as theAMI (or a customized version) we providehttp://www.bioconductor.org/help/bioconductor-cloud-ami/#ami_ids although these have only a subset of packages installed by default. The CRAN thread referenced earlier included this post https://stat.ethz.ch/pipermail/r-devel/2014-March/068605.html which I think makes an important distinction between exact replicationand scientific reproducibility; it is the latter that must be the mostinteresting, and the former that we somehow seem to stumble over. The thread also mentions best practices -- version controlhttp://bioconductor.org/developers/how-to/source-control/ disciplined approach to deprecation http://bioconductor.org/developers/how-to/deprecation/ package versioning http://bioconductor.org/developers/how-to/version-numbering/ and the Bioc-style approach to release that we as developers can acton to enhance reproducibility. What other best pract-- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel[[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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