Re: [Bioc-devel] getting a listing of all src packages
Hi, Darin. You might find these instructions useful: http://www.bioconductor.org/about/mirrors/mirror-how-to/ Basically, you can use rsync to get the repository and keep it up-to-date. Sean On Thu, Oct 30, 2014 at 9:17 AM, Darin Perusich da...@darins.net wrote: Hello All, Would it be possible to get a listing of all package sources from /packages/release/bioc/src/contrib or make the location browseable? I'm trying to download all the bioconductor tarball's so I can create rpm packages of them for inclusion in the openSUSE Build Service. I've already done this for all the CRAN packages and would like to include bioconductor packages as well. https://build.opensuse.org/project/show/devel:languages:R:released https://build.opensuse.org/project/show/devel:languages:R:CRAN-packages -- Later, Darin ___ 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
Re: [Bioc-devel] getting a listing of all src packages
Hi Darin, We're grateful that you're willing to do this! Please be aware that a particular version of BioC is aimed to be used with a particular version of R only. E.g. the current release (BioC 3.0) is aimed to be used with R-3.1.1. Also some BioC packages depend on particular versions of CRAN packages. Only the CRAN packages used by our build system have been tested to be compatible with BioC 3.0: http://bioconductor.org/checkResults/3.0/bioc-LATEST/ You can see the list of CRAN packages used by the latest builds by clicking on the link under 'Installed pkgs' in the top table. Note that, because these builds are currently live (they run every night and will stop in April 2015), the CRAN packages they use are always the latest packages available on CRAN. Cheers, H. On 10/30/2014 06:22 AM, Sean Davis wrote: Hi, Darin. You might find these instructions useful: http://www.bioconductor.org/about/mirrors/mirror-how-to/ Basically, you can use rsync to get the repository and keep it up-to-date. Sean On Thu, Oct 30, 2014 at 9:17 AM, Darin Perusich da...@darins.net wrote: Hello All, Would it be possible to get a listing of all package sources from /packages/release/bioc/src/contrib or make the location browseable? I'm trying to download all the bioconductor tarball's so I can create rpm packages of them for inclusion in the openSUSE Build Service. I've already done this for all the CRAN packages and would like to include bioconductor packages as well. https://build.opensuse.org/project/show/devel:languages:R:released https://build.opensuse.org/project/show/devel:languages:R:CRAN-packages -- Later, Darin ___ 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 -- 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...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] R-devel update schedule/strategy for Bioc devel build machines
Bioc admins, We have an automatic build/test mechanism for our internal packages which we'd like to match the Bioc build machines as closely as possible. AFAIU, the exact commit-specific version of R-devel used on your devel build server changes occasionally within Bioc releases, and we'd like to mirror those changes on our system. Is there a set schedule for when the exact commit of R-devel on your build server changes? Also, do you guys grab them as tarballs, or checkout/update from the svn? Thanks, ~G -- Computational Biologist Genentech Research [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] experiment data package versioning
Dear all, I was under the (wrong) impression that experiment data packages would be following the same versioning convention as software with even/odd for release/devel branches. Would this be something that others would find useful? Best wishes, Laurent ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] experiment data package versioning
On 30 October 2014 17:43, Henrik Bengtsson wrote: On Thu, Oct 30, 2014 at 10:31 AM, Laurent Gatto lg...@cam.ac.uk wrote: Dear all, I was under the (wrong) impression that experiment data packages would be following the same versioning convention as software with even/odd for release/devel branches. Would this be something that others would find useful? Bumping versions of data packages would results in very large amounts of download at every Bioc release, even if there's no actual update to the data packages. I'd vote not a good idea on this one. Good point. But versions are bumped (I think) - two non-random examples: Bioc3.0/AffymetrixDataTestFiles has version 0.3.1 Bioc3.1/AffymetrixDataTestFiles has version 0.4.0 Bioc3.0/pRolocdata has version 1.3.5 Bioc3.1/pRolocdata has version 1.3.6 Laurent /Henrik Best wishes, Laurent ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Laurent Gatto http://cpu.sysbiol.cam.ac.uk/ ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] experiment data package versioning
- Original Message - From: Hervé Pagès hpa...@fredhutch.org To: Laurent Gatto lg...@cam.ac.uk, bioc-devel@r-project.org Sent: Thursday, October 30, 2014 10:52:14 AM Subject: Re: [Bioc-devel] experiment data package versioning Hi Laurent, On 10/30/2014 10:31 AM, Laurent Gatto wrote: Dear all, I was under the (wrong) impression that experiment data packages would be following the same versioning convention as software with even/odd for release/devel branches. You're right! This is what we should have done: https://stat.ethz.ch/pipermail/bioc-devel/2014-April/005452.html And it seems that we actually did this for the previous BioC release (BioC 2.14) back in April. Would this be something that others would find useful? Now that we have branches for experiment data packages, I think it's more important than before that we follow this even/odd versioning convention. That way the maintainers have room to bump the version of their package in release, i.e. they can bump the version of their package in release without the need to re-use a version number that is already (or has already been) used by the devel version of their package. I don't think it's worth fixing in release but we should probably bump y in devel. I have bumped y in devel for the data/experiment packages. My apologies for not doing this properly at release time. I've taken some steps to help ensure this doesn't happen again. Note that we are not bumping these numbers in release, so there are still packages with odd 'y'. But in the interests of not triggering large downloads for all users and mirrors, we are holding off. The data experiment builds will run again on Saturday after which the repository should reflect the bumping I just did in svn. Dan Cheers, H. Best wishes, Laurent ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- 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...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
