biocLite and unknown svn revision
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@michael-lawrence-3846
Last seen 2.4 years ago
United States
Hi, My Linux package manager supports building packages from svn, but it exports the files into a sandbox directory prior to building. This causes 'svn info' to fail in the R build process. (It would probably be cleaner for R to record the svn revision in an svn hook, but that's besides the point). Before October, the unknown revision was indicated by the "unknown" string, and biocLite would emit a warning (but not an error). Since October, the data type of the R_SVN_REVISION has changed to integer, and unknown is indicated by -99. Could this be added to the check in BiocInstaller? Thanks, Michael [[alternative HTML version deleted]]
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@martin-morgan-1513
Last seen 1 day ago
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On 03/08/2013 05:28 AM, Michael Lawrence wrote: > Hi, > > My Linux package manager supports building packages from svn, but it > exports the files into a sandbox directory prior to building. This causes > 'svn info' to fail in the R build process. (It would probably be cleaner This thread https://stat.ethz.ch/pipermail/r-devel/2013-February/065886.html is in essence the same issue (Matrix tests svn revision to determine exports, svn revision is not defined in the way the user is building R), and it might be helpful to bring this up in your context on R-devel. > for R to record the svn revision in an svn hook, but that's besides the > point). Before October, the unknown revision was indicated by the "unknown" > string, and biocLite would emit a warning (but not an error). Since Can you connect the dots a bit more for me, please, I'm not understanding where this warning / error is coming from? Martin > October, the data type of the R_SVN_REVISION has changed to integer, and > unknown is indicated by -99. Could this be added to the check in > BiocInstaller? > > Thanks, > Michael > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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On Fri, Mar 8, 2013 at 6:16 AM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > On 03/08/2013 05:28 AM, Michael Lawrence wrote: >> >> Hi, >> >> My Linux package manager supports building packages from svn, but it >> exports the files into a sandbox directory prior to building. This causes >> 'svn info' to fail in the R build process. (It would probably be cleaner > > > This thread > > https://stat.ethz.ch/pipermail/r-devel/2013-February/065886.html > > is in essence the same issue (Matrix tests svn revision to determine > exports, svn revision is not defined in the way the user is building R), and > it might be helpful to bring this up in your context on R-devel. > > >> for R to record the svn revision in an svn hook, but that's besides the >> point). Before October, the unknown revision was indicated by the >> "unknown" >> string, and biocLite would emit a warning (but not an error). Since > > > Can you connect the dots a bit more for me, please, I'm not understanding > where this warning / error is coming from? > I think from BiocInstaller:::.checkSvnRevision()? Dan > Martin > > >> October, the data type of the R_SVN_REVISION has changed to integer, and >> unknown is indicated by -99. Could this be added to the check in >> BiocInstaller? >> >> Thanks, >> Michael >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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That's correct, sorry that I did not make that more obvious. We just need to change that function to check identical("-99") instead of identical("unknown"). Thanks, Michael On Fri, Mar 8, 2013 at 7:38 AM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > On Fri, Mar 8, 2013 at 6:16 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > > On 03/08/2013 05:28 AM, Michael Lawrence wrote: > >> > >> Hi, > >> > >> My Linux package manager supports building packages from svn, but it > >> exports the files into a sandbox directory prior to building. This > causes > >> 'svn info' to fail in the R build process. (It would probably be cleaner > > > > > > This thread > > > > https://stat.ethz.ch/pipermail/r-devel/2013-February/065886.html > > > > is in essence the same issue (Matrix tests svn revision to determine > > exports, svn revision is not defined in the way the user is building R), > and > > it might be helpful to bring this up in your context on R-devel. > > > > > >> for R to record the svn revision in an svn hook, but that's besides the > >> point). Before October, the unknown revision was indicated by the > >> "unknown" > >> string, and biocLite would emit a warning (but not an error). Since > > > > > > Can you connect the dots a bit more for me, please, I'm not understanding > > where this warning / error is coming from? > > > > I think from BiocInstaller:::.checkSvnRevision()? > > Dan > > > > > > Martin > > > > > >> October, the data type of the R_SVN_REVISION has changed to integer, and > >> unknown is indicated by -99. Could this be added to the check in > >> BiocInstaller? > >> > >> Thanks, > >> Michael > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > > > > -- > > Computational Biology / Fred Hutchinson Cancer Research Center > > 1100 Fairview Ave. N. > > PO Box 19024 Seattle, WA 98109 > > > > Location: Arnold Building M1 B861 > > Phone: (206) 667-2793 > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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On 03/08/2013 09:03 AM, Michael Lawrence wrote: > That's correct, sorry that I did not make that more obvious. We just need to > change that function to check identical("-99") instead of identical("unknown"). Thanks, this was introduced during development of the R-2.14 series, but users of R-3.0 and after automatically satisfy the svn revision requirement and the check has been removed. Martin > > Thanks, > Michael > > > On Fri, Mar 8, 2013 at 7:38 AM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> <mailto:dtenenba at="" fhcrc.org="">> wrote: > > On Fri, Mar 8, 2013 at 6:16 AM, Martin Morgan <mtmorgan at="" fhcrc.org=""> <mailto:mtmorgan at="" fhcrc.org="">> wrote: > > On 03/08/2013 05:28 AM, Michael Lawrence wrote: > >> > >> Hi, > >> > >> My Linux package manager supports building packages from svn, but it > >> exports the files into a sandbox directory prior to building. This causes > >> 'svn info' to fail in the R build process. (It would probably be cleaner > > > > > > This thread > > > > https://stat.ethz.ch/pipermail/r-devel/2013-February/065886.html > > > > is in essence the same issue (Matrix tests svn revision to determine > > exports, svn revision is not defined in the way the user is building R), and > > it might be helpful to bring this up in your context on R-devel. > > > > > >> for R to record the svn revision in an svn hook, but that's besides the > >> point). Before October, the unknown revision was indicated by the > >> "unknown" > >> string, and biocLite would emit a warning (but not an error). Since > > > > > > Can you connect the dots a bit more for me, please, I'm not understanding > > where this warning / error is coming from? > > > > I think from BiocInstaller:::.checkSvnRevision()? > > Dan > > > > > > Martin > > > > > >> October, the data type of the R_SVN_REVISION has changed to integer, and > >> unknown is indicated by -99. Could this be added to the check in > >> BiocInstaller? > >> > >> Thanks, > >> Michael > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > > > > -- > > Computational Biology / Fred Hutchinson Cancer Research Center > > 1100 Fairview Ave. N. > > PO Box 19024 Seattle, WA 98109 > > > > Location: Arnold Building M1 B861 > > Phone: (206) 667-2793 <tel:%28206%29%20667-2793> > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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