On 05.11.2010 20:25, Hervé Pagès wrote: > Hi Uwe, > > On 11/05/2010 06:04 AM, Uwe Ligges wrote: >> Hi, >> >> the binary of SVGAnnotation in >> BioC/packages/2.7/extra/bin/windows/contrib/2.12/SVGAnnotation_0.6- 0.zip >> >> is declared to be built under R-2.10.x (rather than R-2.12.x) > > Thanks for telling us! > > We host a few Omegahat packages in our extra repo and we try to > host the latest versions. This SVGAnnotation Windows binary is > the latest version currently available at Omegahat. > > Unfortunately Omegahat binary packages are often lagging behind > the source packages (when they are available at all). For example, > for the current release, there is only 1 Windows binary at the > moment (out of 84 source packages): > > http://www.omegahat.org/R/bin/windows/contrib/2.12/PACKAGES > > In the case of SVGAnnotation and XMLSchema (the Windows binary > of XMLSchema that we host is also outdated), they don't contain > native code so I should be able to produce updated binaries without > too many problems. I see. A recent XMLSchema binary is on CRAN extras: http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.12/ >> >> which causes update.packages(checkBuilt=TRUE) to reinstall it again and >> again under Windows. > > It sounds like update.packages(checkBuilt=TRUE) could do a better job. > Generally speaking why would an "update tool" replace something by > something that is identical? Well, since update.packages assumes that packages in ./2.12/ have been built with R-2.12.x which is not that unreasonable. ;-) If it is expected to do a better job, we'd need to add the build stamp into the PACKAGES database. Best wishes, Uwe > Cheers, > H. > >> >> Best wishes, >> Uwe >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >

On 05.11.2010 20:49, Hervé Pagès wrote: > On 11/05/2010 12:29 PM, Uwe Ligges wrote: >> >> >> On 05.11.2010 20:25, Hervé Pagès wrote: >>> Hi Uwe, >>> >>> On 11/05/2010 06:04 AM, Uwe Ligges wrote: >>>> Hi, >>>> >>>> the binary of SVGAnnotation in >>>> BioC/packages/2.7/extra/bin/windows/contrib/2.12/SVGAnnotation_0. 6-0.zip >>>> >>>> >>>> is declared to be built under R-2.10.x (rather than R-2.12.x) >>> >>> Thanks for telling us! >>> >>> We host a few Omegahat packages in our extra repo and we try to >>> host the latest versions. This SVGAnnotation Windows binary is >>> the latest version currently available at Omegahat. >>> >>> Unfortunately Omegahat binary packages are often lagging behind >>> the source packages (when they are available at all). For example, >>> for the current release, there is only 1 Windows binary at the >>> moment (out of 84 source packages): >>> >>> http://www.omegahat.org/R/bin/windows/contrib/2.12/PACKAGES >>> >>> In the case of SVGAnnotation and XMLSchema (the Windows binary >>> of XMLSchema that we host is also outdated), they don't contain >>> native code so I should be able to produce updated binaries without >>> too many problems. >> >> I see. >> >> A recent XMLSchema binary is on CRAN extras: >> http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.12/ >> >> >>>> >>>> which causes update.packages(checkBuilt=TRUE) to reinstall it again and >>>> again under Windows. >>> >>> It sounds like update.packages(checkBuilt=TRUE) could do a better job. >>> Generally speaking why would an "update tool" replace something by >>> something that is identical? >> >> >> Well, since update.packages assumes that packages in ./2.12/ have been >> built with R-2.12.x which is not that unreasonable. ;-) > > Yes it's a fair assumption. Even though sometimes it's not the case. > Beside us dropping old binaries in our ./2.12/, the CRAN repository > currently has a symlink from 2.13 to 2.12 so right now packages in > ./2.13/ have not been built with R-2.13.x > I wonder what update.packages(checkBuilt=TRUE) would do for R-devel > users on Windows (I didn't try)... Good, point. It does reinstall the packages again and again. But things are again diferent for R-devel: It may be the case that a package built under a certain svn revision does not work with the next svn revision of R, hence I think it is not the best way but OK to keep R-devel separate. Uwe > H. > > >> If it is expected to do a better job, we'd need to add the build stamp >> into the PACKAGES database. >> >> Best wishes, >> Uwe >> >> >> >>> Cheers, >>> H. >>> >>>> >>>> Best wishes, >>>> Uwe >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> > >