Hi Marc, this is great news! Thank you for your feedback on this. Diego On Fri, Apr 22, 2011 at 3:59 AM, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: > Hi Diego, > > Your requests must have been persuasive since the maintainers at MBNI have > just updated all of their packages again. ?And so there is now a version of > these packages available for Bioconductor 2.8 (R 2.13). > > biocLite() has been updated accordingly and so now you should be able to get > these packages in the very latest release of Bioconductor. > > > ?Marc > > > On 04/20/2011 08:54 PM, Diego Diez wrote: >> >> Hi Marc >> >> Of course, I understand (and support) the idea behind biocLite() and >> that for the bioconductor installation to properly work it is needed >> to ensure appropriate version of the packages to be installed. The >> problem here is that the custom cdf packages are not - to the best of >> my understanding- official bioconductor packages, but the repository >> is provided in biocReposList() as a convenience. Therefore the lack of >> support for custom cdf packages in this bioconductor version was not >> mentioned in the release announcement. It may have been worth >> mentioning since this may have a big impact on users. >> >> Obviously, removing the repository while not suitable packages exists >> makes all the sense. However, biocReposList() also provides a >> repository for cran, and any package present in cran will be installed >> by biocLite() whether it is compatible with the bioconductor version >> or not. Even there is a recent thread in the list about an old (non >> compatible) version of the graph package present in cran being >> installed because the official one was missing in the repositories. >> Unfortunately I cannot think on a way to overcome this limitation. >> That being said I myself never had a problem using biocLite() on a >> number of year of use. >> >> Two additional comments: >> >> - The help page for biocReposList() might be a bit old since it lists >> two repositories not presently found: >> ----------- >> oh : URL for Bioc Omegahat package repository. ?This repository >> ? ? ? ? ? contains the versions of Omegahat packages that were tested >> ? ? ? ? ? with the current Bioc release. >> >> li : URL for Bioc Lindsey package repository. >> ------------ >> >> whereas the repository "extra" is missing. >> >> - The cran repository is forced to be "http://cran.fhcrc.org". >> Wouldn't be better to try to get the default CRAN repository selected >> by the user in case that option is set? >> >> >> Anyway, to finish this lengthy email just let you know that I >> contacted the custom cdf people and they are working on providing >> packages for bioconductor 2.8 soon! >> >> Diego >> >> >> On Thu, Apr 21, 2011 at 1:55 AM, Marc Carlson<mcarlson at="" fhcrc.org=""> ?wrote: >>> >>> Hi Diego, >>> >>> You can always throw caution to the wind and just forcibly install any >>> tarball (if downloaded manually). ?Although that would be taking matters >>> into your own hands, and you would obviously have to live with any of the >>> consequences that might result. >>> >>> But you should *not* normally be able to get these package using >>> biocLite() >>> if there is not an appropriate version available. ?This is because >>> correct >>> version matching is part of what people depend on when using biocLite(). >>> ?And in this case the problem is indeed because of the issue that you >>> mentioned. ?The .db packages would have been built using sources >>> appropriate >>> for the Bioc 2.7 and so if you installed them with Bioc 2.8, the GO and >>> KEGG >>> terms etc. would be out of sync with the rest of the build. >>> >>> It is also true that the cdf and probe packages might be ok for some >>> things >>> in Bioc 2.8. ?But without the corresponding .db package you will not >>> really >>> be able to really use them fully. ?And if you did use them and then tried >>> to >>> use those remapped probe and cdf packages with the wrong (default) .db >>> style >>> packages the result could be quite chaotic. ?So I can't really recommend >>> that either unless you have some very specialized usage in mind. >>> >>> >>> ?Marc >>> >>> >>> >>> >>> On 04/19/2011 07:29 PM, Diego Diez wrote: >>>> >>>> Hi Marc >>>> >>>> On Wed, Apr 20, 2011 at 1:10 AM, Marc Carlson<mcarlson at="" fhcrc.org=""> >>>> ?wrote: >>>>> >>>>> Hi Diego, >>>>> >>>>> The brainarray CDFs are only missing from the 2.8 build of Bioconductor >>>>> because there is not yet a brainarray build that matches that. ?There >>>>> is >>>>> a >>>>> recent brainarray build that matches Bioconductor 2.7 though, so we >>>>> have >>>>> of >>>>> course provided access to that for the older 2.7 branch. >>>> >>>> Do you mean that the recent brainarray build was not generated using >>>> the latest versions of the framework in Bioconductor 2.8 (like GO.db, >>>> KEGG.db, etc.)? Because other than that I can install those packages >>>> without problem in R2.13/Bioc2.8. I imagine this may create some >>>> problems with unmatched entries... >>>> >>>>> If you are interested in access to a set of brainarray packages that >>>>> match >>>>> Bioconductor 2.8, then I would recommend that you contact them and let >>>>> them >>>>> know how much you appreciate their hard work. ? ;) >>>> >>>> I will, since I really appreciate their hard work! >>>> >>>>> We will of course make such packages available as soon as it is >>>>> possible >>>>> to >>>>> do so. >>>> >>>> Thank you for the clarification. >>>> >>>> Diego >>>> >>>>> ?Marc >>>>> >>>>> >>>>> On 04/18/2011 11:20 PM, Diego Diez wrote: >>>>>> >>>>>> Hi all, >>>>>> >>>>>> I noticed that the mirror for the custom CDFs available at the >>>>>> BrainArray Microarray laboratory is missing in BioC 2.8, and wonder >>>>>> whether this is intentional and permanent. >>>>>> >>>>>> Thank you, >>>>>> >>>>>> -- >>>>>> Diego Diez, PhD >>>>>> Bioinformatics center, >>>>>> Institute for Chemical Research, >>>>>> Kyoto University. >>>>>> Gokasho, Uji, Kyoto 611-0011 JAPAN >>>>>> diez at kuicr.kyoto-u.ac.jp >>>>>> >>>>>> >>>>>>> library(Biobase) >>>>>> >>>>>> Welcome to Bioconductor >>>>>> >>>>>> ?Vignettes contain introductory material. To view, type >>>>>> ?'browseVignettes()'. To cite Bioconductor, see >>>>>> ?'citation("Biobase")' and for packages 'citation("pkgname")'. >>>>>> >>>>>>> biocReposList() >>>>>> >>>>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bioc >>>>>> ? ? ? ? ? "http://bioconductor.org/packages/2.8/bioc" >>>>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? aData >>>>>> "http://bioconductor.org/packages/2.8/data/annotation" >>>>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? eData >>>>>> "http://bioconductor.org/packages/2.8/data/experiment" >>>>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? extra >>>>>> ? ? ? ? ?"http://bioconductor.org/packages/2.8/extra" >>>>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?cran >>>>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? "http://cran.fhcrc.org" >>>>>>> >>>>>>> sessionInfo() >>>>>> >>>>>> R version 2.13.0 Patched (2011-04-13 r55441) >>>>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>>>>> >>>>>> locale: >>>>>> [1] C/UTF-8/C/C/C/C >>>>>> >>>>>> attached base packages: >>>>>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>>>>> >>>>>> other attached packages: >>>>>> [1] Biobase_2.12.1 >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>>> _______________________________________________ >>>>> 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 >>>>> >>> > >