On Fri, Feb 19, 2010 at 10:26 AM, Nicolas Delhomme <[email protected]> wrote: > Hi folks, just to clarify. > > 1) I'm extensively working with Rsamtools and this package is in very active > development (Thanks Martin!) which means that I do not want to wait for the > package to be available through biocLite (which for me is 1 and 1/2 day > after any bug correction has been published on the mailing list). So, thanks > Sean, but I need the SVN checkout , so a life with a production R and > biocLite will remain an utopia for me... Luckily, I have no problem dealing > with the dependancies by myself.
Cool. So just use R-devel (see below) and know that the SVN version of any package may be broken. Even in devel, the build process can be helpful because if a package version is available via biocLite(), then the version actually built; this is not guaranteed with an SVN checkout, though most authors are as careful as possible to check in working code. > 2) Kasper, maybe I was naive, but well, I expected that patching a > "production" R with the latest development patch (the R-release.diff.gz) > would result in the same as using a "development" R. I mean, that is the > whole purpose of that diff file, right? Actually, that diff file is just to patch the release version of R; it does not end up being equal to R-devel, I don't think. In any case, he final major version of R that you need (currently) to be truly using R-devel is 2.11 in your sessionInfo() and yours is reported as 2.10. > So, either I might have been expecting too much, or (thanks Arnaud for > making me feel less alone and, well, possibly not that crazy ;-) ) that > might be an R related issue (r51142 fails for me, r51149 works for you). > > Since I've "faith" in R, I got the latest R-release.diff.gz and I've patched > my R 2.10.1 again. I'll let you know if that fixes the issue. Otherwise, > I'll just get the R-devel; it's not like the download bandwidth would be an > issue anyway. Actually, since bioc-devel is being developed on R-devel (currently 2.11), there is a possibility (especially for packages that use C code and rely on the underlying R API) that a previous version of R will not work with a bioc-devel package because of changes in R that occur between releases (and also in the development of R). I'm not sure what is going on here, specifically, but Kasper's advice to stick with R-devel when using Bioc devel packages (via SVN or biocLite()) is a good rule-of-thumb. After getting there, it will be easier to see what issues might remain. Sean > --------------------------------------------------------------- > Nicolas Delhomme > > High Throughput Functional Genomics Center > > European Molecular Biology Laboratory > > Tel: +49 6221 387 8426 > Email: [email protected] > Meyerhofstrasse 1 - Postfach 10.2209 > 69102 Heidelberg, Germany > --------------------------------------------------------------- > > > > On 19 Feb 2010, at 15:30, Kasper Daniel Hansen wrote: > >> You should _always_ use R-devel when using Bioc-devel. >> >> Kasper >> >> On Fri, Feb 19, 2010 at 9:20 AM, Droit Arnaud <[email protected]> >> wrote: >>> >>> Hi Nicolas, >>> >>> I had the same problem with the BSgenome packages from SVN. >>> I tried different installation and desinstallation with different version >>> of BSgenome, Biostrings, IRanges.... >>> >>> Finally, I resolved my problem by installing the latest build of R-dev >>> (version.string R version 2.11.0 Under development (unstable) (2010-02-18 >>> r51149). >>> >>> Good luck, >>> >>> Arnaud. >>> >>>> sessionInfo() >>> >>> R version 2.11.0 Under development (unstable) (2010-02-18 r51149) >>> >>> x86_64-apple-darwin10.2.0 >>> >>> locale: >>> >>> [1] fr_CA.UTF-8/fr_CA.UTF-8/C/C/fr_CA.UTF-8/fr_CA.UTF-8 >>> >>> attached base packages: >>> >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> >>> [1] BSgenome_1.15.7 Biostrings_2.15.21 IRanges_1.5.47 >>> >>> loaded via a namespace (and not attached): >>> >>> [1] Biobase_2.7.4 >>> >>> >>> >>> >>> Le 2010-02-19 à 08:51, Nicolas Delhomme a écrit : >>> >>> Hi all, >>> >>> Since a few days, I get the following error message when trying to >>> install BSgenome from my svn checkout directory (R CMD INSTALL -- >>> preclean --clean BSgenome): >>> >>> installing *source* package ‘BSgenome’ ... >>> ** R >>> ** inst >>> ** preparing package for lazy loading >>> Error in conformMethod(signature, mnames, fnames, f, fdef, definition) : >>> in method for ‘start<-’ with signature ‘x="GRanges"’: formal >>> arguments (check = "NA") omitted in the method definition cannot bein >>> the signature >>> Error : unable to load R code in package 'BSgenome' >>> ERROR: lazy loading failed for package ‘BSgenome’ >>> >>> The details about the checkout are (svn info BSgenome/): >>> >>> Path: BSgenome >>> URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BSgenome >>> Repository Root: https://hedgehog.fhcrc.org/bioconductor >>> Repository UUID: bc3139a8-67e5-0310-9ffc-ced21a209358 >>> Revision: 44766 >>> >>> My current sessionInfo: >>> >>> R version 2.10.1 Patched (2010-02-14 r51142) >>> x86_64-unknown-linux-gnu >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] BSgenome_1.15.4 Biostrings_2.15.21 IRanges_1.5.47 >>> >>> loaded via a namespace (and not attached): >>> [1] Biobase_2.7.4 tools_2.10.1 >>> >>> Any idea what is happening there? Instead of patching my R with the R- >>> release.diff.gz, should I install R-devel? >>> >>> Thanks for any help, >>> >>> Cheers, >>> >>> --------------------------------------------------------------- >>> Nicolas Delhomme >>> >>> High Throughput Functional Genomics Center >>> >>> European Molecular Biology Laboratory >>> >>> Tel: +49 6221 387 8426 >>> Email: [email protected]<mailto:[email protected]> >>> Meyerhofstrasse 1 - Postfach 10.2209 >>> 69102 Heidelberg, Germany >>> >>> _______________________________________________ >>> Bioc-sig-sequencing mailing list >>> >>> [email protected]<mailto:[email protected] >>> > >>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >>> >>> _______________________________________________ >>> Bioc-sig-sequencing mailing list >>> [email protected] >>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >>> > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
