Hi all, if you want to work with "devel" versions: on most days, I get good results by running the following shell script in the morning while I go get my coffee. (Important disclaimer: this procedure is not 100% safe and on some days, you'll have to do manually reinstall packages that rely on properties of R that have changed 'under them'; or, to "make distclean" instead of "make clean"; or wipe out and again check out the whole R svn tree):
## -------------------------------- ## Update shell script ## -------------------------------- #!/bin/bash set -e set -o errexit cd $HOME svn up madman # https://hedgehog.fhcrc.org/bioconductor/trunk/madman svn up R # https://svn.r-project.org/R/trunk cd R ./tools/rsync-recommended make clean if [ "$(uname)" = "Darwin" ]; then ./configure --x-includes=/usr/X11/include --x-libraries=/usr/X11/lib else ./configure fi make echo "update.packages(ask=F)" | R --no-save ## -------------------------------- ## Furthermore, I have these lines in ~/.Rprofile: ## (you need to update this with every Bioconductor release) ## -------------------------------- Rvers = as.numeric(version$minor) basename = "http://bioconductor.org/packages"; biocUrls = c("bioc", "data/annotation", "data/experiment", "extra") if(Rvers >=11.0) repos=paste(basename, biocUrls, sep="/2.6/") else if(Rvers >=10.0) repos=paste(basename, biocUrls, sep="/2.5/") else stop("Zapperlot") options(repos=c(CRAN="http://cran.fhcrc.org";, repos, OMEGAHT="http://www.omegahat.org/R";)) rm(list=c("Rvers", "basename", "biocUrls", "repos")) Il giorno Feb 19, 2010, alle ore 5:07 PM, Nicolas Delhomme ha scritto: Hi Kasper, Thanks for refreshing my confused mind (not that I didn't know it); seems like some of my synapses must have misfired one day because I was convinced that the diff file had to do with devel. I'll RTFM more attentively next time. Cheers, Nico --------------------------------------------------------------- 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 16:50, Kasper Daniel Hansen wrote: > 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. >> >> 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? > > Well, your expectation is completely wrong which is why you are > running into this issue. > > Let me do a short recap of what happens, since you are clearly a bit confused. > > When R-2.10 was released, they immediately created two branches of R: > 2.10-patched (known as R-patched) and devel. These branches are > separate. The only things that enter into the 2.10 branch is bug > fixes. When enough bug fixes has accumulated a minor version of R > gets release (like R-2.10.1). All new functionality is in devel. > This is an extremely big difference. All the release-diff does, is > track the difference between the R-2.10 release and the patch branch > of 2.10. So applying the diff means you essentially create the latest > R-patched. Devel is completely different. > > All of this is done to make sure that a user of R-2.10 can get bug > fixes, without getting new - perhaps non-compatible - functionality > changes. > > Bioc-devel uses R-devel, not R-patched. > > Kasper > >> 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. >> >> Cheers, >> >> Nico >> >> --------------------------------------------------------------- >> 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 be in >>>> 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 Wolfgang Huber [email protected] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
