Herve Pages wrote: > Hi Joao, > > Please don't email me privately for those matters. Use the mailing list > where other people might be able to help you. Also other people that > have the same problem (today or in 2 years -- the mailing list is > archived) could benefit from your experience. > > Jo?o Fadista wrote: >> Hi Herve, >> >> I downloaded the package as you told me but it gave an error: >> >> >> 'tar' is not recognized as an internal or external command, >> operable program or batch file. >> Error: cannot untar the package >> >> The downloaded packages are in >> C:\Documents and Settings\jofa\Local Settings\Temp\RtmpNdyPKI\downloaded_packages >> Warning message: >> In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : >> installation of package 'BSgenome.Btaurus.UCSC.bosTau3' had non- zero exit status > > > You need to provide your sessionInfo() + the exact commands that produced > this error. Without this information, there is no way anybody can help you. > > It looks like you tried to install a source packages on a Windows machine > that doesn't have the required tools for doing this but it's hard to know > with so little information provided. > > The important part of the instructions I gave you in my previous email > was: "... if your Windows box is configured to install from source ..." > Getting your Windows box properly configured to install from source is an > _absolute requirement_ if you want to use BioC devel. > This requires that you first install R devel from source (+ all the R tools). This isn't quite true. You don't need to install R-devel from source. You can just install R-devel and then go to Duncan Murdoch's site to get and then run the Rtools installer, and then you should be ready to go. Note that you may or may not be able to install a source package from within an R session. Sometimes you have to do Rcmd install <thepackagename> at a dos prompt. In which case it is much easier if you have R installed in e.g., C:\R-devel rather than in C:\Program Files\... And also note that you will need to use forward slashes and short path names. So let's say the file is on the desktop and your R is in C:\R-devel. At a dos prompt: cd \R-devel\bin rcmd install -l C:\R-devel\library C:/docume~1/<username>/desktop/<packagename> <==this all on one line should work. Or maybe just biocLite("thepackagename", type="source") from within R. Best, Jim > See section 3 of the "R Installation and Administration" for how to do this. > Otherwise, just wait the next BioC release (end of April). Also it could be > that a Windows version of BSgenome.Btaurus.UCSC.bosTau3 is made available > in BioC devel before the release but there is no precise plan for this. > > Cheers, > H. > > >> >> Is there something I did wrong? >> >> Best regards, >> Jo?o Fadista >> >> >> >> >> >> -----Original Message----- >> From: Herve Pages [mailto:hpages at fhcrc.org] >> Sent: Saturday, March 15, 2008 2:12 AM >> To: Jo?o Fadista >> Cc: bioc >> Subject: Re: [BioC] BSgenome package - add the bos taurus genome >> >> Hi Jo?o, >> >> Sorry I forgot to mention that the package is only available as a source package. The Windows and Mac OS X binaries will come later. >> In the mean time, if your Windows box is configured to install from source, you can do: >> >> > options(pkgType="source") >> > library(BSgenome) >> > available.genomes() # now you should see it! >> > source("http://bioconductor.org/biocLite.R") >> > biocLite("BSgenome.Btaurus.UCSC.bosTau3") >> >> Cheers, >> H. >> >> >> Jo?o Fadista wrote: >>> Dear Herve, >>> >>> I Installed the R devel and the BioC devel (I suppose) but I was not able to get the package: >>> >>>> library(BSgenome) >>>> available.genomes() >>> [1] "BSgenome.Amellifera.UCSC.apiMel2" >>> [2] "BSgenome.Athaliana.TAIR.01222004" >>> [3] "BSgenome.Celegans.UCSC.ce2" >>> [4] "BSgenome.Dmelanogaster.BDGP.Release5" >>> [5] "BSgenome.Dmelanogaster.FlyBase.r51" >>> [6] "BSgenome.Dmelanogaster.UCSC.dm2" >>> [7] "BSgenome.Ggallus.UCSC.galGal3" >>> [8] "BSgenome.Hsapiens.UCSC.hg16" >>> [9] "BSgenome.Hsapiens.UCSC.hg17" >>> [10] "BSgenome.Hsapiens.UCSC.hg18" >>> [11] "BSgenome.Mmusculus.UCSC.mm6" >>> [12] "BSgenome.Mmusculus.UCSC.mm7" >>> [13] "BSgenome.Mmusculus.UCSC.mm8" >>> [14] "BSgenome.Mmusculus.UCSC.mm9" >>> [15] "BSgenome.Scerevisiae.UCSC.sacCer1" >>> >>>> source("http://bioconductor.org/biocLite.R") >>> Warning messages: >>> 1: In safeSource() : Redefining 'biocinstall' >>> 2: In safeSource() : Redefining 'biocinstallPkgGroups' >>> 3: In safeSource() : Redefining 'biocinstallRepos' >>> >>>> biocLite("BSgenome.Btaurus.UCSC.bosTau3") >>> Running biocinstall version 2.2.2 with R version 2.7.0 (under >>> development) Your version of R requires version 2.2 of Bioconductor. >>> Warning message: >>> package 'BSgenome.Btaurus.UCSC.bosTau3' is not available >>> >>>> sessionInfo() >>> R version 2.7.0 Under development (unstable) (2008-03-11 r44737) >>> i386-pc-mingw32 >>> >>> locale: >>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >>> States.1252;LC_MONETARY=English_United >>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >>> >>> attached base packages: >>> [1] tools stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] BSgenome_1.7.4 Biostrings_2.7.32 Biobase_1.99.2 >>> >>> >>> >>> Did I make something wrong? >>> >>> >>> Best regards, >>> Jo?o >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> -----Original Message----- >>> From: Herve Pages [mailto:hpages at fhcrc.org] >>> Sent: Wednesday, March 12, 2008 4:21 AM >>> To: Jo?o Fadista >>> Cc: bioconductor at stat.math.ethz.ch >>> Subject: Re: [BioC] BSgenome package - add the bos taurus genome >>> >>> Hi Jo?o, >>> >>> Jo?o Fadista wrote: >>>> Yes, it?s that version. Thanks a lot. When you add the package please let me know. >>> I've just added BSgenome.Btaurus.UCSC.bosTau3 to our public repository (for BioC devel only). From R 2.7.0: >>> >>> > library(BSgenome) >>> > available.genomes() >>> [1] "BSgenome.Amellifera.UCSC.apiMel2" >>> [2] "BSgenome.Athaliana.TAIR.01222004" >>> [3] "BSgenome.Btaurus.UCSC.bosTau3" >>> [4] "BSgenome.Celegans.UCSC.ce2" >>> [5] "BSgenome.Dmelanogaster.BDGP.Release5" >>> [6] "BSgenome.Dmelanogaster.FlyBase.r51" >>> [7] "BSgenome.Dmelanogaster.UCSC.dm2" >>> [8] "BSgenome.Ggallus.UCSC.galGal3" >>> [9] "BSgenome.Hsapiens.UCSC.hg16" >>> [10] "BSgenome.Hsapiens.UCSC.hg17" >>> [11] "BSgenome.Hsapiens.UCSC.hg18" >>> [12] "BSgenome.Mmusculus.UCSC.mm6" >>> [13] "BSgenome.Mmusculus.UCSC.mm7" >>> [14] "BSgenome.Mmusculus.UCSC.mm8" >>> [15] "BSgenome.Mmusculus.UCSC.mm9" >>> [16] "BSgenome.Scerevisiae.UCSC.sacCer1" >>> >>> Install as usual with biocLite(): >>> >>> > source("http://bioconductor.org/biocLite.R") >>> > biocLite("BSgenome.Btaurus.UCSC.bosTau3") >>> >>> It's big (736.7 Mb) so depending on your connection it might take a while. >>> Let me know in case of problems. >>> >>> Cheers, >>> H. > > _______________________________________________ > 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 -- James W. 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