Hi Florian, Fixed BSgenome.Mmusculus.UCSC.mm8 (version 1.3.2) and new BSgenome.Mmusculus.UCSC.mm9 are available. Let me know in case of problems. Cheers, H. Quoting Herve Pages <hpages at="" fhcrc.org="">: > Hi Florian, > > Florian Markowetz wrote: > > Hi list, > > > > I have some trouble with the Mouse genome version 'mm8' (Feb 2006), > > v1.3.1, which is the newest assembly on bioconductor (even though there > > is an assembly from Jul 2007 at the UCSC genome browser). > > Ooops. Thanks for reporting this! We need to build a BSgenome package for > mm9. I'll post again here when it is ready. > > > > > Somehow the Biostring object is broken: > > > > > library("BSgenome.Mmusculus.UCSC.mm8") > > > Mmusculus$chr1 > > 197069962-letter "DNAString" instanceError in XRaw.read(x at data, > > x at offset + i, x at offset + imax, dec_lkup = dec_lkup(x)) : > > RAW() can only be applied to a 'raw', not a 'char' > > Ugly! I'll look into this and let you know. > > > > > The problem is not specific to chromosome 1 and does not appear with the > > older versions 'mm7' and 'mm6' > > > > Additionally, when installing 'BSgenome' (v1.6.0) it got a message about > > wrong MD5 checksums: > > > > package 'BSgenome' successfully unpacked and MD5 sums checked > > Note that this is a Windows specific message only... > > > files extdata/chr10.rda, extdata/upstream5000.rda have the wrong MD5 > > checksums > > ... so I tried on a Windows machine but I didn't get the "wrong MD5 > checksums" message. > Note that this last message is probably related to the installation of > the BSgenome.Mmusculus.UCSC.mm8 package, not the BSgenome package > (there are no chr10.rda or upstream5000.rda files in BSgenome). > But I don't get the "wrong MD5 checksums" message when I install > BSgenome.Mmusculus.UCSC.mm8 on Windows. > > Can you reproduce the problem? Maybe these files were corrupted because > of temporary download problems? > > The MD5 sum for these files are: > > b3db5d4de17aba4dc503e45e39ae93da chr10.rda > 27de5d07fc68449329fb5e489b82400f upstream5000.rda > > You need the md5sum command for this (part of the Rtools on Windows, > standard command on Linux). Locate the folder where > BSgenome.Mmusculus.UCSC.mm8 > is installed, go in the extdata/ subfolder and run md5sum on chr10.rda > and upstream5000.rda. If you don't get the same MD5 sums as the ones > above then try to reinstall the package. > > > > > I don't know how serious that is ... > > It is serious since it probably means that your chr10.rda and > upstream5000.rda are corrupted. But this package is broken anyway > so maybe you want to wait until I fix it before you download it again. > > I'm going to fix it ASAP and will let you know. > > Cheers, > H. > > > > > Thanks for any input, > > Florian > > > > > sessionInfo() > > R version 2.6.0 (2007-10-03) > > 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 > > [8] base > > > > other attached packages: > > [1] BSgenome.Mmusculus.UCSC.mm8_1.3.1 BSgenome_1.6.0 > > [3] Biobase_1.16.1 Biostrings_2.6.3 > > > > _______________________________________________ > 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 >