[BioC] BSgenome.Mmusculus.UCSC.mm8 and BSgenome

[hpages at fhcrc.org]

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
> >
> 
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