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

[Florian Markowetz]

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).

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'

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
  files extdata/chr10.rda, extdata/upstream5000.rda have the wrong MD5 
checksums

I don't know how serious that is ...

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

-- 
Florian Markowetz

Princeton University
Lewis-Sigler-Institute, Carl Icahn Lab
Princeton, NJ, 08544

609-258-8236 (lab phone)
609-258-8004 (fax)

email: florian at genomics.princeton.edu
web  : http://genomics.princeton.edu/~florian
skype: florian.markowetz