[BioC] Error in masks for Dmelanogaster BSGenome

[Hervé Pagès]

Hi David and users of the BSgenome data packages,

I've pushed a new roster of BSgenome data packages (v 1.3.13) to the
current BioC release (2.4). This fixes the mask problem that David
reported here. As usual, please update with (from R-2.9.0):

   source("http://bioconductor.org/biocLite.R")
   update.packages(rep=biocinstallRepos())

Only the source packages of this new roster are available for now.
The binaries for Windows and Mac will follow soon. In the meantime
the binaries for the old roster (< 1.3.13) are still available.

Also I've added hg19 (released in Feb. 2009) to this new roster:

   > library(BSgenome.Hsapiens.UCSC.hg19)
   > Hsapiens
   Human genome
   |
   | organism: Homo sapiens (Human)
   | provider: UCSC
   | provider version: hg19
   | release date: Feb. 2009
   | release name: Genome Reference Consortium GRCh37
   ...

Note that BioC devel is still using the old roster and will be updated
at some point too.

Please let me know if you find any issue.

Cheers,
H.


Hervé Pagès wrote:
> Hi David,
> 
> Thanks for the report!
> The error is indeed occurring in the "show" method for IRanges objects.
> It is occurring because the content of the NAMES slots of the IRanges
> objects that are stored in the serialized MaskCollection objects found
> in the BSgenome.* data packages is not valid anymore (because of changes
> in the IRanges container).
> 
> I will fix this. Thanks again.
> 
> Cheers,
> H.
> 
> 
> David Rossell wrote:
>> I just installed BSgenome.Dmelanogaster.UCSC.dm3, where there appears 
>> to be
>> some bug in the masks. For instance,
>>
>>> masks(Dmelanogaster$chr2L)$RM
>> NormalIRanges object:
>> Error in width(x) : NAs in 'x' are not supported
>>
>> Same happens with other masks (TR etc.). Curiously, there are no NAs 
>> in the
>> width slot
>>
>>> table(is.na(width(masks(Dmelanogaster$chr2L)$RM)))
>>
>> FALSE
>> 12044
>>
>> This seems to be an issue of the show method, as I can save the object 
>> and
>> work normally with it
>>
>>> aa <- masks(Dmelanogaster$chr2L)$RM
>>> head(start(aa))
>> [1]    2  313  457  771  915 1229
>>> head(width(aa))
>> [1] 153  96 156  96 156  96
>>> head(end(aa))
>> [1]  154  408  612  866 1070 1324
>>
>> My session info is below. Best,
>>
>> David
>>
>>> sessionInfo()
>> R version 2.9.0 (2009-04-17)
>> i386-apple-darwin8.11.1
>>
>> locale:
>> C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>>  [1] BSgenome.Dmelanogaster.UCSC.dm3_1.3.11
>>  [2] ACME_1.10.0
>>  [3] MDA_1.0.1
>>  [4] multicore_0.1-3
>>  [5] ShortRead_1.2.0
>>  [6] lattice_0.17-22
>>  [7] BSgenome_1.12.0
>>  [8] Biostrings_2.12.3
>>  [9] IRanges_1.2.2
>> [10] gdata_2.4.2
>> [11] GEOquery_2.8.0
>> [12] RCurl_0.94-1
>> [13] Biobase_2.4.1
>>
>> loaded via a namespace (and not attached):
>> [1] grid_2.9.0   gtools_2.6.1 hwriter_1.1  tools_2.9.0
>>
> 

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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