[Bioc-devel] Error when reading BAM files with readGAlignmentPairs

[Leonard Goldstein]

Hi Hervé,

Thanks for the quick reply - I didn't notice the build reports.

Best wishes

Leonard


On Fri, Dec 12, 2014 at 12:55 PM, Hervé Pagès <hpages at fredhutch.org> wrote:
> Hi Leonard,
>
> You can also see this error on the build report:
>
>
> http://bioconductor.org/checkResults/3.1/bioc-LATEST/GenomicAlignments/zin2-buildsrc.html
>
> This is a known issue that is the consequence of a recent change in
> Rsamtools. We'll sort it out.
>
> Thanks for your patience,
> H.
>
>
>
> On 12/12/2014 12:51 PM, Leonard Goldstein wrote:
>>
>> Dear Bioc developers,
>>
>> There seems to be an issue with GenomicAlignments or dependent
>> packages as I can no longer read BAM files with readGAlignmentPairs
>> that could be read without problems previously (see example below). I
>> assume this is a general problem but can provide test files if
>> necessary.
>>
>> Leonard
>>
>>
>>> readGAlignmentPairs(file)
>>
>> Error in .Call2("Integer_explode_bits", x, bitpos, PACKAGE = "S4Vectors")
>> :
>>    'bitpos' must contain values >= 1
>>>
>>>
>>> sessionInfo()
>>
>> R Under development (unstable) (2014-11-04 r66932)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats4    parallel  stats     graphics  grDevices utils     datasets
>> [8] methods   base
>>
>> other attached packages:
>> [1] GenomicAlignments_1.3.14 Rsamtools_1.19.14        Biostrings_2.35.6
>> [4] XVector_0.7.3            GenomicRanges_1.19.21    GenomeInfoDb_1.3.7
>> [7] IRanges_2.1.32           S4Vectors_0.5.14         BiocGenerics_0.13.3
>>
>> loaded via a namespace (and not attached):
>>   [1] base64enc_0.1-2    BatchJobs_1.5      BBmisc_1.8
>> BiocParallel_1.1.9
>>   [5] bitops_1.0-6       brew_1.0-6         checkmate_1.5.0
>> codetools_0.2-9
>>   [9] DBI_0.3.1          digest_0.6.6       fail_1.2
>> foreach_1.4.2
>> [13] iterators_1.0.7    RSQLite_1.0.0      sendmailR_1.2-1
>> stringr_0.6.2
>> [17] tools_3.2.0        zlibbioc_1.13.0
>>>
>>>
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319