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

[Hervé Pagès]

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