[Bioc-devel] Error when reading BAM files with readGAlignmentPairs
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-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_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] stats4parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] GenomicAlignments_1.3.14 Rsamtools_1.19.14Biostrings_2.35.6
[4] XVector_0.7.3GenomicRanges_1.19.21GenomeInfoDb_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_0.1-2BatchJobs_1.5 BBmisc_1.8 BiocParallel_1.1.9
[5] bitops_1.0-6 brew_1.0-6 checkmate_1.5.0codetools_0.2-9
[9] DBI_0.3.1 digest_0.6.6 fail_1.2 foreach_1.4.2
[13] iterators_1.0.7RSQLite_1.0.0 sendmailR_1.2-1stringr_0.6.2
[17] tools_3.2.0zlibbioc_1.13.0
>
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Re: [Bioc-devel] Error when reading BAM files with readGAlignmentPairs
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-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_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] stats4parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] GenomicAlignments_1.3.14 Rsamtools_1.19.14Biostrings_2.35.6
[4] XVector_0.7.3GenomicRanges_1.19.21GenomeInfoDb_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_0.1-2BatchJobs_1.5 BBmisc_1.8
BiocParallel_1.1.9
[5] bitops_1.0-6 brew_1.0-6 checkmate_1.5.0codetools_0.2-9
[9] DBI_0.3.1 digest_0.6.6 fail_1.2 foreach_1.4.2
[13] iterators_1.0.7RSQLite_1.0.0 sendmailR_1.2-1stringr_0.6.2
[17] tools_3.2.0zlibbioc_1.13.0
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--
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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319
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Re: [Bioc-devel] Error when reading BAM files with readGAlignmentPairs
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 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-8LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=en_US.UTF-8LC_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] stats4parallel stats graphics grDevices utils datasets
>> [8] methods base
>>
>> other attached packages:
>> [1] GenomicAlignments_1.3.14 Rsamtools_1.19.14Biostrings_2.35.6
>> [4] XVector_0.7.3GenomicRanges_1.19.21GenomeInfoDb_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_0.1-2BatchJobs_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_1.0.7RSQLite_1.0.0 sendmailR_1.2-1
>> stringr_0.6.2
>> [17] tools_3.2.0zlibbioc_1.13.0
>>>
>>>
>>
>> ___
>> Bioc-devel@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: hpa...@fredhutch.org
> Phone: (206) 667-5791
> Fax:(206) 667-1319
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