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
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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
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E-mail: hpa...@fredhutch.org
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Fax: (206) 667-1319
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