[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-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

--
Herv? Pag?s

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