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

Leonard Goldstein goldstein.leonard at gene.com
Fri Dec 12 21:51:24 CET 2014

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


> 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)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=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

More information about the Bioc-devel mailing list