[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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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 ___ 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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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 hpa...@fredhutch.org 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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
