[Bioc-devel] MacOS-specific error in VariantAnnotation::locateVariants() in devel
Robert Castelo
robert.castelo at upf.edu
Sat Nov 22 00:27:26 CET 2014
hi Dan,
you're right, I updated the packages this morning (european time) before
the test, but with the very last update of GenomicRanges and IRanges
this evening the error goes away. I should have waited one day more.
Sorry for the noise and thanks for the help!!
robert.
On 11/21/14 7:48 PM, Dan Tenenbaum wrote:
> Hi Robert,
>
> ----- Original Message -----
>> From: "Robert Castelo" <robert.castelo at upf.edu>
>> To: bioc-devel at r-project.org
>> Sent: Friday, November 21, 2014 8:40:07 AM
>> Subject: [Bioc-devel] MacOS-specific error in VariantAnnotation::locateVariants() in devel
>>
>> hi,
>>
>> I have encountered an error using the function locateVariants in the
>> latest version of VariantAnnotation in the devel branch. I know this
>> is
>> a "moving target" but it occurs only in the MacOS system and,
>> moreover,
>> the package builds fine in the BioC Mac OS machines, so I guess I
>> must
>> be dealing with something specific of my Mac OS system (a Mountain
>> Lion
>> 10.8.5) so any hint will be very much appreciated.
>>
>> The following code runs fine with the release version:
>>
>> library(VariantAnnotation)
>> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
>>
>> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
>> gr <- GRanges(seqnames="chr20", IRanges(44501458, 44501458),
>> strand="*")
>> locateVariants(gr, txdb, AllVariants(intergenic=IntergenicVariants(0,
>> 0)))
>> GRanges object with 2 ranges and 9 metadata columns:
>> seqnames ranges strand | LOCATION LOCSTART
>> LOCEND QUERYID TXID CDSID GENEID
>> <Rle> <IRanges> <Rle> | <factor> <integer>
>> <integer> <integer> <integer> <integer> <character>
>> [1] chr20 [44501458, 44501458] + | intron 14839
>> 14839 1 71208 <NA> 140831
>> [2] chr20 [44501458, 44501458] + | coding 131
>> 131 1 71209 208174 140831
>> PRECEDEID FOLLOWID
>> <CharacterList> <CharacterList>
>> [1]
>> [2]
>> -------
>> seqinfo: 1 sequence from an unspecified genome; no seqlengths
>> R version 3.1.1 Patched (2014-10-14 r66765)
>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] stats4 parallel stats graphics grDevices utils datasets
>> methods base
>>
>> other attached packages:
>> [1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.0.0 GenomicFeatures_1.18.2
>> AnnotationDbi_1.28.1
>> [4] Biobase_2.26.0 VariantAnnotation_1.12.4 Rsamtools_1.18.2
>> [7] Biostrings_2.34.0 XVector_0.6.0 GenomicRanges_1.18.3
>> [10] GenomeInfoDb_1.2.3 IRanges_2.0.0 S4Vectors_0.4.0
>> [13] BiocGenerics_0.12.1 BiocInstaller_1.16.1 vimcom_1.0-0
>> [16] setwidth_1.0-3 colorout_1.0-3
>>
>> loaded via a namespace (and not attached):
>> [1] base64enc_0.1-2 BatchJobs_1.5 BBmisc_1.8
>> BiocParallel_1.0.0 biomaRt_2.22.0
>> [6] bitops_1.0-6 brew_1.0-6 BSgenome_1.34.0
>> checkmate_1.5.0 codetools_0.2-9
>> [11] DBI_0.3.1 digest_0.6.4 fail_1.2
>> foreach_1.4.2 GenomicAlignments_1.2.1
>> [16] iterators_1.0.7 RCurl_1.95-4.3 RSQLite_1.0.0
>> rtracklayer_1.26.2 sendmailR_1.2-1
>> [21] stringr_0.6.2 tools_3.1.1 XML_3.98-1.1
>> zlibbioc_1.12.0
>>
>> while the same code gives an error with the devel version:
>>
>> library(VariantAnnotation)
>> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
>>
>> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
>> gr <- GRanges(seqnames="chr20", IRanges(44501458, 44501458),
>> strand="*")
>> locateVariants(gr, txdb, AllVariants(intergenic=IntergenicVariants(0,
>> 0)))
>> Error in DataFrame(...) : different row counts implied by arguments
>> traceback()
>> 17: stop("different row counts implied by arguments")
>> 16: DataFrame(...)
>> 15: newGRanges("GRanges", seqnames = seqnames, ranges = ranges,
>> strand =
>> strand,
>> mcols = DataFrame(...), seqlengths = seqlengths, seqinfo =
>> seqinfo)
>> 14: GRanges(seqnames = seqnames(query)[queryid], ranges =
>> IRanges(ranges(query)[queryid]),
>> strand = strand(usub)[solap], LOCATION =
>> .location(length(queryid),
>> vtype), LOCSTART = start(map), LOCEND = end(map),
>> QUERYID =
>> queryid,
>> TXID = as.integer(txid[solap]), CDSID = cdsid, GENEID =
>> NA_character_,
>> PRECEDEID = CharacterList(character(0)), FOLLOWID =
>> CharacterList(character(0)))
>> 13: .makeResult(query, subject, "coding", ignore.strand =
>> ignore.strand,
>> asHits = asHits)
>> 12: .local(query, subject, region, ...)
>> 11: locateVariants(query, cache[["cdsbytx"]], region, ...,
>> ignore.strand
>> = ignore.strand,
>> asHits = asHits)
>> 10: locateVariants(query, cache[["cdsbytx"]], region, ...,
>> ignore.strand
>> = ignore.strand,
>> asHits = asHits)
>> 9: eval(expr, envir, enclos)
>> 8: eval(call, sys.frame(sys.parent()))
>> 7: callGeneric(query, cache[["cdsbytx"]], region, ..., ignore.strand
>> =
>> ignore.strand,
>> asHits = asHits)
>> 6: .local(query, subject, region, ...)
>> 5: locateVariants(query, subject, CodingVariants(), cache = cache,
>> ignore.strand = ignore.strand)
>> 4: locateVariants(query, subject, CodingVariants(), cache = cache,
>> ignore.strand = ignore.strand)
>> 3: .local(query, subject, region, ...)
>> 2: locateVariants(gr, txdb, AllVariants(intergenic =
>> IntergenicVariants(0,
>> 0)))
>> 1: locateVariants(gr, txdb, AllVariants(intergenic =
>> IntergenicVariants(0,
>> 0)))
>> R Under development (unstable) (2014-10-14 r66765)
>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] stats4 parallel stats graphics grDevices utils datasets
>> methods base
>>
>> other attached packages:
>> [1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.0.0 GenomicFeatures_1.19.6
>> AnnotationDbi_1.29.5
>> [4] Biobase_2.27.0 VariantAnnotation_1.13.12 Rsamtools_1.19.10
>> [7] Biostrings_2.35.4 XVector_0.7.2 GenomicRanges_1.19.10
>> [10] GenomeInfoDb_1.3.7 IRanges_2.1.17 S4Vectors_0.5.9
>> [13] BiocGenerics_0.13.2 vimcom_1.0-0 setwidth_1.0-3
>> [16] colorout_1.0-3
>>
>> loaded via a namespace (and not attached):
>> [1] base64enc_0.1-2 BatchJobs_1.4 BBmisc_1.7
>> BiocParallel_1.1.6 biomaRt_2.23.4
>> [6] bitops_1.0-6 brew_1.0-6 BSgenome_1.35.7
>> checkmate_1.5.0 codetools_0.2-9
>> [11] DBI_0.3.1 digest_0.6.4 fail_1.2
>> foreach_1.4.2 GenomicAlignments_1.3.9
>> [16] iterators_1.0.7 RCurl_1.95-4.3 RSQLite_1.0.0
>> rtracklayer_1.27.5 sendmailR_1.2-1
>> [21] stringr_0.6.2 tools_3.2.0 XML_3.98-1.1
>> zlibbioc_1.13.0
>>
> This code works for me with the exact same R. However, I have a newer GenomicRanges and IRanges and maybe other things, so try updating your packages? Here's my sessionInfo():
>
> R Under development (unstable) (2014-10-14 r66765)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats4 parallel stats graphics grDevices utils datasets
> [8] methods base
>
> other attached packages:
> [1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.0.0
> [2] GenomicFeatures_1.19.6
> [3] VariantAnnotation_1.13.12
> [4] AnnotationDbi_1.29.5
> [5] Biobase_2.27.0
> [6] Rsamtools_1.19.10
> [7] Biostrings_2.35.4
> [8] XVector_0.7.2
> [9] GenomicRanges_1.19.13
> [10] GenomeInfoDb_1.3.7
> [11] IRanges_2.1.18
> [12] S4Vectors_0.5.10
> [13] BiocGenerics_0.13.2
> [14] BiocInstaller_1.17.1
> [15] BiocContributions_0.99.3
>
> loaded via a namespace (and not attached):
> [1] base64enc_0.1-2 BatchJobs_1.4 BBmisc_1.7
> [4] BiocParallel_1.1.8 biomaRt_2.23.4 bitops_1.0-6
> [7] brew_1.0-6 BSgenome_1.35.8 checkmate_1.5.0
> [10] codetools_0.2-9 DBI_0.3.1 digest_0.6.4
> [13] fail_1.2 foreach_1.4.2 GenomicAlignments_1.3.10
> [16] iterators_1.0.7 RCurl_1.95-4.3 RSQLite_1.0.0
> [19] rtracklayer_1.27.5 sendmailR_1.2-1 stringr_0.6.2
>
> Dan
>
>
>>
>> thanks!!
>> robert.
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
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