[Bioc-devel] MacOS-specific error in VariantAnnotation::locateVariants() in devel
Dan Tenenbaum
dtenenba at fredhutch.org
Fri Nov 21 19:48:34 CET 2014
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.
>
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