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