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Richard Birnie
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@richard-birnie-5827
Last seen 9.7 years ago
Dear all,
Please ignore my previous message I've found the cause of the issue.
It looks like it was an issue with packages not being reloaded quite
as I thought hence my workspace didn't contain quite what I thought it
did. Running the test case in a clean session works as expected.
regards,
Richard
________________________________________
From: Richard Birnie [guest] [guest@bioconductor.org]
Sent: 14 March 2013 16:20
To: bioconductor at r-project.org; Richard Birnie
Subject: GRanges error - Error: identical(colnames(classinfo),
colnames(out)) is not TRUE
Dear all,
I've come up against an error I can't explain trying to extract
transcript/gene IDs for a given set of genomic coordinates. I checked
the coordinates against the UCSC genome browser so I know that this
region does actually contain some genes. The curious thing is that
this worked yesterday and doesn't work today. I did upgrade several
bioconductor packages overnight and I think it may be down to a change
in the version of GenomicRanges but I'm not certain.
The code below shows a minimal case that reproduces the error message.
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
library(GenomicRanges)
#absolute minimal GRanges object
gr <- GRanges(seqnames='chr1', ranges=IRanges(start=40221856,
end=40502499), strand='*')
#attempt to get transcript IDs and gene IDs out of
TxDb.Hsapiens.UCSC.hg19.knownGene
result <- transcriptsByOverlaps(txdb, gr, columns=c('tx_id',
'tx_name', 'gene_id'))
If I try to display the contents of the object 'result' then I ge t
the following:
> result
GRanges with 0 ranges and 3 metadata columns:
Error: identical(colnames(classinfo), colnames(out)) is not TRUE
Output of traceback()
> traceback()
5: stop(paste0(ch, " is not ", if (length(r) > 1L) "all ", "TRUE"),
call. = FALSE)
4: stopifnot(identical(colnames(classinfo), colnames(out)))
3: showGenomicRanges(object, margin = " ", with.classinfo = TRUE,
print.seqlengths = TRUE)
2: function (object)
standardGeneric("show")(<s4 object="" of="" class="" "granges"="">)
1: function (object)
standardGeneric("show")(<s4 object="" of="" class="" "granges"="">)
I did do some searching before posting this and found this in the
archives https://stat.ethz.ch/pipermail/bioc-
devel/2012-April/003344.html which seems related. I had a look into
the GenomicRanges source code and the error seems to occur in the
function showGenomicRanges around lines 729-731:
classinfo <- makeClassinfoRowForCompactPrinting(x, .COL2CLASS)
## A sanity check, but this should never happen!
stopifnot(identical(colnames(classinfo), colnames(out)))
out <- rbind(classinfo, out)
That's as far as I've been able to get.
So, two related questions
1)Am I doing something wrong and if so what can I do to get around
this error?
2)Is it possible to install older versions of bioconductor packages
and if so how? I'd like to see if I can reprodce this with the
previous version of GenomicRanges
Any help appreciated,
Richard
-- output of sessionInfo():
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=C LC_NAME=C
LC_ADDRESS=C LC_TELEPHONE=C
LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets
methods base
other attached packages:
[1] org.Hs.eg.db_2.8.0 RSQLite_0.11.2
DBI_0.2-5
TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0
[5] GenomicFeatures_1.10.2 AnnotationDbi_1.20.6
Biobase_2.18.0 biomaRt_2.14.0
[9] ggbio_1.6.6 gridExtra_0.9.1
scales_0.2.3 ggplot2_0.9.3.1
[13] GenomicRanges_1.10.7 IRanges_1.16.6
BiocGenerics_0.4.0 knitr_1.1
loaded via a namespace (and not attached):
[1] Biostrings_2.26.3 biovizBase_1.6.2 bitops_1.0-5
BSgenome_1.26.1 cluster_1.14.3 colorspace_1.2-1
[7] dichromat_2.0-0 digest_0.6.3 evaluate_0.4.3
formatR_0.7 gtable_0.1.2 Hmisc_3.10-1
[13] labeling_0.1 lattice_0.20-13 MASS_7.3-23
munsell_0.4 parallel_2.15.2 plyr_1.8
[19] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1
reshape2_1.2.2 Rsamtools_1.10.2 rtracklayer_1.18.2
[25] stats4_2.15.2 stringr_0.6.2 tools_2.15.2
VariantAnnotation_1.4.12 XML_3.95-0.2 zlibbioc_1.4.0
--
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