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Michael Steeves
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40
@michael-steeves-5969
Last seen 10.2 years ago
On OS X (10.8.4) with R 3.0.1, I'm getting an error when running the
following three lines of code:
library(GenomicRanges)
library(GenomicFeatures)
txdb <- makeTxDbPackageFromUCSC(genome = 'mm9', tablename = 'refGene')
Download the refGene table ... OK
Download the refLink table ... OK
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TranscriptDb object ... OK
Error in list(PKGTITLE = paste("Annotation package for", dbType,
"object(s)"), :
'version' is missing
In addition: There were 50 or more warnings (use warnings() to see the
first 50)
If I run this on RHEL5, the same code fails in the same place, though
with a slightly different error message:
> txdb <- makeTxDbPackageFromUCSC(genome = 'mm9', tablename =
'refGene')
Download the refGene table ... OK
Download the refLink table ... OK
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TranscriptDb object ... Error in .Call2("svn_time", PACKAGE =
"IRanges") :
IRanges internal error in svn_time(): get_svn_time() failed
In addition: There were 50 or more warnings (use warnings() to see the
first 50)
For OS X:
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin12.4.0 (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] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] GenomicFeatures_1.12.3 AnnotationDbi_1.22.6 Biobase_2.20.1
[4] GenomicRanges_1.12.5 IRanges_1.18.1 BiocGenerics_0.6.0
loaded via a namespace (and not attached):
[1] biomaRt_2.16.0 Biostrings_2.28.0 bitops_1.0-5
BSgenome_1.28.0
[5] DBI_0.2-7 RCurl_1.95-4.1 Rsamtools_1.12.3
RSQLite_0.11.4
[9] rtracklayer_1.20.3 stats4_3.0.1 tools_3.0.1 XML_3.98-1.1
[13] zlibbioc_1.6.0
For RHEL:
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] GenomicFeatures_1.12.2 AnnotationDbi_1.22.5 Biobase_2.20.0
[4] GenomicRanges_1.12.4 IRanges_1.18.3 BiocGenerics_0.6.0
loaded via a namespace (and not attached):
[1] BSgenome_1.28.0 Biostrings_2.28.0 DBI_0.2-7 RCurl_1.95-4.1
[5] RSQLite_0.11.4 Rsamtools_1.12.3 XML_3.96-1.1
biomaRt_2.16.0
[9] bitops_1.0-5 rtracklayer_1.20.2 stats4_3.0.1 tools_3.0.1
[13] zlibbioc_1.6.0
The warnings referenced don't look related, I don't think:
43: In .extractUCSCCdsStartEnd(cdsStart[i], cdsEnd[i],
exon_locs$start[[i]], ... :
UCSC data anomaly in transcript NM_010707: the cds cumulative
length
is not a multiple of 3
-Mike
--
Michael Steeves (steeves at raingods.net)
