Hi Sonali, Michael,
Tried on Linux and Windows with BioC 3.3 and couldn't reproduce
this either (got the expected/usual warning about the cds cumulative
length not being a multiple of 3).
BTW I think GenomicRanges is failing in the devel builds because
of some issues with AnnotationHub. I don't think this is related
to the error you got with makeTxDbFromUCSC() though.
H.
On 10/16/2015 12:55 PM, Michael Lawrence wrote:
Seemed to work for me. Could just be a transient issue with UCSC?
On Fri, Oct 16, 2015 at 12:02 PM, Arora, Sonali <sar...@fredhutch.org> wrote:
Hi ,
I get an error when creating a txdb object for hg19 from the refGene Table
txdb <- makeTxDbFromUCSC(genome = "hg19", tablename = "refGene")
Error in tableNames(ucscTableQuery(session, track = track)) :
error in evaluating the argument 'object' in selecting a method for
function 'tableNames': Error in relist(ans_unlistData, ans_partitioning) :
shape of 'skeleton' is not compatible with 'NROW(flesh)'
Is this because GenomicRanges() is broken in devel ? Please advise.
sessionInfo()
R Under development (unstable) (2015-10-15 r69519)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United
States.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
methods base
other attached packages:
[1] GenomicFeatures_1.23.1 AnnotationDbi_1.33.0 Biobase_2.31.0
GenomicRanges_1.21.32 GenomeInfoDb_1.7.0
[6] IRanges_2.5.0 S4Vectors_0.9.0 BiocGenerics_0.17.0
BiocInstaller_1.21.1
loaded via a namespace (and not attached):
[1] XVector_0.11.0 zlibbioc_1.17.0 GenomicAlignments_1.7.0
BiocParallel_1.5.0
[5] tools_3.3.0 SummarizedExperiment_1.1.0 DBI_0.3.1
lambda.r_1.1.7
[9] futile.logger_1.4.1 rtracklayer_1.31.0 futile.options_1.0.0
bitops_1.0-6
[13] RCurl_1.95-4.7 biomaRt_2.27.0 RSQLite_1.0.0
Biostrings_2.39.0
[17] Rsamtools_1.23.0 XML_3.98-1.3
--
Thanks and Regards,
Sonali
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
