[Bioc-devel] Error in GenomicFeatures::makeTxDbFromUCSC()

[Hervé Pagès]

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 <sarora at 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
>>
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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