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

[Arora, Sonali]

Thanks Herve and Michael,

I'll just use my linux box.


Sonali.

On 10/16/2015 1:15 PM, Hervé Pagès wrote:
> 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
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>

-- 
Thanks and Regards,
Sonali
Office: C2-169
http://tinyurl.com/sonali-hb-calendar