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

5 messages · Michael Lawrence, Hervé Pagès, Arora, Sonali

Original
Arora, Sonali
# 
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
Arora, Sonali
# 
Update , I just see a warning on my linux box ( see the error only on 
windows)

 > txdb <- makeTxDbFromUCSC(genome = "hg19", 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 TxDb object ... OK
Warning message:
In .extractCdsLocsFromUCSCTxTable(ucsc_txtable, exon_locs) :
   UCSC data anomaly in 359 transcript(s): the cds cumulative length is
   not a multiple of 3 for transcripts ?NM_001037501? ?NM_001277444?
   ?NM_001037675? ?NM_001271872? ?NM_001170637? ?NM_001300952?
   ?NM_015326? ?NM_017940? ?NM_001271870? ?NM_001143962? ?NM_001305275?
   ?NM_001146344? ?NM_001300891? ?NM_001010890? ?NM_001300891?
   ?NM_001289974? ?NM_001291281? ?NM_001301371? ?NM_016178?
   ?NM_001134939? ?NM_001080427? ?NM_001145710? ?NM_001291328?
   ?NM_001271466? ?NM_001017915? ?NM_005541? ?NM_000348? ?NM_001145051?
   ?NM_001135649? ?NM_001128929? ?NM_001080423? ?NM_001144382?
   ?NM_001291661? ?NM_002958? ?NM_001005861? ?NM_004636? ?NM_001005914?
   ?NM_001290060? ?NM_001290061? ?NM_001289930? ?NM_003715?
   ?NM_001290049? ?NM_001286054? ?NM_001286053? ?NM_001286052?
   ?NM_182524? ?NM_001075? ?NM_00 [... truncated]
 > sessionInfo()
R Under development (unstable) (2015-10-15 r69519)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils datasets
[8] methods   base

other attached packages:
[1] GenomicFeatures_1.23.1 AnnotationDbi_1.33.0   Biobase_2.31.0
[4] GenomicRanges_1.21.32  GenomeInfoDb_1.7.0     IRanges_2.5.0
[7] 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
  [3] GenomicAlignments_1.7.0    BiocParallel_1.5.0
  [5] tools_3.3.0                SummarizedExperiment_1.1.0
  [7] DBI_0.3.1                  lambda.r_1.1.7
  [9] futile.logger_1.4.1        rtracklayer_1.31.0
[11] futile.options_1.0.0       bitops_1.0-6
[13] RCurl_1.95-4.7             biomaRt_2.27.0
[15] RSQLite_1.0.0              Biostrings_2.39.0
[17] Rsamtools_1.23.0           XML_3.98-1.3


Sonali.
On 10/16/2015 12:02 PM, Arora, Sonali wrote:
Michael Lawrence
# 
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:
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:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Arora, Sonali
    

    

      
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Thanks Herve and Michael,

I'll just use my linux box.


Sonali.

        
On 10/16/2015 1:15 PM, Herv? Pag?s wrote: