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

[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:
> 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
>