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
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