I've been using the makeTranscriptDbFromUCSC function to retrieve ensembl genes from UCSC for over two years as part of our RNA-Seq expression profiling pipeline. Suddenly, last week, it started generating the following error:
> txdb <- makeTranscriptDbFromUCSC(genome="hg19", tablename="ensGene")
Warning message:
In .local(.Object, ...) : NAs introduced by coercion
Error in genome(ucscCart(x)) :
error in evaluating the argument 'x' in selecting a method for function 'genome': Error in matrix(unlist(pairs), nrow = 2) :
'data' must be of a vector type
Has anyone seen this? Any idea why it just started happening and how to fix it?
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-redhat-linux-gnu (64-bit)
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=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] GenomicFeatures_1.10.2 AnnotationDbi_1.20.7 Biobase_2.18.0
[4] GenomicRanges_1.10.7 IRanges_1.16.6 BiocGenerics_0.4.0
loaded via a namespace (and not attached):
[1] biomaRt_2.14.0 Biostrings_2.26.3 bitops_1.0-6 BSgenome_1.26.1
[5] DBI_0.2-7 parallel_2.15.2 RCurl_1.95-4.1 Rsamtools_1.10.2
[9] RSQLite_0.11.4 rtracklayer_1.18.2 stats4_2.15.2 tools_2.15.2
[13] XML_3.98-1.1 zlibbioc_1.4.0
> txdb <- makeTranscriptDbFromUCSC(genome="hg19", tablename="ensGene")
Warning message:
In .local(.Object, ...) : NAs introduced by coercion
Error in genome(ucscCart(x)) :
error in evaluating the argument 'x' in selecting a method for function 'genome': Error in matrix(unlist(pairs), nrow = 2) :
'data' must be of a vector type
Has anyone seen this? Any idea why it just started happening and how to fix it?
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-redhat-linux-gnu (64-bit)
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=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] GenomicFeatures_1.10.2 AnnotationDbi_1.20.7 Biobase_2.18.0
[4] GenomicRanges_1.10.7 IRanges_1.16.6 BiocGenerics_0.4.0
loaded via a namespace (and not attached):
[1] biomaRt_2.14.0 Biostrings_2.26.3 bitops_1.0-6 BSgenome_1.26.1
[5] DBI_0.2-7 parallel_2.15.2 RCurl_1.95-4.1 Rsamtools_1.10.2
[9] RSQLite_0.11.4 rtracklayer_1.18.2 stats4_2.15.2 tools_2.15.2
[13] XML_3.98-1.1 zlibbioc_1.4.0
