[BioC] Error in makeTranscriptDbFromBiomart

Fabrice Tourre fabrice.ciup at gmail.com
Mon Oct 1 19:19:56 CEST 2012


hg19Ensembl <- makeTranscriptDbFromBiomart(biomart = "ensembl",
dataset = "hsapiens_gene_ensembl")

Download and preprocess the 'transcripts' data frame ... Error in
scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  line 197870 did not have 5 elements


sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-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_1.8.3 AnnotationDbi_1.18.4  Biobase_2.16.0
[4] GenomicRanges_1.8.13  IRanges_1.14.4        BiocGenerics_0.2.0

loaded via a namespace (and not attached):
 [1] biomaRt_2.12.0     Biostrings_2.24.1  bitops_1.0-4.1     BSgenome_1.24.0
 [5] DBI_0.2-5          RCurl_1.95-0       Rsamtools_1.8.6    RSQLite_0.11.2
 [9] rtracklayer_1.16.3 stats4_2.15.1      tools_2.15.1       XML_3.95-0
[13] zlibbioc_1.2.0



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