[BioC] Error in makeTranscriptDbFromBiomart

[Cook, Malcolm]

> -----Original Message-----
> From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Fabrice Tourre
> Sent: Monday, October 01, 2012 12:20 PM
> To: Bioconductor mailing list
> Subject: [BioC] Error in makeTranscriptDbFromBiomart
> 
> 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
> 

Fabrice,

I just had the same issue.

install.packages('XML',type='source')

... fixed for me

Similarly bitten,

--Malcolm

PS (I was on a OSX Mac though)

> 
> 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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