[BioC] Error in makeTranscriptDbFromBiomart

[Martin Morgan]

On 10/3/2012 10:25 AM, Cook, Malcolm wrote:
>> -----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')

The problem is with RCurl; probably you were 'updated' when you did the 
install.packages(). so biocLite('RCurl') and look for a version number > 
1.95.0.1. Also, though, I think the most recent version of XML also has problems 
(in parsing the Namespace) but this seems to be less dramatic.

Martin

>
> ... 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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-- 
Dr. Martin Morgan, PhD
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109