[BioC] Error in makeTranscriptDbFromBiomart

[Cook, Malcolm]

Fabrice,

I think Martin was observing that RCurl needs to be upgraded....

Try again:

install.packages('RCurl')

Let us know....

All this written at the risk of my making another error....

' evening,

Malcolm
________________________________________
From: hiekeen at gmail.com [hiekeen at gmail.com] On Behalf Of Fabrice Tourre [fabrice.ciup at gmail.com]
Sent: Wednesday, October 03, 2012 5:51 PM
To: Martin Morgan
Cc: Cook, Malcolm; Bioconductor mailing list
Subject: Re: [BioC] Error in makeTranscriptDbFromBiomart

It seems it does not work for me.

install.packages('XML',type='source')
source("http://bioconductor.org/biocLite.R")
biocLite('RCurl')
library(GenomicFeatures)
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] BiocInstaller_1.4.8   GenomicFeatures_1.8.3 AnnotationDbi_1.18.4
[4] Biobase_2.16.0        GenomicRanges_1.8.13  IRanges_1.14.4
[7] 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_1.95-0.1.2   Rsamtools_1.8.6    RSQLite_0.11.2
 [9] rtracklayer_1.16.3 stats4_2.15.1      tools_2.15.1       XML_3.95-0.1
[13] zlibbioc_1.2.0



On Wed, Oct 3, 2012 at 5:29 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> 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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>>
>>
>> _______________________________________________
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>>
>
>
> --
> Dr. Martin Morgan, PhD
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109