[BioC] Error in makeTranscriptDbFromBiomart

[Fabrice Tourre]

Now it works for me according to your suggestions.

Thank you.

On Wed, Oct 3, 2012 at 9:19 PM, Cook, Malcolm <MEC at stowers.org> wrote:
> 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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>>>> Search the archives:
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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