On Oct 3, 2012 6:22 PM, "Cook, Malcolm" <MEC@stowers.org> wrote:
>
> Fabrice,
>
> I think Martin was observing that RCurl needs to be upgraded....
>
> Try again:
>
> install.packages('RCurl')

According to Fabrice's sessionInfo, he has the latest RCurl.  But it would
not hurt to reinstall, and start a fresh session.

However,  the non broken version is available via biocLite,  not
install.packages.

Dan

>
> Let us know....
>
> All this written at the risk of my making another error....
>
> ' evening,
>
> Malcolm
> ________________________________________
> From: hiekeen@gmail.com [hiekeen@gmail.com] On Behalf Of Fabrice Tourre [
fabrice.ciup@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@fhcrc.org> wrote:
> > On 10/3/2012 10:25 AM, Cook, Malcolm wrote:
> >>>
> >>> -----Original Message-----
> >>> From: bioconductor-bounces@r-project.org
> >>> [mailto:bioconductor-bounces@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
> >>>
> >>> _______________________________________________
> >>> Bioconductor mailing list
> >>> Bioconductor@r-project.org
> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>> Search the archives:
> >>> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >
> >
> > --
> > Dr. Martin Morgan, PhD
> > Fred Hutchinson Cancer Research Center
> > 1100 Fairview Ave. N.
> > PO Box 19024 Seattle, WA 98109
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
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