Error in makeTranscriptDbFromBiomart
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@fabrice-tourre-4394
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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] 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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Malcolm Cook ★ 1.6k
@malcolm-cook-6293
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> -----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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at 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 at 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
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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 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at 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 at 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
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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@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 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 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at 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 at 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
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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 > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
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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 >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at 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 at 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
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