Error in makeTranscriptDbFromBiomart
1
0
Entering edit mode
@fabrice-tourre-4394
Last seen 10.2 years ago
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
• 1.6k views
ADD COMMENT •
0
Entering edit mode
Malcolm Cook ★ 1.6k
@malcolm-cook-6293
Last seen 4 months ago
United States
> -----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
ADD COMMENT •
0
Entering edit mode
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
ADD REPLY •
0
Entering edit mode
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
ADD REPLY •
0
Entering edit mode
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
ADD REPLY •
0
Entering edit mode
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]]
ADD REPLY •
0
Entering edit mode
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
ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 499 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6