biomaRt - current devel version of biomaRt+RCurl don't work
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@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
Hi just to warn all users of the development version of biomaRt, please wait a few days before updating your RCurl, the current devel versions of these two packages do not work together. We are sorting it out. An example for the error that is produced, with RCurl_0.97-2 and biomaRt_2.1.0, is shown below. With a previous version of RCurl, the problem should not arise. library("biomaRt") mart = useMart("ensembl") ensembl = useDataset("hsapiens_gene_ensembl", mart=mart) EGsub = c("1635_at"="25", "39329_at"="87", "40797_at"="102") utr = getSequence(id=EGsub, seqType="3utr", mart=ensembl, type="entrezgene") CAGCAGTCAGGGGTCAGGTGTCAGGCCCGTCGGAGCT... 25 CTGCAGCTTTTGCCTTGGTTCTTCCTAGTGCCTACAA... 102 TCCACCCCGCCCGGCCGCCCTCGTCTTGTGCGCCGTG... 87 TCCACCCCGCCCGGCCGCCCTCGTCTTGTGCGCCGTG... 87 V1 1 HTTP/1.1 200 OK 2 Date: Thu, 28 May 2009 11:57:58 GMT 3 Server: Apache/2.2.9 (Debian) mod_perl/2.0.4 Perl/v5.10.0 4 Connection: close 5 Transfer-Encoding: chunked 6 Content-Type: text/plain Errore in getBM(c(seqType, type), filters = type, values = id, mart = mart, : The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing list. > sessionInfo() R version 2.10.0 Under development (unstable) (2009-05-28 r48665) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=C LC_NUMERIC=C LC_TIME=C [4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=it_IT.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] biomaRt_2.1.0 fortunes_1.3-6 loaded via a namespace (and not attached): [1] RCurl_0.97-2 XML_2.3-0 > -- Best wishes Wolfgang ------------------------------------------------ Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber
biomaRt biomaRt • 1.1k views
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@james-bullard-1231
Last seen 9.6 years ago
Hi, I am having problems with biomaRt and based on Wolfgang's post it looks like I shouldn't be (or am I being completely naive?): Thanks, jim > library("biomaRt") > mart = useMart("ensembl") > ensembl = useDataset("hsapiens_gene_ensembl", + mart=mart) Checking attributes ... ok Checking filters ... ok > EGsub = c("1635_at"="25", "39329_at"="87", "40797_at"="102") > utr = getSequence(id=EGsub, seqType="3utr", + mart=ensembl, type="entrezgene") CA ..... I cut out a lot of the sequence ... GTGCCCTGCCTTGCACCTCCGCCTTATTTTCTGC 87 V1 1 HTTP/1.1 200 OK 2 Date: Thu, 28 May 2009 20:56:08 GMT 3 Server: Apache/2.2.9 (Debian) mod_perl/2.0.4 Perl/v5.10.0 4 Connection: close 5 Transfer-Encoding: chunked 6 Content-Type: text/plain Error in getBM(c(seqType, type), filters = type, values = id, mart = mart, : The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing list. > sessionInfo() R version 2.9.0 Patched (2009-05-28 r48678) x86_64-unknown-linux-gnu locale: LC_CTYPE = en_US .UTF -8 ;LC_NUMERIC = C ;LC_TIME = en_US .UTF -8 ;LC_COLLATE = en_US .UTF -8 ;LC_MONETARY = C ;LC_MESSAGES = en_US .UTF -8 ;LC_PAPER = en_US .UTF -8 ;LC_NAME = C ;LC_ADDRESS =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.0.0 loaded via a namespace (and not attached): [1] RCurl_0.95-1 tools_2.9.0 XML_2.3-0 On May 28, 2009, at 5:01 AM, Wolfgang Huber wrote: > Hi > > just to warn all users of the development version of biomaRt, please > wait a few days before updating your RCurl, the current devel > versions of these two packages do not work together. We are sorting > it out. > > An example for the error that is produced, with RCurl_0.97-2 and > biomaRt_2.1.0, is shown below. With a previous version of RCurl, the > problem should not arise. > > > library("biomaRt") > mart = useMart("ensembl") > ensembl = useDataset("hsapiens_gene_ensembl", > mart=mart) > EGsub = c("1635_at"="25", "39329_at"="87", "40797_at"="102") > utr = getSequence(id=EGsub, seqType="3utr", > mart=ensembl, type="entrezgene") > > CAGCAGTCAGGGGTCAGGTGTCAGGCCCGTCGGAGCT... 25 > CTGCAGCTTTTGCCTTGGTTCTTCCTAGTGCCTACAA... 102 > TCCACCCCGCCCGGCCGCCCTCGTCTTGTGCGCCGTG... 87 > TCCACCCCGCCCGGCCGCCCTCGTCTTGTGCGCCGTG... 87 > V1 > 1 HTTP/1.1 200 OK > 2 Date: Thu, 28 May 2009 11:57:58 GMT > 3 Server: Apache/2.2.9 (Debian) mod_perl/2.0.4 Perl/v5.10.0 > 4 Connection: close > 5 Transfer-Encoding: chunked > 6 Content-Type: text/plain > > Errore in getBM(c(seqType, type), filters = type, values = id, mart > = mart, : > The query to the BioMart webservice returned an invalid result: the > number of columns in the result table does not equal the number of > attributes in the query. Please report this to the mailing list. > > > > sessionInfo() > R version 2.10.0 Under development (unstable) (2009-05-28 r48665) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=C LC_NUMERIC=C LC_TIME=C > [4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=it_IT.UTF-8 > [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C > [10] LC_TELEPHONE=C LC_MEASUREMENT=C > LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] biomaRt_2.1.0 fortunes_1.3-6 > > loaded via a namespace (and not attached): > [1] RCurl_0.97-2 XML_2.3-0 > > > > > -- > > Best wishes > Wolfgang > > ------------------------------------------------ > Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi James, It would be worthwhile to provide a reproducible piece of code that generates an error; this way the folks who maintain the package will have a better position to fix things. Otherwise, only reporting that you have problems with the software makes it entirely inefficient for the maintainers. Cheers, --tony On Thu, May 28, 2009 at 2:00 PM, James Bullard <bullard@berkeley.edu> wrote: > Hi, I am having problems with biomaRt and based on Wolfgang's post it looks > like I shouldn't be (or am I being completely naive?): > > Thanks, jim > > > library("biomaRt") > > mart = useMart("ensembl") > > ensembl = useDataset("hsapiens_gene_ensembl", > + mart=mart) > Checking attributes ... ok > Checking filters ... ok > > EGsub = c("1635_at"="25", "39329_at"="87", "40797_at"="102") > > utr = getSequence(id=EGsub, seqType="3utr", > + mart=ensembl, type="entrezgene") > CA ..... I cut out a lot of the sequence ... > GTGCCCTGCCTTGCACCTCCGCCTTATTTTCTGC 87 > V1 > 1 HTTP/1.1 200 OK > 2 Date: Thu, 28 May 2009 20:56:08 GMT > 3 Server: Apache/2.2.9 (Debian) mod_perl/2.0.4 Perl/v5.10.0 > 4 Connection: close > 5 Transfer-Encoding: chunked > 6 Content-Type: text/plain > Error in getBM(c(seqType, type), filters = type, values = id, mart = mart, > : > The query to the BioMart webservice returned an invalid result: the number > of columns in the result table does not equal the number of attributes in > the query. Please report this to the mailing list. > > sessionInfo() > R version 2.9.0 Patched (2009-05-28 r48678) > x86_64-unknown-linux-gnu > > locale: > > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.0.0 > > loaded via a namespace (and not attached): > [1] RCurl_0.95-1 tools_2.9.0 XML_2.3-0 > > > > On May 28, 2009, at 5:01 AM, Wolfgang Huber wrote: > > Hi >> >> just to warn all users of the development version of biomaRt, please wait >> a few days before updating your RCurl, the current devel versions of these >> two packages do not work together. We are sorting it out. >> >> An example for the error that is produced, with RCurl_0.97-2 and >> biomaRt_2.1.0, is shown below. With a previous version of RCurl, the problem >> should not arise. >> >> >> library("biomaRt") >> mart = useMart("ensembl") >> ensembl = useDataset("hsapiens_gene_ensembl", >> mart=mart) >> EGsub = c("1635_at"="25", "39329_at"="87", "40797_at"="102") >> utr = getSequence(id=EGsub, seqType="3utr", >> mart=ensembl, type="entrezgene") >> >> CAGCAGTCAGGGGTCAGGTGTCAGGCCCGTCGGAGCT... 25 >> CTGCAGCTTTTGCCTTGGTTCTTCCTAGTGCCTACAA... 102 >> TCCACCCCGCCCGGCCGCCCTCGTCTTGTGCGCCGTG... 87 >> TCCACCCCGCCCGGCCGCCCTCGTCTTGTGCGCCGTG... 87 >> V1 >> 1 HTTP/1.1 200 OK >> 2 Date: Thu, 28 May 2009 11:57:58 GMT >> 3 Server: Apache/2.2.9 (Debian) mod_perl/2.0.4 Perl/v5.10.0 >> 4 Connection: close >> 5 Transfer-Encoding: chunked >> 6 Content-Type: text/plain >> >> Errore in getBM(c(seqType, type), filters = type, values = id, mart = >> mart, : >> The query to the BioMart webservice returned an invalid result: the >> number of columns in the result table does not equal the number of >> attributes in the query. Please report this to the mailing list. >> >> >> > sessionInfo() >> R version 2.10.0 Under development (unstable) (2009-05-28 r48665) >> x86_64-unknown-linux-gnu >> >> locale: >> [1] LC_CTYPE=C LC_NUMERIC=C LC_TIME=C >> [4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=it_IT.UTF-8 >> [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C >> [10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods base >> >> other attached packages: >> [1] biomaRt_2.1.0 fortunes_1.3-6 >> >> loaded via a namespace (and not attached): >> [1] RCurl_0.97-2 XML_2.3-0 >> > >> >> >> -- >> >> Best wishes >> Wolfgang >> >> ------------------------------------------------ >> Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > 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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I (and I assume most) have no problem with the "standard" config below. Worth depreciating ? > sessionInfo() R version 2.9.0 (2009-04-17) x86_64-pc-linux-gnu locale: LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_AU .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_AU.UTF-8;LC_PAPER=en_AU.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.0.0 loaded via a namespace (and not attached): [1] RCurl_0.94-1 XML_1.95-3 > -----Original Message----- From: James Bullard <bullard@berkeley.edu> To: whuber at embl.de Cc: Bioconductor <bioconductor at="" stat.math.ethz.ch=""> Subject: Re: [BioC] biomaRt - current devel version of biomaRt+RCurl don't work Date: Thu, 28 May 2009 14:00:04 -0700 Hi, I am having problems with biomaRt and based on Wolfgang's post it looks like I shouldn't be (or am I being completely naive?): Thanks, jim > library("biomaRt") > mart = useMart("ensembl") > ensembl = useDataset("hsapiens_gene_ensembl", + mart=mart) Checking attributes ... ok Checking filters ... ok > EGsub = c("1635_at"="25", "39329_at"="87", "40797_at"="102") > utr = getSequence(id=EGsub, seqType="3utr", + mart=ensembl, type="entrezgene") CA ..... I cut out a lot of the sequence ... GTGCCCTGCCTTGCACCTCCGCCTTATTTTCTGC 87 V1 1 HTTP/1.1 200 OK 2 Date: Thu, 28 May 2009 20:56:08 GMT 3 Server: Apache/2.2.9 (Debian) mod_perl/2.0.4 Perl/v5.10.0 4 Connection: close 5 Transfer-Encoding: chunked 6 Content-Type: text/plain Error in getBM(c(seqType, type), filters = type, values = id, mart = mart, : The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing list. > sessionInfo() R version 2.9.0 Patched (2009-05-28 r48678) x86_64-unknown-linux-gnu locale: LC_CTYPE = en_US .UTF -8 ;LC_NUMERIC = C ;LC_TIME = en_US .UTF -8 ;LC_COLLATE = en_US .UTF -8 ;LC_MONETARY = C ;LC_MESSAGES = en_US .UTF -8 ;LC_PAPER = en_US .UTF -8 ;LC_NAME = C ;LC_ADDRESS =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.0.0 loaded via a namespace (and not attached): [1] RCurl_0.95-1 tools_2.9.0 XML_2.3-0 On May 28, 2009, at 5:01 AM, Wolfgang Huber wrote: > Hi > > just to warn all users of the development version of biomaRt, please > wait a few days before updating your RCurl, the current devel > versions of these two packages do not work together. We are sorting > it out. > > An example for the error that is produced, with RCurl_0.97-2 and > biomaRt_2.1.0, is shown below. With a previous version of RCurl, the > problem should not arise. > > > library("biomaRt") > mart = useMart("ensembl") > ensembl = useDataset("hsapiens_gene_ensembl", > mart=mart) > EGsub = c("1635_at"="25", "39329_at"="87", "40797_at"="102") > utr = getSequence(id=EGsub, seqType="3utr", > mart=ensembl, type="entrezgene") > > CAGCAGTCAGGGGTCAGGTGTCAGGCCCGTCGGAGCT... 25 > CTGCAGCTTTTGCCTTGGTTCTTCCTAGTGCCTACAA... 102 > TCCACCCCGCCCGGCCGCCCTCGTCTTGTGCGCCGTG... 87 > TCCACCCCGCCCGGCCGCCCTCGTCTTGTGCGCCGTG... 87 > V1 > 1 HTTP/1.1 200 OK > 2 Date: Thu, 28 May 2009 11:57:58 GMT > 3 Server: Apache/2.2.9 (Debian) mod_perl/2.0.4 Perl/v5.10.0 > 4 Connection: close > 5 Transfer-Encoding: chunked > 6 Content-Type: text/plain > > Errore in getBM(c(seqType, type), filters = type, values = id, mart > = mart, : > The query to the BioMart webservice returned an invalid result: the > number of columns in the result table does not equal the number of > attributes in the query. Please report this to the mailing list. > > > > sessionInfo() > R version 2.10.0 Under development (unstable) (2009-05-28 r48665) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=C LC_NUMERIC=C LC_TIME=C > [4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=it_IT.UTF-8 > [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C > [10] LC_TELEPHONE=C LC_MEASUREMENT=C > LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] biomaRt_2.1.0 fortunes_1.3-6 > > loaded via a namespace (and not attached): > [1] RCurl_0.97-2 XML_2.3-0 > > > > > -- > > Best wishes > Wolfgang > > ------------------------------------------------ > Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi Paul, the issue is fixed in the latest RCurl which you can install by source("http://www.bioconductor.org/biocLite.R") biocLite("RCurl") For some reason this didn't pick up the dependency on bitops on my my machine, so to be safe you might want to do biocLite(c("bitops", "RCurl")) Please check if the fixes the problem on your end, if not we need the reproducible example Tony was suggesting before. Florian On 28.05.2009, at 21:56, Paul Leo wrote: > I (and I assume most) have no problem with the "standard" config > below. > Worth depreciating ? > >> sessionInfo() > R version 2.9.0 (2009-04-17) > x86_64-pc-linux-gnu > > locale: > LC_CTYPE > = > en_AU > .UTF > -8 > ;LC_NUMERIC > = > C > ;LC_TIME > = > en_AU > .UTF > -8 > ;LC_COLLATE > = > en_AU > .UTF > -8 > ;LC_MONETARY > = > C > ;LC_MESSAGES > = > en_AU > .UTF > -8 > ;LC_PAPER > = > en_AU > .UTF > -8 > ;LC_NAME > = > C > ;LC_ADDRESS > =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.0.0 > > loaded via a namespace (and not attached): > [1] RCurl_0.94-1 XML_1.95-3 >> > > > -----Original Message----- > From: James Bullard <bullard at="" berkeley.edu=""> > To: whuber at embl.de > Cc: Bioconductor <bioconductor at="" stat.math.ethz.ch=""> > Subject: Re: [BioC] biomaRt - current devel version of biomaRt+RCurl > don't work > Date: Thu, 28 May 2009 14:00:04 -0700 > > Hi, I am having problems with biomaRt and based on Wolfgang's post it > looks like I shouldn't be (or am I being completely naive?): > > Thanks, jim > >> library("biomaRt") >> mart = useMart("ensembl") >> ensembl = useDataset("hsapiens_gene_ensembl", > + mart=mart) > Checking attributes ... ok > Checking filters ... ok >> EGsub = c("1635_at"="25", "39329_at"="87", "40797_at"="102") >> utr = getSequence(id=EGsub, seqType="3utr", > + mart=ensembl, type="entrezgene") > CA ..... I cut out a lot of the sequence ... > GTGCCCTGCCTTGCACCTCCGCCTTATTTTCTGC 87 > V1 > 1 HTTP/1.1 200 OK > 2 Date: Thu, 28 May 2009 20:56:08 GMT > 3 Server: Apache/2.2.9 (Debian) mod_perl/2.0.4 Perl/v5.10.0 > 4 Connection: close > 5 Transfer-Encoding: chunked > 6 Content-Type: text/plain > Error in getBM(c(seqType, type), filters = type, values = id, mart = > mart, : > The query to the BioMart webservice returned an invalid result: the > number of columns in the result table does not equal the number of > attributes in the query. Please report this to the mailing list. >> sessionInfo() > R version 2.9.0 Patched (2009-05-28 r48678) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE > = > en_US > .UTF > -8 > ;LC_NUMERIC > = > C > ;LC_TIME > = > en_US > .UTF > -8 > ;LC_COLLATE > = > en_US > .UTF > -8 > ;LC_MONETARY > = > C > ;LC_MESSAGES > = > en_US > .UTF > -8 > ;LC_PAPER > = > en_US > .UTF > -8 > ;LC_NAME > = > C > ;LC_ADDRESS > =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.0.0 > > loaded via a namespace (and not attached): > [1] RCurl_0.95-1 tools_2.9.0 XML_2.3-0 > > > On May 28, 2009, at 5:01 AM, Wolfgang Huber wrote: > >> Hi >> >> just to warn all users of the development version of biomaRt, please >> wait a few days before updating your RCurl, the current devel >> versions of these two packages do not work together. We are sorting >> it out. >> >> An example for the error that is produced, with RCurl_0.97-2 and >> biomaRt_2.1.0, is shown below. With a previous version of RCurl, the >> problem should not arise. >> >> >> library("biomaRt") >> mart = useMart("ensembl") >> ensembl = useDataset("hsapiens_gene_ensembl", >> mart=mart) >> EGsub = c("1635_at"="25", "39329_at"="87", "40797_at"="102") >> utr = getSequence(id=EGsub, seqType="3utr", >> mart=ensembl, type="entrezgene") >> >> CAGCAGTCAGGGGTCAGGTGTCAGGCCCGTCGGAGCT... 25 >> CTGCAGCTTTTGCCTTGGTTCTTCCTAGTGCCTACAA... 102 >> TCCACCCCGCCCGGCCGCCCTCGTCTTGTGCGCCGTG... 87 >> TCCACCCCGCCCGGCCGCCCTCGTCTTGTGCGCCGTG... 87 >> V1 >> 1 HTTP/1.1 200 OK >> 2 Date: Thu, 28 May 2009 11:57:58 GMT >> 3 Server: Apache/2.2.9 (Debian) mod_perl/2.0.4 Perl/v5.10.0 >> 4 Connection: close >> 5 Transfer-Encoding: chunked >> 6 Content-Type: text/plain >> >> Errore in getBM(c(seqType, type), filters = type, values = id, mart >> = mart, : >> The query to the BioMart webservice returned an invalid result: the >> number of columns in the result table does not equal the number of >> attributes in the query. Please report this to the mailing list. >> >> >>> sessionInfo() >> R version 2.10.0 Under development (unstable) (2009-05-28 r48665) >> x86_64-unknown-linux-gnu >> >> locale: >> [1] LC_CTYPE=C LC_NUMERIC=C LC_TIME=C >> [4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=it_IT.UTF-8 >> [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C >> [10] LC_TELEPHONE=C LC_MEASUREMENT=C >> LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods base >> >> other attached packages: >> [1] biomaRt_2.1.0 fortunes_1.3-6 >> >> loaded via a namespace (and not attached): >> [1] RCurl_0.97-2 XML_2.3-0 >>> >> >> >> -- >> >> Best wishes >> Wolfgang >> >> ------------------------------------------------ >> Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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