getBM returns error
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Wasco Wruck ▴ 30
@wasco-wruck-4800
Last seen 7.2 years ago
Hi, I am getting an error for a biomaRt getBM() call which used to work before. Has something changed in getBM() or the corresponding web services - or might there be firewall problems? I have the environment variable http_proxy set and other commands through the firewall, e.g. package installations work. Also getting the same information from biomart via wget and a xml query works through http_proxy. Here is the output: > library("biomaRt") > mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl") Checking attributes ... ok Checking filters ... ok > o=getBM(c("ensembl_gene_id", "ensembl_transcript_id", "illumina_humanwg_6_v2"), mart=mart) V1 1 <html><head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8"> <title>FEHLER: Die angeforderte URL konnte nicht gefunden werden</title> <style type="text/css">
biomaRt biomaRt • 793 views
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@steffen-durinck-4465
Last seen 7.2 years ago
Hi Wasco, This works for me, maybe the server was temporarily down, any chance you can try again? Steffen On Wed, Aug 10, 2011 at 5:16 AM, Wasco Wruck <wasco.wruck@charite.de> wrote: > Hi, > > I am getting an error for a biomaRt getBM() call which used to work before. > Has something changed in getBM() or the corresponding web services - or > might there be firewall problems? I have the environment variable http_proxy > set and other commands through the firewall, e.g. package installations > work. Also getting the same information from biomart via wget and a xml > query works through http_proxy. Here is the output: > > > library("biomaRt") > > mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > Checking attributes ... ok > Checking filters ... ok > > o=getBM(c("ensembl_gene_id", "ensembl_transcript_id", > "illumina_humanwg_6_v2"), mart=mart) > > > > V1 > 1 http://www.w3.org/TR/html4/**strict.dtd<http: www.w3.org="" tr="" html4="" s="" trict.dtd="">"> > <html><head> <meta http-equiv="Content-Type" content="text/html; &gt; charset=utf-8"> FEHLER: Die angeforderte URL konnte nicht gefunden > werden <style type="text/css">
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Hi Steffen , hi Johannes, I consistently get the same error. Something must have changed because before some days it worked fine. Maybe I have to update. Wasco Am 8/10/2011 5:17 PM, schrieb Steffen Durinck: > Hi Wasco, > > This works for me, maybe the server was temporarily down, any chance > you can try again? > > Steffen > > On Wed, Aug 10, 2011 at 5:16 AM, Wasco Wruck <wasco.wruck@charite.de> <mailto:wasco.wruck@charite.de>> wrote: > > Hi, > > I am getting an error for a biomaRt getBM() call which used to > work before. Has something changed in getBM() or the corresponding > web services - or might there be firewall problems? I have the > environment variable http_proxy set and other commands through the > firewall, e.g. package installations work. Also getting the same > information from biomart via wget and a xml query works through > http_proxy. Here is the output: > > > library("biomaRt") > > mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > Checking attributes ... ok > Checking filters ... ok > > o=getBM(c("ensembl_gene_id", "ensembl_transcript_id", > "illumina_humanwg_6_v2"), mart=mart) > > > > > V1 > 1 "http://www.w3.org/TR/html4/strict.dtd"> <html><head> <meta> http-equiv="Content-Type" content="text/html; FEHLER: Die > angeforderte URL konnte nicht gefunden werden <style> type="text/css">
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Hi Wasco well, it works for me as well (using R 2.13.1 and biomaRt_2.8.1), see below. I suggest to upgrade, most likely your R 2.11.0 and biomaRt_2.4.0 doesn't work with the Biomart database from ensembl 63 (which was released a few weeks ago)....on the other hand the error message you provide: "Die angeforderte URL konnte nicht gefunden werden" does sound like a firewall problem on your side...... Regards, Hans > library("biomaRt") > mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > o=getBM(c("ensembl_gene_id", "ensembl_transcript_id", + "illumina_humanwg_6_v2"), mart=mart) > head(o) ensembl_gene_id ensembl_transcript_id illumina_humanwg_6_v2 1 ENSG00000203347 ENST00000366172 2 ENSG00000256017 ENST00000379355 ILMN_1676712 3 ENSG00000236057 ENST00000537266 4 ENSG00000236057 ENST00000446137 5 ENSG00000245602 ENST00000500835 6 ENSG00000247217 ENST00000499475 > sessionInfo() R version 2.13.1 (2011-07-08) 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=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 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] biomaRt_2.8.1 loaded via a namespace (and not attached): [1] RCurl_1.6-6 XML_3.4-0 > On 08/10/2011 06:00 PM, Wasco Wruck wrote: > Hi Steffen , hi Johannes, > > I consistently get the same error. Something must have changed because > before some days it worked fine. Maybe I have to update. > > Wasco > > Am 8/10/2011 5:17 PM, schrieb Steffen Durinck: >> Hi Wasco, >> >> This works for me, maybe the server was temporarily down, any chance >> you can try again? >> >> Steffen >> >> On Wed, Aug 10, 2011 at 5:16 AM, Wasco Wruck<wasco.wruck at="" charite.de="">> <mailto:wasco.wruck at="" charite.de="">> wrote: >> >> Hi, >> >> I am getting an error for a biomaRt getBM() call which used to >> work before. Has something changed in getBM() or the corresponding >> web services - or might there be firewall problems? I have the >> environment variable http_proxy set and other commands through the >> firewall, e.g. package installations work. Also getting the same >> information from biomart via wget and a xml query works through >> http_proxy. Here is the output: >> >> > library("biomaRt") >> > mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl") >> Checking attributes ... ok >> Checking filters ... ok >> > o=getBM(c("ensembl_gene_id", "ensembl_transcript_id", >> "illumina_humanwg_6_v2"), mart=mart) >> >> >> >> >> V1 >> 1> "http://www.w3.org/TR/html4/strict.dtd"> <html><head> <meta>> http-equiv="Content-Type" content="text/html;FEHLER: Die >> angeforderte URL konnte nicht gefunden werden <style>> type="text/css">
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Hi Hans-Rudolf, Steffen, Johannes, thank you for your answers and testing! I upgraded to the newest versions but still got the same error. Using only one attribute to useMart() I got a html error page which our network admin could interpret - it was a not-easy-to-detect firewall problem concerning HTTP1.1 expect! Best wishes, Wasco Am 8/10/2011 6:48 PM, schrieb Hans-Rudolf Hotz: > Hi Wasco > > well, it works for me as well (using R 2.13.1 and biomaRt_2.8.1), see below. > > I suggest to upgrade, most likely your R 2.11.0 and biomaRt_2.4.0 > doesn't work with the Biomart database from ensembl 63 (which was > released a few weeks ago)....on the other hand the error message you > provide: "Die angeforderte URL konnte nicht gefunden werden" does sound > like a firewall problem on your side...... > > > Regards, Hans > > > > library("biomaRt") > > mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > > o=getBM(c("ensembl_gene_id", "ensembl_transcript_id", > + "illumina_humanwg_6_v2"), mart=mart) > > head(o) > ensembl_gene_id ensembl_transcript_id illumina_humanwg_6_v2 > 1 ENSG00000203347 ENST00000366172 > 2 ENSG00000256017 ENST00000379355 ILMN_1676712 > 3 ENSG00000236057 ENST00000537266 > 4 ENSG00000236057 ENST00000446137 > 5 ENSG00000245602 ENST00000500835 > 6 ENSG00000247217 ENST00000499475 > > sessionInfo() > R version 2.13.1 (2011-07-08) > 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=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 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] biomaRt_2.8.1 > > loaded via a namespace (and not attached): > [1] RCurl_1.6-6 XML_3.4-0 > > > > > > On 08/10/2011 06:00 PM, Wasco Wruck wrote: >> Hi Steffen , hi Johannes, >> >> I consistently get the same error. Something must have changed because >> before some days it worked fine. Maybe I have to update. >> >> Wasco >> >> Am 8/10/2011 5:17 PM, schrieb Steffen Durinck: >>> Hi Wasco, >>> >>> This works for me, maybe the server was temporarily down, any chance >>> you can try again? >>> >>> Steffen >>> >>> On Wed, Aug 10, 2011 at 5:16 AM, Wasco Wruck<wasco.wruck at="" charite.de="">>> <mailto:wasco.wruck at="" charite.de="">> wrote: >>> >>> Hi, >>> >>> I am getting an error for a biomaRt getBM() call which used to >>> work before. Has something changed in getBM() or the corresponding >>> web services - or might there be firewall problems? I have the >>> environment variable http_proxy set and other commands through the >>> firewall, e.g. package installations work. Also getting the same >>> information from biomart via wget and a xml query works through >>> http_proxy. Here is the output: >>> >>> > library("biomaRt") >>> > mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl") >>> Checking attributes ... ok >>> Checking filters ... ok >>> > o=getBM(c("ensembl_gene_id", "ensembl_transcript_id", >>> "illumina_humanwg_6_v2"), mart=mart) >>> >>> >>> >>> >>> V1 >>> 1>> "http://www.w3.org/TR/html4/strict.dtd"> <html><head> <meta>>> http-equiv="Content-Type" content="text/html;FEHLER: Die >>> angeforderte URL konnte nicht gefunden werden <style>>> type="text/css">
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@freudenberg-johannes-nihniehs-e-4789
Last seen 7.2 years ago
Hi Wasco, I have tried your example just now and it worked fine. But I'm running more current versions of R and Bioconductor. Have you tried updating R/Bioconductor? > library("biomaRt") > mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > mart Object of class 'Mart': Using the ensembl BioMart database Using the hsapiens_gene_ensembl dataset > o=getBM(c("ensembl_gene_id", "ensembl_transcript_id", "illumina_humanwg_6_v2"), mart=mart) > head(o) ensembl_gene_id ensembl_transcript_id illumina_humanwg_6_v2 1 ENSG00000203347 ENST00000366172 2 ENSG00000256017 ENST00000379355 ILMN_1676712 3 ENSG00000236057 ENST00000537266 4 ENSG00000236057 ENST00000446137 5 ENSG00000245602 ENST00000500835 6 ENSG00000247217 ENST00000499475 > sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-pc-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=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 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] biomaRt_2.8.1 loaded via a namespace (and not attached): [1] RCurl_1.5-0 tools_2.13.0 XML_3.2-0 > --Johannes -----Original Message----- From: Wasco Wruck [mailto:wasco.wruck@charite.de] Sent: Wednesday, August 10, 2011 8:17 AM To: bioconductor at r-project.org Subject: [BioC] getBM returns error Hi, I am getting an error for a biomaRt getBM() call which used to work before. Has something changed in getBM() or the corresponding web services - or might there be firewall problems? I have the environment variable http_proxy set and other commands through the firewall, e.g. package installations work. Also getting the same information from biomart via wget and a xml query works through http_proxy. Here is the output: > library("biomaRt") > mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl") Checking attributes ... ok Checking filters ... ok > o=getBM(c("ensembl_gene_id", "ensembl_transcript_id", "illumina_humanwg_6_v2"), mart=mart) V1 1 <html><head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8"> <title>FEHLER: Die angeforderte URL konnte nicht gefunden werden</title> <style type="text/css">

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