getBM no connection but listMarts has
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@cristobal-fresno-rodriguez-3838
Last seen 8.7 years ago
Argentina/Cordoba/Universidad Católica …
Hi, I'm trying to use biomaRt but get the following error, when I try getBM statement but the connectivity seems ok according to listMarts(). library("biomaRt") listMarts()[1:4,] biomart version 1 ensembl ENSEMBL 56 GENES (SANGER UK) 2 snp ENSEMBL 56 VARIATION (SANGER UK) 3 functional_genomics ENSEMBL 56 FUNCTIONAL GENOMICS (SANGER UK) 4 vega VEGA 36 (SANGER UK) ensembl = useMart("ensembl") ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl) Checking attributes ... ok Checking filters ... ok affyids = c("202763_at", "209310_s_at", "207500_at") getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters = "affy_hg_u133_plus_2", values = affyids, mart = ensembl) Error in value[[3L]](cond) : Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down. Calls: getBM ... tryCatch -> tryCatchList -> tryCatchOne -> <anonymous> I search a little bit and found that on the postForm call on getBM got the error; probably RCurl compatibility issue? > sessionInfo() R version 2.9.2 (2009-08-24) i486-pc-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=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. UTF-8;LC_NAME=en_US.UTF-8;LC_ADDRESS=en_US.UTF-8;LC_TELEPHONE=en_US.UT F-8;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.2.0 rkward_0.5.1 loaded via a namespace (and not attached): [1] RCurl_1.3-0 tools_2.9.2 XML_2.6-0 Thanks, Cristobal [[alternative HTML version deleted]]
SNP biomaRt Vega SNP biomaRt Vega • 1.7k views
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@james-w-macdonald-5106
Last seen 3 days ago
United States
Hi Cristobal, Cristobal Fresno Rodr?guez wrote: > Hi, > > I'm trying to use biomaRt but get the following error, when I try getBM > statement but the connectivity seems ok according to listMarts(). > > library("biomaRt") > listMarts()[1:4,] > biomart > version > 1 ensembl ENSEMBL 56 GENES (SANGER UK) > 2 snp ENSEMBL 56 VARIATION (SANGER UK) > 3 functional_genomics ENSEMBL 56 FUNCTIONAL GENOMICS (SANGER UK) > 4 vega VEGA 36 (SANGER UK) > ensembl = useMart("ensembl") > ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl) > Checking attributes ... ok > Checking filters ... ok > affyids = c("202763_at", "209310_s_at", "207500_at") > getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters = > "affy_hg_u133_plus_2", values = affyids, mart = ensembl) > Error in value[[3L]](cond) : > Request to BioMart web service failed. Verify if you are still connected > to the internet. Alternatively the BioMart web service is temporarily down. > Calls: getBM ... tryCatch -> tryCatchList -> tryCatchOne -> <anonymous> > > > I search a little bit and found that on the postForm call on getBM got the > error; probably RCurl compatibility issue? Possibly. You have a previous version of R and a current version of biomaRt and RCurl. This works for me with packages installed using biocLite(): > library(biomaRt) > ensembl <- useMart("ensembl", "hsapiens_gene_ensembl") Checking attributes ... ok Checking filters ... ok > affyids = c("202763_at", "209310_s_at", "207500_at") > > getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters ="affy_hg_u133_plus_2", values = affyids, mart = ensembl) affy_hg_u133_plus_2 entrezgene 1 202763_at 836 2 202763_at NA 3 209310_s_at 837 4 209310_s_at NA 5 207500_at 838 6 207500_at NA > > > sessionInfo() R version 2.10.0 Patched (2009-11-05 r50317) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] biomaRt_2.2.0 loaded via a namespace (and not attached): [1] RCurl_1.2-1 XML_2.6-0 Best, Jim > > >> sessionInfo() > R version 2.9.2 (2009-08-24) > i486-pc-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=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U S.UTF-8;LC_NAME=en_US.UTF-8;LC_ADDRESS=en_US.UTF-8;LC_TELEPHONE=en_US. UTF-8;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.2.0 rkward_0.5.1 > > loaded via a namespace (and not attached): > [1] RCurl_1.3-0 tools_2.9.2 XML_2.6-0 > > > Thanks, > > Cristobal > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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Hi Jim, I updated the packages as recommended, and still have the same error. > library(biomaRt) > sessionInfo() R version 2.10.1 RC (2009-12-06 r50681) i686-pc-linux-gnu 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_2.2.0 loaded via a namespace (and not attached): [1] RCurl_1.3-0 XML_2.6-0 > ensembl <- useMart("ensembl", "hsapiens_gene_ensembl") Checking attributes ... ok Checking filters ... ok > affyids = c("202763_at", "209310_s_at", "207500_at") > getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters ="affy_hg_u133_plus_2", values = affyids, mart = ensembl) Error in value[[3L]](cond) : Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down. > Can you tell me what curl and xml are on your system? I have $ xml2-config --version 2.7.5 $ curl --version curl 7.19.7 (i686-pc-linux-gnu) libcurl/7.19.7 Protocols: tftp ftp telnet dict http file Features: IPv6 Largefile Best, Cristobal El 7 de diciembre de 2009 14:37, James W. MacDonald <jmacdon@med.umich.edu>escribió: > Hi Cristobal, > > > Cristobal Fresno Rodríguez wrote: > >> Hi, >> >> I'm trying to use biomaRt but get the following error, when I try getBM >> statement but the connectivity seems ok according to listMarts(). >> >> library("biomaRt") >> listMarts()[1:4,] >> biomart >> version >> 1 ensembl ENSEMBL 56 GENES (SANGER UK) >> 2 snp ENSEMBL 56 VARIATION (SANGER UK) >> 3 functional_genomics ENSEMBL 56 FUNCTIONAL GENOMICS (SANGER UK) >> 4 vega VEGA 36 (SANGER UK) >> ensembl = useMart("ensembl") >> ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl) >> Checking attributes ... ok >> Checking filters ... ok >> affyids = c("202763_at", "209310_s_at", "207500_at") >> getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters = >> "affy_hg_u133_plus_2", values = affyids, mart = ensembl) >> Error in value[[3L]](cond) : >> Request to BioMart web service failed. Verify if you are still connected >> to the internet. Alternatively the BioMart web service is temporarily >> down. >> Calls: getBM ... tryCatch -> tryCatchList -> tryCatchOne -> <anonymous> >> >> >> I search a little bit and found that on the postForm call on getBM got the >> error; probably RCurl compatibility issue? >> > > Possibly. You have a previous version of R and a current version of biomaRt > and RCurl. This works for me with packages installed using biocLite(): > > > library(biomaRt) > > ensembl <- useMart("ensembl", "hsapiens_gene_ensembl") > > Checking attributes ... ok > Checking filters ... ok > > affyids = c("202763_at", "209310_s_at", "207500_at") > > > > getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters > ="affy_hg_u133_plus_2", values = affyids, mart = ensembl) > affy_hg_u133_plus_2 entrezgene > 1 202763_at 836 > 2 202763_at NA > 3 209310_s_at 837 > 4 209310_s_at NA > 5 207500_at 838 > 6 207500_at NA > > > > sessionInfo() > R version 2.10.0 Patched (2009-11-05 r50317) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > > other attached packages: > [1] biomaRt_2.2.0 > > loaded via a namespace (and not attached): > [1] RCurl_1.2-1 XML_2.6-0 > > Best, > > Jim > >> >> >> sessionInfo() >>> >> R version 2.9.2 (2009-08-24) >> i486-pc-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=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_ US.UTF-8;LC_NAME=en_US.UTF-8;LC_ADDRESS=en_US.UTF-8;LC_TELEPHONE=en_US .UTF-8;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=en_US.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] biomaRt_2.2.0 rkward_0.5.1 >> >> loaded via a namespace (and not attached): >> [1] RCurl_1.3-0 tools_2.9.2 XML_2.6-0 >> >> >> Thanks, >> >> Cristobal >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >> > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues > [[alternative HTML version deleted]]
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Hi Cristobal, Earlier I was using my Windows box. For comparison I switched to our ROCKS cluster: $ xml2-config --version 2.6.23 Not sure that is correct - I seem to recall having to link against a newer version of libxml2, but I don't see one in my home directory. $ curl --version curl 7.19.5 (i686-pc-linux-gnu) libcurl/7.19.5 OpenSSL/0.9.7a zlib/1.2.1.2 Protocols: tftp ftp telnet dict ldap http file https ftps Features: IPv6 Largefile NTLM SSL libz > getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters = "affy_hg_u133_plus_2", values = affyids, mart = ensembl) affy_hg_u133_plus_2 entrezgene 1 202763_at 836 2 202763_at NA 3 209310_s_at 837 4 209310_s_at NA 5 207500_at 838 6 207500_at NA > sessionInfo() R version 2.10.0 alpha (2009-09-30 r49906) i686-pc-linux-gnu locale: [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 [5] LC_MONETARY=C LC_MESSAGES=en_US.iso885915 [7] LC_PAPER=en_US.iso885915 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.1.0 loaded via a namespace (and not attached): [1] RCurl_1.2-0 XML_2.6-0 Best, Jim Cristobal Fresno Rodr?guez wrote: > Hi Jim, > > I updated the packages as recommended, and still have the same error. > > > library(biomaRt) > > sessionInfo() > R version 2.10.1 RC (2009-12-06 r50681) > i686-pc-linux-gnu > > 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_2.2.0 > > loaded via a namespace (and not attached): > [1] RCurl_1.3-0 XML_2.6-0 > > ensembl <- useMart("ensembl", "hsapiens_gene_ensembl") > Checking attributes ... ok > Checking filters ... ok > > affyids = c("202763_at", "209310_s_at", "207500_at") > > getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters > ="affy_hg_u133_plus_2", values = affyids, mart = ensembl) > Error in value[[3L]](cond) : > Request to BioMart web service failed. Verify if you are still > connected to the internet. Alternatively the BioMart web service is > temporarily down. > > > > Can you tell me what curl and xml are on your system? > I have > $ xml2-config --version > 2.7.5 > $ curl --version > curl 7.19.7 (i686-pc-linux-gnu) libcurl/7.19.7 > Protocols: tftp ftp telnet dict http file > Features: IPv6 Largefile > > Best, > Cristobal > > > > El 7 de diciembre de 2009 14:37, James W. MacDonald > <jmacdon at="" med.umich.edu="" <mailto:jmacdon="" at="" med.umich.edu="">> escribi?: > > Hi Cristobal, > > > Cristobal Fresno Rodr?guez wrote: > > Hi, > > I'm trying to use biomaRt but get the following error, when I > try getBM > statement but the connectivity seems ok according to listMarts(). > > library("biomaRt") > listMarts()[1:4,] > biomart > version > 1 ensembl ENSEMBL 56 GENES (SANGER UK) > 2 snp ENSEMBL 56 VARIATION (SANGER UK) > 3 functional_genomics ENSEMBL 56 FUNCTIONAL GENOMICS (SANGER UK) > 4 vega VEGA 36 (SANGER UK) > ensembl = useMart("ensembl") > ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl) > Checking attributes ... ok > Checking filters ... ok > affyids = c("202763_at", "209310_s_at", "207500_at") > getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters = > "affy_hg_u133_plus_2", values = affyids, mart = ensembl) > Error in value[[3L]](cond) : > Request to BioMart web service failed. Verify if you are still > connected > to the internet. Alternatively the BioMart web service is > temporarily down. > Calls: getBM ... tryCatch -> tryCatchList -> tryCatchOne -> > <anonymous> > > > I search a little bit and found that on the postForm call on > getBM got the > error; probably RCurl compatibility issue? > > > Possibly. You have a previous version of R and a current version of > biomaRt and RCurl. This works for me with packages installed using > biocLite(): > > > library(biomaRt) > > ensembl <- useMart("ensembl", "hsapiens_gene_ensembl") > > Checking attributes ... ok > Checking filters ... ok > > affyids = c("202763_at", "209310_s_at", "207500_at") > > > > getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), > filters ="affy_hg_u133_plus_2", values = affyids, mart = ensembl) > affy_hg_u133_plus_2 entrezgene > 1 202763_at 836 > 2 202763_at NA > 3 209310_s_at 837 > 4 209310_s_at NA > 5 207500_at 838 > 6 207500_at NA > > > > sessionInfo() > R version 2.10.0 Patched (2009-11-05 r50317) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > > other attached packages: > [1] biomaRt_2.2.0 > > loaded via a namespace (and not attached): > [1] RCurl_1.2-1 XML_2.6-0 > > Best, > > Jim > > > > sessionInfo() > > R version 2.9.2 (2009-08-24) > i486-pc-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COL LATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PA PER=en_US.UTF-8;LC_NAME=en_US.UTF-8;LC_ADDRESS=en_US.UTF-8;LC_TELEPHON E=en_US.UTF-8;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.2.0 rkward_0.5.1 > > loaded via a namespace (and not attached): > [1] RCurl_1.3-0 tools_2.9.2 XML_2.6-0 > > > Thanks, > > Cristobal > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > <mailto: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 > > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should > not be used for urgent or sensitive issues > > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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