Question: getBM no connection but listMarts has
0
gravatar for Cristobal Fresno Rodríguez
9.9 years ago by
Argentina/Cordoba/Universidad Católica de Córdoba (CONICET)
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 • 1.1k views
ADD COMMENTlink modified 9.9 years ago by James W. MacDonald51k • written 9.9 years ago by Cristobal Fresno Rodríguez360
Answer: getBM no connection but listMarts has
0
gravatar for James W. MacDonald
9.9 years ago by
United States
James W. MacDonald51k wrote:
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
ADD COMMENTlink written 9.9 years ago by James W. MacDonald51k
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]]
ADD REPLYlink written 9.9 years ago by Cristobal Fresno Rodríguez360
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
ADD REPLYlink written 9.9 years ago by James W. MacDonald51k
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