Dear Steffen, I had the same problem as Ana. I did as you suggested and installed the dev version of biomaRt (downloading the .tar.gz and installing with R CMD INSTALL, running Debian Linux). Now I cannot even connect to BioMart anymore (I checked with another machine, there connecting still works, so it's not BioMart being down): > library(biomaRt) > listMarts() Error in value[[3]](cond) : Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down. > sessionInfo() R version 2.7.1 (2008-06-23) i486-pc-linux-gnu locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_1.99.4 loaded via a namespace (and not attached): [1] RCurl_0.94-0 XML_1.99-0 After getting this error, i also installed the dev versions of the packages XML and RCurl, but the error remains. Do you have any idea how to solve this? Could it be because of the base package "methods", which is not dev as well? Thanks, Christof steffen at stat.berkeley.edu wrote, On 28.01.2009 06:37: > Dear Ana, > > It looks like there is a problem with the XML configuration file for that > dataset. If you upgrade to using the dev version of biomaRt > (http://bioconductor.org/packages/2.4/bioc/html/biomaRt.html) you should > be fine for this dataset, as that version does not depend on this XML file > anymore. > > worbase_gene works for me see below: > >> library(biomaRt) >> >> wormbase = useMart("wormbase_current", dataset = "wormbase_gene") > > Checking attributes ... ok > Checking filters ... ok >> att = listAttributes(wormbase) >> att[1:10,] > name description > 1 species Species > 2 gene Gene WB ID > 3 sequence_name Sequence Name (Gene) > 4 public_name Gene Public Name > 5 cds Sequence Name (CDS) > 6 cgc_name Gene CGC Name > 7 transcript Sequence Name (Transcript) > 8 name_dmlist Gene Names (merged) > 9 cds_dmlist Sequence Names (CDS) (merged) > 10 transcript_dmlist Sequence Names (Transcript) (merged) > >> sessionInfo() > \R version 2.8.0 (2008-10-20) > powerpc-apple-darwin8.11.1 > > locale: > C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_1.99.4 > > loaded via a namespace (and not attached): > [1] RCurl_0.92-0 XML_1.98-1 > > > >> Dear all, >> >> I've been experience a problem with BioMart when I tried to access >> wormbase. I am getting an error when I tried to use a specific dataset >> (wormbase_gene). This problem do not exist when I access any other >> dataset from wormbase. Besides, few months ago a used this code without >> problems. >> >> >>> library(biomaRt) >>> wormbase = useMart("wormbase_current", dataset = "wormbase_gene") >> Checking attributes and filters ...Error in if (xmlGetAttr(xml, >> "displayType") == "list" && type != "boolean") options = >> parseOptions(xml) : >> missing value where TRUE/FALSE needed >> >>> listDatasets(wormbase) >> dataset description version >> 1 wormbase_paper Paper >> 2 wormbase_gene Gene >> 3 wormbase_anatomy_term Anatomy Term >> 4 wormbase_expr_pattern Expression Pattern >> 5 wormbase_go_term GO Term >> 6 wormbase_rnai RNAi >> 7 wormbase_phenotype Phenotype >> 8 wormbase_variation Variation >> >>> wormbase = useMart("wormbase_current", dataset = "wormbase_paper") >> Checking attributes and filters ... Ok >> >> >> >> I will appreciate any help. >> >> Ana. >> >> >> ############################## >>> sessionInfo() >> R version 2.8.0 (2008-10-20) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=Dutch_Netherlands.1252;LC_CTYPE=Dutch_Netherlands.1252;L C_MON >> ETARY=Dutch_Netherlands.1252;LC_NUMERIC=C;LC_TIME=Dutch_Netherlands .1252 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> >> other attached packages: >> [1] biomaRt_1.16.0 >> >> loaded via a namespace (and not attached): >> [1] RCurl_0.91-0 XML_1.94-0.1 >> >> _______________________________________________ >> 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 >

Hi Christof, I am not sure what sort of data you were looking for from biomaRt, but there is also an organism annotation package for worm. http://www.bioconductor.org/packages/release/data/annotation/html/org. Ce.eg.db.html Marc Christof Winter wrote: > Dear Steffen, > > I had the same problem as Ana. I did as you suggested and installed > the dev version of biomaRt (downloading the .tar.gz and installing > with R CMD INSTALL, running Debian Linux). Now I cannot even connect > to BioMart anymore (I checked with another machine, there connecting > still works, so it's not BioMart being down): > > > library(biomaRt) > > listMarts() > Error in value[[3]](cond) : > Request to BioMart web service failed. Verify if you are still > connected to the internet. Alternatively the BioMart web service is > temporarily down. > > sessionInfo() > R version 2.7.1 (2008-06-23) > i486-pc-linux-gnu > > locale: > C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_1.99.4 > > loaded via a namespace (and not attached): > [1] RCurl_0.94-0 XML_1.99-0 > > After getting this error, i also installed the dev versions of the > packages XML and RCurl, but the error remains. > > Do you have any idea how to solve this? Could it be because of the > base package "methods", which is not dev as well? > > Thanks, > Christof > > steffen at stat.berkeley.edu wrote, On 28.01.2009 06:37: >> Dear Ana, >> >> It looks like there is a problem with the XML configuration file for >> that >> dataset. If you upgrade to using the dev version of biomaRt >> (http://bioconductor.org/packages/2.4/bioc/html/biomaRt.html) you should >> be fine for this dataset, as that version does not depend on this XML >> file >> anymore. >> >> worbase_gene works for me see below: >> >>> library(biomaRt) >>> >>> wormbase = useMart("wormbase_current", dataset = "wormbase_gene") >> >> Checking attributes ... ok >> Checking filters ... ok >>> att = listAttributes(wormbase) >>> att[1:10,] >> name description >> 1 species Species >> 2 gene Gene WB ID >> 3 sequence_name Sequence Name (Gene) >> 4 public_name Gene Public Name >> 5 cds Sequence Name (CDS) >> 6 cgc_name Gene CGC Name >> 7 transcript Sequence Name (Transcript) >> 8 name_dmlist Gene Names (merged) >> 9 cds_dmlist Sequence Names (CDS) (merged) >> 10 transcript_dmlist Sequence Names (Transcript) (merged) >> >>> sessionInfo() >> \R version 2.8.0 (2008-10-20) >> powerpc-apple-darwin8.11.1 >> >> locale: >> C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] biomaRt_1.99.4 >> >> loaded via a namespace (and not attached): >> [1] RCurl_0.92-0 XML_1.98-1 >> >> >> >>> Dear all, >>> >>> I've been experience a problem with BioMart when I tried to access >>> wormbase. I am getting an error when I tried to use a specific dataset >>> (wormbase_gene). This problem do not exist when I access any other >>> dataset from wormbase. Besides, few months ago a used this code without >>> problems. >>> >>> >>>> library(biomaRt) >>>> wormbase = useMart("wormbase_current", dataset = "wormbase_gene") >>> Checking attributes and filters ...Error in if (xmlGetAttr(xml, >>> "displayType") == "list" && type != "boolean") options = >>> parseOptions(xml) : >>> missing value where TRUE/FALSE needed >>> >>>> listDatasets(wormbase) >>> dataset description version >>> 1 wormbase_paper Paper >>> 2 wormbase_gene Gene >>> 3 wormbase_anatomy_term Anatomy Term >>> 4 wormbase_expr_pattern Expression Pattern >>> 5 wormbase_go_term GO Term >>> 6 wormbase_rnai RNAi >>> 7 wormbase_phenotype Phenotype >>> 8 wormbase_variation Variation >>> >>>> wormbase = useMart("wormbase_current", dataset = "wormbase_paper") >>> Checking attributes and filters ... Ok >>> >>> >>> >>> I will appreciate any help. >>> >>> Ana. >>> >>> >>> ############################## >>>> sessionInfo() >>> R version 2.8.0 (2008-10-20) >>> i386-pc-mingw32 >>> >>> locale: >>> LC_COLLATE=Dutch_Netherlands.1252;LC_CTYPE=Dutch_Netherlands.1252; LC_MON >>> >>> ETARY=Dutch_Netherlands.1252;LC_NUMERIC=C;LC_TIME=Dutch_Netherland s.1252 >>> >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> >>> other attached packages: >>> [1] biomaRt_1.16.0 >>> >>> loaded via a namespace (and not attached): >>> [1] RCurl_0.91-0 XML_1.94-0.1 >>> >>> _______________________________________________ >>> 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 >

Hi Christof, Either you are not online or Ensembl was temporary down when you did your query. Can you check if you're online and try it again? I get: > listMarts() biomart version 1 ensembl ENSEMBL 52 GENES (SANGER UK) 2 snp ENSEMBL 52 VARIATION (SANGER UK) 3 vega VEGA 33 (SANGER UK) 4 msd MSD PROTOTYPE (EBI UK) 5 htgt HIGH THROUGHPUT GENE TARGETING AND TRAPPING (SANGER UK) 6 ENSEMBL_MART_ENSEMBL GRAMENE GENES (CSHL US) 7 ENSEMBL_MART_SNP GRAMENE SNPS (CSHL US) 8 REACTOME REACTOME (CSHL US) 9 wormbase_current WORMBASE (CSHL US) 10 dicty DICTYBASE (NORTHWESTERN US) 11 rgd__mart RGD GENES (MCW US) 12 ipi_rat__mart RGD IPI MART (MCW US) 13 SSLP__mart RGD MICROSATELLITE MARKERS (MCW US) 14 g4public HGNC (EBI UK) 15 pride PRIDE (EBI UK) 16 uniprot_mart UNIPROT (EBI UK) 17 ensembl_expressionmart_48 EURATMART (EBI UK) 18 biomartDB PARAMECIUM GENOME (CNRS FRANCE) 19 Eurexpress Biomart EUREXPRESS (MRC EDINBURGH UK) 20 pepseekerGOLD_mart06 PEPSEEKER (UNIVERSITY OF MANCHESTER UK) 21 Pancreatic_Expression PANCREATIC EXPRESSION DATABASE (INSTITUTE OF CANCER UK) > sessionInfo() R version 2.8.0 (2008-10-20) 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_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_1.99.4 loaded via a namespace (and not attached): [1] RCurl_0.91-0 XML_1.98-1 Cheers, Steffen > Dear Steffen, > > I had the same problem as Ana. I did as you suggested and installed the > dev > version of biomaRt (downloading the .tar.gz and installing with R CMD > INSTALL, > running Debian Linux). Now I cannot even connect to BioMart anymore (I > checked > with another machine, there connecting still works, so it's not BioMart > being down): > > > library(biomaRt) > > listMarts() > Error in value[[3]](cond) : > Request to BioMart web service failed. Verify if you are still > connected to > the internet. Alternatively the BioMart web service is temporarily down. > > sessionInfo() > R version 2.7.1 (2008-06-23) > i486-pc-linux-gnu > > locale: > C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_1.99.4 > > loaded via a namespace (and not attached): > [1] RCurl_0.94-0 XML_1.99-0 > > After getting this error, i also installed the dev versions of the > packages XML > and RCurl, but the error remains. > > Do you have any idea how to solve this? Could it be because of the base > package > "methods", which is not dev as well? > > Thanks, > Christof > > steffen at stat.berkeley.edu wrote, On 28.01.2009 > 06:37: >> Dear Ana, >> >> It looks like there is a problem with the XML configuration file for >> that >> dataset. If you upgrade to using the dev version of biomaRt >> (http://bioconductor.org/packages/2.4/bioc/html/biomaRt.html) you should >> be fine for this dataset, as that version does not depend on this XML >> file >> anymore. >> >> worbase_gene works for me see below: >> >>> library(biomaRt) >>> >>> wormbase = useMart("wormbase_current", dataset = "wormbase_gene") >> >> Checking attributes ... ok >> Checking filters ... ok >>> att = listAttributes(wormbase) >>> att[1:10,] >> name description >> 1 species Species >> 2 gene Gene WB ID >> 3 sequence_name Sequence Name (Gene) >> 4 public_name Gene Public Name >> 5 cds Sequence Name (CDS) >> 6 cgc_name Gene CGC Name >> 7 transcript Sequence Name (Transcript) >> 8 name_dmlist Gene Names (merged) >> 9 cds_dmlist Sequence Names (CDS) (merged) >> 10 transcript_dmlist Sequence Names (Transcript) (merged) >> >>> sessionInfo() >> \R version 2.8.0 (2008-10-20) >> powerpc-apple-darwin8.11.1 >> >> locale: >> C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] biomaRt_1.99.4 >> >> loaded via a namespace (and not attached): >> [1] RCurl_0.92-0 XML_1.98-1 >> >> >> >>> Dear all, >>> >>> I've been experience a problem with BioMart when I tried to access >>> wormbase. I am getting an error when I tried to use a specific dataset >>> (wormbase_gene). This problem do not exist when I access any other >>> dataset from wormbase. Besides, few months ago a used this code without >>> problems. >>> >>> >>>> library(biomaRt) >>>> wormbase = useMart("wormbase_current", dataset = "wormbase_gene") >>> Checking attributes and filters ...Error in if (xmlGetAttr(xml, >>> "displayType") == "list" && type != "boolean") options = >>> parseOptions(xml) : >>> missing value where TRUE/FALSE needed >>> >>>> listDatasets(wormbase) >>> dataset description version >>> 1 wormbase_paper Paper >>> 2 wormbase_gene Gene >>> 3 wormbase_anatomy_term Anatomy Term >>> 4 wormbase_expr_pattern Expression Pattern >>> 5 wormbase_go_term GO Term >>> 6 wormbase_rnai RNAi >>> 7 wormbase_phenotype Phenotype >>> 8 wormbase_variation Variation >>> >>>> wormbase = useMart("wormbase_current", dataset = "wormbase_paper") >>> Checking attributes and filters ... Ok >>> >>> >>> >>> I will appreciate any help. >>> >>> Ana. >>> >>> >>> ############################## >>>> sessionInfo() >>> R version 2.8.0 (2008-10-20) >>> i386-pc-mingw32 >>> >>> locale: >>> LC_COLLATE=Dutch_Netherlands.1252;LC_CTYPE=Dutch_Netherlands.1252; LC_MON >>> ETARY=Dutch_Netherlands.1252;LC_NUMERIC=C;LC_TIME=Dutch_Netherland s.1252 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> >>> other attached packages: >>> [1] biomaRt_1.16.0 >>> >>> loaded via a namespace (and not attached): >>> [1] RCurl_0.91-0 XML_1.94-0.1 >>> >>> _______________________________________________ >>> 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 >

Hi all: Problem solved. With the help of Steffen, I got rid of the "Request to BioMart web service failed." error. The trick is to add an explicit library(RCurl): > library(biomaRt) > listMarts() Error in value[[3]](cond) : Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down. > library(RCurl) > listMarts() biomart 1 ensembl 2 snp 3 vega 4 msd ... > wormbase = useMart("wormbase_current", dataset = "wormbase_gene") Checking attributes ... ok Checking filters ... ok The last line of code was the problem of Ana's initial post. > sessionInfo() R version 2.7.1 (2008-06-23) i486-pc-linux-gnu locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RCurl_0.94-0 biomaRt_1.99.4 loaded via a namespace (and not attached): [1] XML_1.99-0 Interestingly, when comparing this sessionInfo with the one below, now RCurl is attached instead of loaded via namespace. But I'm not sure if that's the reason for fixing it. Christof Christof Winter wrote, On 04.02.2009 10:59: > Dear Steffen, > > I had the same problem as Ana. I did as you suggested and installed the dev > version of biomaRt (downloading the .tar.gz and installing with R CMD INSTALL, > running Debian Linux). Now I cannot even connect to BioMart anymore (I checked > with another machine, there connecting still works, so it's not BioMart being down): > > > library(biomaRt) > > listMarts() > Error in value[[3]](cond) : > Request to BioMart web service failed. Verify if you are still connected to > the internet. Alternatively the BioMart web service is temporarily down. > > sessionInfo() > R version 2.7.1 (2008-06-23) > i486-pc-linux-gnu > > locale: > C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_1.99.4 > > loaded via a namespace (and not attached): > [1] RCurl_0.94-0 XML_1.99-0 > > After getting this error, i also installed the dev versions of the packages XML > and RCurl, but the error remains. > > Do you have any idea how to solve this? Could it be because of the base package > "methods", which is not dev as well? > > Thanks, > Christof > > steffen at stat.berkeley.edu wrote, On 28.01.2009 > 06:37: >> Dear Ana, >> >> It looks like there is a problem with the XML configuration file for that >> dataset. If you upgrade to using the dev version of biomaRt >> (http://bioconductor.org/packages/2.4/bioc/html/biomaRt.html) you should >> be fine for this dataset, as that version does not depend on this XML file >> anymore. >> >> worbase_gene works for me see below: >> >>> library(biomaRt) >>> >>> wormbase = useMart("wormbase_current", dataset = "wormbase_gene") >> Checking attributes ... ok >> Checking filters ... ok >>> att = listAttributes(wormbase) >>> att[1:10,] >> name description >> 1 species Species >> 2 gene Gene WB ID >> 3 sequence_name Sequence Name (Gene) >> 4 public_name Gene Public Name >> 5 cds Sequence Name (CDS) >> 6 cgc_name Gene CGC Name >> 7 transcript Sequence Name (Transcript) >> 8 name_dmlist Gene Names (merged) >> 9 cds_dmlist Sequence Names (CDS) (merged) >> 10 transcript_dmlist Sequence Names (Transcript) (merged) >> >>> sessionInfo() >> \R version 2.8.0 (2008-10-20) >> powerpc-apple-darwin8.11.1 >> >> locale: >> C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] biomaRt_1.99.4 >> >> loaded via a namespace (and not attached): >> [1] RCurl_0.92-0 XML_1.98-1 >> >> >> >>> Dear all, >>> >>> I've been experience a problem with BioMart when I tried to access >>> wormbase. I am getting an error when I tried to use a specific dataset >>> (wormbase_gene). This problem do not exist when I access any other >>> dataset from wormbase. Besides, few months ago a used this code without >>> problems. >>> >>> >>>> library(biomaRt) >>>> wormbase = useMart("wormbase_current", dataset = "wormbase_gene") >>> Checking attributes and filters ...Error in if (xmlGetAttr(xml, >>> "displayType") == "list" && type != "boolean") options = >>> parseOptions(xml) : >>> missing value where TRUE/FALSE needed >>> >>>> listDatasets(wormbase) >>> dataset description version >>> 1 wormbase_paper Paper >>> 2 wormbase_gene Gene >>> 3 wormbase_anatomy_term Anatomy Term >>> 4 wormbase_expr_pattern Expression Pattern >>> 5 wormbase_go_term GO Term >>> 6 wormbase_rnai RNAi >>> 7 wormbase_phenotype Phenotype >>> 8 wormbase_variation Variation >>> >>>> wormbase = useMart("wormbase_current", dataset = "wormbase_paper") >>> Checking attributes and filters ... Ok >>> >>> >>> >>> I will appreciate any help. >>> >>> Ana. >>> >>> >>> ############################## >>>> sessionInfo() >>> R version 2.8.0 (2008-10-20) >>> i386-pc-mingw32 >>> >>> locale: >>> LC_COLLATE=Dutch_Netherlands.1252;LC_CTYPE=Dutch_Netherlands.1252; LC_MON >>> ETARY=Dutch_Netherlands.1252;LC_NUMERIC=C;LC_TIME=Dutch_Netherland s.1252 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> >>> other attached packages: >>> [1] biomaRt_1.16.0 >>> >>> loaded via a namespace (and not attached): >>> [1] RCurl_0.91-0 XML_1.94-0.1 >>> >>> _______________________________________________ >>> 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 >