Dear Wolfgang, You were right, the error was due to the proxy settings. We have another proxy on the site (in case of breakdown of the main one) It works only with the second one. No ideas why. Thank you very much. Anthony On 24 March 2010 22:08, Wolfgang Huber <whuber@embl.de> wrote: > Dear Anthony > > I just tried your code example (as requoted in cleaned up form below) from > a computer 'directly on the internet', and got a result, so your problem > appears to be related to your particular site (i.e. internet connection). > > I am sorry that I cannot help further with that, as I have not recently had > the need to use proxies. Maybe someone else has an idea...? > > Wolfgang > > > > library("biomaRt") > > > listMarts(host="may2009.archive.ensembl.org", > path="/biomart/martservice",archive=FALSE) > > ensembl = useMart("ENSEMBL_MART_ENSEMBL", > dataset="hsapiens_gene_ensembl", > host="may2009.archive.ensembl.org", > path="/biomart/martservice", > archive=FALSE) > > chrom <- 5 > chr.start <- 110000000 > chr.stop <- 113000000 > > r = getBM(attributes="hgnc_symbol", > > filters=c("chromosome_name","start","end"), > values=list(chrom,chr.start,chr.stop),mart=ensembl) > > > r > hgnc_symbol > 1 TSSK1B > 2 YTHDC2 > 3 MCC > 4 DCP2 > 5 ZRSR1 > 6 REEP5 > 7 SRP19 > 8 APC > 9 EPB41L4A > 10 C5orf13 > 11 STARD4 > 12 CAMK4 > 13 WDR36 > 14 TSLP > 15 SLC25A46 > > > sessionInfo() > R version 2.11.0 Under development (unstable) (2010-03-23 r51373) > 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_2.3.4 fortunes_1.3-7 > > > loaded via a namespace (and not attached): > [1] RCurl_1.3-1 XML_2.8-1 > > > > Ferrari ha scritto: > >> (Sorry if you received this email twice) >> >> Hi all, >> >> I am currently experiencing problems running biomaRt package. >> I have a simple task to do which consists in retrieving all hgnc symbols >> between two genomic positions on a chromosome. >> >> My genomic positions are mapped to NCBI36/hg18 so I want to use an >> archived >> version of ensembl database to be able to query this human genome version. >> >> I am behind a proxy. I am using a windows PC, pentium 4, 3.2 Ghz, 1 Go >> RAM. >> >> I have already been through the archived mailing list to find useful >> information about problems running biomaRt. And this allowed me to get >> started and below you will find the scripts I used and my sessionInfo(). >> >> >> I can connect to the release 54 (NCBI36) of ensembl database, create a >> 'biomart object' but the getBM function fails. A traceback() call >> indicates >> that the error comes from a call to tryCatch(..). The error is the >> following >> : >> >> *Erreur dans 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. >> De plus : Message d'avis : >> In getStatus(status) : NAs introduits lors de la conversion automatique* >> >> But it seems that my internet connection is not down and neither is >> biomart >> web service. >> >> Does anyone know why I am getting this message ? >> Any help would be appreciated. Thank you very much. >> >> >> Anthony Ferrari >> >> >> >> >> Sys.time() >>> >> [1] "2010-03-24 09:57:42 CET" >> >>> library(biomaRt); >>> Sys.setenv("http_proxy"="http://195.220.67.254:8247"); >>> >>> listMarts(host="may2009.archive.ensembl.org",path="/ >>> >> biomart/martservice",archive=FALSE); >> biomart version >> 1 ENSEMBL_MART_ENSEMBL Ensembl 54 >> 2 ENSEMBL_MART_SNP Ensembl Variation 54 >> 3 ENSEMBL_MART_VEGA Vega 35 >> 4 REACTOME Reactome(CSHL US) >> 5 wormbase_current WormBase (CSHL US) >> 6 pride PRIDE (EBI UK) >> >>> ensembl = >>> >> useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl",host=" >> may2009.archive.ensembl.org",path="/biomart/martservice",archive=FA LSE); >> Checking attributes ... ok >> Checking filters ... ok >> >>> chrom <- 5; >>> chr.start <- 110000000; >>> chr.stop <- 113000000; >>> >>> >>> getBM(attributes="hgnc_symbol",filters=c("chromosome_name","start" ,"end"),values=list(chrom,chr.start,chr.stop),mart=ensembl); >> Erreur dans 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. >> De plus : Message d'avis : >> In getStatus(status) : NAs introduits lors de la conversion automatique >> >>> traceback() >>> >> 6: stop("Request to BioMart web service failed. Verify if you are still >> connected to the internet. Alternatively the BioMart web service is >> temporarily down.") >> 5: value[[3L]](cond) >> 4: tryCatchOne(expr, names, parentenv, handlers[[1L]]) >> 3: tryCatchList(expr, classes, parentenv, handlers) >> 2: tryCatch(postForm(paste(martHost(mart), "?", sep = ""), query = >> xmlQuery), >> error = function(e) { >> stop("Request to BioMart web service failed. Verify if you are >> still connected to the internet. Alternatively the BioMart web service is >> temporarily down.") >> }) >> 1: getBM(attributes = "hgnc_symbol", filters = c("chromosome_name", >> "start", "end"), values = list(chrom, chr.start, chr.stop), >> mart = ensembl) >> >>> Sys.time() >>> >> [1] "2010-03-24 09:57:47 CET" >> >>> sessionInfo() >>> >> R version 2.10.0 (2009-10-26) >> i386-pc-mingw32 >> >> locale: >> [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 >> LC_MONETARY=French_France.1252 LC_NUMERIC=C >> [5] LC_TIME=French_France.1252 >> >> 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_1.3-1 XML_2.8-1 >> >> [[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 >> > > -- > > Best wishes > Wolfgang > > > -- > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber/contact > > > [[alternative HTML version deleted]]