Hi Juerg, Stefan, Thanks for providing those details, that helps a lot. So it looks you guys are guilty, like me and the build machines, of keeping your installation up-to-date. More precisely we are all using the latest version of RCurl (1.6-1, from May 15), but the postForm() function in this package seems to be broken (it doesn't *return* the text from the HTTP response anymore, it only *displays* it and returns NULL). One way to workaround the problem is to download and install the previous version of RCurl (1.6-0) available here: http://cran.fhcrc.org/src/contrib/Archive/RCurl/ You will need to download the source tarball manually and then install it from the command line with: R CMD INSTALL RCurl_1.6-0.tar.gz Another way is to wait for the RCurl maintainer to fix the package but it might takes a few days before the fix shows up on CRAN... I'll contact him right now. Cheers, H. On 11-05-18 07:34 AM, Straubhaar, Juerg wrote: > Hi Herve, > > code: > > library(biomaRt) > mart<- useMart("ensembl","rnorvegicus_gene_ensembl") > attr.g<- c("rgd_symbol","ensembl_gene_id","chromosome_name","start_position", > "end_position","strand") > ensGene<- getBM(attributes=attr.g,mart=mart) > > I run the code on the commandline > > R --no-save< processSeq.R 1>process.out 2>error.out > > process.out contains > > LOC682397 ENSRNOG00000043314 13 1120899 1121213 -1 > LOC304725 ENSRNOG00000031539 13 1192186 2293551 -1 > ENSRNOG00000031539 13 1192186 2293551 -1 > ENSRNOG00000028603 13 3174383 3175216 1 > ENSRNOG00000030028 13 4377731 4379174 -1 > ENSRNOG00000040235 13 4866302 4866586 -1 > ENSRNOG00000040233 13 5486651 5487388 1 > RGD1561440 ENSRNOG00000033336 13 5488973 5493293 -1 > ENSRNOG00000021163 13 5972234 6066767 -1 > ENSRNOG00000030239 13 7099478 7102595 1 > ... > > all 36669 rows from getBM function which should be stored in the ensGene variable. The ensGene variable is empty > because of the error. > > error.out contains > > Error in getBM(attributes = attr.g, mart = mart) : > The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this to the mailing list. > > Connection worked fine until beginning of this week when error appeared. > >> sessionInfo() > R version 2.12.2 (2011-02-25) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] C > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] annaffy_1.22.0 KEGG.db_2.4.5 GO.db_2.4.5 > [4] AnnotationDbi_1.12.1 ShortRead_1.8.2 Rsamtools_1.2.3 > [7] Biostrings_2.18.4 GenomicRanges_1.2.3 Genominator_1.4.2 > [10] GenomeGraphs_1.10.0 biomaRt_2.6.0 IRanges_1.8.9 > [13] RSQLite_0.9-4 DBI_0.2-5 DESeq_1.2.1 > [16] locfit_1.5-6 lattice_0.19-26 akima_0.5-4 > [19] Biobase_2.10.0 multicore_0.1-5 > > loaded via a namespace (and not attached): > [1] RColorBrewer_1.0-2 RCurl_1.6-1 XML_3.4-0 annotate_1.28.1 > [5] genefilter_1.32.0 geneplotter_1.28.0 hwriter_1.3 splines_2.12.2 > [9] survival_2.36-5 xtable_1.5-6 > > > Kind regards, > Juerg Straubhaar > UMASS Med School > ________________________________________ > From: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] On Behalf Of Hervé Pagès [hpages at fhcrc.org] > Sent: Tuesday, May 17, 2011 9:50 PM > To: s.kroeger at drfz.de > Cc: bioconductor at r-project.org > Subject: Re: [BioC] connecting to ensembl > > Hi Stefan, > > On 11-05-17 01:57 AM, Stefan Kroeger wrote: >> Does anybody else has problem with connecting to ensembl (since yesterday)? >> >> example code: >> myMart<- useMart("ensembl", dataset = "mmusculus_gene_ensembl") > > Please show the output or the error message you get. > > Yes we see problems in our daily build reports e.g. > > > http://bioconductor.org/checkResults/2.8/bioc- LATEST/GenomicFeatures/lamb1-checksrc.html > > AFAICT for at least the last couple of days, biomaRt and all the > packages that depend on it seem to have problems to connect to the > ensembl Mart during the builds :-/ > > H. > >> >> Best >> Stefan >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages at fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319