Dear Forum, I have installed biomart, in the begining I had problems because some libraries the Rcurl and the xml were missing. But now I am getting the same error with biocLite("org.Hs.eg.db") I get that is missing a library but I am not understanding which, can someone help me? I run Ubuntu 9.04 Thanks Andreia Below is the messages after > source ("http://bioconductor.org/biocLite.R") > biocLite("org.Hs.eg.db") Running biocinstall version 2.3.14 with R version 2.8.1 Your version of R requires version 2.3 of Bioconductor. Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using '/home/user/R/x86_64-pc-linux-gnu-library/2.8' trying URL ' http://bioconductor.org/packages/2.3/data/annotation/src/contrib/org.H s.eg.db_2.2.6.tar.gz ' Content type 'application/x-gzip' length 31989336 bytes (30.5 Mb) opened URL ================================================== downloaded 30.5 Mb * Installing *source* package 'org.Hs.eg.db' ... ** R ** inst ** preparing package for lazy loading Loading required package: AnnotationDbi Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. ** help >>> Building/Updating help pages for package 'org.Hs.eg.db' Formats: text html latex example org.Hs.egACCNUM text html latex example org.Hs.egALIAS2EG text html latex example org.Hs.egBASE text html latex example org.Hs.egCHR text html latex example org.Hs.egCHRLENGTHS text html latex example org.Hs.egCHRLOC text html latex example org.Hs.egENSEMBL text html latex example org.Hs.egENSEMBLPROT text html latex example org.Hs.egENSEMBLTRANS text html latex example org.Hs.egENZYME text html latex example org.Hs.egGENENAME text html latex example org.Hs.egGO text html latex example org.Hs.egGO2ALLEGS text html latex example org.Hs.egMAP text html latex example org.Hs.egMAPCOUNTS text html latex example org.Hs.egOMIM text html latex example org.Hs.egORGANISM text html latex example org.Hs.egPATH text html latex example org.Hs.egPFAM text html latex example org.Hs.egPMID text html latex example org.Hs.egPROSITE text html latex example org.Hs.egREFSEQ text html latex example org.Hs.egSYMBOL text html latex example org.Hs.egUNIGENE text html latex example org.Hs.egUNIPROT text html latex example org.Hs.eg_dbconn text html latex example ** building package indices ... * DONE (org.Hs.eg.db) The downloaded packages are in /tmp/RtmpqsEDGq/downloaded_packages [[alternative HTML version deleted]]

Dear Andreia, the warning is simply informing you that the package will be installed into the default library because you have not specified a 'lib' argument. No need to worry about that. Try: library("org.Hs.eg.db") and you will see that it works... hopefully... :-) Cheers, - axel Axel Klenk Research Informatician Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / Switzerland Andreia Fonseca <andreia.fonseca@ gmail.com=""> To Sent by: bioconductor at stat.math.ethz.ch bioconductor-boun cc ces at stat.math.eth z.ch Subject [BioC] installation of org.Hs.eg.db 11/26/2009 04:31 PM Dear Forum, I have installed biomart, in the begining I had problems because some libraries the Rcurl and the xml were missing. But now I am getting the same error with biocLite("org.Hs.eg.db") I get that is missing a library but I am not understanding which, can someone help me? I run Ubuntu 9.04 Thanks Andreia Below is the messages after > source ("http://bioconductor.org/biocLite.R") > biocLite("org.Hs.eg.db") Running biocinstall version 2.3.14 with R version 2.8.1 Your version of R requires version 2.3 of Bioconductor. Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using '/home/user/R/x86_64-pc-linux-gnu-library/2.8' trying URL ' http://bioconductor.org/packages/2.3/data/annotation/src/contrib/org.H s.eg.db_2.2.6.tar.gz ' Content type 'application/x-gzip' length 31989336 bytes (30.5 Mb) opened URL ================================================== downloaded 30.5 Mb * Installing *source* package 'org.Hs.eg.db' ... ** R ** inst ** preparing package for lazy loading Loading required package: AnnotationDbi Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. ** help >>> Building/Updating help pages for package 'org.Hs.eg.db' Formats: text html latex example org.Hs.egACCNUM text html latex example org.Hs.egALIAS2EG text html latex example org.Hs.egBASE text html latex example org.Hs.egCHR text html latex example org.Hs.egCHRLENGTHS text html latex example org.Hs.egCHRLOC text html latex example org.Hs.egENSEMBL text html latex example org.Hs.egENSEMBLPROT text html latex example org.Hs.egENSEMBLTRANS text html latex example org.Hs.egENZYME text html latex example org.Hs.egGENENAME text html latex example org.Hs.egGO text html latex example org.Hs.egGO2ALLEGS text html latex example org.Hs.egMAP text html latex example org.Hs.egMAPCOUNTS text html latex example org.Hs.egOMIM text html latex example org.Hs.egORGANISM text html latex example org.Hs.egPATH text html latex example org.Hs.egPFAM text html latex example org.Hs.egPMID text html latex example org.Hs.egPROSITE text html latex example org.Hs.egREFSEQ text html latex example org.Hs.egSYMBOL text html latex example org.Hs.egUNIGENE text html latex example org.Hs.egUNIPROT text html latex example org.Hs.eg_dbconn text html latex example ** building package indices ... * DONE (org.Hs.eg.db) The downloaded packages are in /tmp/RtmpqsEDGq/downloaded_packages [[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 The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. The content of this email is not legally binding unless confirmed by letter. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com