Hello, I have ran into problems trying to use the bioconductor install script as found on the web site: http://www.bioconductor.org/ These are the errors I saw when running under the bash shell and zsh. Running under bash shell: sh-2.05a$ source getBioC.R sh: getBioC.R: line 55: syntax error near unexpected token `(l' sh: getBioC.R: line 55: `getBioC <- function (libName = "all", relLevel = "release",' Running under zsh: source getBioC.R [ 7:56] getBioC.R:55: number expected getBioC.R:62: no such file or directory: - getBioC.R:69: bad pattern: writeLines(paste(Running getBioC version ,getBioCVersion,....\n,\n If you encounter problems, first make sure that\n,\n you are running the latest version of getBioC()\n,\n which can be found at: www.bioconductor.org/getBioC.R\n \n\n,\n Please direct any concerns or questions to,\n bioconductor@stat.math.ethz.ch.\n,sep=)) Just thought I'd let you know. Bela ************************* Dr. Bela Tiwari Lead Bioinformatician CEH Oxford Mansfield Road Oxford, OX1 3SR 01865 281975

> Running under bash shell: Have you tried running it in R?

Hi Bela, have you tried running the script on the R interpreter rather than on a unix shell? i.e., start R and then type 'source("getBioC.R")'. Best regards Wolfgang ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/mga/whuber

getBioC is an R script and is supposed to be run with R. After starting R, source("http://www.bioconductor.org/getBioC.R") will load the script into R and getBioC("all", "release") will get all the released packages from Bioconductor. >Date: Fri, 13 Jun 2003 16:42:30 +0100 >From: "Bela Tiwari" <btiwari@ceh.ac.uk> >To: <bioconductor@stat.math.ethz.ch> >Mime-Version: 1.0 >Content-Transfer-Encoding: 7bit >Content-Disposition: inline >X-MailScanner-NERC: Found to be clean >X-Virus-Scanned: by amavisd-milter (http://amavis.org/) >X-Virus-Scanned: by amavisd-milter (http://amavis.org/) >X-Spam-Status: No, hits=0.0 required=5.0 tests=none version=2.54 >X-Spam-Level: >X-Spam-Checker-Version: SpamAssassin 2.54 (1.174.2.17-2003-05-11-exp) >X-Mailman-Approved-At: Fri, 13 Jun 2003 17:44:58 +0200 >Subject: [BioC] problem with bioconductor install script >X-BeenThere: bioconductor@stat.math.ethz.ch >X-Mailman-Version: 2.1.2 >List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> >List-Help: <mailto:bioconductor- request@stat.math.ethz.ch?subject="help"> >List-Post: <mailto:bioconductor@stat.math.ethz.ch> >List-Subscribe: <https: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=subscribe> >List-Archive: <https: www.stat.math.ethz.ch="" pipermail="" bioconductor=""> >List-Unsubscribe: <https: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=unsubscribe> > > >Hello, > >I have ran into problems trying to use the bioconductor install script >as found on the web site: http://www.bioconductor.org/ > >These are the errors I saw when running under the bash shell and zsh. > > >Running under bash shell: > >sh-2.05a$ source getBioC.R >sh: getBioC.R: line 55: syntax error near unexpected token `(l' >sh: getBioC.R: line 55: `getBioC <- function (libName = "all", >relLevel = "release",' > > >Running under zsh: > > source getBioC.R [ 7:56] >getBioC.R:55: number expected >getBioC.R:62: no such file or directory: - >getBioC.R:69: bad pattern: writeLines(paste(Running getBioC version >,getBioCVersion,....\n,\n If you encounter problems, >first make sure that\n,\n you are running the latest >version of getBioC()\n,\n which can be found at: >www.bioconductor.org/getBioC.R\n \n\n,\n > Please direct any concerns or questions to,\n > bioconductor@stat.math.ethz.ch.\n,sep=)) > > >Just thought I'd let you know. > >Bela > > > > >************************* >Dr. Bela Tiwari >Lead Bioinformatician > >CEH Oxford >Mansfield Road >Oxford, OX1 3SR >01865 281975 > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

Hi Bela, Were you running it from within R because if not that may solve your problems claire > -----Original Message----- > From: Bela Tiwari [mailto:btiwari@ceh.ac.uk] > Sent: 13 June 2003 16:43 > To: bioconductor@stat.math.ethz.ch > Subject: [BioC] problem with bioconductor install script > > > > Hello, > > I have ran into problems trying to use the bioconductor install script > as found on the web site: http://www.bioconductor.org/ > > These are the errors I saw when running under the bash shell and zsh. > > > Running under bash shell: > > sh-2.05a$ source getBioC.R > sh: getBioC.R: line 55: syntax error near unexpected token `(l' > sh: getBioC.R: line 55: `getBioC <- function (libName = "all", > relLevel = "release",' > > > Running under zsh: > > source getBioC.R [ 7:56] > getBioC.R:55: number expected > getBioC.R:62: no such file or directory: - > getBioC.R:69: bad pattern: writeLines(paste(Running getBioC version > ,getBioCVersion,....\n,\n If you > encounter problems, > first make sure that\n,\n you are running > the latest > version of getBioC()\n,\n which can be found at: > www.bioconductor.org/getBioC.R\n \n\n,\n > Please direct any concerns or questions to,\n > > bioconductor@stat.math.ethz.ch.\n,sep=)) > > > Just thought I'd let you know. > > Bela > > > > > ************************* > Dr. Bela Tiwari > Lead Bioinformatician > > CEH Oxford > Mansfield Road > Oxford, OX1 3SR > 01865 281975 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > -------------------------------------------------------- This email is confidential and intended solely for the use of th... {{dropped}}