Hi, I'm trying to install bioconductor on RedHat 7.3. Installation of reposTools gives the following message: --------------------------------------- > getBioC(relLevel="release") Running getBioC version 1.2.55.... If you encounter problems, first make sure that you are running the latest version of getBioC() which can be found at: www.bioconductor.org/getBioC.R Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. [1] "Installing reposTools ..." * Installing *source* package 'reposTools' ... ** R Error: couldn't find function ".installPackageCodeFiles" Execution halted ERROR: unable to collate files for package 'reposTools' ** Removing '/usr/lib/R/library/reposTools' Error in getReposTools(relLevel, PLATFORM, destdir, method = method, bioCoption = bioCoption) : Failed to install package reposTools -------------------------------------------- I recompiled R (1.8.1) and installed it correctly as far as I can see. I tried to find a solution on the net, but I was unable to find it. Could you help me on track? Victor de Jager ---------------------------------- V.C.L. de Jager Erasmus MC Dr. Molewaterplein 50 3015 GE Rotterdam tel: 31-10-4088454 fax: 31-10-4089468 email: v.dejager@erasmusmc.nl

> Error: couldn't find function ".installPackageCodeFiles" > Execution halted I believe that your R installation is somehow broken. The .installPackageCodeFiles function gets called by the "INSTALL" script in R/bin, which in turn gets called by install.packages() (which itself is part of a chain of calls from getBioC). If that function doesn't exist, it would seem that your 'tools' package (part of the base installation of R) is somehow not installed properly most likely. What happens if you do a 'R INSTALL XXXXX' (where XXXXX is a package) from the command line? Or run 'install.packages()' on a non-Bioconductor package? -J

Thanks, that did the trick, it works now, although I have some issues with running R from batch mode. It can't find the Limma library if I invoke R from a PHP script where it can if I run the same command from the commandline (R CMD BATCH script.R) Victor Kathy Dawson, Ph.D. wrote: >I think you need to install R (1.9) and then everything will install correctly. > >kathy > >"V.C.L. de Jager" wrote: > > > >>Hi, >> >>I'm trying to install bioconductor on RedHat 7.3. Installation of reposTools >>gives the following message: >>--------------------------------------- >> >> >>>getBioC(relLevel="release") >>> >>> >>Running getBioC version 1.2.55.... >>If you encounter problems, first make sure that >>you are running the latest version of getBioC() >>which can be found at: www.bioconductor.org/getBioC.R >> >>Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. >> >>[1] "Installing reposTools ..." >>* Installing *source* package 'reposTools' ... >>** R >>Error: couldn't find function ".installPackageCodeFiles" >>Execution halted >>ERROR: unable to collate files for package 'reposTools' >>** Removing '/usr/lib/R/library/reposTools' >>Error in getReposTools(relLevel, PLATFORM, destdir, method = method, >>bioCoption = bioCoption) : >> Failed to install package reposTools >>-------------------------------------------- >> >>I recompiled R (1.8.1) and installed it correctly as far as I can see. >>I tried to find a solution on the net, but I was unable to find it. Could >>you help me on track? >> >>Victor de Jager >>---------------------------------- >>V.C.L. de Jager >>Erasmus MC >>Dr. Molewaterplein 50 >>3015 GE Rotterdam >> >>tel: 31-10-4088454 >>fax: 31-10-4089468 >>email: v.dejager@erasmusmc.nl >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor@stat.math.ethz.ch >>https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >> >>