Hello, I am attempting to install Bioconductor on 64 bit R. The installation of some bioconductor packages fails with the errors below. I would be very grateful for any help on how to resolve the issue. Best regards, Octavio Espinosa --------------------- Most of the bioconductor packages won't install, for examples 'Biobase' errors with: ** building package indices ... Loading required package: methods Error in dim(robj) <- c(dX, dY) : dims [product 8] do not match the length of object [16] Calls: <anonymous> ... list_files_with_type -> .make_file_exts -> switch -> outer Execution halted ERROR: installing package indices failed ** Removing '/usr/local/lib/R/library/Biobase' The downloaded packages are in /tmp/RtmpHGbpND/downloaded_packages Updating HTML index of packages in '.Library' Warning message: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'Biobase' had non-zero exit status It looks like it doesn't work with 64bit stuff (the byte lengths mismatch) [[alternative HTML version deleted]] [[alternative HTML version deleted]]

On Mon, Oct 6, 2008 at 8:17 AM, Octavio Espinosa <o.espinosa at="" har.mrc.ac.uk=""> wrote: > Hello, > > I am attempting to install Bioconductor on 64 bit R. The installation of some bioconductor packages fails with the errors below. I would be very grateful for any help on how to resolve the issue. > Hi, Octavio. You need to post the output of sessionInfo() in order to get any help. Also, how did you install R? Sean > > > Most of the bioconductor packages won't install, for examples 'Biobase' > errors with: > > ** building package indices ... > Loading required package: methods > Error in dim(robj) <- c(dX, dY) : > dims [product 8] do not match the length of object [16] > Calls: <anonymous> ... list_files_with_type -> .make_file_exts -> switch > -> outer > Execution halted > ERROR: installing package indices failed > ** Removing '/usr/local/lib/R/library/Biobase' > > The downloaded packages are in > /tmp/RtmpHGbpND/downloaded_packages > Updating HTML index of packages in '.Library' > Warning message: > In install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > installation of package 'Biobase' had non-zero exit status > > > It looks like it doesn't work with 64bit stuff (the byte lengths > mismatch) > > [[alternative HTML version deleted]] > > > > [[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 >

Hi Octavio, Not without knowing a lot more about how you installed R, which version of R, whether it works, and many other details omitted from your email. Please read the posting guide for information on how to post questions. On a practical note, the first thing to do is to install a new R (2.7.2 is the current release, 2.8.0 is less than one month away). Run the make check target to ensure that R has correctly installed. Then use biocLite - and if errors persist - post again (after reading the posting guide so you include enough information for someone to help you). There are no known problems with 64 bit R or Bioconductor on 64 bit machines (which you can easily verify by looking at the package check pages). best wishes Robert Octavio Espinosa wrote: > Hello, > > I am attempting to install Bioconductor on 64 bit R. The installation of some bioconductor packages fails with the errors below. I would be very grateful for any help on how to resolve the issue. > > Best regards, > > Octavio Espinosa > > > > --------------------- > > > Most of the bioconductor packages won't install, for examples 'Biobase' > errors with: > > ** building package indices ... > Loading required package: methods > Error in dim(robj) <- c(dX, dY) : > dims [product 8] do not match the length of object [16] > Calls: <anonymous> ... list_files_with_type -> .make_file_exts -> switch > -> outer > Execution halted > ERROR: installing package indices failed > ** Removing '/usr/local/lib/R/library/Biobase' > > The downloaded packages are in > /tmp/RtmpHGbpND/downloaded_packages > Updating HTML index of packages in '.Library' > Warning message: > In install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > installation of package 'Biobase' had non-zero exit status > > > It looks like it doesn't work with 64bit stuff (the byte lengths > mismatch) > > [[alternative HTML version deleted]] > > > > [[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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

Hi Octavio, looks to me like this is not a Bioconductor issue, but that your R is not working properly as the "methods" package cannot be attached (do you get the same error message, when starting R and typing 'library("methods")'? ). How did you install R? Did you get it from some RPM or other pre-built source? Maybe this R does not match your system architecture. I would recommend to get the R .tar.gz from the CRAN web site. Unpack it, run "configure", then "make", "make check" to see if it works, and optionally "make install". You may need to install some other libraries of your Linux for the "configure" to succeed, but the configure script will probably tell you what you are missing. If you are stuck, I am sure that people on the R help list will be helpful regarding the installation. If you still face the issue with installing Biobase with the custom-built R, please get back to this list and provide the output of "sessionInfo()" as well. Regards, Joern Octavio Espinosa wrote: > Hello, > > I am attempting to install Bioconductor on 64 bit R. The installation of some bioconductor packages fails with the errors below. I would be very grateful for any help on how to resolve the issue. > > Best regards, > > Octavio Espinosa > > > > --------------------- > > > Most of the bioconductor packages won't install, for examples 'Biobase' > errors with: > > ** building package indices ... > Loading required package: methods > Error in dim(robj) <- c(dX, dY) : > dims [product 8] do not match the length of object [16] > Calls: <anonymous> ... list_files_with_type -> .make_file_exts -> switch > -> outer > Execution halted > ERROR: installing package indices failed > ** Removing '/usr/local/lib/R/library/Biobase' > > The downloaded packages are in > /tmp/RtmpHGbpND/downloaded_packages > Updating HTML index of packages in '.Library' > Warning message: > In install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > installation of package 'Biobase' had non-zero exit status > > > It looks like it doesn't work with 64bit stuff (the byte lengths > mismatch) > -- Joern Toedling EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Phone +44(0)1223 492566 Email toedling at ebi.ac.uk