[BioC] Bioconductor installation on 64 bit R problem

Joern Toedling toedling at ebi.ac.uk
Mon Oct 6 14:44:39 CEST 2008

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.


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

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