[BioC] Bioconductor installation on 64 bit R problem

[Robert Gentleman]

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