[BioC] trouble with installing Biobase package

[Robert Gentleman]

Hi,
   Yes, I believe you need to update your R. But since you did not 
follow the advice on the posting guide, I cannot be sure.

The addition of the numeric_version class was pretty recent (about one 
week ago), so you need to update.

   During the lead up to the release you can expect that changes to R 
will necessitate updating more often.
   The other choice is to work off of the release branches of both R and 
Bioconductor.

   best wishes
     Robert

Tena Sakai wrote:
> Hi Everybody,
> 
> I am having a problem with loading Biobase package.  I typed
> 2 lines below at R prompt
> 
>  > source ("http://boconductor.org/biocLite.R")
>  > biocLite (lib="/usr/local/lib/R/library")
> 
> which attempted to install a bunch of packages with varying
> degree of success.  Out of 29, 13 failed.  Biobase is one of
> them.  As a matter of fact, when I looked at logs, most other
> failures seemed due to the fact Biobase not being there.  So,
> why is Biobase failing to compile?  Here's the complaint:
> 
>  * Installing *source* package 'Biobase' ...
>  ** libs
>  gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include  -I/usr/local/include    -fpic  -g -O2 -c anyMissing.c -o anyMissing.o
>  gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include  -I/usr/local/include    -fpic  -g -O2 -c envir.c -o envir.o
>  gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include  -I/usr/local/include    -fpic  -g -O2 -c matchpt.c -o matchpt.o
>  gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include  -I/usr/local/include    -fpic  -g -O2 -c Rinit.c -o Rinit.o
>  gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include  -I/usr/local/include    -fpic  -g -O2 -c rowMedians.c -o rowMedians.o
>  gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include  -I/usr/local/include    -fpic  -g -O2 -c sublist_extract.c -o sublist_extract.o
>  gcc -std=gnu99 -shared -L/usr/local/lib64 -o Biobase.so anyMissing.o envir.o matchpt.o Rinit.o rowMedians.o sublist_extract.o 
>  ** R
>  ** data
>  ** inst
>  ** preparing package for lazy loading
>  Loading required package: tools
>  Error : could not find function "numeric_version"
>  Error: unable to load R code in package 'Biobase'
>  Execution halted
>  ERROR: lazy loading failed for package 'Biobase'
>  ** Removing '/usr/local/lib/R/library/Biobase'
> 
> It is choking at not finding a function "numeric_version".  Has anybody
> seen this before and have any insight to the solution?  I would appreciate
> a bit of helping hand.
> 
> The platform I am on is Dell 64-bit server, running redhat enterprise
> server.
> 
> Regards,
> 
> Tena Sakai
> tsakai at gallo.ucsf.edu
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
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