Hi Tena -- Please use the Bioconductor mailing list for Bioconductor
questions.
You need to update your development version of R to the prerelease
version (provide the output of sessionInfo() with problem reports).
Martin
"Tena Sakai" <[EMAIL PROTECTED]> writes:
> 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
> [EMAIL PROTECTED]
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@r-project.org mailing list
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
--
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org
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