[BioC] Building BioC 2.2 with R 2.7.0

Kasper Daniel Hansen khansen at stat.Berkeley.EDU
Mon May 26 19:55:02 CEST 2008

The first thing to understand is that in some case R CMD INSTALL can  
seem sucessful, but when you to to do the librray command from within  
R it fails, ie.


This typically happens when a package is dynamically linked to  
something that R cannot find when it tries to load the package. Now,  
the slightly confusing issue that may happen is that when package XX  
depends on package YY, R will try to load the YY package when it tries  
to install XX. So if YY has the problem I just mention you will not  
discover it when you install YY but rather when you install something  
that depends on YY.

See below for rest of comments

On May 26, 2008, at 4:03 AM, Atro Tossavainen wrote:

> I've successfully built R 2.7.0 for x86 Linux (RHEL4), x86_64 Linux
> (RHEL4), Solaris 8 SPARC and IRIX 6.5.  The Bioconductor installation
> process works fine on x86_64 Linux and IRIX.
> Building annaffy fails on x86 Linux, and building annaffy and  
> simpleaffy
> fail on Solaris 8.  In both cases, the annaffy error message is as  
> follows:
> Loading required package: GO.db
> Loading required package: AnnotationDbi
> Loading required package: DBI
> Loading required package: RSQLite
> Error in sqliteExecStatement(con, statement, bind.data) :
>  RS-DBI driver: (error in statement: no such table: metadata)
> Error : .onLoad failed in 'loadNamespace' for 'GO.db'
> Error: package 'GO.db' could not be loaded
> Execution halted
> ERROR: lazy loading failed for package 'annaffy'
> ** Removing '/.../R/2.7.0/lib/R/library/annaffy'

Here it seems like you GO.db installation is wrong. This is not a  
dynamically linked issue, but something else. My guess is that you  
have some version mismatch.

> The simpleaffy installation attempt ends with:
> Loading required package: splines
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>  unable to load shared library '/.../R/2.7.0/lib/R/library/ 
> genefilter/libs/genefilter.so':
>  ld.so.1: /.../R/2.7.0/lib. at sys/R/bin/exec/R: fatal: relocation  
> error: file /.../R/2.7.0/lib/R/library/genefilter/libs/ 
> genefilter.so: symbol __1cDstdJexceptionG__vtbl_: referenced symbol  
> not found
> Error: package 'genefilter' could not be loaded
> Execution halted
> ERROR: lazy loading failed for package 'simpleaffy'
> ** Removing '/.../R/2.7.0/lib/R/library/simpleaffy'

Looking at the error, it happens when you try to load genefilter. I  
will bet that if you open up R and do
R> library(genefilter)
you will get the same error.

Now, why genefilter does not install properly, I have no idea about.

> All help appreciated.
> -- 
> Atro Tossavainen (Mr.)               / The Institute of  
> Biotechnology at
> Systems Analyst, Techno-Amish &     / the University of Helsinki,  
> Finland,
> +358-9-19158939  UNIX Dinosaur     / employs me, but my opinions are  
> my own.
> < URL : http : / / www . helsinki . fi / %7E atossava / > NO FILE  
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