[BioC] preprocessCore "Undefined log2" installation error

[Bruce Hayward]

Ben,
The installation script says:
 > trying URL 
'http://www.bioconductor.org/packages/2.7/bioc/src/contrib/preprocessCore_1.12.0.tar.gz'

On 03/21/11 13:34, Bruce Hayward wrote:
> I'm running FreeBSD8.2 on an Intel Core2Duo
> I have installed the basic R package via the FreeBSD ports to version 
> 2.12.2
> My attempts to install the basic Bioconductor package fails when 
> preprocessCore installation fails.
>
> Followed the standard installation instructions at Bioconductor:
>
> > source("http://bioconductor.org/biocLite.R")
> > biocLite("preprocessCore")
>
> which generated the following complaint in amongst the rest of the build:
>
> gcc45 -std=gnu99 -I/usr/local/lib/R/include     -g -O2  
> -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" 
> -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 
> -DUSE_PTHREADS=1 -fpic  -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc45 
> -fno-strict-aliasing -c median_log.c -o median_log.o
> median_log.c: In function 'medianlog':
> median_log.c:137:7: warning: implicit declaration of function 'log2'
> median_log.c:137:19: warning: incompatible implicit declaration of 
> built-in function 'log2'
> median_log.c: In function 'medianlog_no_copy':
> median_log.c:154:25: warning: incompatible implicit declaration of 
> built-in function 'log2'
> gcc45 -std=gnu99 -I/usr/local/lib/R/include     -g -O2  
> -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" 
> -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 
> -DUSE_PTHREADS=1 -fpic  -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc45 
> -fno-strict-aliasing -c medianpolish.c -o medianpolish.o
>
> leading to:
>
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices ...
> ** testing if installed package can be loaded
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>   unable to load shared object 
> '/usr/local/lib/R/library/preprocessCore/libs/preprocessCore.so':
>   /usr/local/lib/R/library/preprocessCore/libs/preprocessCore.so: 
> Undefined symbol "log2"
> ERROR: loading failed
> * removing '/usr/local/lib/R/library/preprocessCore'
>
>
> Any suggestions?
>
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