[BioC] preprocessCore "Undefined log2" installation error

[bmb at bmbolstad.com]

I believe I may have already addressed this in the development branch
(meaning it will be fixed in the next BioC release), but please do confirm
for me the version of preprocessCore that you are using.

Best,

Ben


> 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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