[Bioc-devel] build/check fails for multiscan package on Mac OSX

[Richard Pearson]

It seems the problem is with the build system. If you take a look at

http://bioconductor.org/checkResults/2.4/bioc-LATEST/index.html

There are lots of packages that have failed on the Mac machines. Anyone know what's happened?

Cheers

Richard

Mizanur Khondoker wrote:
> Dear list,
> 
> The Bioc 2.4 package 'multiscan' was working OK so far on Windows,
> Linux and MacOS X.
> 
> I received an automated message today reporting a problem with
> Multiple platform build/check of the package.
> Build/check of the packages fails for Bioc platforms pitt (Mac OS X
> Tiger (10.4.11) / i386) and   pelham  (Mac OS X Leopard (10.5.7) /
> i386).
> 
> I  haven't got a clue whether  it is a problem with the package or the
> build system. Any help would be appreciated.
> 
> Please see the build/check report below:
> (Same error from both pitt and pelham)
> ====================================================================
> * checking for file 'multiscan/DESCRIPTION' ... OK
> * preparing 'multiscan':
> * checking DESCRIPTION meta-information ... OK
> * cleaning src
> * installing the package to re-build vignettes
> * Installing *source* package 'multiscan' ...
> ** libs
> ** arch - i386
> gcc -arch i386 -std=gnu99
> -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include
> -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386
> -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c multiscan.c -o
> multiscan.o
> gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names
> -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module
> -multiply_defined suppress -L/usr/local/lib -o multiscan.so
> multiscan.o -F/Library/Frameworks/R.framework/.. -framework R
> -Wl,-framework -Wl,CoreFoundation
> ** arch - ppc
> gcc -arch ppc -std=gnu99
> -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include
> -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc
> -I/usr/local/include    -fPIC  -g -O2 -c multiscan.c -o multiscan.o
> gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names
> -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module
> -multiply_defined suppress -L/usr/local/lib -o multiscan.so
> multiscan.o -F/Library/Frameworks/R.framework/.. -framework R
> -Wl,-framework -Wl,CoreFoundation
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
>  >>> Building/Updating help pages for package 'multiscan'
>      Formats: text html latex example
>   multiscan                         text    html    latex   example
>   murine                            text    html    latex
>   plot.multiscan                    text    html    latex   example
> ** building package indices ...
> * DONE (multiscan)
> * creating vignettes ... ERROR
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>   unable to load shared library
> '/tmp/Rinst2461267252/multiscan/libs/i386/multiscan.so':
>   dlopen(/tmp/Rinst2461267252/multiscan/libs/i386/multiscan.so, 6):
> Library not loaded:
> /Library/Frameworks/R.framework/Versions/2.10/Resources/lib/libR.dylib
>   Referenced from: /tmp/Rinst2461267252/multiscan/libs/i386/multiscan.so
>   Reason: Incompatible library version: multiscan.so requires version
> 2.10.0 or later, but libR.dylib provides version 2.9.0
> 
> Error: processing vignette 'multiscan.Rnw' failed with diagnostics:
>  chunk 1
> Error : package/namespace load failed for 'multiscan'
> Execution halted
> 
> 

-- 
Richard D Pearson                          richard.pearson at well.ox.ac.uk
Wellcome Trust Centre for Human Genetics   http://www.well.ox.ac.uk/~rpearson
University of Oxford                       Tel: +44 (0)1865 287575
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