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

[Patrick Aboyoun]

This was my bad. I had recently updated R-devel on the two Mac OS X 
build machines and I forgot to change the symbolic link 
/Library/Frameworks/R.framework/Versions/Current to point to 2.9 rather 
than 2.10. I made the correction just now and today's BioC 2.4 builds 
should run much smoother.


Patrick



Richard Pearson wrote:
> 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
>>
>>
>