[BioC] rsbml installation fails on MacOS with libsbml 3

[Dan Tenenbaum]

Hi all,


On Wed, May 29, 2013 at 7:25 AM, Michael Lawrence
<lawrence.michael at gene.com> wrote:
> This is probably an incompatibility between the version of libsbml used by
> the build machines for compiling the package and the version installed on
> your system. Maybe Dan can figure out the version on the build machines?
>

OK. Hannes, it would help to know the output of sessionInfo() on your machine.

Both our release and devel build machines use libsbml 3.4.1.

Dan




> Michael
>
>
>
>
> On Wed, May 29, 2013 at 6:32 AM, Hannes Hettling [guest] <
> guest at bioconductor.org> wrote:
>
>>
>> Dear all,
>>
>> we have a problem with installing rsbml on MacOS using libsbml 3.4.1.
>>
>> The error message (pasted below) is similar to the one in an older post:
>>
>> http://article.gmane.org/gmane.science.biology.informatics.conductor/33187/match=rsbml
>>
>> Error : .onLoad failed in loadNamespace() for 'rsbml', details:
>>   call: dyn.load(file, DLLpath = DLLpath, ...)
>>   error: unable to load shared object
>> '/Library/Frameworks/R.framework/Versions/2.15/Resources/library/rsbml/libs/x86_64/rsbml.so':
>>
>> dlopen(/Library/Frameworks/R.framework/Versions/2.15/Resources/library/rsbml/libs/x86_64/rsbml.so,
>> 6): Symbol not found: _ASTNode_addChild
>>   Referenced from:
>> /Library/Frameworks/R.framework/Versions/2.15/Resources/library/rsbml/libs/x86_64/rsbml.so
>>   Expected in: dynamic lookup
>>
>> We set the environment variables LIBSBML3_CFLAGS=/usr/local/lib/ and
>> LIBSBML3_LIBS=/usr/local/include/ and the directories contain the library
>> files and the headers, respectively.
>>
>> Unfortunately, we are not able to build the package from source, since we
>> cannot get access to Xcode (development tools) on that machine.
>>
>> With which sbml version was the current macos rsbml package compiled?
>>
>> Hope someone can help us,
>> many thanks in advance,
>>
>> Farah and Hannes
>>
>>  -- output of sessionInfo():
>>
>> R version 2.15.1 (2012-06-22)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>
>> locale:
>> [1] C/UTF-8/C/C/C/C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] BiocGenerics_0.4.0  BiocInstaller_1.8.3
>>
>> loaded via a namespace (and not attached):
>> [1] graph_1.36.2  stats4_2.15.1 tools_2.15.1
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
>
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