[Bioc-devel] BioC 2.2 (Devel): Rdisop build on leopard [was: xcms package update for Mac OS X 10.5.1 (Re: netCDF on pelham)

[Kasper Daniel Hansen]

On Feb 1, 2008, at 4:42 AM, sneumann wrote:

> On Do, 2008-01-24 at 12:13 -0800, Patrick Aboyoun wrote:
>> Steffen,
>> I installed universal binaries (i386, x86_64, ppc) for the NetCDF
> Many thanks!
>
>> Keep in mind that the xcms package is not passing check on any of  
>> OS for
> Until yesterday they were not even passing the build stage,
> so once we're sober from celebrating successful builds,
> we'll go after the check/warnings ;-)
>
>> the BioC 2.2 (Devel) builds, so you may want to use the BioC 2.1
>> (Release) build of xcms with R 2.6.1 (Release) until that has been
>> rectified.
> We're maintainers of xcms, just waiting won't help ;-)
>
> Thanks for your efforts,
> I might approach you later for some help with Rdisop.
> Rdisop is shipping a library in Rdisop/src/imslib
> which is successfully built using libtool:
>
> 	g++ -dynamiclib -single_module  -o src/.libs/libims.0.0.0.dylib   
> src/ims/.libs/element.o ... src/ims/.libs/nitrogenrulefilter.o   - 
> install_name  /usr/local/lib/libims.0.dylib -Wl,- 
> compatibility_version -Wl,1 -Wl,-current_version -Wl,1.0
> 	(cd src/.libs && rm -f libims.0.dylib && ln -s libims.0.0.0.dylib  
> libims.0.dylib)
> 	(cd src/.libs && rm -f libims.dylib && ln -s libims.0.0.0.dylib  
> libims.dylib)
>
> Then it is successfully building Rdisop.so using the
> newly built -L./imslib/src/.libs/ -lims:
>
> 	g++-4.0 -arch i386 -dynamiclib -Wl,-headerpad_max_install_names  - 
> undefined dynamic_lookup -single_module -multiply_defined suppress - 
> L/usr/local/lib -o Rdisop.so disop.o -L../RcppSrc -lRcpp -L./imslib/ 
> src/.libs/ -lims   -F/Library/Frameworks/R.framework/.. -framework  
> R -lintl -liconv -lc -Wl,-framework -Wl,CoreFoundation
>
> and copied to the Rdisop/src/ directory:
>
> 	ls -l ./imslib/src/.libs/
> 	total 6448
> 	-rwxr-xr-x  1 biocbuild  staff   318092 Jan 31 03:27 libims. 
> 0.0.0.dylib
> 	lrwxr-xr-x  1 biocbuild  staff       18 Jan 31 03:27 libims. 
> 0.dylib -> libims.0.0.0.dylib
> 	-rw-r--r--  1 biocbuild  staff  2963884 Jan 31 03:27 libims.a
> 	lrwxr-xr-x  1 biocbuild  staff       18 Jan 31 03:27 libims.dylib - 
> > libims.0.0.0.dylib
> 	lrwxr-xr-x  1 biocbuild  staff       12 Jan 31 03:27 libims.la - 
> > ../libims.la
> 	-rw-r--r--  1 biocbuild  staff      813 Jan 31 03:27 libims.lai
> 	cp -rv ./imslib/src/.libs/libims*.dylib* .
> 	./imslib/src/.libs/libims.dylib -> ./libims.dylib
> 	./imslib/src/.libs/libims.0.dylib -> ./libims.0.dylib
> 	./imslib/src/.libs/libims.0.0.0.dylib -> ./libims.0.0.0.dylib
>
> It is, however, _not_ copied into the installed package as on linux:
> or not found under the name "libims":
>
> 	* creating vignettes ... ERROR
> 	Error in library.dynam(lib, package, package.lib) :
> 	  shared library 'libims' not found
>
> I suspect that either the libims*dylib* are not copied
> into the package, or that library.dynam() resolving has a problem.
>
> On Windows I needed to copy the DLLs explicitely in configure.win:
> 	mkdir ${DPKG}/libs
> 	cp src/win/libims*.dll ${DPKG}/libs/
> do I have to do that on leopard as well ?
>
> Since I don't have leopard access, I'd appreciate any hints.

On the Mac you need to be able to build universal binaries (ie. you  
need to compile for several architectures). The suffix for a library  
can both be .a and .dylib. What you seem to be doing above is  
probably extremely non-portable.

Kasper


> Yours,
> Steffen
>
> -- 
> IPB Halle                    AG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann          http://www.IPB-Halle.DE
> Weinberg 3                   http://msbi.bic-gh.de
> 06120 Halle                  Tel. +49 (0) 345 5582 - 1470
>                                   +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
>
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