[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)

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.

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

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

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.

On Fri, 2008-02-01 at 07:47 -0800, Kasper Daniel Hansen wrote:

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

...

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.

I am open for anz suggestions to improve the BioC 
experience for Mac Users. 

Is there a way to build the universal binaries with configure/make ?

Are there other packages in BioC that build complex libraries 
which I could use as example ? Or some Mac specific 
documentation links ?

Actually I have in src/Makevars

  cp -r ./imslib/src/.libs/libims*$(DYLIB_EXT)*

so I use whatever extension R has configured.

Yours,
Steffen