[Bioc-devel] Mac build (xcms)
Patrick Aboyoun
paboyoun at fhcrc.org
Mon Feb 22 19:59:06 CET 2010
Steffen,
I am unable to reproduce the problem. Currently the builds are fine and
when I run R-2.10/R-devel --arch=ppc, download xcms via biocLite, and
run the RUnit tests everything seems to be in order. Perhaps there is
some confusion over the warning messages you are receiving during the
build process? The BioC build process occurs in three stages for Mac OS
X 10.4 and 10.5.
1) Build package source tarball, which is *not* distributed at
bioconductor.org. At this step we only test arch=i386 and so the ld
warning messages for arch=ppc are not meaningful.
2) Check package source tarball that was built in first step. Again we
only test arch=i386.
3) Build binary package tarball. At this step, the build for each
architecture (i386, pcc for Mac OS X 10.4 and i386, ppc, x86_64 for Mac
OS X 10.5) is performed separately using the (parameterized) command
R_ARCH=/{i386/ppc} R CMD INSTALL --preclean
--library=xcms.buildbin-libdir --libs-only xcms_VERSION.tar.gz
The resulting shared objects from each of the architecture builds are
then bundled together in the *.tgz Mac OS X binary package tarball. It
is this multi-architecture collection that is distributed at
bioconductor.org.
If I am misunderstanding your concerns, let me know.
Cheers,
Patrick
On 2/20/10 11:52 AM, Steffen Neumann wrote:
> Hi,
>
> XCMS has link problems on MacOS ppc build, see Ralf's mail below.
>
> We had a similar issue april last year
> http://groups.google.de/group/xcms-devel/browse_thread/thread/bb2584a7c015e56e/a24d1436bfc5d552?hl=de&ie=UTF-8&oe=utf-8&q=Re:+xcms+and+parallel+make#a24d1436bfc5d552
> which got fixed by Patrick Aboyoun back then. Patrick's answer
> back then is at the end of this mail.
>
> Since R-2.10 or so R CMD build moved over to some perl code,
> which might have re-introduced this similar problem unnoticed.
> Could that be ?
>
> If we'd add a unit test to XCMS (which are disabled
> in the BioC builds ?!) or added that obiwarp() call to a vignette,
> we'd have a broken ("ERROR") build on MacOS. This way
> only the users will notice, which is even worse.
>
> Any clues ?
>
> Yours,
> Steffen
>
> On Fri, 2010-02-19 at 16:10 -0800, Ralf Tautenhahn wrote:
>
>> I am not a Mac person, and I am not familiar with these multiarch
>> builds that Mac seems to use.
>>
>> It seems the current builds of release and devel for Mac
>> http://bioconductor.org/checkResults/2.5/bioc-LATEST/xcms/pelham-buildsrc.html
>> http://bioconductor.org/checkResults/2.6/bioc-LATEST/xcms/pelham-buildsrc.html
>> are not compiled/linked correctly.
>>
>> g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c obiwarp/mat.cpp -o obiwarp/mat.o
>> g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c obiwarp/vec.cpp -o obiwarp/vec.o
>> g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
>> g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
>> g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c obiwarp/xcms_obiwarp.cpp -o obiwarp/xcms_obiwarp.o
>> gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -Wall -c mzClust_hclust.c -o mzClust_hclust.o
>> gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -Wall -c mzROI.c -o mzROI.o
>> gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -Wall -c netCDF.c -o netCDF.o
>> g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c ramp_base64.cpp -o ramp_base64.o
>> g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c ramp.cpp -o ramp.o
>> ramp.cpp: In function ‘char* rampValidFileType(const char*)’:
>> ramp.cpp:1459: warning: ‘result’ may be used uninitialized in this function
>> g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c rampR.cpp -o rampR.o
>> gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -Wall -c util.c -o util.o
>> gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -Wall -c xcms.c -o xcms.o
>> g++-4.2 -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o xcms.so obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o obiwarp/xcms_obiwarp.o mzClust_hclust.o mzROI.o netCDF.o ramp_base64.o ramp.o rampR.o util.o xcms.o -L/usr/local/lib -L/sw/lib -lnetcdf -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
>> ** arch - ppc
>> gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c mzClust_hclust.c -o mzClust_hclust.o
>> gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c mzROI.c -o mzROI.o
>> gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c netCDF.c -o netCDF.o
>> g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c ramp_base64.cpp -o ramp_base64.o
>> g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c ramp.cpp -o ramp.o
>> g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c rampR.cpp -o rampR.o
>> gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c util.c -o util.o
>> gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c xcms.c -o xcms.o
>> g++-4.2 -arch ppc -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o xcms.so obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o obiwarp/xcms_obiwarp.o mzClust_hclust.o mzROI.o netCDF.o ramp_base64.o ramp.o rampR.o util.o xcms.o -L/usr/local/lib -L/sw/lib -lnetcdf -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
>> ld: warning in obiwarp/mat.o, file is not of required architecture
>> ld: warning in obiwarp/vec.o, file is not of required architecture
>> ld: warning in obiwarp/xcms_dynprog.o, file is not of required architecture
>> ld: warning in obiwarp/xcms_lmat.o, file is not of required architecture
>> ld: warning in obiwarp/xcms_obiwarp.o, file is not of required architecture
>>
>> As you can see, the obiwarp part is build for 32 bit, only.
>>
>> As a result you get this kind of error message on Mac's when trying to
>> use obiwarp:
>> Error in .Call("R_set_from_xcms", valscantime1, scantime1, mzval,
>> mz, :
>> C symbol name "R_set_from_xcms" not in load table
>>
>> (defined in src/obiwarp/xcms_obiwarp.cpp:extern "C" SEXP
>> R_set_from_xcms(SEXP valscantime, SEXP scantime, SEXP mzrange, SEXP
>> mz, SEXP intensity)
>>
>> It builds correctly (for the main architecture, only)
>> when the --no-multiarch option is used for R CMD INSTALL.
>>
>>
>> Any Mac build gurus out there ?
>>
> ######################################################################################
> # This is Patrick's answer from last year, which I can't find
> # in any of the public archives:
> #
>
> On Fri, 2009-04-24 at 09:54 -0700, Patrick Aboyoun wrote:
>
>> Steffen,
>> Per Brian suggestion I changed the build universal binary script on the
>> BioC Mac OS X nodes to use the (variable regulated) command
>>
>> R_ARCH=/$arch $R_CMD CMD INSTALL --preclean --library="$R_LIBS"
>> --libs-only "$srcpkg_filepath"
>>
>> The addition of the --preclean flag solved the problem. There are other
>> BioC packages with similar issues that need to be cleaned out now in a
>> similar manner, but it appears that BioC packages with embedded source
>> libraries no longer have to concern themselves with multi-architecture
>> builds. (Problems will still exist for packages that expect the Mac OS X
>> machines to have pre-built multi-architecture shared libraries, but that
>> is another issue.)
>>
>>
>> Patrick
>>
>>
>> Steffen Neumann wrote:
>>
>>> Hi,
>>>
>>> the problem we (Patrick) solved with "all: clean $(SHLIB)"
>>> was that we have a subdirectory "xcms/src/obiwarp"
>>> which contains *.c files and *.o fies after "make all".
>>>
>>> BUT because MacOS BioC is building i386/PPC/PPC64 consecutively,
>>> and presumably calling something like
>>>
>>> make clean
>>> for ARCH in (i386 ppc ppc64) {
>>> make all
>>> }
>>>
>>> and *not*
>>>
>>> for ARCH in (i386 ppc ppc64) {
>>> make clean
>>> make all
>>> }
>>>
>>> we had linker warnings in http://bioconductor.org/.../xcms/pelham-buildsrc.html
>>> about those leftover *.o in the obiwarp subdirectory:
>>>
>>> g++-4.2 -arch ppc -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o xcms.so obiwarp/cmdparser.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o obiwarp/xcms_obiwarp.o mzClust_hclust.o mzROI.o netCDF.o ramp_base64.o ramp.o rampR.o util.o xcms.o -L/usr/local/lib -L/sw/lib -lnetcdf -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
>>>
>>>
>>>> ld: warning in obiwarp/cmdparser.o, file is not of required architecture
>>>> ld: warning in obiwarp/mat.o, file is not of required architecture
>>>>
>>>>
>>> I am happy to get suggestions for a better solution,
>>> which 1) allows to organise C sources in subdirectories
>>> and 2) works with multiple Arch builds. Maybe these
>>> multiarch builds need to call make clean explicitely inbetween ?
>>>
>>> Yours,
>>> Steffen
>>>
>>>
>>>
>>
>
>
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