Normally one doesn't have to do anything at all with the Makefile.config.incl file. I'd suspect that the changes you're making there are only driving you further into the woods. What happens when you start with that file empty?
On Wed, Feb 9, 2011 at 9:25 AM, Andreas Quandt <[email protected]> wrote: > hey brian, > thanks for the update. > unfortunately this does not (fully) solve the compiling errors. > i had to 'fix' to other external programs (gsl-1.14 and fann-2.0.0/): > > cd trans_proteomic_pipeline/src > touch Makefile.config.incl > vim Makefile.config.incl > .... > TPP_ROOT=/cluster/apps/tpp/r5304/ > TPP_WEB=/tpp/ > ## for Boost > BOOST_INCL=-I/cluster/apps/tpp/r5304/boost/ > BOOST_LIBDIR=/cluster/apps/tpp/r5304/boost/lib > BOOST_LIBSPEC=-gcc43 > #BOOST_INCL=-I/opt/boost/ > #BOOST_LIBDIR=/opt/boost/lib > #BOOST_LIBSPEC=-gcc43 > LINK=shared > LIBEXT=so > PERL_LIB_CORE=/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE > .... > cd /cluster/apps/tpp/trans_proteomic_pipeline/src/../extern/gsl-1.14/ > ./configure > cd /cluster/apps/tpp/trans_proteomic_pipeline/src/../extern/fann-2.0.0/ > ./configure > > however now i am stuck with compiling parts of the boost library (although > it compiles successful when using ./build_dist.sh): > ...done building FANN library source > mkdir -p /cluster/apps/tpp/trans_proteomic_pipeline/src/../build/linux > building boost bjam... > ### > ### Using 'gcc' toolset. > ### > rm -rf bootstrap > mkdir bootstrap > gcc -o bootstrap/jam0 command.c compile.c debug.c expand.c glob.c hash.c > hdrmacro.c headers.c jam.c jambase.c jamgram.c lists.c make.c make1.c > newstr.c option.c output.c parse.c pathunix.c pathvms.c regexp.c rules.c > scan.c search.c subst.c timestamp.c variable.c modules.c strings.c filesys.c > builtins.c pwd.c class.c native.c w32_getreg.c modules/set.c modules/path.c > modules/regex.c modules/property-set.c modules/sequence.c modules/order.c > execunix.c fileunix.c > ./bootstrap/jam0 -f build.jam --toolset=gcc --toolset-root= clean > build.jam:174: in module scope > *** argument error > * rule toolset ( name command .type ? : opt.out + : opt.define * : flags * : > linklibs * ) > * called with: ( cc g++ -D__LINUX__ > -DDEFAULT_TPP_INSTALL_ROOT=\"/cluster/apps/tpp/r5304/\" > -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D__INTEL__ -DINLINING -DTPPLIB > -fPIC -I. -I/cluster/apps/tpp/trans_proteomic_pipeline/src/ > -I../extern/gzstream -I../extern/libarchive-2.2.7/libarchive > -I/cluster/apps/tpp/trans_proteomic_pipeline/src/../extern/expat-2.0.1/lib > -I/cluster/apps/tpp/trans_proteomic_pipeline/src/../extern/boost_1_39_0/boost > -I/cluster/apps/tpp/trans_proteomic_pipeline/src/../extern/boost_1_39_0/ > -I/cluster/apps/tpp/trans_proteomic_pipeline/src/../extern/fann-2.0.0//src/include/ > -I/cluster/apps/tpp/trans_proteomic_pipeline/src/../extern/gsl-1.14/ > -iprefix > /cluster/apps/tpp/trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz/ > -iwithprefix pwiz/data/msdata -iwithprefix pwiz/data > -I/cluster/apps/tpp/trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz > -iwithprefix pwiz -iwithprefix pwiz/utility/misc -iwithprefix > pwiz/utility/math > -I/cluster/apps/tpp/trans_proteomic_pipeline/src/../extern/boost_1_39_0/boost > -I/cluster/apps/tpp/trans_proteomic_pipeline/src/../extern/boost_1_39_0/ > -iwithprefix libraries/boost_aux > -I/cluster/apps/tpp/trans_proteomic_pipeline/src/Parsers/ramp -iwithprefix > libraries/libsvm-3.0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE > -DPWIZ_USER_VERSION_INFO_H=\"common/TPPVersion.h\" -Werror -Dlint -Wformat > -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts : -o : -D : -s -O : > ) > * extra argument -DDEFAULT_TPP_INSTALL_ROOT=\"/cluster/apps/tpp/r5304/\" > build.jam:138:see definition of rule 'toolset' being called > ...done building boost bjam > Error: Boost bjam build failed > make: *** > [/cluster/apps/tpp/trans_proteomic_pipeline/src/../extern/boost_1_39_0/tools/jam/src/bin.linuxx86_64/bjam] > Error 255 > could you or someone else probably point me in the right direction to fix > this? > also i am not sure if it is related but i switched to gcc 4.4.4. therefore, > do you think it might help adapting the Makefile.config.incl accordingly? > cheers, > andreas > On Sun, Feb 6, 2011 at 8:31 AM, Brian Pratt <[email protected]> > wrote: >> >> That single quote is certainly incorrect. I have fixed that, not sure >> if it also corrects your other issues but you should try again with >> r5304. >> >> Brian >> >> On Sat, Feb 5, 2011 at 10:03 AM, Andreas Quandt >> <[email protected]> wrote: >> > dear list, >> > i tried to comile the r5303 from the trunk repositor but unfortunately i >> > got >> > compiling errors. >> > here is what i did: >> > >> > svn -r 5303 co >> > >> > https://sashimi.svn.sourceforge.net/svnroot/sashimi/trunk/trans_proteomic_pipeline >> > trans_proteomic_pipeline >> > >> > cd trans_proteomic_pipeline/src >> > touch Makefile.config.incl >> > vim Makefile.config.incl >> > .... >> > TPP_ROOT=/cluster/apps/tpp/r5303/ >> > TPP_WEB=/tpp/ >> > ## for Boost >> > BOOST_INCL=-I/cluster/apps/tpp/r5303/boost/ >> > BOOST_LIBDIR=/cluster/apps/tpp/r5303/boost/lib >> > BOOST_LIBSPEC=-gcc43 >> > #BOOST_INCL=-I/opt/boost/ >> > #BOOST_LIBDIR=/opt/boost/lib >> > #BOOST_LIBSPEC=-gcc43 >> > LINK=shared >> > LIBEXT=so >> > PERL_LIB_CORE=/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE >> > .... >> > make 2>&1 | tee make.log >> > >> > and here the compilation error i got: >> > >> > checking for gcc... g++ -D__LINUX__ >> > -DDEFAULT_TPP_INSTALL_ROOT=\"/usr/local/tpp/\" -D_FILE_OFFSET_BITS=64 >> > -D_LARGEFILE_SOURCE -D__INTEL__ -DINLINING -DTPPLIB -fPIC -I. >> > -I/cluster/apps/tpp/trans_proteomic_pipeline/src/ -I../extern/gz >> > >> > stream -I../extern/libarchive-2.2.7/libarchive >> > >> > -I/cluster/apps/tpp/trans_proteomic_pipeline/src/../extern/expat-2.0.1/lib >> > >> > -I/cluster/apps/tpp/trans_proteomic_pipeline/src/../extern/boost_1_39_0/boost >> > -I/cluster/apps/tpp/trans_proteomic_p >> > >> > ipeline/src/../extern/boost_1_39_0/ >> > >> > -I/cluster/apps/tpp/trans_proteomic_pipeline/src/../extern/fann-2.0.0//src/include/ >> > -I/cluster/apps/tpp/trans_proteomic_pipeline/src/../extern/gsl-1.14/ >> > -iprefix /cluster/apps/tpp/trans_proteomic_pipe >> > >> > line/src/../extern/ProteoWizard/pwiz/ -iwithprefix pwiz/data/msdata >> > -iwithprefix pwiz/data >> > >> > -I/cluster/apps/tpp/trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz >> > -iwithprefix pwiz -iwithprefix pwiz/utility/misc -iwithprefix pwiz/ut >> > >> > ility/math >> > >> > -I/cluster/apps/tpp/trans_proteomic_pipeline/src/../extern/boost_1_39_0/boost >> > -I/cluster/apps/tpp/trans_proteomic_pipeline/src/../extern/boost_1_39_0/ >> > -iwithprefix libraries/boost_aux >> > -I/cluster/apps/tpp/trans_proteomic_pipeli >> > >> > ne/src/Parsers/ramp -iwithprefix libraries/libsvm-3.0 >> > -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE >> > -DPWIZ_USER_VERSION_INFO_H=\"common/TPPVersion.h\" -Werror -Dlint >> > -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts >> > >> > checking whether the C compiler works... no >> > >> > configure: error: in >> > `/cluster/apps/tpp/trans_proteomic_pipeline/extern/gsl-1.14': >> > >> > configure: error: C compiler cannot create executables >> > >> > See `config.log' for more details. >> > >> > make: *** >> > >> > [/cluster/apps/tpp/trans_proteomic_pipeline/src/../extern/gsl-1.14/Makefile] >> > Error 77 >> > >> > i checked back with our system administrators and the problem does not >> > seem >> > to come form the gcc (4.4.4) as gsl-1.14 compiles fine when done >> > separately. >> > however our experts pointed to possible problems in the makefile (such >> > as >> > the single "'") >> > >> > mkdir -p $(OBJ_ARCH)/PepcView ; \ >> > rm -f $(OBJ_ARCH)/PepcView/* ' \ >> > cp -f >> > >> > Quantitation/Pepc/PepcView/GWTCompilerOutputpepcview/com.insilicos.PepcView/* >> > $(OBJ_ARCH)/PepcView \ >> > >> > hence, i wanted to ask you if this might be the correct answer or if >> > there >> > is some other explanation that i cannot compile this version of the tpp? >> > many thanks for your help in advance, >> > andreas >> > >> > -- >> > You received this message because you are subscribed to the Google >> > Groups >> > "spctools-discuss" group. >> > To post to this group, send email to [email protected]. >> > To unsubscribe from this group, send email to >> > [email protected]. >> > For more options, visit this group at >> > http://groups.google.com/group/spctools-discuss?hl=en. >> > >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To post to this group, send email to [email protected]. >> To unsubscribe from this group, send email to >> [email protected]. >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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