hey brian, i still generated the file as this was (at least for 4.3.1) mandatory for us. however i will check for the next compilation round if i can skip this part of the installation procedure. also i was now able to compile successfully after i made sure to use the old gcc version (4.1).
thanks again for all the help! cheers, andreas On Wed, Feb 9, 2011 at 8:23 PM, Brian Pratt <[email protected]>wrote: > 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. > 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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