On the server, another type of flex related err: :o( Martin Making install in io make[2]: Entering directory `/home/maasha/maasha_install/tmp/mira-3rc2/src/io' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3rc2\" -DPACKAGE_STRING=\"mira\ 3rc2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3rc2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -DENABLE64=1 -I. -I../ -DPUBLICQUIET -DAJ_Linux64 -O3 -funroll-loops -pthread -I/home/maasha/maasha_install/include/boost-1_39 -MT gbf.o -MD -MP -MF .deps/gbf.Tpo -c -o gbf.o gbf.C In file included from ../io/gbf.H:38, from gbf.C:28: ../io/exp.H:49:23: error: FlexLexer.h: No such file or directory ../io/exp.H:163: error: ‘FlexLexer’ has not been declared ../io/exp.H:164: error: ‘FlexLexer’ has not been declared make[2]: *** [gbf.o] Error 1 make[2]: Leaving directory `/home/maasha/maasha_install/tmp/mira-3rc2/src/io' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/home/maasha/maasha_install/tmp/mira-3rc2/src' make: *** [install-recursive] Error 1 On Thu, Aug 13, 2009 at 12:04 PM, Martin A. Hansen <mail@xxxxxxxxx> wrote: > Nay, still problems :o( > > Anyway, I was just playing around trying to install MIRA on my Mac, but now > I am going to try the Linux server. > > > Martin > > > maasha@cletus:/tmp/mira-3rc2$ make > Making all in src > Making all in lec > make[2]: Nothing to be done for `all'. > Making all in io > make[2]: Nothing to be done for `all'. > Making all in stdinc > make[2]: Nothing to be done for `all'. > Making all in errorhandling > make[2]: Nothing to be done for `all'. > Making all in util > make[2]: Nothing to be done for `all'. > Making all in mira > make[2]: Nothing to be done for `all'. > Making all in EdIt > make[2]: Nothing to be done for `all'. > Making all in caf > make[2]: Nothing to be done for `all'. > Making all in examine > make[2]: Nothing to be done for `all'. > Making all in knn_abi373 > make[2]: Nothing to be done for `all'. > Making all in knn_alf > make[2]: Nothing to be done for `all'. > Making all in examples_programming > /bin/sh ../../libtool --tag=CXX --mode=link g++ -pthread > -I/tmp/fisk//include/boost-1_39 -DPUBLICQUIET -O2 -pthread > -I/tmp/fisk//include/boost-1_39 -L../io/ -L../util/ -L../errorhandling/ > -L../mira -L../examine/ -L../EdIt/ -L../caf/ -L../knn_abi373 -L../knn_alf > -L/tmp/fisk//lib -L/tmp/fisk//lib -lboost_thread-xgcc40-mt-1_39 -o mira_101 > mira_101.o -lmira -lEdIt -lExamine -lmsupport -lestass -lerrorhandling > -lutil -ldptools -lfio -lcaf -lKNN_abi373 -lm -lexpat -lz > -lboost_thread-xgcc40-mt-1_39 > libtool: link: g++ -pthread -I/tmp/fisk//include/boost-1_39 -DPUBLICQUIET > -O2 -pthread -I/tmp/fisk//include/boost-1_39 -o mira_101 mira_101.o > -Wl,-bind_at_load -L/tmp/mira-3rc2/src/io -L/tmp/mira-3rc2/src/util > -L/tmp/mira-3rc2/src/errorhandling -L/tmp/mira-3rc2/src/mira > -L/tmp/mira-3rc2/src/examine -L/tmp/mira-3rc2/src/EdIt > -L/tmp/mira-3rc2/src/caf -L/tmp/mira-3rc2/src/knn_abi373 > -L/tmp/mira-3rc2/src/knn_alf -L/tmp/fisk//lib -lmira -lEdIt -lExamine > -lmsupport -lestass -lerrorhandling -lutil -ldptools -lfio -lcaf > -lKNN_abi373 -lm /usr/lib/libexpat.dylib -lz -lboost_thread-xgcc40-mt-1_39 > -pthread > Undefined symbols: > "byteToHumanReadableSize(double, std::basic_ostream<char, > std::char_traits<char> >&)", referenced from: > Assembly::dmi_dumpALine(std::basic_ostream<char, > std::char_traits<char> >&, char const*, unsigned long, unsigned long, > unsigned long, unsigned long)in libmira.a(assembly.o) > Assembly::dmi_dumpALine(std::basic_ostream<char, > std::char_traits<char> >&, char const*, unsigned long, unsigned long, > unsigned long, unsigned long)in libmira.a(assembly.o) > Assembly::dmi_dumpALine(std::basic_ostream<char, > std::char_traits<char> >&, char const*, unsigned long, unsigned long, > unsigned long, unsigned long)in libmira.a(assembly.o) > Assembly::dumpMemInfo() in libmira.a(assembly.o) > Assembly::dumpMemInfo() in libmira.a(assembly.o) > Assembly::loadAlignmentsFromFile(int, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >)in libmira.a(assembly.o) > "dateStamp(std::basic_ostream<char, std::char_traits<char> >&)", > referenced from: > Assembly::loadExternalSCFQualities() in libmira.a(assembly_io.o) > Assembly::loadSequenceData() in libmira.a(assembly_io.o) > Assembly::loadSequenceData() in libmira.a(assembly_io.o) > Assembly::loadSequenceData() in libmira.a(assembly_io.o) > Assembly::loadSequenceData() in libmira.a(assembly_io.o) > Assembly::saveResults() in libmira.a(assembly.o) > Assembly::saveResults() in libmira.a(assembly.o) > Assembly::saveResults() in libmira.a(assembly.o) > Assembly::saveResults() in libmira.a(assembly.o) > Assembly::saveResults() in libmira.a(assembly.o) > Assembly::saveResults() in libmira.a(assembly.o) > Assembly::saveResults() in libmira.a(assembly.o) > Assembly::saveResults() in libmira.a(assembly.o) > Assembly::saveResults() in libmira.a(assembly.o) > Assembly::saveResults() in libmira.a(assembly.o) > Assembly::saveResults() in libmira.a(assembly.o) > Assembly::saveResults() in libmira.a(assembly.o) > Assembly::saveResults() in libmira.a(assembly.o) > Assembly::huntPossibleContigJoinGrinches(int, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >)in libmira.a(assembly.o) > Assembly::huntPossibleContigJoinGrinches(int, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >)in libmira.a(assembly.o) > Assembly::buildFirstContigs(int, EDITParameters const&, bool)in > libmira.a(assembly.o) > Assembly::buildFirstContigs(int, EDITParameters const&, bool)in > libmira.a(assembly.o) > Assembly::buildFirstContigs(int, EDITParameters const&, bool)in > libmira.a(assembly.o) > Assembly::buildFirstContigs(int, EDITParameters const&, bool)in > libmira.a(assembly.o) > Assembly::buildFirstContigs(int, EDITParameters const&, bool)in > libmira.a(assembly.o) > Assembly::buildFirstContigs(int, EDITParameters const&, bool)in > libmira.a(assembly.o) > Assembly::buildFirstContigs(int, EDITParameters const&, bool)in > libmira.a(assembly.o) > Assembly::buildFirstContigs(int, EDITParameters const&, bool)in > libmira.a(assembly.o) > Assembly::buildFirstContigs(int, EDITParameters const&, bool)in > libmira.a(assembly.o) > Assembly::buildFirstContigs(int, EDITParameters const&, bool)in > libmira.a(assembly.o) > Assembly::buildFirstContigs(int, EDITParameters const&, bool)in > libmira.a(assembly.o) > Assembly::buildFirstContigs(int, EDITParameters const&, bool)in > libmira.a(assembly.o) > Assembly::loadAlignmentsFromFile(int, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >)in libmira.a(assembly.o) > Assembly::loadAlignmentsFromFile(int, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >)in libmira.a(assembly.o) > Assembly::loadAlignmentsFromFile(int, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >)in libmira.a(assembly.o) > Assembly::loadAlignmentsFromFile(int, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >)in libmira.a(assembly.o) > Assembly::reduceSkimHits2(int, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >)in libmira.a(assembly.o) > Assembly::reduceSkimHits2(int, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >)in libmira.a(assembly.o) > Assembly::reduceSkimHits2(int, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >)in libmira.a(assembly.o) > Assembly::reduceSkimHits2(int, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >)in libmira.a(assembly.o) > Assembly::reduceSkimHits2(int, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >)in libmira.a(assembly.o) > Assembly::reduceSkimHits2(int, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >)in libmira.a(assembly.o) > Assembly::reduceSkimHits2(int, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >)in libmira.a(assembly.o) > Assembly::findPossibleOverlaps(int, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >)in libmira.a(assembly.o) > Assembly::makeAlignments(bool (*)(Assembly&, int, int), bool, bool, > int, std::basic_string<char, std::char_traits<char>, std::allocator<char> >, > std::basic_string<char, std::char_traits<char>, std::allocator<char> >, > std::basic_string<char, std::char_traits<char>, std::allocator<char> >)in > libmira.a(assembly.o) > Assembly::makeAlignments(bool (*)(Assembly&, int, int), bool, bool, > int, std::basic_string<char, std::char_traits<char>, std::allocator<char> >, > std::basic_string<char, std::char_traits<char>, std::allocator<char> >, > std::basic_string<char, std::char_traits<char>, std::allocator<char> >)in > libmira.a(assembly.o) > Assembly::makeAlignments(bool (*)(Assembly&, int, int), bool, bool, > int, std::basic_string<char, std::char_traits<char>, std::allocator<char> >, > std::basic_string<char, std::char_traits<char>, std::allocator<char> >, > std::basic_string<char, std::char_traits<char>, std::allocator<char> >)in > libmira.a(assembly.o) > Assembly::calcPossibleSeqVectorClipoffs(int, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >)in > libmira.a(dataprocessing.o) > Assembly::correctContigs() in libmira.a(dataprocessing.o) > Assembly::extendADS(int, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >)in > libmira.a(dataprocessing.o) > Assembly::performNewProposedCutbackClips(std::basic_string<char, > std::char_traits<char>, std::allocator<char> > const&, > std::basic_string<char, std::char_traits<char>, std::allocator<char> > > const&)in libmira.a(dataprocessing.o) > assout::saveAssemblyInfo(AssemblyInfo&, std::basic_string<char, > std::char_traits<char>, std::allocator<char> > const&, bool)in > libmsupport.a(assembly_output.o) > ReadPool::makeTemplateIDs() in libmsupport.a(readpool.o) > ReadPool::makeStrainIDs() in libmsupport.a(readpool.o) > Skim::skimGo(ReadPool&, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >&, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >&, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >&, > std::vector<std::set<unsigned int, std::less<unsigned int>, > std::allocator<unsigned int> >, std::allocator<std::set<unsigned int, > std::less<unsigned int>, std::allocator<unsigned int> > > >&, > std::vector<unsigned int, std::allocator<unsigned int> >&, > std::vector<unsigned int, std::allocator<unsigned int> >&, std::vector<int, > std::allocator<int> >&, std::vector<int, std::allocator<int> >&, unsigned > int, unsigned int, bool, unsigned char, unsigned char, std::vector<int, > std::allocator<int> > const&, std::vector<int, std::allocator<int> > const&, > unsigned int)in libmira.a(skim.o) > Skim::skimGo(ReadPool&, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >&, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >&, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >&, > std::vector<std::set<unsigned int, std::less<unsigned int>, > std::allocator<unsigned int> >, std::allocator<std::set<unsigned int, > std::less<unsigned int>, std::allocator<unsigned int> > > >&, > std::vector<unsigned int, std::allocator<unsigned int> >&, > std::vector<unsigned int, std::allocator<unsigned int> >&, std::vector<int, > std::allocator<int> >&, std::vector<int, std::allocator<int> >&, unsigned > int, unsigned int, bool, unsigned char, unsigned char, std::vector<int, > std::allocator<int> > const&, std::vector<int, std::allocator<int> > const&, > unsigned int)in libmira.a(skim.o) > Skim::analyseHashes(ReadPool&, bool, unsigned char, unsigned char, > unsigned int, std::basic_string<char, std::char_traits<char>, > std::allocator<char> > const&)in libmira.a(skim.o) > "dumpFile(char const*, std::basic_ostream<char, std::char_traits<char> > >&)", referenced from: > Assembly::dumpMemInfo() in libmira.a(assembly.o) > Assembly::dumpMemInfo() in libmira.a(assembly.o) > "splitFullPathAndFileName(std::basic_string<char, std::char_traits<char>, > std::allocator<char> > const&, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >&, std::basic_string<char, > std::char_traits<char>, std::allocator<char> >&)", referenced from: > ReadPool::mergeXMLTraceInfo(std::basic_string<char, > std::char_traits<char>, std::allocator<char> > const&)in > libmsupport.a(readpool.o) > "editContigBack(Contig&, EDITParameters&)", referenced from: > Assembly::buildFirstContigs(int, EDITParameters const&, bool)in > libmira.a(assembly.o) > Assembly::correctContigs() in libmira.a(dataprocessing.o) > "EDITParameters::EDITParameters()", referenced from: > Assembly::assemble() in libmira.a(assembly.o) > Assembly::correctContigs() in libmira.a(dataprocessing.o) > "EDITParameters::~EDITParameters()", referenced from: > Assembly::assemble() in libmira.a(assembly.o) > Assembly::assemble() in libmira.a(assembly.o) > Assembly::assemble() in libmira.a(assembly.o) > Assembly::correctContigs() in libmira.a(dataprocessing.o) > Assembly::correctContigs() in libmira.a(dataprocessing.o) > "diffsuseconds(timeval&)", referenced from: > Pathfinder::n4_buildContigStartWithStrongGood(std::vector<Align, > std::allocator<Align> >&, int, Contig&)in libmira.a(newpathfinder.o) > Pathfinder::n4_buildContigStartWithStrongGood(std::vector<Align, > std::allocator<Align> >&, int, Contig&)in libmira.a(newpathfinder.o) > Pathfinder::n4_buildContigStartWithStrongGood(std::vector<Align, > std::allocator<Align> >&, int, Contig&)in libmira.a(newpathfinder.o) > Pathfinder::buildContig(std::vector<Align, std::allocator<Align> >&, > int, Contig&)in libmira.a(newpathfinder.o) > Pathfinder::buildContig(std::vector<Align, std::allocator<Align> >&, > int, Contig&)in libmira.a(newpathfinder.o) > Pathfinder::buildContig(std::vector<Align, std::allocator<Align> >&, > int, Contig&)in libmira.a(newpathfinder.o) > "conditionalStrCpy(char const*)", referenced from: > Notify::Notify(unsigned char, char const*)in > liberrorhandling.a(errorhandling.o) > Notify::Notify(unsigned char, char const*, char const*)in > liberrorhandling.a(errorhandling.o) > Notify::Notify(unsigned char, char const*, char const*)in > liberrorhandling.a(errorhandling.o) > Notify::Notify(unsigned char, char const*, char const*, char > const*)in liberrorhandling.a(errorhandling.o) > Notify::Notify(unsigned char, char const*, char const*, char > const*)in liberrorhandling.a(errorhandling.o) > Notify::Notify(unsigned char, char const*, char const*, char > const*)in liberrorhandling.a(errorhandling.o) > Notify::operator=(Notify const&)in > liberrorhandling.a(errorhandling.o) > Notify::operator=(Notify const&)in > liberrorhandling.a(errorhandling.o) > Notify::operator=(Notify const&)in > liberrorhandling.a(errorhandling.o) > ReadPool::makeTemplateIDs() in libmsupport.a(readpool.o) > Contig::operator=(Contig const&)in libmsupport.a(contig.o) > "avg_suseconds(std::vector<int, std::allocator<int> >&)", referenced > from: > Pathfinder::n4_buildContigStartWithStrongGood(std::vector<Align, > std::allocator<Align> >&, int, Contig&)in libmira.a(newpathfinder.o) > Pathfinder::n4_buildContigStartWithStrongGood(std::vector<Align, > std::allocator<Align> >&, int, Contig&)in libmira.a(newpathfinder.o) > Pathfinder::n4_buildContigStartWithStrongGood(std::vector<Align, > std::allocator<Align> >&, int, Contig&)in libmira.a(newpathfinder.o) > Pathfinder::buildContig(std::vector<Align, std::allocator<Align> >&, > int, Contig&)in libmira.a(newpathfinder.o) > Pathfinder::buildContig(std::vector<Align, std::allocator<Align> >&, > int, Contig&)in libmira.a(newpathfinder.o) > Pathfinder::buildContig(std::vector<Align, std::allocator<Align> >&, > int, Contig&)in libmira.a(newpathfinder.o) > ld: symbol(s) not found > collect2: ld returned 1 exit status > make[2]: *** [mira_101] Error 1 > make[1]: *** [all-recursive] Error 1 > make: *** [all-recursive] Error 1 > > On Thu, Aug 13, 2009 at 11:29 AM, Bastien Chevreux <bach@xxxxxxxxxxxx>wrote: > >> > From: Martin A. Hansen >> > I am battling to compile MIRA against a locally compiled version of >> libboost. >> > [...] >> > exp_flexer.flex.C >> > exp_flexer.flex.C:324: error: no 'int EXPFlexLexer::yywrap()' member >> function declared in class 'EXPFlexLexer' >> > make[2]: *** [exp_flexer.flex.o] Error 1 >> > make[1]: *** [all-recursive] Error 1 >> > make: *** [all-recursive] Error 1 >> > This is a Mac Intel running OSX 10.5.7 >> >> Hello Martin, >> >> that's fortunately not a problem with boost, but something I discovered >> myself only beginning of this week: the mira source package is distributed >> with pre-flexed source files ... which should not happen. I've corrected >> that in the current development tree and this will ship in the next release. >> >> In the mean time, the solution for you is fortunately pretty simple: in >> the top directory of mira, do the following >> >> find . -name "*.flex.C" -exec rm -f {} \; >> >> This particular problem should then be solved and you can run make. I'll >> cross fingers for it to link, this has been pretty difficult in the past on >> OSX. >> >> Regards, >> Bastien >> >> >> -- >> You have received this mail because you are subscribed to the mira_talk >> mailing list. For information on how to subscribe or unsubscribe, please >> visit http://www.chevreux.org/mira_mailinglists.html >> > >