Hello Andreas, I have fixed the problem in trunk's Makefile.incl. Please note that we're still waiting for another fix to get trunk working again; as you know, trunk is the "bleeding edge" and not guaranteed to build.
It seems that on Ubuntu, make and/or make's shell incorrectly interprets redirections (stderr, stdout ) which use '&' as the 'background' directive. I've simplly taken them out and things work fine now. Previously, make was executing shell commands out-of- sequence. Also, this fixes the strange behavior in which you would see the shell prompt again, but the build was not really complete done. And I've also taken the opportunity to update our included sqlite3 to the latest, 3.6.15. You'll either need to do a "make distclean" (always a good idea with big trunk changes) or manually rm build/linux/libsqlite3.a, and then "make all". -Natalie On Jun 24, 2009, at 11:31 AM, andreas quandt wrote: > > hi brian, > > i tried the compilation but it fails with sqlite-3.6.11: > do you have potentially any suggestion what the cause might be? > > > cheers, > andreas > > building SQLite3 library > cp > /usr/local/src/tpp-trunk-rev4391/src/../extern/sqlite-3.6.11/.libs/ > libsqlite3.a > /usr/local/src/tpp-trunk-rev4391/src/../build/linux/libsqlite3.a > cp: cannot stat > `/usr/local/src/tpp-trunk-rev4391/src/../extern/sqlite-3.6.11/.libs/ > libsqlite3.a': > No such file or directory > make: *** > [/usr/local/src/tpp-trunk-rev4391/src/../build/linux/libsqlite3.a] > Error 1 > make[1]: Entering directory > `/usr/local/src/tpp-trunk-rev4391/extern/sqlite-3.6.11' > r...@neo:/usr/local/src/tpp-trunk-rev4391/src# rm -f sqlite3 sqlite3 > test -z "libsqlite3.la" || rm -f libsqlite3.la > rm -f "./so_locations" > rm -rf .libs _libs > rm -f *.o > rm -f *.lo > if /bin/bash ./libtool --tag=CC --mode=compile gcc > -DPACKAGE_NAME=\"sqlite\" -DPACKAGE_TARNAME=\"sqlite\" > -DPACKAGE_VERSION=\"3.6.11\" -DPACKAGE_STRING=\"sqlite\ 3.6.11\" > -DPACKAGE_BUGREPORT=\"http://www.sqlite.org\"; -DPACKAGE=\"sqlite\" > -DVERSION=\"3.6.11\" -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 - > DHAVE_FDATASYNC=1 > -DHAVE_USLEEP=1 -DHAVE_LOCALTIME_R=1 -DHAVE_GMTIME_R=1 -I. -I. > -DSQLITE_THREADSAFE=1 -g -O2 -MT sqlite3.lo -MD -MP -MF > ".deps/sqlite3.Tpo" -c -o sqlite3.lo sqlite3.c; \ > then mv -f ".deps/sqlite3.Tpo" ".deps/sqlite3.Plo"; else rm -f > ".deps/sqlite3.Tpo"; exit 1; fi > checking for a BSD-compatible install... /usr/bin/install -c > checking whether build environment is sane... mkdir .libs > gcc -DPACKAGE_NAME=\"sqlite\" -DPACKAGE_TARNAME=\"sqlite\" > -DPACKAGE_VERSION=\"3.6.11\" "-DPACKAGE_STRING=\"sqlite 3.6.11\"" > -DPACKAGE_BUGREPORT=\"http://www.sqlite.org\"; -DPACKAGE=\"sqlite\" > -DVERSION=\"3.6.11\" -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 - > DHAVE_FDATASYNC=1 > -DHAVE_USLEEP=1 -DHAVE_LOCALTIME_R=1 -DHAVE_GMTIME_R=1 -I. -I. > -DSQLITE_THREADSAFE=1 -g -O2 -MT sqlite3.lo -MD -MP -MF > .deps/sqlite3.Tpo -c sqlite3.c -fPIC -DPIC -o .libs/sqlite3.o > yes > checking for gawk... gawk > checking whether make sets $(MAKE)... yes > checking for style of include used by make... GNU > checking for gcc... gcc > checking for C compiler default output file name... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ISO C89... none needed > checking dependency style of gcc... gcc3 > checking for special C compiler options needed for large files... no > checking for _FILE_OFFSET_BITS value needed for large files... no > checking for gcc... (cached) gcc > checking whether we are using the GNU C compiler... (cached) yes > checking whether gcc accepts -g... (cached) yes > checking for gcc option to accept ISO C89... (cached) none needed > checking dependency style of gcc... (cached) gcc3 > checking for ranlib... ranlib > checking build system type... x86_64-unknown-linux-gnu > checking host system type... x86_64-unknown-linux-gnu > checking for a sed that does not truncate output... /bin/sed > checking for grep that handles long lines and -e... /bin/grep > checking for egrep... /bin/grep -E > checking for ld used by gcc... /usr/bin/ld > checking if the linker (/usr/bin/ld) is GNU ld... yes > checking for /usr/bin/ld option to reload object files... -r > checking for BSD-compatible nm... /usr/bin/nm -B > checking whether ln -s works... yes > checking how to recognise dependent libraries... pass_all > checking how to run the C preprocessor... gcc -E > checking for ANSI C header files... yes > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking dlfcn.h usability... yes > checking dlfcn.h presence... yes > checking for dlfcn.h... yes > checking for g++... g++ > checking whether we are using the GNU C++ compiler... yes > checking whether g++ accepts -g... yes > checking dependency style of g++... gcc3 > checking how to run the C++ preprocessor... g++ -E > checking for g77... no > checking for xlf... no > checking for f77... no > checking for frt... no > checking for pgf77... no > checking for cf77... no > checking for fort77... no > checking for fl32... no > checking for af77... no > checking for xlf90... no > checking for f90... no > checking for pgf90... no > checking for pghpf... no > checking for epcf90... no > checking for gfortran... gfortran > checking whether we are using the GNU Fortran 77 compiler... yes > checking whether gfortran accepts -g... yes > checking the maximum length of command line arguments... 32768 > checking command to parse /usr/bin/nm -B output from gcc object... ok > checking for objdir... .libs > checking for ar... ar > checking for ranlib... (cached) ranlib > checking for strip... strip > checking if gcc supports -fno-rtti -fno-exceptions... no > checking for gcc option to produce PIC... -fPIC > checking if gcc PIC flag -fPIC works... yes > checking if gcc static flag -static works... yes > checking if gcc supports -c -o file.o... yes > checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports > shared libraries... yes > checking whether -lc should be explicitly linked in... no > checking dynamic linker characteristics... GNU/Linux ld.so > checking how to hardcode library paths into programs... immediate > checking whether stripping libraries is possible... yes > checking if libtool supports shared libraries... yes > checking whether to build shared libraries... yes > checking whether to build static libraries... yes > configure: creating libtool > appending configuration tag "CXX" to libtool > checking for ld used by g++... /usr/bin/ld -m elf_x86_64 > checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes > checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports > shared libraries... yes > checking for g++ option to produce PIC... -fPIC > checking if g++ PIC flag -fPIC works... yes > checking if g++ static flag -static works... yes > checking if g++ supports -c -o file.o... yes > checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports > shared libraries... yes > checking dynamic linker characteristics... GNU/Linux ld.so > checking how to hardcode library paths into programs... immediate > appending configuration tag "F77" to libtool > checking if libtool supports shared libraries... yes > checking whether to build shared libraries... yes > checking whether to build static libraries... yes > checking for gfortran option to produce PIC... -fPIC > checking if gfortran PIC flag -fPIC works... yes > checking if gfortran static flag -static works... yes > checking if gfortran supports -c -o file.o... yes > checking whether the gfortran linker (/usr/bin/ld -m elf_x86_64) > supports shared libraries... yes > checking dynamic linker characteristics... GNU/Linux ld.so > checking how to hardcode library paths into programs... immediate > checking for fdatasync... yes > checking for usleep... yes > checking for fullfsync... no > checking for localtime_r... yes > checking for gmtime_r... yes > checking for library containing tgetent... no > checking for library containing readline... no > checking for readline... no > checking for library containing pthread_create... -lpthread > checking for library containing dlopen... -ldl > checking for whether to support dynamic extensions... yes > configure: creating ./config.status > config.status: creating Makefile > config.status: creating sqlite3.pc > config.status: executing depfiles commands > Assembler messages: > Fatal error: can't create .libs/sqlite3.o: No such file or directory > make[1]: *** [sqlite3.lo] Error 1 > make[1]: Leaving directory > `/usr/local/src/tpp-trunk-rev4391/extern/sqlite-3.6.11' > > > > Brian Pratt wrote: >> Customizing the makefile.config.incl is usually not necessary, and >> when it >> is it's because a system is unusual so there's not really any >> standard >> advice I can offer. >> >> BTW trunk is just plain broken at the moment (developer forgot to >> add a >> newly created file) - I've alerted the developer responsible for >> the error >> and I'm sure it will be corrected soonest. For the moment, add "-R >> 4391" to >> your subversion statement to grab the code from just before the >> change that >> broke the build. >> >> From there a "make all install" should be all you need. >> Conceivably you'll >> hit some bumps due to gcc version, I'm not sure what ubuntu 9.04 >> ships with. >> >> Brian >> >> -----Original Message----- >> From: [email protected] >> [mailto:[email protected]] On Behalf Of andreas >> quandt >> Sent: Wednesday, June 24, 2009 9:28 AM >> To: [email protected] >> Subject: [spctools-discuss] Re: building tpp from svn (rev 4395) on >> ubuntu >> 9.04 >> >> >> hey brian, >> >> thanks for the fast reply. >> also it would be great if you could send me a short howto for >> compiling >> from trunk as i am not sure if it is still necessary to create >> Makefile.config.incl and to define its content respectively. >> >> many thanks in advance (again), >> andreas >> >> >> Brian Pratt wrote: >> >>> Hi Andreas, >>> >>> You shouldn't need to mess with Boost config any more, TPP builds >>> its own >>> copy for stability. >>> >>> I'm hitting the same issue (such is life on the bleeding edge with >>> trunk), >>> let me have a quick go at cleaning it up... >>> >>> Brian >>> >>> -----Original Message----- >>> From: [email protected] >>> [mailto:[email protected]] On Behalf Of andreas >>> quandt >>> Sent: Wednesday, June 24, 2009 8:35 AM >>> To: [email protected] >>> Subject: [spctools-discuss] building tpp from svn (rev 4395) on >>> ubuntu >>> >> 9.04 >> >>> dear list, >>> >>> i would like to test the trunk version of the tpp but have some >>> trouble >>> to build it. >>> i was following the instructions for the installation of 4.2.1 on >>> ubuntu >>> 9.04 (specifying the latest boost library in the >>> Makefile.config.incl) >>> but get following error during the compilation process: >>> >>> In file included from >>> ./Validation/DiscriminateFunction/DiscrimValMixtureDistr.h:6, >>> from ./Validation/MixtureModel/MixtureModel.h:14, >>> from >>> Validation/PeptideProphet/PeptideProphetParser/ >>> PeptideProphetParser.h:47, >>> from >>> >>> >> Validation/PeptideProphet/PeptideProphetParser/ >> PeptideProphetParserMain.cxx: >> >>> 2: >>> ./Validation/Distribution/NonParametricDistribution.h:84: error: >>> 'Fit' >>> has not been declared >>> ./Validation/Distribution/NonParametricDistribution.h:85: error: >>> expected ';' before '(' token >>> ./Validation/Distribution/NonParametricDistribution.h:86: error: >>> expected ';' before '(' token >>> ./Validation/Distribution/NonParametricDistribution.h:87: error: >>> expected ';' before '(' token >>> ./Validation/Distribution/NonParametricDistribution.h:90: error: >>> 'Fit' >>> has not been declared >>> ./Validation/Distribution/NonParametricDistribution.h:92: error: >>> 'Fit' >>> has not been declared >>> ./Validation/Distribution/NonParametricDistribution.h:94: error: >>> 'Fit' >>> has not been declared >>> ./Validation/Distribution/NonParametricDistribution.h:106: error: >>> ISO >>> C++ forbids declaration of 'Fit' with no type >>> ./Validation/Distribution/NonParametricDistribution.h:106: error: >>> expected ';' before '*' token >>> ./Validation/Distribution/NonParametricDistribution.h:107: error: >>> ISO >>> C++ forbids declaration of 'Fit' with no type >>> ./Validation/Distribution/NonParametricDistribution.h:107: error: >>> expected ';' before '*' token >>> In file included from >>> ./Validation/MixtureDistribution/ >>> AccurateMassDiffDiscrMixtureDistr.h:7, >>> from ./Validation/MixtureModel/MixtureModel.h:23, >>> from >>> Validation/PeptideProphet/PeptideProphetParser/ >>> PeptideProphetParser.h:47, >>> from >>> >>> >> Validation/PeptideProphet/PeptideProphetParser/ >> PeptideProphetParserMain.cxx: >> >>> 2: >>> ./Validation/InterProphet/InterProphetParser/KDModel.h:118: error: >>> ISO >>> C++ forbids declaration of 'Fit' with no type >>> ./Validation/InterProphet/InterProphetParser/KDModel.h:118: error: >>> expected ';' before '*' token >>> ./Validation/InterProphet/InterProphetParser/KDModel.h:119: error: >>> ISO >>> C++ forbids declaration of 'Fit' with no type >>> ./Validation/InterProphet/InterProphetParser/KDModel.h:119: error: >>> expected ';' before '*' token >>> make[1]: *** >>> >>> >> [/usr/local/src/tpp-trunk-rev4395/src/../build/linux/ >> PeptideProphetParserMai >> >>> n.o] >>> Error 1 >>> make[1]: Leaving directory `/usr/local/src/tpp-trunk-rev4395/src' >>> make: *** [default] Error 2 >>> >>> >>> does anyone might have an idea what i am doing wrong? >>> and furthermore, i would like to ask if it is still necessary to >>> build >>> the boost library separately and to set the Makefile.config.incl? >>> if not, i would very much appreciate if one of you could send me a >>> brief >>> howto as i did not find any further information about this on the >>> spc-wiki... >>> >>> >>> many thanks in advance for any kind of help! >>> >>> cheers, >>> andreas >>> >>> >>> >>> >>> >>> >>> >>> >> >> >> >> >> >>> >> > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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