Heh - got my wires crossed, you're working on ubuntu build issues, not msvc, but the message is the same: we'll get this sorted. Natalie is looking into the sqlite issue now.
Brian -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of andreas quandt Sent: Wednesday, June 24, 2009 11:44 AM To: [email protected] Subject: [spctools-discuss] Re: building tpp from svn (rev 4395) on ubuntu 9.04 awesome, many thanks brian! cheers, andreas Brian Pratt wrote: > I should note that while I do build with MSVC, I also build with MinGW/gcc > and you're probably just hitting things I missed in MSVC because I built > with gcc first (that was the case with the boost decompression, for > example). We'll work through this and get it cleaned up. > > Brian > > -----Original Message----- > From: Brian Pratt [mailto:[email protected]] On Behalf Of > Brian Pratt > Sent: Wednesday, June 24, 2009 11:38 AM > To: [email protected] > Subject: RE: [spctools-discuss] Re: building tpp from svn (rev 4395) on > ubuntu 9.04 > > Can you show me the subversion statement you used to grab the source code > tree? > > Brian > > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of andreas quandt > Sent: Wednesday, June 24, 2009 11:31 AM > To: [email protected] > Subject: [spctools-discuss] Re: building tpp from svn (rev 4395) on ubuntu > 9.04 > > > 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/libsqlite > 3.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/libsqlit > e3.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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