Hello Andreas, As of trunk rev. 4414, the TPP builds successfully. This was tested on Ubuntu 9.04.
-Natalie On Jun 24, 2009, at 2:33 PM, Andreas Quandt wrote: > > Hi Natalie > > Many thanks for the fast bugfix. > Also it would be great if you (or brian) could let me know when the > other bugfix is comitted so that I can continue with some small > tests ;-) > > Cheers > Andreas > > > > On Jun 24, 2009, at 9:49 PM, Natalie Tasman <[email protected] >> wrote: > >> >> 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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