hey brian, now i know what you mean. i did not see that the tpp binary folder is automatically created in the parent directory.... so this seems to work fine.
many thanks! andreas Andreas Quandt wrote: > Hey Natalie, hello Brian > > Sorry for getting back to you so late. > I tried the compilation and it worked like a charm :-) > I am only a little bit confused about the structure as it completely > differs from the stable branch. > Hence I am not exactly sure how to best integrate the trunk in an > existing installation or to replace it respectively. > It would be great if one of you guys could give me a short explanation. > > Cheers > Andreas > > > > > On Jun 26, 2009, at 12:26 AM, Natalie Tasman > <[email protected]> wrote: > >> >> 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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