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. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
