Hey Natalie Many thanks for the info! I will check it out in a few hours ;-)
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. 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 -~----------~----~----~----~------~----~------~--~---
