Actually we've been seeing some problems with the latest versions of gcc. You might be running into some of the same issues.
-Joe On Mon, Oct 14, 2013 at 11:47 AM, Han Jo <sven.gies...@gmail.com> wrote: > I am using 4.5... good guess. I will give it a shot with a later version! > > > 2013/10/14 Joseph Slagel <joseph.sla...@systemsbiology.org> > >> What version of gcc are you using to do the build? >> >> -Joe >> >> >> On Mon, Oct 14, 2013 at 8:21 AM, Han Jo <sven.gies...@gmail.com> wrote: >> >>> Okay, after finding the line: >>> >>> "libs/regex/build/has_icu_test.cpp:12:30: fatal error: >>> unicode/uversion.h: No such file or directory". I tried to remove -q flag >>> from the bjam command as suggested here( >>> http://boost.2283326.n4.nabble.com/error-unicode-uversion-h-No-such-file-building-Boost-1-44-0-td2581731.html), >>> but without success. >>> As far as I understood with the current version the makefile.config.inc >>> does not need to contain the boost dirs... since boost is now part of the >>> distributed tar. So my config file is as sparse as: >>> >>> TPP_ROOT=/data/software/TPP/bin/ >>> TPP_WEB=/data/software/TPP/web/ >>> >>> >>> And I only do the following commands: >>> >>> >>> 1. tar xzf TPP-4.6.3.tgz >>> 2. cd TPP-4.6.3/trans_proteomic_pipeline/src >>> 3. make ARCH=x86_64 >>> >>> >>> >>> ...done building FANN library source >>> mkdir -p >>> /data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../build/x86_64 >>> unpacking Boost source (this may take a few minutes)... >>> ...applying Boost patch >>> /data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../extern/boost_1_45_0.gcc47patch >>> done unpacking Boost source >>> building boost bjam... >>> ### >>> ### Using 'gcc' toolset. >>> ### >>> rm -rf bootstrap >>> mkdir bootstrap >>> gcc -o bootstrap/jam0 command.c compile.c debug.c expand.c glob.c hash.c >>> hdrmacro.c headers.c jam.c jambase.c jamgram.c lists.c make.c make1.c >>> newstr.c option.c output.c parse.c pathunix.c pathvms.c regexp.c rules.c >>> scan.c search.c subst.c timestamp.c variable.c modules.c strings.c >>> filesys.c builtins.c pwd.c class.c native.c md5.c w32_getreg.c >>> modules/set.c modules/path.c modules/regex.c modules/property-set.c >>> modules/sequence.c modules/order.c execunix.c fileunix.c >>> ./bootstrap/jam0 -f build.jam --toolset=gcc --toolset-root= clean >>> ...found 1 target... >>> ...updating 1 target... >>> ...updated 1 target... >>> ./bootstrap/jam0 -f build.jam --toolset=gcc --toolset-root= >>> ...found 48 targets... >>> ...updating 2 targets... >>> [MKDIR] bin.linuxx86_64 >>> [COMPILE] bin.linuxx86_64/bjam >>> ...updated 2 targets... >>> ...done building boost bjam >>> >>> building boost libraries... >>> warning: No toolsets are configured. >>> warning: Configuring default toolset "gcc". >>> warning: If the default is wrong, your build may not work correctly. >>> warning: Use the "toolset=xxxxx" option to override our guess. >>> warning: For more configuration options, please consult >>> warning: >>> http://boost.org/boost-build2/doc/html/bbv2/advanced/configuration.html >>> libs/regex/build/has_icu_test.cpp:12:30: fatal error: >>> unicode/uversion.h: No such file or directory >>> compilation terminated. >>> ...skipped >>> <p/data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/build/x86_64/boost/obj/boost/bin.v2/libs/regex/build/gcc-4.5/debug>has_icu >>> for lack of >>> <p/data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/build/x86_64/boost/obj/boost/bin.v2/libs/regex/build/gcc-4.5/debug>has_icu_test.o... >>> ...failed updating 1 target... >>> >>> Performing configuration checks >>> >>> - has_icu builds : no >>> >>> Component configuration: >>> >>> - date_time : building >>> - filesystem : building >>> - graph : not building >>> - graph_parallel : not building >>> - iostreams : building >>> - math : not building >>> - mpi : not building >>> - program_options : building >>> - python : not building >>> - random : not building >>> - regex : building >>> - serialization : building >>> - signals : not building >>> - system : not building >>> - test : not building >>> - thread : building >>> - wave : not building >>> >>> In file included from ./boost/thread/pthread/mutex.hpp:14:0, >>> from ./boost/thread/mutex.hpp:16, >>> from ./boost/thread/pthread/thread_data.hpp:12, >>> from ./boost/thread/thread.hpp:17, >>> from libs/thread/src/pthread/thread.cpp:10: >>> ./boost/thread/xtime.hpp:23:5: error: expected identifier before numeric >>> constant >>> ./boost/thread/xtime.hpp:23:5: error: expected ‘}’ before numeric >>> constant >>> ./boost/thread/xtime.hpp:23:5: error: expected unqualified-id before >>> numeric constant >>> ./boost/thread/xtime.hpp:46:14: error: expected type-specifier before >>> ‘system_time’ >>> In file included from ./boost/thread/pthread/mutex.hpp:14:0, >>> from ./boost/thread/mutex.hpp:16, >>> from ./boost/thread/pthread/thread_data.hpp:12, >>> from ./boost/thread/thread.hpp:17, >>> from libs/thread/src/pthread/thread.cpp:10: >>> ./boost/thread/xtime.hpp: In function ‘int xtime_get(xtime*, int)’: >>> ./boost/thread/xtime.hpp:73:40: error: ‘get_system_time’ was not >>> declared in this scope >>> ./boost/thread/xtime.hpp: At global scope: >>> ./boost/thread/xtime.hpp:88:1: error: expected declaration before ‘}’ >>> token >>> ...failed updating 1 target... >>> >>> real 0m48.564s >>> user 1m21.641s >>> sys 0m6.872s >>> [ERROR] Boost libary build failed (missing >>> /data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../build/x86_64/boost/lib/libboost_filesystem.a), >>> please report the results of manually running the following commands: >>> cd >>> /data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../extern/boost_1_45_0; >>> time >>> /data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../extern/boost_1_45_0/tools/build/v2/engine/src/bin.linuxx86_64/bjam >>> -q -d0 >>> --stagedir=/data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../build/x86_64/boost >>> --build-dir=/data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../build/x86_64/boost/obj >>> --layout=system --build-type=minimal -j3 variant=release link=static >>> runtime-link=shared --with-filesystem --with-date_time --with-iostreams >>> --with-program_options --with-regex --with-serialization --with-thread stage >>> >>> make: *** [boost-build-libs] Error 255 >>> >>> >>> When I execute the last command again the following, with no direct >>> errors appears: (but I still cannot build TPP) >>> >>> cd >>> /data/NG4/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../extern/boost_1_45_0; >>> time >>> /data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../extern/boost_1_45_0/tools/build/v2/engine/src/bin.linuxx86_64/bjam >>> -q -d0 >>> --stagedir=/data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../build/x86_64/boost >>> --build-dir=/data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../build/x86_64/boost/obj >>> --layout=system --build-type=minimal -j3 variant=release link=static >>> runtime-link=shared --with-filesystem --with-date_time --with-iostreams >>> --with-program_options --with-regex --with-serialization --with-thread stage >>> >>> warning: No toolsets are configured. >>> warning: Configuring default toolset "gcc". >>> warning: If the default is wrong, your build may not work correctly. >>> warning: Use the "toolset=xxxxx" option to override our guess. >>> warning: For more configuration options, please consult >>> warning: >>> http://boost.org/boost-build2/doc/html/bbv2/advanced/configuration.html >>> Performing configuration checks >>> >>> - has_icu builds : no >>> >>> Component configuration: >>> >>> - date_time : building >>> - filesystem : building >>> - graph : not building >>> - graph_parallel : not building >>> - iostreams : building >>> - math : not building >>> - mpi : not building >>> - program_options : building >>> - python : not building >>> - random : not building >>> - regex : building >>> - serialization : building >>> - signals : not building >>> - system : not building >>> - test : not building >>> - thread : building >>> - wave : not building >>> >>> In file included from ./boost/thread/pthread/mutex.hpp:14:0, >>> from ./boost/thread/mutex.hpp:16, >>> from ./boost/thread/pthread/thread_data.hpp:12, >>> from ./boost/thread/thread.hpp:17, >>> from libs/thread/src/pthread/thread.cpp:10: >>> ./boost/thread/xtime.hpp:23:5: error: expected identifier before numeric >>> constant >>> ./boost/thread/xtime.hpp:23:5: error: expected ‘}’ before numeric >>> constant >>> ./boost/thread/xtime.hpp:23:5: error: expected unqualified-id before >>> numeric constant >>> ./boost/thread/xtime.hpp:46:14: error: expected type-specifier before >>> ‘system_time’ >>> In file included from ./boost/thread/pthread/mutex.hpp:14:0, >>> from ./boost/thread/mutex.hpp:16, >>> from ./boost/thread/pthread/thread_data.hpp:12, >>> from ./boost/thread/thread.hpp:17, >>> from libs/thread/src/pthread/thread.cpp:10: >>> ./boost/thread/xtime.hpp: In function ‘int xtime_get(xtime*, int)’: >>> ./boost/thread/xtime.hpp:73:40: error: ‘get_system_time’ was not >>> declared in this scope >>> ./boost/thread/xtime.hpp: At global scope: >>> ./boost/thread/xtime.hpp:88:1: error: expected declaration before ‘}’ >>> token >>> ...failed updating 1 target... >>> >>> real 0m10.936s >>> user 0m6.284s >>> sys 0m1.288s >>> >>> >>> >>> Am Montag, 14. Oktober 2013 15:46:00 UTC+2 schrieb Han Jo: >>> >>>> Thanks for sharing! But this still would't let me build TPP. >>>> >>>> Did you download boost by yourself (as described in your quoted text) >>>> or did you just go straight to the src dir of TPP and perform the >>>> installations steps? >>>> >>>> >>>> Am Samstag, 12. Oktober 2013 11:38:49 UTC+2 schrieb ChargedPeptide: >>>>> >>>>> Also, I quoted the wrong text. This is in reply to Han Jo. >>>>> >>>>> -- >>> You received this message because you are subscribed to the Google >>> Groups "spctools-discuss" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to spctools-discuss+unsubscr...@googlegroups.com. >>> To post to this group, send email to spctools-discuss@googlegroups.com. >>> Visit this group at http://groups.google.com/group/spctools-discuss. >>> For more options, visit https://groups.google.com/groups/opt_out. >>> >> >> >> >> -- >> Joe Slagel >> Institute for Systems Biology >> jsla...@systemsbiology.org >> (206) 732-1362 >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to spctools-discuss+unsubscr...@googlegroups.com. >> To post to this group, send email to spctools-discuss@googlegroups.com. >> Visit this group at http://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/groups/opt_out. >> > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > Visit this group at http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/groups/opt_out. > -- Joe Slagel Institute for Systems Biology jsla...@systemsbiology.org (206) 732-1362 -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out.
