I am using 4.5... good guess. I will give it a shot with a later version!
2013/10/14 Joseph Slagel <[email protected]> > What version of gcc are you using to do the build? > > -Joe > > > On Mon, Oct 14, 2013 at 8:21 AM, Han Jo <[email protected]> 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 [email protected]. >> To post to this group, send email to [email protected]. >> 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 > [email protected] > (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 [email protected]. > To post to this group, send email to [email protected]. > 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out.
