I've identified one problem with compiling with recent versions of gcc. It has to do with a new macro TIME_UTC conflicting with a enum in boost. You can read about it here (with a workaround):
https://svn.boost.org/trac/boost/ticket/6940 https://bbs.archlinux.org/viewtopic.php?pid=1126374 I'm working on fixing it on TPP's trunk now. -Joe On Mon, Oct 14, 2013 at 11:49 AM, Joseph Slagel < [email protected]> wrote: > 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 <[email protected]> wrote: > >> 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. >> > > > > -- > Joe Slagel > Institute for Systems Biology > [email protected] > (206) 732-1362 > -- 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.
