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. 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