Robert, My recommendation would be to use the version of boost that's packaged with the source of TPP. Getting TPP to build against the local systems version of boost is a bit challenging as things are TPP's Proteowizard and source code is pretty coupled to the packaged version. If you were seeing compilation errors when building TPP you could try applying a recent patch I made. Starting with a freshly unpacked copy of the TPP source simply copy the attached file into the directory trans_proteomic_pipeline/extern (next to the file boost_1_54_0.tar.bz2). When you run make it should apply the patch automatically.
(Incidentally this patch is the same change mentioned earlier). -Joe On Tue, Jun 24, 2014 at 7:56 AM, Robert Winkler < [email protected]> wrote: > Dear Joe, > > my first try was with the official libboost 1.54 packages of Ubuntu 14.04. > Since this make gave the mentioned thread.a missing problem, I built the > 1.55 version; however, during compilation of TPP the error returned. > > Might it be an idea to build the libboost 1.54 and to try again? > > Best, Robert > > > On Mo 23 Jun 2014 19:57:26 CDT, Joseph Slagel wrote: > >> Hi Robert, >> >> It sounds like you built your own version of boost as we're still on >> 1.54.0? If so getting the right packages built and linked with the >> TPP might be a bit challenging. Any reason for not going with the >> stock boost that built in TPP? >> >> -Joe >> >> >> On Mon, Jun 23, 2014 at 4:16 PM, Robert <[email protected] >> <mailto:[email protected]>> wrote: >> >> Hi, same here. I compiled and installed the boost libraries 1.55.0 >> on Ubuntu 14.04. >> The compilation of TPP 4.7.1 stops with >> [ERROR] Boost libary build failed (missing >> /home/rob/Downloads/tpp_4.7.1/src/../build/Ubuntu-x86_64/ >> boost/lib/libboost_thread.a), >> please report the results of manually running the following commands: >> >> Any ideas (downgrade to 12.04 is not an option for me)? >> >> Best Regards, >> >> obert >> >> >> >> Am Montag, 12. Mai 2014 10:42:39 UTC-5 schrieb Will Fondrie: >> >> Hello, >> >> I am trying to install TPP on a machine running 64bit Ubuntu >> 14.04 LTS. I keep running into the error below when I try >> compiling using the make command. >> I've tried using gcc-4.8 and gcc-4.4 as well as boost 1.54 and >> 1.55 with no luck. >> >> Thank you for the help. >> >> -Will >> >> building boost libraries... >> Performing configuration checks >> >> - zlib : yes (cached) >> - has_icu builds : yes (cached) >> >> Component configuration: >> >> - atomic : not building >> - chrono : not building >> - context : not building >> - coroutine : not building >> - date_time : building >> - exception : not building >> - filesystem : building >> - graph : not building >> - graph_parallel : not building >> - iostreams : building >> - locale : not building >> - log : not 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 >> - timer : not building >> - wave : not building >> >> In file included from ./boost/atomic.hpp:12, >> from ./boost/thread/pthread/once___ >> atomic.hpp:20, >> from ./boost/thread/once.hpp:20, >> from >> libs/thread/src/pthread/./__once_atomic.cpp:9, >> from libs/thread/src/pthread/once.__cpp:8: >> >> ./boost/atomic/atomic.hpp:202: error: ‘uintptr_t’ was not >> declared in this scope >> ./boost/atomic/atomic.hpp:202: error: template argument 1 is >> invalid >> ./boost/atomic/atomic.hpp:202: error: invalid type in >> declaration before ‘;’ token >> In file included from ./boost/atomic.hpp:12, >> from ./boost/thread/pthread/once___ >> atomic.hpp:20, >> from ./boost/thread/once.hpp:20, >> from libs/thread/src/pthread/__thread.cpp:17: >> >> ./boost/atomic/atomic.hpp:202: error: ‘uintptr_t’ was not >> declared in this scope >> ./boost/atomic/atomic.hpp:202: error: template argument 1 is >> invalid >> ./boost/atomic/atomic.hpp:202: error: invalid type in >> declaration before ‘;’ token >> ./boost/system/error_code.hpp:__222: warning: >> ‘boost::system::posix___category’ defined but not used >> ./boost/system/error_code.hpp:__223: warning: >> >> ‘boost::system::errno_ecat’ defined but not used >> ./boost/system/error_code.hpp:__224: warning: >> >> ‘boost::system::native_ecat’ defined but not used >> ...failed updating 2 targets... >> Command exited with non-zero status 1 >> 1.03user 0.09system 0:00.97elapsed 116%CPU (0avgtext+0avgdata >> 164912maxresident)k >> 0inputs+32outputs (0major+62861minor)pagefaults 0swaps >> [ERROR] Boost libary build failed (missing >> /usr/local/src/TPP-4.7.0/__trans_proteomic_pipeline/src/. >> __./build/Ubuntu-x86_64/boost/__lib/libboost_thread.a), >> >> please report the results of manually running the following >> commands: >> cd >> /usr/local/src/TPP-4.7.0/__trans_proteomic_pipeline/src/. >> __./extern/boost_1_54_0; >> time >> /usr/local/src/TPP-4.7.0/__trans_proteomic_pipeline/src/. >> __./extern/boost_1_54_0/tools/__build/v2/engine/bin.linuxx86___64/bjam >> -q -d0 >> --stagedir=/usr/local/src/TPP-__4.7.0/trans_proteomic___ >> pipeline/src/../build/Ubuntu-__x86_64/boost >> --build-dir=/usr/local/src/__TPP-4.7.0/trans_proteomic___ >> pipeline/src/../build/Ubuntu-__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 >> /bin/sh: 1: exit: Illegal number: -1 >> make: *** [boost-build-libs] Error 2 >> >> Running the commands above results in: >> >> >> Performing configuration checks >> >> - zlib : yes (cached) >> - has_icu builds : yes (cached) >> >> Component configuration: >> >> - atomic : not building >> - chrono : not building >> - context : not building >> - coroutine : not building >> - date_time : building >> - exception : not building >> - filesystem : building >> - graph : not building >> - graph_parallel : not building >> - iostreams : building >> - locale : not building >> - log : not 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 >> - timer : not building >> - wave : not building >> >> In file included from ./boost/atomic.hpp:12, >> from ./boost/thread/pthread/once___ >> atomic.hpp:20, >> from ./boost/thread/once.hpp:20, >> from >> libs/thread/src/pthread/./__once_atomic.cpp:9, >> from libs/thread/src/pthread/once.__cpp:8: >> >> ./boost/atomic/atomic.hpp:202: error: ‘uintptr_t’ was not >> declared in this scope >> ./boost/atomic/atomic.hpp:202: error: template argument 1 is >> invalid >> ./boost/atomic/atomic.hpp:202: error: invalid type in >> declaration before ‘;’ token >> In file included from ./boost/atomic.hpp:12, >> from ./boost/thread/pthread/once___ >> atomic.hpp:20, >> from ./boost/thread/once.hpp:20, >> from libs/thread/src/pthread/__thread.cpp:17: >> >> ./boost/atomic/atomic.hpp:202: error: ‘uintptr_t’ was not >> declared in this scope >> ./boost/atomic/atomic.hpp:202: error: template argument 1 is >> invalid >> ./boost/atomic/atomic.hpp:202: error: invalid type in >> declaration before ‘;’ token >> ./boost/system/error_code.hpp:__222: warning: >> ‘boost::system::posix___category’ defined but not used >> ./boost/system/error_code.hpp:__223: warning: >> >> ‘boost::system::errno_ecat’ defined but not used >> ./boost/system/error_code.hpp:__224: warning: >> >> ‘boost::system::native_ecat’ defined but not used >> ...failed updating 2 targets... >> >> real 0m0.997s >> user 0m1.062s >> sys 0m0.099s >> >> -- >> 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] >> <mailto:[email protected]>. >> >> To post to this group, send email to >> [email protected] >> <mailto:[email protected]>. >> >> Visit this group at http://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> >> >> >> >> -- >> Joe Slagel >> Institute for Systems Biology >> [email protected] <mailto:[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] >> <mailto:[email protected]>. >> >> To post to this group, send email to [email protected] >> <mailto:[email protected]>. >> >> Visit this group at http://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > -- 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/d/optout.
boost_1_54_0.ubuntupatch
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