After having the same problem as Will and others in this thread I realized that the problem with the boost patch not working is that we are using a local install of boost as per the instructions on the SPCTools Wiki here:http://tools.proteomecenter.org/wiki/index.php?title=TPP_4.5.2:_Installing_on_Ubuntu_10.04.3. Or at least we think we are.
However, when I compile TPP I noticed that it uses the boost that actually ships with the TPP! So the local system's boost install isn't used at all and therefore changes to that local boost cstdint.hpp file are ignored. There most likely is a more elegant solution, but the way I worked around this was to do the following: 1. extract TPP_4.7.1-src.tgz 2. cd into tpp tpp_4.7.1/extern and extract boost_1_54_0.tar.bz2 (tar xvf boost_1_54_0.tar.bz2) 3. cd into tpp_4.7.1/extern/boost_1_54_0/boost 4. edit the file cstdint.hpp as per: https://svn.boost.org/trac/boost/changeset/84950 (replacing the red text with the green) 5. save the file and cd back up to tpp_4.7.1/extern and delete boost_1_54_0.tar.bz2 6. compress the boost directory containing the modified cstdint.hpp (tar xjf boost_1_54_0.tar.bz2 boost_1_54_0) 7. edit the Makefile.config.incl file to remove the three lines referencing boost and place it in tpp_4.7.1/src contents of new Makefile.config.incl TPP_ROOT=/usr/local/tpp/ TPP_WEB=/tpp/ LINK=shared LIBEXT=so PERL_LIB_CORE= /usr/lib/perl/5.18/CORE/ PERL_BIN=/usr/bin/perl 8. in the tpp_4.7.1/src directory, issue make && make install. TPP now successfully compiles. I hope this helps some one, and that a fix is coming for the next version of TPP. Cheers, Brian On Tuesday, June 24, 2014 12:42:32 PM UTC-4, [email protected] wrote: > > 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] > <javascript:>> 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] >>> <javascript:> >>> <mailto:[email protected] <javascript:>>> 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] <javascript:> >>> <mailto:[email protected] <javascript:> >>> >. >>> >>> To post to this group, send email to >>> [email protected] <javascript:> >>> <mailto:[email protected] <javascript:>>. >>> >>> 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] <javascript:> <mailto:jsl...@ >>> systemsbiology.org <javascript:>> >>> (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] <javascript:> >>> <mailto:[email protected] <javascript:>>. >>> >>> To post to this group, send email to [email protected] >>> <javascript:> >>> <mailto:[email protected] <javascript:>>. >>> >>> 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] <javascript:> > (206) 732-1362 > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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