Peter, Can you tell me how you are getting the code and building?
Did you export the source code from our SVN repository with svn? Such as: *svn checkout https://svn.code.sf.net/p/sashimi/code/trunk/trans_proteomic_pipeline <https://svn.code.sf.net/p/sashimi/code/trunk/trans_proteomic_pipeline> trans_proteomic_pipeline* Then cd to the directory with the code: *cd trans_proteomic_pipeline* Then run: *make all* This is how the we build the TPP on a nightly basis. Please send the exact errors you encounter. -David On Mon, Jun 11, 2018 at 1:12 PM, David Shteynberg < [email protected]> wrote: > Peter, > > Did you export the source code from our SVN repository with : > > > On Mon, Jun 11, 2018 at 12:42 PM, Peter Sudmant <[email protected]> > wrote: > >> gcc version 6.3.0 (GCC) >> >> Hopefully that's helpful. >> >> On Mon, Jun 11, 2018 at 2:50 PM David Shteynberg < >> [email protected]> wrote: >> >>> Hello Peter, >>> >>> Which compiler version are you using? >>> >>> Thanks, >>> -David >>> >>> On Mon, Jun 11, 2018 at 11:16 AM, Peter Sudmant <[email protected]> >>> wrote: >>> >>>> I seem to be having the same problem, with and without line 301 >>>> commented out. has anyone found a solution for this? >>>> >>>> On Tuesday, November 28, 2017 at 3:17:18 PM UTC-5, David Shteynberg >>>> wrote: >>>>> >>>>> Hello lejeczek, >>>>> >>>>> Our nightly build executes without any issues using gcc 4.4.7 on linux >>>>> using mingw64. Which version of gcc do you have on your system? It seems >>>>> to be complaining of not finding the boost_filesystem library when >>>>> compiling msconvert "undefined reference to >>>>> `boost::filesystem::detail::copy_file". >>>>> This build product should be getting built in >>>>> /home.sysops/appmgr/rpmbuild/t >>>>> ar.src/TransProteomicPipeline/TPP_5.1.0-srcbuild/linux-x86_64/lib/libboostfilesystem.a >>>>> , can you verify it exists on your system? Google pointed me to an >>>>> article >>>>> with a possible solution: http://stackoverflow.com/quest >>>>> ions/35007134/c-boost-undefined-reference-to-boostfilesystem >>>>> detailcopy-file >>>>> >>>>> The suggested solution is to add -DBOOST_NO_CXX11_SCOPED_ENUMS to >>>>> your compiler flags. However, common.mk already has this flag >>>>> enabled on line 301 for ur >>>>> >>>>> Can you try to comment out this line in common.mk file in case that >>>>> your more modern compiler compiles with -std=c++11 in which case this >>>>> definition should be disabled? >>>>> >>>>> -David >>>>> >>>>> >>>>> On Mon, Nov 20, 2017 at 9:41 AM, lejeczek <[email protected]> wrote: >>>>> >>>>>> hi, I wonder.. >>>>>> if it fails for you too? >>>>>> Is it purely boost problem/failure? >>>>>> And lastly, how to solve it? >>>>>> I'm on Centos 7.4 >>>>>> >>>>>> error: >>>>>> ... >>>>>> g++ -L/home.sysops/appmgr/rpmbuild >>>>>> /tar.src/TransProteomicPipeline/TPP_5.1.0-src/build/linux-x86_64/lib >>>>>> -o /home.sysops/appmgr/rpmbuild/tar.src/TransProteomicPipeline/ >>>>>> TPP_5.1.0-src/build/linux-x86_64/bin/msconvert >>>>>> /home.sysops/appmgr/rpmbuild/tar.src/TransProteomicPipeline/ >>>>>> TPP_5.1.0-src/build/linux-x86_64/artifacts/pwiz/pwiz_tools/commandline/msconvert.o >>>>>> /home.sysops/appmgr/rpmbuild/tar.src/TransProteomicPipeline/ >>>>>> TPP_5.1.0-src/build/linux-x86_64/lib/libpwiz.a \ >>>>>> -L/home.sysops/appmgr/rpmbuild/tar.src/TransProteomicPipelin >>>>>> e/TPP_5.1.0-src/build/linux-x86_64/lib \ >>>>>> -lboost_system -lboost_program_options \ >>>>>> -lboost_filesystem -lboost_iostreams -lboost_regex -lboost_thread >>>>>> -lboost_chrono \ >>>>>> -lboost_serialization \ >>>>>> -lm -lrt -lz -lpthread >>>>>> /home.sysops/appmgr/rpmbuild/tar.src/TransProteomicPipeline/ >>>>>> TPP_5.1.0-src/build/linux-x86_64/lib/libpwiz.a(Filesystem.o): In >>>>>> function `boost::filesystem::copy_file(boost::filesystem::path >>>>>> const&, boost::filesystem::path const&, boost::system::error_code&)': >>>>>> /home.sysops/appmgr/rpmbuild/tar.src/TransProteomicPipeline/ >>>>>> TPP_5.1.0-src/extern/ProteoWizard/pwiz-src/ >>>>>> libraries/boost_1_56_0/boost/filesystem/operations.hpp:502: >>>>>> undefined reference to `boost::filesystem::detail::co >>>>>> py_file(boost::filesystem::path const&, boost::filesystem::path >>>>>> const&, boost::filesystem::copy_option::enum_type, >>>>>> boost::system::error_code*)' >>>>>> /home.sysops/appmgr/rpmbuild/tar.src/TransProteomicPipeline/ >>>>>> TPP_5.1.0-src/build/linux-x86_64/lib/libpwiz.a(Filesystem.o): In >>>>>> function `boost::filesystem::copy_file(boost::filesystem::path >>>>>> const&, boost::filesystem::path const&)': >>>>>> /home.sysops/appmgr/rpmbuild/tar.src/TransProteomicPipeline/ >>>>>> TPP_5.1.0-src/extern/ProteoWizard/pwiz-src/ >>>>>> libraries/boost_1_56_0/boost/filesystem/operations.hpp:495: >>>>>> undefined reference to `boost::filesystem::detail::co >>>>>> py_file(boost::file,system::path const&, boost::filesystem::path >>>>>> const&, boost::filesystem::copy_option::enum_type, >>>>>> boost::system::error_code*)' >>>>>> collect2: error: ld returned 1 exit status >>>>>> make: *** [/home.sysops/appmgr/rpmbuild/ >>>>>> tar.src/TransProteomicPipeline/TPP_5.1.0-src/build/linux-x86_64/bin/msconvert] >>>>>> Error 1 >>>>>> /home.sysops/appmgr/rpmbuild/tar.src/TransProteomicPipeline/ >>>>>> TPP_5.1.0-src/extern/ProteoWizard/Makefile:334: recipe for target >>>>>> '/home.sysops/appmgr/rpmbuild/tar.src/TransProteomicPipeline >>>>>> /TPP_5.1.0-src/build/linux-x86_64/bin/msconvert' failed >>>>>> >>>>>> -- >>>>>> 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 https://groups.google.com/group/spctools-discuss. >>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>> >>>>> >>>>> -- >>>> 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 https://groups.google.com/group/spctools-discuss. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> -- >>> 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 https://groups.google.com/group/spctools-discuss. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> >> -- >> Peter >> >> -- >> 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 https://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > > -- 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 https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
