Hi David; I'm trying to compile TPP on a Windows machine, I'm following the instructions on BUILD_WIN.txt file (gcc 5.2) and I'm getting several compilation errors, including the one reported above. Any suggestions on how to fix it ?
Thanks On Monday, June 11, 2018 at 4:17:41 PM UTC-4, David Shteynberg wrote: > > 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 < > david.sh...@systemsbiology.org <javascript:>> wrote: > >> Peter, >> >> Did you export the source code from our SVN repository with : >> >> >> On Mon, Jun 11, 2018 at 12:42 PM, Peter Sudmant <psud...@gmail.com >> <javascript:>> wrote: >> >>> gcc version 6.3.0 (GCC) >>> >>> Hopefully that's helpful. >>> >>> On Mon, Jun 11, 2018 at 2:50 PM David Shteynberg < >>> david.sh...@systemsbiology.org <javascript:>> wrote: >>> >>>> Hello Peter, >>>> >>>> Which compiler version are you using? >>>> >>>> Thanks, >>>> -David >>>> >>>> On Mon, Jun 11, 2018 at 11:16 AM, Peter Sudmant <psud...@gmail.com >>>> <javascript:>> 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/tar.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/questions/35007134/c-boost-undefined-reference-to-boostfilesystemdetailcopy-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 <pel...@gmail.com> 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/TransProteomicPipeline/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::copy_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::copy_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 spctools-discu...@googlegroups.com. >>>>>>> To post to this group, send email to spctools...@googlegroups.com. >>>>>>> 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 spctools-discu...@googlegroups.com <javascript:>. >>>>> To post to this group, send email to spctools...@googlegroups.com >>>>> <javascript:>. >>>>> 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 spctools-discu...@googlegroups.com <javascript:>. >>>> To post to this group, send email to spctools...@googlegroups.com >>>> <javascript:>. >>>> 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 spctools-discu...@googlegroups.com <javascript:>. >>> To post to this group, send email to spctools...@googlegroups.com >>> <javascript:>. >>> 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. 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