sorry I meant to say MSYS 5.2, GCC 8.2. I downloaded the release_5.1, not the trunk
On Thu, Sep 27, 2018 at 1:11 PM David Shteynberg < [email protected]> wrote: > Which source code are you using? Have you tried building the latest SVN > version of the code? I compile regularly on windows (MSYS2 and mingw64) > using gcc 8.2 and also using gcc 5.4, I have not tried it with gcc 5.2. > > On Thu, Sep 27, 2018 at 9:52 AM Felipe da Veiga Leprevost < > [email protected]> wrote: > >> 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 < >>> [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/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 <[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/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 [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. >> > -- > 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. > -- Felipe da Veiga Leprevost, Ph.D. www.leprevost.com.br Proteome Bioinformatics Lab University of Michigan -- 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.
