ok, thanks On Thu, Sep 27, 2018 at 1:35 PM David Shteynberg < david.shteynb...@systemsbiology.org> wrote:
> The code in the release will not compile on that system without some major > changes. Try with trunk and see if that works. Let us know! > > On Thu, Sep 27, 2018 at 10:19 AM Felipe da Veiga Leprevost < > leprevos...@gmail.com> wrote: > >> 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 < >> david.shteynb...@systemsbiology.org> 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 < >>> leprevos...@gmail.com> 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 < >>>>> david.sh...@systemsbiology.org> 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> >>>>>> 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> 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> >>>>>>>> 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. >>>>>>>>> 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. >>>>>>>> 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. >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> 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. >>>>>>> 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-discuss+unsubscr...@googlegroups.com. >>>> To post to this group, send email to spctools-discuss@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-discuss+unsubscr...@googlegroups.com. >>> To post to this group, send email to spctools-discuss@googlegroups.com. >>> 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 spctools-discuss+unsubscr...@googlegroups.com. >> To post to this group, send email to spctools-discuss@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-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > 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 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