tpp 5.1 compilation fails - operations.hpp:502: undefined reference to `boost::filesystem:....

[lejeczek]

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::filesystem::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

[David Shteynberg]

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

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[Peter Sudmant]

I seem to be having the same problem, with and without line 301 commented out. has anyone found a solution for this? 

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[David Shteynberg]

Hello Peter,

Which compiler version are you using?

Thanks,

-David

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[Peter Sudmant]

gcc version 6.3.0 (GCC) 

Hopefully that's helpful. 

Peter

[David Shteynberg]

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. 

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[David Shteynberg]

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 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

[Felipe da Veiga Leprevost]

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 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. 

--

Peter

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[David Shteynberg]

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.

[Felipe da Veiga Leprevost]

sorry I meant to say MSYS 5.2, GCC 8.2.

I downloaded the release_5.1, not the trunk

Felipe da Veiga Leprevost, Ph.D.

www.leprevost.com.br

Proteome Bioinformatics Lab

University of Michigan

[David Shteynberg]

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!

[Felipe da Veiga Leprevost]

ok, thanks