Hi, I solved it..I was trying to overwrite an old installation. Thank you
very much for your help!
Elisa
On Tue, Feb 13, 2018 at 3:03 PM, Elisa Pieri <elisa.pieri90.gmail.com>
wrote:
> Now I have this:
>
> Final compiler envs
> CXX = g++
>
> CC = gcc
>
> COMPILER =
> install = True
> set rpath to /home/elisa/amber16/lib
> running install
> running build
> running build_py
> copying pytraj/version.py -> build/lib.linux-x86_64-2.7/pytraj
> running build_ext
> building 'pytraj.cpp_options' extension
> gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall
> -Wstrict-prototypes -fPIC -I/home/elisa/amber16/AmberTools/src/cpptraj/src
> -I/home/elisa/amber16/AmberTools/src/pytraj/pytraj -I/home/elisa/amber16/miniconda/include/python2.7
> -c pytraj/cpp_options.cpp -o build/temp.linux-x86_64-2.7/pytraj/cpp_options.o
> -O0 -ggdb -Wl,-rpath=/home/elisa/amber16/lib
> cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for
> C/ObjC but not for C++
> pytraj/cpp_options.cpp: In function ‘PyObject* __pyx_pf_6pytraj_11cpp_
> options_2set_error_silent(PyObject*, PyObject*)’:
> pytraj/cpp_options.cpp:803:28: error: ‘SupressErrorMsg’ was not declared
> in this scope
> SupressErrorMsg(__pyx_t_1);
> ^
> error: command 'gcc' failed with exit status 1
> Makefile:508: recipe for target 'pytraj' failed
> make[2]: *** [pytraj] Error 1
> make[2]: Leaving directory '/home/elisa/amber16/AmberTools/src'
> Makefile:17: recipe for target 'serial' failed
> make[1]: *** [serial] Error 2
> make[1]: Leaving directory '/home/elisa/amber16/AmberTools/src'
> Makefile:7: recipe for target 'install' failed
> make: *** [install] Error 2
>
>
> On Tue, Feb 13, 2018 at 2:27 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
>> ah, I found this command useful too
>>
>> cd $HOME
>> find . -type f -name libcpptraj.so
>>
>> Hai
>>
>> On Tue, Feb 13, 2018 at 8:22 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>>
>> >
>> >
>> > On Tue, Feb 13, 2018 at 8:11 AM, Elisa Pieri <elisa.pieri90.gmail.com>
>> > wrote:
>> >
>> >> Hi and thanks Hai,
>> >>
>> >> now I'm getting get this error:
>> >>
>> >> creating build/lib.linux-x86_64-2.7/pytraj/utils/css
>> >> copying pytraj/utils/css/oceans16.css ->
>> >> build/lib.linux-x86_64-2.7/pytraj/utils/css
>> >> running build_ext
>> >> building 'pytraj.cpp_options' extension
>> >> creating build/temp.linux-x86_64-2.7
>> >> creating build/temp.linux-x86_64-2.7/pytraj
>> >> gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall
>> >> -Wstrict-prototypes -fPIC -I/home/elisa/amber16/AmberToo
>> >> ls/src/cpptraj/src
>> >> -I/home/elisa/amber16/AmberTools/src/pytraj/pytraj
>> >> -I/home/elisa/amber16/miniconda/include/python2.7 -c
>> >> pytraj/cpp_options.cpp
>> >> -o build/temp.linux-x86_64-2.7/pytraj/cpp_options.o -O0 -ggdb
>> >> -Wl,-rpath=/home/elisa/amber16/lib
>> >> cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid
>> for
>> >> C/ObjC but not for C++
>> >> pytraj/cpp_options.cpp: In function ‘PyObject*
>> >> __pyx_pf_6pytraj_11cpp_options_2set_error_silent(PyObject*,
>> PyObject*)’:
>> >> pytraj/cpp_options.cpp:803:28: error: ‘SupressErrorMsg’ was not
>> declared
>> >> in
>> >> this scope
>> >> SupressErrorMsg(__pyx_t_1);
>> >>
>> >
>> >
>> > Hi, this means that you have an old libcpptraj.so somewhere. Can you
>> find
>> > it (e.g: locate libcpptraj.so) and delete it, then "make install" again?
>> >
>> > Hai
>> >
>> >
>> >> ^
>> >> error: command 'gcc' failed with exit status 1
>> >> Makefile:508: recipe for target 'pytraj' failed
>> >> make[2]: *** [pytraj] Error 1
>> >> make[2]: Leaving directory '/home/elisa/amber16/AmberTools/src'
>> >> Makefile:17: recipe for target 'serial' failed
>> >> make[1]: *** [serial] Error 2
>> >> make[1]: Leaving directory '/home/elisa/amber16/AmberTools/src'
>> >> Makefile:7: recipe for target 'install' failed
>> >> make: *** [install] Error 2
>> >>
>> >> Is there a problem with my gcc compiler? Its version is "gcc (Ubuntu
>> >> 5.4.0-6ubuntu1~16.04.6) 5.4.0 20160609"
>> >>
>> >> Elisa
>> >>
>> >> On Tue, Feb 13, 2018 at 1:30 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>> >>
>> >> > Hi, can you try remove that bin/FEW.pl and “make install” again?
>> >> >
>> >> > Hai
>> >> >
>> >> > On Tue, Feb 13, 2018 at 4:46 AM Elisa Pieri <elisa.pieri90.gmail.com
>> >
>> >> > wrote:
>> >> >
>> >> > > Hello,
>> >> > >
>> >> > > apparently I'm not lucky with this reinstallation..everything in
>> the
>> >> > > "./configure gnu" was fine, but then I get this from the "make
>> >> install":
>> >> > >
>> >> > > make[4]: Entering directory
>> >> > >
>> >> > > '/home/elisa/amber16/AmberTools/src/FEW/additional_
>> >> > libs/PerlMol-0.3500/Parse-Yapp-1.05'
>> >> > > Manifying 1 pod document
>> >> > > Manifying 1 pod document
>> >> > > make[4]: Leaving directory
>> >> > >
>> >> > > '/home/elisa/amber16/AmberTools/src/FEW/additional_
>> >> > libs/PerlMol-0.3500/Parse-Yapp-1.05'
>> >> > > Manifying 1 pod document
>> >> > > Appending installation info to
>> >> > >
>> >> > > /home/elisa/amber16/lib/perl//lib/x86_64-linux-gnu/perl/5.
>> >> > 22.1/perllocal.pod
>> >> > > make[3]: Leaving directory
>> >> > > '/home/elisa/amber16/AmberTools/src/FEW/additional_libs/
>> >> PerlMol-0.3500'
>> >> > > cp -f /home/elisa/amber16/AmberTools/src/FEW/FEW.pl
>> >> > /home/elisa/amber16/bin
>> >> > > cp: '/home/elisa/amber16/AmberTools/src/FEW/FEW.pl' and
>> >> > > '/home/elisa/amber16/bin/FEW.pl' are the same file
>> >> > > Makefile:5: recipe for target 'install' failed
>> >> > > make[2]: *** [install] Error 1
>> >> > > make[2]: Leaving directory '/home/elisa/amber16/AmberTool
>> s/src/FEW'
>> >> > > Makefile:17: recipe for target 'serial' failed
>> >> > > make[1]: *** [serial] Error 2
>> >> > > make[1]: Leaving directory '/home/elisa/amber16/AmberTools/src'
>> >> > > Makefile:7: recipe for target 'install' failed
>> >> > > make: *** [install] Error 2
>> >> > >
>> >> > > Can you help me?
>> >> > > Elisa
>> >> > > _______________________________________________
>> >> > > AMBER mailing list
>> >> > > AMBER.ambermd.org
>> >> > > http://lists.ambermd.org/mailman/listinfo/amber
>> >> > >
>> >> > _______________________________________________
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>> >> > AMBER.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >> >
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>> >
>> >
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Received on Tue Feb 13 2018 - 07:00:04 PST
