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/AmberTools/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
> >> > >
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 13 2018 - 06:30:04 PST
