Comments (4)
Need to update https://github.com/Electrostatics/apbs-pdb2pqr/blob/master/pdb2pqr/README.md after we confirm that Cmake is working.
from apbs-pdb2pqr.
I'm posting instructions on the Cmake build from @intendo here:
rm -rf build && mkdir build && cd build && cmake -DENABLE_PYTHON=ON .. && cmake --build . && ctest . && cd ..
from apbs-pdb2pqr.
When running WSL Ubuntu 18.04 on Windows 10, I run the following commands:
rm -rf build/
. ~/venvs/apbs/bin/activate
mkdir build
cd build
cmake -DENABLE_PYTHON=ON ..
cmake --build .
Everything goes well until the end, when I receive the error:
[100%] Linking C shared library ../../lib/_apbslib.so
/usr/bin/cc -fPIC -O2 -g -DNDEBUG -shared -Wl,-soname,_apbslib.so -o ../../lib/_apbslib.so CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -L/mnt/c/Users/bake113/Git/apbs-pdb2pqr/apbs/externals/fetk/maloc/lib
-Wl,-rpath,/mnt/c/Users/bake113/Git/apbs-pdb2pqr/apbs/externals/fetk/maloc/lib:/home/bake113/venvs/apbs/lib/python3.6/config-3.6m-x86_64-linux-gnu -lm -lstdc++ ../../../../apbs/externals/fetk/maloc/lib/libmaloc.a ../../lib/libapbs_generic.a ../../lib/libapbs_pmgc.a ../../lib/libapbs_mg.a ../../lib/libapbs_routines.a /home/bake113/venvs/apbs/lib/python3.6/config-3.6m-x86_64-linux-gnu/libpython3.6m.so ../../lib/libapbs_generic.a ../../lib/libapbs_pmgc.a -lm -lstdc++ ../../../../apbs/externals/fetk/maloc/lib/libmaloc.a
/usr/bin/ld: ../../lib/libapbs_generic.a(mgparm.c.o): relocation R_X86_64_PC32 against symbol `stderr@@GLIBC_2.2.5' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: Bad value
collect2: error: ld returned 1 exit status
apbs/tools/python/CMakeFiles/_apbslib.dir/build.make:115: recipe for target 'apbs/lib/_apbslib.so' failed
make[2]: *** [apbs/lib/_apbslib.so] Error 1
CMakeFiles/Makefile2:1133: recipe for target 'apbs/tools/python/CMakeFiles/_apbslib.dir/all' failed
make[1]: *** [apbs/tools/python/CMakeFiles/_apbslib.dir/all] Error 2
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2
Adding -DCMAKE_C_FLAGS="-fPIC"
to the initial cmake command fixed this problem.
from apbs-pdb2pqr.
Since this is working in Github Actions and we made the releases for 3.0.0, I think the CMake builds are correct.
from apbs-pdb2pqr.
Related Issues (20)
- Add testing for extensions
- PDB2PQR tests don't actually work HOT 1
- PDB2PQR --assign-only does not assign charges or radii
- PDB2PQR doesn't recognize HETATM with --drop-water HOT 2
- Problem with pdb2pqr.utilities.getFFfile HOT 1
- Please fix really ugly code HOT 1
- Replace C++ clique-finding with Python
- Possibly reinstate PDB2PKA ligand support
- Large apbs .dx file downloads fail from web server due to server-side error? HOT 8
- APBS and Python3 HOT 7
- PyMOL 2.4.0 APBS plug-in not recognising PDB2PQR HOT 4
- Remove binaries from Git repo HOT 9
- NotImplementedError: PDB2PKA not implemented. HOT 12
- Move PDB2PQR back to its own repo? HOT 10
- Positive potential on hydrophobic protein interfaces HOT 3
- Remove PDB2PQR code from this repo
- Create separate apbs repo
- Update README.md and documentation for this repo HOT 1
- Remove APBS code from this repo
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