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Nandha Kumar
Jun 21, 2023, 1:55:21 AM6/21/23
to gmx_MMPBSA
During gmx_MMPBSA installation, after this, I got an error, and I stacked with this command line.
Input command;
python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4
Collecting git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4
Collecting git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4
Error:
(gmxMMPBSA) bubblu@Nandha:~$ python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4
Collecting git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4
Cloning https://github.com/Valdes-Tresanco-MS/ParmEd.git (to revision v3.4) to /tmp/pip-req-build-_9q8cz86
Running command git clone --filter=blob:none --quiet https://github.com/Valdes-Tresanco-MS/ParmEd.git /tmp/pip-req-build-_9q8cz86
Running command git checkout -b v3.4 --track origin/v3.4
Switched to a new branch 'v3.4'
Branch 'v3.4' set up to track remote branch 'v3.4' from 'origin'.
Resolved https://github.com/Valdes-Tresanco-MS/ParmEd.git to commit 41cc9ab1fe930f0c13c36433148d4601307d60c3
Preparing metadata (setup.py) ... done
Building wheels for collected packages: ParmEd
Building wheel for ParmEd (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [167 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-cpython-39
creating build/lib.linux-x86_64-cpython-39/parmed
copying parmed/periodic_table.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/symmetry.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/exceptions.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/_version.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/scripts.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/residue.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/vec3.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/geometry.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/structure.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/parameters.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/constants.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/topologyobjects.py -> build/lib.linux-x86_64-cpython-39/parmed
creating build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/_chamberparm.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/_tinkerparm.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/offlib.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/_amberparm.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/titratable_residues.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/asciicrd.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/amberformat.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/parameters.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/netcdffiles.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/readparm.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/mask.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
creating build/lib.linux-x86_64-cpython-39/parmed/modeller
copying parmed/modeller/standardtemplates.py -> build/lib.linux-x86_64-cpython-39/parmed/modeller
copying parmed/modeller/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/modeller
copying parmed/modeller/residue.py -> build/lib.linux-x86_64-cpython-39/parmed/modeller
creating build/lib.linux-x86_64-cpython-39/parmed/tinker
copying parmed/tinker/system.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
copying parmed/tinker/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
copying parmed/tinker/parameterfile.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
copying parmed/tinker/tinkerfiles.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
copying parmed/tinker/topologyobjects.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
creating build/lib.linux-x86_64-cpython-39/parmed/unit
copying parmed/unit/mymatrix.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
copying parmed/unit/standard_dimensions.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
copying parmed/unit/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
copying parmed/unit/quantity.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
copying parmed/unit/unit_operators.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
copying parmed/unit/prefix.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
copying parmed/unit/unit_math.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
copying parmed/unit/baseunit.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
copying parmed/unit/unit_definitions.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
copying parmed/unit/basedimension.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
copying parmed/unit/constants.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
copying parmed/unit/unit.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
creating build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
copying parmed/amber/mdin/mdin.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
copying parmed/amber/mdin/pb.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
copying parmed/amber/mdin/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
copying parmed/amber/mdin/gbnsr6.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
copying parmed/amber/mdin/cntrl.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
copying parmed/amber/mdin/qmmm.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
copying parmed/amber/mdin/rism.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
copying parmed/amber/mdin/ewald.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
creating build/lib.linux-x86_64-cpython-39/parmed/charmm
copying parmed/charmm/_charmmfile.py -> build/lib.linux-x86_64-cpython-39/parmed/charmm
copying parmed/charmm/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/charmm
copying parmed/charmm/psf.py -> build/lib.linux-x86_64-cpython-39/parmed/charmm
copying parmed/charmm/parameters.py -> build/lib.linux-x86_64-cpython-39/parmed/charmm
copying parmed/charmm/charmmcrds.py -> build/lib.linux-x86_64-cpython-39/parmed/charmm
creating build/lib.linux-x86_64-cpython-39/parmed/formats
creating build/lib.linux-x86_64-cpython-39/parmed/formats/pdbx
copying parmed/formats/pdbx/PdbxReader.py -> build/lib.linux-x86_64-cpython-39/parmed/formats/pdbx
copying parmed/formats/pdbx/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/formats/pdbx
copying parmed/formats/pdbx/PdbxContainers.py -> build/lib.linux-x86_64-cpython-39/parmed/formats/pdbx
copying parmed/formats/pdbx/PdbxWriter.py -> build/lib.linux-x86_64-cpython-39/parmed/formats/pdbx
creating build/lib.linux-x86_64-cpython-39/parmed/rosetta
copying parmed/rosetta/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/rosetta
copying parmed/rosetta/pose.py -> build/lib.linux-x86_64-cpython-39/parmed/rosetta
creating build/lib.linux-x86_64-cpython-39/parmed/rdkit
copying parmed/rdkit/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/rdkit
copying parmed/rdkit/rdkit.py -> build/lib.linux-x86_64-cpython-39/parmed/rdkit
copying parmed/formats/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
copying parmed/formats/registry.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
copying parmed/formats/sdf.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
copying parmed/formats/pqr.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
copying parmed/formats/pdb.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
copying parmed/formats/psf.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
copying parmed/formats/mol2.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
creating build/lib.linux-x86_64-cpython-39/parmed/utils
creating build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
copying parmed/utils/fortranformat/_input.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
copying parmed/utils/fortranformat/_misc.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
copying parmed/utils/fortranformat/_parser.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
copying parmed/utils/fortranformat/FortranRecordWriter.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
copying parmed/utils/fortranformat/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
copying parmed/utils/fortranformat/FortranRecordReader.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
copying parmed/utils/fortranformat/_edit_descriptors.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
copying parmed/utils/fortranformat/_lexer.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
copying parmed/utils/fortranformat/_output.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
copying parmed/utils/fortranformat/config.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
copying parmed/utils/fortranformat/_exceptions.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
creating build/lib.linux-x86_64-cpython-39/parmed/openmm
copying parmed/openmm/topsystem.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
copying parmed/openmm/xmlfile.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
copying parmed/openmm/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
copying parmed/openmm/reporters.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
copying parmed/openmm/utils.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
copying parmed/openmm/parameters.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
copying parmed/utils/six.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
copying parmed/utils/netcdf.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
copying parmed/utils/pairlist.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
copying parmed/utils/decorators.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
copying parmed/utils/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
copying parmed/utils/io.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
copying parmed/utils/timer.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
copying parmed/utils/pandautils.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
creating build/lib.linux-x86_64-cpython-39/parmed/gromacs
copying parmed/gromacs/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
copying parmed/gromacs/_cpp.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
copying parmed/gromacs/gromacsgro.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
copying parmed/gromacs/gromacstop.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
copying parmed/gromacs/_gromacsfile.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
creating build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/addljtype.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/logos.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/parmed_cmd.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/exceptions.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/changeradii.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/checkvalidity.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/parmlist.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/argumentlist.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/actions.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/coarsegrain.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/add1264.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
creating build/lib.linux-x86_64-cpython-39/parmed/namd
copying parmed/namd/namdbinfiles.py -> build/lib.linux-x86_64-cpython-39/parmed/namd
copying parmed/namd/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/namd
creating build/lib.linux-x86_64-cpython-39/parmed/tools/gui
copying parmed/tools/gui/_guiwidgets.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/gui
copying parmed/tools/gui/guifiletools.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/gui
copying parmed/tools/gui/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/gui
copying parmed/tools/gui/guitools.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/gui
copying parmed/tools/gui/guiactions.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/gui
copying parmed/tools/gui/_guiactions.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/gui
creating build/lib.linux-x86_64-cpython-39/parmed/tools/simulations
copying parmed/tools/simulations/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/simulations
copying parmed/tools/simulations/sanderapi.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/simulations
copying parmed/tools/simulations/openmm.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/simulations
creating build/lib.linux-x86_64-cpython-39/parmed/modeller/data
copying parmed/modeller/data/standard_residues.lib -> build/lib.linux-x86_64-cpython-39/parmed/modeller/data
UPDATING build/lib.linux-x86_64-cpython-39/parmed/_version.py
set build/lib.linux-x86_64-cpython-39/parmed/_version.py to '3.4.3+11.g41cc9ab'
running build_ext
building 'parmed.amber._rdparm' extension
creating build/temp.linux-x86_64-cpython-39
creating build/temp.linux-x86_64-cpython-39/src
/home/bubblu/miniconda3/envs/gmxMMPBSA/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/bubblu/miniconda3/envs/gmxMMPBSA/include -fPIC -O2 -isystem /home/bubblu/miniconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/bubblu/miniconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/bubblu/miniconda3/envs/gmxMMPBSA/include -fPIC -I/tmp/pip-req-build-_9q8cz86/src -I/home/bubblu/miniconda3/envs/gmxMMPBSA/include/python3.9 -c src/_rdparm.cpp -o build/temp.linux-x86_64-cpython-39/src/_rdparm.o
In file included from /home/bubblu/miniconda3/envs/gmxMMPBSA/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/locale_facets_nonio.h:39,
from /home/bubblu/miniconda3/envs/gmxMMPBSA/x86_64-conda-linux-gnu/include/c++/11.2.0/locale:41,
from src/readparm.h:5,
from src/_rdparm.cpp:17:
/home/bubblu/miniconda3/envs/gmxMMPBSA/x86_64-conda-linux-gnu/include/c++/11.2.0/ctime:80:11: error: 'timespec_get' has not been declared in '::'
80 | using ::timespec_get;
| ^~~~~~~~~~~~
error: command '/home/bubblu/miniconda3/envs/gmxMMPBSA/bin/x86_64-conda-linux-gnu-cc' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for ParmEd
Running setup.py clean for ParmEd
Failed to build ParmEd
ERROR: Could not build wheels for ParmEd, which is required to install pyproject.toml-based projects
Collecting git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4
Cloning https://github.com/Valdes-Tresanco-MS/ParmEd.git (to revision v3.4) to /tmp/pip-req-build-_9q8cz86
Running command git clone --filter=blob:none --quiet https://github.com/Valdes-Tresanco-MS/ParmEd.git /tmp/pip-req-build-_9q8cz86
Running command git checkout -b v3.4 --track origin/v3.4
Switched to a new branch 'v3.4'
Branch 'v3.4' set up to track remote branch 'v3.4' from 'origin'.
Resolved https://github.com/Valdes-Tresanco-MS/ParmEd.git to commit 41cc9ab1fe930f0c13c36433148d4601307d60c3
Preparing metadata (setup.py) ... done
Building wheels for collected packages: ParmEd
Building wheel for ParmEd (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [167 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-cpython-39
creating build/lib.linux-x86_64-cpython-39/parmed
copying parmed/periodic_table.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/symmetry.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/exceptions.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/_version.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/scripts.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/residue.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/vec3.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/geometry.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/structure.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/parameters.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/constants.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/topologyobjects.py -> build/lib.linux-x86_64-cpython-39/parmed
creating build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/_chamberparm.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/_tinkerparm.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/offlib.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/_amberparm.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/titratable_residues.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/asciicrd.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/amberformat.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/parameters.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/netcdffiles.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/readparm.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/mask.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
creating build/lib.linux-x86_64-cpython-39/parmed/modeller
copying parmed/modeller/standardtemplates.py -> build/lib.linux-x86_64-cpython-39/parmed/modeller
copying parmed/modeller/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/modeller
copying parmed/modeller/residue.py -> build/lib.linux-x86_64-cpython-39/parmed/modeller
creating build/lib.linux-x86_64-cpython-39/parmed/tinker
copying parmed/tinker/system.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
copying parmed/tinker/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
copying parmed/tinker/parameterfile.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
copying parmed/tinker/tinkerfiles.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
copying parmed/tinker/topologyobjects.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
creating build/lib.linux-x86_64-cpython-39/parmed/unit
copying parmed/unit/mymatrix.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
copying parmed/unit/standard_dimensions.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
copying parmed/unit/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
copying parmed/unit/quantity.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
copying parmed/unit/unit_operators.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
copying parmed/unit/prefix.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
copying parmed/unit/unit_math.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
copying parmed/unit/baseunit.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
copying parmed/unit/unit_definitions.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
copying parmed/unit/basedimension.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
copying parmed/unit/constants.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
copying parmed/unit/unit.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
creating build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
copying parmed/amber/mdin/mdin.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
copying parmed/amber/mdin/pb.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
copying parmed/amber/mdin/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
copying parmed/amber/mdin/gbnsr6.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
copying parmed/amber/mdin/cntrl.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
copying parmed/amber/mdin/qmmm.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
copying parmed/amber/mdin/rism.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
copying parmed/amber/mdin/ewald.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
creating build/lib.linux-x86_64-cpython-39/parmed/charmm
copying parmed/charmm/_charmmfile.py -> build/lib.linux-x86_64-cpython-39/parmed/charmm
copying parmed/charmm/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/charmm
copying parmed/charmm/psf.py -> build/lib.linux-x86_64-cpython-39/parmed/charmm
copying parmed/charmm/parameters.py -> build/lib.linux-x86_64-cpython-39/parmed/charmm
copying parmed/charmm/charmmcrds.py -> build/lib.linux-x86_64-cpython-39/parmed/charmm
creating build/lib.linux-x86_64-cpython-39/parmed/formats
creating build/lib.linux-x86_64-cpython-39/parmed/formats/pdbx
copying parmed/formats/pdbx/PdbxReader.py -> build/lib.linux-x86_64-cpython-39/parmed/formats/pdbx
copying parmed/formats/pdbx/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/formats/pdbx
copying parmed/formats/pdbx/PdbxContainers.py -> build/lib.linux-x86_64-cpython-39/parmed/formats/pdbx
copying parmed/formats/pdbx/PdbxWriter.py -> build/lib.linux-x86_64-cpython-39/parmed/formats/pdbx
creating build/lib.linux-x86_64-cpython-39/parmed/rosetta
copying parmed/rosetta/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/rosetta
copying parmed/rosetta/pose.py -> build/lib.linux-x86_64-cpython-39/parmed/rosetta
creating build/lib.linux-x86_64-cpython-39/parmed/rdkit
copying parmed/rdkit/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/rdkit
copying parmed/rdkit/rdkit.py -> build/lib.linux-x86_64-cpython-39/parmed/rdkit
copying parmed/formats/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
copying parmed/formats/registry.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
copying parmed/formats/sdf.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
copying parmed/formats/pqr.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
copying parmed/formats/pdb.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
copying parmed/formats/psf.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
copying parmed/formats/mol2.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
creating build/lib.linux-x86_64-cpython-39/parmed/utils
creating build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
copying parmed/utils/fortranformat/_input.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
copying parmed/utils/fortranformat/_misc.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
copying parmed/utils/fortranformat/_parser.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
copying parmed/utils/fortranformat/FortranRecordWriter.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
copying parmed/utils/fortranformat/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
copying parmed/utils/fortranformat/FortranRecordReader.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
copying parmed/utils/fortranformat/_edit_descriptors.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
copying parmed/utils/fortranformat/_lexer.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
copying parmed/utils/fortranformat/_output.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
copying parmed/utils/fortranformat/config.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
copying parmed/utils/fortranformat/_exceptions.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
creating build/lib.linux-x86_64-cpython-39/parmed/openmm
copying parmed/openmm/topsystem.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
copying parmed/openmm/xmlfile.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
copying parmed/openmm/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
copying parmed/openmm/reporters.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
copying parmed/openmm/utils.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
copying parmed/openmm/parameters.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
copying parmed/utils/six.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
copying parmed/utils/netcdf.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
copying parmed/utils/pairlist.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
copying parmed/utils/decorators.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
copying parmed/utils/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
copying parmed/utils/io.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
copying parmed/utils/timer.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
copying parmed/utils/pandautils.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
creating build/lib.linux-x86_64-cpython-39/parmed/gromacs
copying parmed/gromacs/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
copying parmed/gromacs/_cpp.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
copying parmed/gromacs/gromacsgro.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
copying parmed/gromacs/gromacstop.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
copying parmed/gromacs/_gromacsfile.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
creating build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/addljtype.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/logos.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/parmed_cmd.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/exceptions.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/changeradii.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/checkvalidity.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/parmlist.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/argumentlist.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/actions.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/coarsegrain.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/add1264.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
creating build/lib.linux-x86_64-cpython-39/parmed/namd
copying parmed/namd/namdbinfiles.py -> build/lib.linux-x86_64-cpython-39/parmed/namd
copying parmed/namd/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/namd
creating build/lib.linux-x86_64-cpython-39/parmed/tools/gui
copying parmed/tools/gui/_guiwidgets.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/gui
copying parmed/tools/gui/guifiletools.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/gui
copying parmed/tools/gui/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/gui
copying parmed/tools/gui/guitools.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/gui
copying parmed/tools/gui/guiactions.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/gui
copying parmed/tools/gui/_guiactions.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/gui
creating build/lib.linux-x86_64-cpython-39/parmed/tools/simulations
copying parmed/tools/simulations/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/simulations
copying parmed/tools/simulations/sanderapi.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/simulations
copying parmed/tools/simulations/openmm.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/simulations
creating build/lib.linux-x86_64-cpython-39/parmed/modeller/data
copying parmed/modeller/data/standard_residues.lib -> build/lib.linux-x86_64-cpython-39/parmed/modeller/data
UPDATING build/lib.linux-x86_64-cpython-39/parmed/_version.py
set build/lib.linux-x86_64-cpython-39/parmed/_version.py to '3.4.3+11.g41cc9ab'
running build_ext
building 'parmed.amber._rdparm' extension
creating build/temp.linux-x86_64-cpython-39
creating build/temp.linux-x86_64-cpython-39/src
/home/bubblu/miniconda3/envs/gmxMMPBSA/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/bubblu/miniconda3/envs/gmxMMPBSA/include -fPIC -O2 -isystem /home/bubblu/miniconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/bubblu/miniconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/bubblu/miniconda3/envs/gmxMMPBSA/include -fPIC -I/tmp/pip-req-build-_9q8cz86/src -I/home/bubblu/miniconda3/envs/gmxMMPBSA/include/python3.9 -c src/_rdparm.cpp -o build/temp.linux-x86_64-cpython-39/src/_rdparm.o
In file included from /home/bubblu/miniconda3/envs/gmxMMPBSA/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/locale_facets_nonio.h:39,
from /home/bubblu/miniconda3/envs/gmxMMPBSA/x86_64-conda-linux-gnu/include/c++/11.2.0/locale:41,
from src/readparm.h:5,
from src/_rdparm.cpp:17:
/home/bubblu/miniconda3/envs/gmxMMPBSA/x86_64-conda-linux-gnu/include/c++/11.2.0/ctime:80:11: error: 'timespec_get' has not been declared in '::'
80 | using ::timespec_get;
| ^~~~~~~~~~~~
error: command '/home/bubblu/miniconda3/envs/gmxMMPBSA/bin/x86_64-conda-linux-gnu-cc' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for ParmEd
Running setup.py clean for ParmEd
Failed to build ParmEd
ERROR: Could not build wheels for ParmEd, which is required to install pyproject.toml-based projects
Mario Sergio Valdes
Jun 21, 2023, 2:02:04 AM6/21/23
to gmx_MMPBSA
Please, check this thread https://groups.google.com/g/gmx_mmpbsa/c/ZohP_GQvUEc/m/yW7GeWR4BAAJ
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