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Sarthak Trivedi SVNIT
Jan 7, 2023, 5:46:33 AM1/7/23
to gmx_MMPBSA
Hello,
I can't install gmx_MMPBSA on other device having Ubuntu 20.04 LTS. When i apply following command it shows an error.
(gmxMMPBSA) drr-18@xyz-System-Product-Name:~$ 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-ezrloct2
Running command git clone --filter=blob:none --quiet https://github.com/Valdes-Tresanco-MS/ParmEd.git /tmp/pip-req-build-ezrloct2
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 a195c7ec07b22da09678c5562367f44a068bce19
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/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/scripts.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/topologyobjects.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/periodic_table.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/_version.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/parameters.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/symmetry.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/constants.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/residue.py -> build/lib.linux-x86_64-cpython-39/parmed
creating 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/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/_amberparm.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/__init__.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/offlib.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/mask.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/_chamberparm.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/netcdffiles.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/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
copying parmed/tinker/topologyobjects.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/system.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
creating 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/mymatrix.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/unit_definitions.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/unit.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/prefix.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/unit_math.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/baseunit.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/qmmm.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/mdin.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/pb.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
copying parmed/amber/mdin/rism.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
creating 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/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
copying parmed/charmm/_charmmfile.py -> build/lib.linux-x86_64-cpython-39/parmed/charmm
copying parmed/charmm/psf.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/__init__.py -> 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/PdbxWriter.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
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/pdb.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/mol2.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
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/pqr.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
copying parmed/formats/psf.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/_output.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/FortranRecordWriter.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
copying parmed/utils/fortranformat/FortranRecordReader.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/config.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/_parser.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
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/__init__.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/parameters.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/reporters.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
copying parmed/utils/io.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/timer.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
copying parmed/utils/six.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/netcdf.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/pandautils.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
creating 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/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
copying parmed/gromacs/_gromacsfile.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
copying parmed/gromacs/gromacstop.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
creating 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/add1264.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/__init__.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/coarsegrain.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/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/addljtype.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/parmlist.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/guitools.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/guiactions.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/_guiactions.py -> 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
creating 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
copying parmed/tools/simulations/sanderapi.py -> 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
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+10.ga195c7e'
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/drr-18/miniconda3/envs/gmxMMPBSA/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/drr-18/miniconda3/envs/gmxMMPBSA/include -I/home/drr-18/miniconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/drr-18/miniconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/drr-18/miniconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/drr-18/miniconda3/envs/gmxMMPBSA/include -fPIC -I/tmp/pip-req-build-ezrloct2/src -I/home/drr-18/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/drr-18/miniconda3/envs/gmxMMPBSA/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/locale_facets_nonio.h:39,
from /home/drr-18/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/drr-18/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/drr-18/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
Installing collected packages: ParmEd
Attempting uninstall: ParmEd
Found existing installation: ParmEd 3.4.3
Uninstalling ParmEd-3.4.3:
Successfully uninstalled ParmEd-3.4.3
Running setup.py install for ParmEd ... error
error: subprocess-exited-with-error
× Running setup.py install for ParmEd did not run successfully.
│ exit code: 1
╰─> [169 lines of output]
running install
/home/drr-18/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
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/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/scripts.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/topologyobjects.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/periodic_table.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/_version.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/parameters.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/symmetry.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/constants.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/residue.py -> build/lib.linux-x86_64-cpython-39/parmed
creating 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/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/_amberparm.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/__init__.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/offlib.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/mask.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/_chamberparm.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/netcdffiles.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/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
copying parmed/tinker/topologyobjects.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/system.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
creating 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/mymatrix.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/unit_definitions.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/unit.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/prefix.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/unit_math.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/baseunit.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/qmmm.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/mdin.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/pb.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
copying parmed/amber/mdin/rism.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
creating 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/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
copying parmed/charmm/_charmmfile.py -> build/lib.linux-x86_64-cpython-39/parmed/charmm
copying parmed/charmm/psf.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/__init__.py -> 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/PdbxWriter.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
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/pdb.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/mol2.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
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/pqr.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
copying parmed/formats/psf.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/_output.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/FortranRecordWriter.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
copying parmed/utils/fortranformat/FortranRecordReader.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/config.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/_parser.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
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/__init__.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/parameters.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/reporters.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
copying parmed/utils/io.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/timer.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
copying parmed/utils/six.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/netcdf.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/pandautils.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
creating 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/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
copying parmed/gromacs/_gromacsfile.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
copying parmed/gromacs/gromacstop.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
creating 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/add1264.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/__init__.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/coarsegrain.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/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/addljtype.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/parmlist.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/guitools.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/guiactions.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/_guiactions.py -> 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
creating 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
copying parmed/tools/simulations/sanderapi.py -> 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
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+10.ga195c7e'
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/drr-18/miniconda3/envs/gmxMMPBSA/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/drr-18/miniconda3/envs/gmxMMPBSA/include -I/home/drr-18/miniconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/drr-18/miniconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/drr-18/miniconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/drr-18/miniconda3/envs/gmxMMPBSA/include -fPIC -I/tmp/pip-req-build-ezrloct2/src -I/home/drr-18/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/drr-18/miniconda3/envs/gmxMMPBSA/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/locale_facets_nonio.h:39,
from /home/drr-18/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/drr-18/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/drr-18/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.
Rolling back uninstall of ParmEd
Moving to /home/drr-18/miniconda3/envs/gmxMMPBSA/bin/parmed
from /tmp/pip-uninstall-_vhu95rt/parmed
Moving to /home/drr-18/miniconda3/envs/gmxMMPBSA/bin/xparmed
from /tmp/pip-uninstall-_vhu95rt/xparmed
Moving to /home/drr-18/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/ParmEd-3.4.3.dist-info/
from /home/drr-18/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/~armEd-3.4.3.dist-info
Moving to /home/drr-18/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/
from /home/drr-18/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/~armed
error: legacy-install-failure
× Encountered error while trying to install package.
╰─> ParmEd
note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.
(gmxMMPBSA) xyz@xyz-System-Product-Name:~$
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-ezrloct2
Running command git clone --filter=blob:none --quiet https://github.com/Valdes-Tresanco-MS/ParmEd.git /tmp/pip-req-build-ezrloct2
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 a195c7ec07b22da09678c5562367f44a068bce19
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/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/scripts.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/topologyobjects.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/periodic_table.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/_version.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/parameters.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/symmetry.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/constants.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/residue.py -> build/lib.linux-x86_64-cpython-39/parmed
creating 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/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/_amberparm.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/__init__.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/offlib.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/mask.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/_chamberparm.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/netcdffiles.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/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
copying parmed/tinker/topologyobjects.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/system.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
creating 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/mymatrix.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/unit_definitions.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/unit.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/prefix.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/unit_math.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/baseunit.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/qmmm.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/mdin.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/pb.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
copying parmed/amber/mdin/rism.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
creating 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/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
copying parmed/charmm/_charmmfile.py -> build/lib.linux-x86_64-cpython-39/parmed/charmm
copying parmed/charmm/psf.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/__init__.py -> 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/PdbxWriter.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
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/pdb.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/mol2.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
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/pqr.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
copying parmed/formats/psf.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/_output.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/FortranRecordWriter.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
copying parmed/utils/fortranformat/FortranRecordReader.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/config.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/_parser.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
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/__init__.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/parameters.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/reporters.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
copying parmed/utils/io.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/timer.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
copying parmed/utils/six.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/netcdf.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/pandautils.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
creating 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/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
copying parmed/gromacs/_gromacsfile.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
copying parmed/gromacs/gromacstop.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
creating 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/add1264.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/__init__.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/coarsegrain.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/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/addljtype.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/parmlist.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/guitools.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/guiactions.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/_guiactions.py -> 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
creating 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
copying parmed/tools/simulations/sanderapi.py -> 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
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+10.ga195c7e'
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/drr-18/miniconda3/envs/gmxMMPBSA/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/drr-18/miniconda3/envs/gmxMMPBSA/include -I/home/drr-18/miniconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/drr-18/miniconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/drr-18/miniconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/drr-18/miniconda3/envs/gmxMMPBSA/include -fPIC -I/tmp/pip-req-build-ezrloct2/src -I/home/drr-18/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/drr-18/miniconda3/envs/gmxMMPBSA/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/locale_facets_nonio.h:39,
from /home/drr-18/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/drr-18/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/drr-18/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
Installing collected packages: ParmEd
Attempting uninstall: ParmEd
Found existing installation: ParmEd 3.4.3
Uninstalling ParmEd-3.4.3:
Successfully uninstalled ParmEd-3.4.3
Running setup.py install for ParmEd ... error
error: subprocess-exited-with-error
× Running setup.py install for ParmEd did not run successfully.
│ exit code: 1
╰─> [169 lines of output]
running install
/home/drr-18/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
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/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/scripts.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/topologyobjects.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/periodic_table.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/_version.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/parameters.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/symmetry.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/constants.py -> build/lib.linux-x86_64-cpython-39/parmed
copying parmed/residue.py -> build/lib.linux-x86_64-cpython-39/parmed
creating 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/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/_amberparm.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/__init__.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/offlib.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/mask.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/_chamberparm.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
copying parmed/amber/netcdffiles.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/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
copying parmed/tinker/topologyobjects.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/system.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
creating 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/mymatrix.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/unit_definitions.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/unit.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/prefix.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/unit_math.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/baseunit.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/qmmm.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/mdin.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/pb.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
copying parmed/amber/mdin/rism.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
creating 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/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
copying parmed/charmm/_charmmfile.py -> build/lib.linux-x86_64-cpython-39/parmed/charmm
copying parmed/charmm/psf.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/__init__.py -> 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/PdbxWriter.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
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/pdb.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/mol2.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
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/pqr.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
copying parmed/formats/psf.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/_output.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/FortranRecordWriter.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
copying parmed/utils/fortranformat/FortranRecordReader.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/config.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/_parser.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
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/__init__.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/parameters.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/reporters.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
copying parmed/utils/io.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/timer.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
copying parmed/utils/six.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/netcdf.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/pandautils.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
creating 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/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
copying parmed/gromacs/_gromacsfile.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
copying parmed/gromacs/gromacstop.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
creating 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/add1264.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/__init__.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/coarsegrain.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/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/addljtype.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
copying parmed/tools/parmlist.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/guitools.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/guiactions.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/_guiactions.py -> 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
creating 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
copying parmed/tools/simulations/sanderapi.py -> 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
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+10.ga195c7e'
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/drr-18/miniconda3/envs/gmxMMPBSA/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/drr-18/miniconda3/envs/gmxMMPBSA/include -I/home/drr-18/miniconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/drr-18/miniconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/drr-18/miniconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/drr-18/miniconda3/envs/gmxMMPBSA/include -fPIC -I/tmp/pip-req-build-ezrloct2/src -I/home/drr-18/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/drr-18/miniconda3/envs/gmxMMPBSA/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/locale_facets_nonio.h:39,
from /home/drr-18/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/drr-18/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/drr-18/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.
Rolling back uninstall of ParmEd
Moving to /home/drr-18/miniconda3/envs/gmxMMPBSA/bin/parmed
from /tmp/pip-uninstall-_vhu95rt/parmed
Moving to /home/drr-18/miniconda3/envs/gmxMMPBSA/bin/xparmed
from /tmp/pip-uninstall-_vhu95rt/xparmed
Moving to /home/drr-18/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/ParmEd-3.4.3.dist-info/
from /home/drr-18/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/~armEd-3.4.3.dist-info
Moving to /home/drr-18/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/
from /home/drr-18/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/~armed
error: legacy-install-failure
× Encountered error while trying to install package.
╰─> ParmEd
note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.
(gmxMMPBSA) xyz@xyz-System-Product-Name:~$
Please help me to solve this error. Thank you in advance. 
Mario Sergio Valdes
Jan 7, 2023, 8:13:51 AM1/7/23
to gmx_MMPBSA
Please check this thread (https://groups.google.com/g/gmx_mmpbsa/c/I5-lVPUcHts)
Sarthak Trivedi SVNIT
Jan 7, 2023, 9:04:17 AM1/7/23
to gmx_MMPBSA
(base) drr-18@drr18-System-Product-Name:~/Downloads$ conda env create -n gmxMMPBSA --file env.yml
Collecting package metadata (repodata.json): done
Solving environment: done
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Installing pip dependencies: / Ran pip subprocess with arguments:
['/home/drr-18/miniconda3/envs/gmxMMPBSA/bin/python', '-m', 'pip', 'install', '-U', '-r', '/home/drr-18/Downloads/condaenv.dx_j942a.requirements.txt', '--exists-action=b']
Pip subprocess output:
WARNING: No ICDs were found. Either,
- Install a conda package providing a OpenCL implementation (pocl, oclgrind, intel-compute-runtime, beignet) or
- Make your system-wide implementation visible by installing ocl-icd-system conda package.
Collecting git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4 (from -r /home/drr-18/Downloads/condaenv.dx_j942a.requirements.txt (line 3))
Cloning https://github.com/Valdes-Tresanco-MS/ParmEd.git (to revision v3.4) to /tmp/pip-req-build-2gu4m69c
Pip subprocess error:
ERROR: Error [Errno 2] No such file or directory: 'git' while executing command git version
ERROR: Cannot find command 'git' - do you have 'git' installed and in your PATH?
failed
CondaEnvException: Pip failed
Collecting package metadata (repodata.json): done
Solving environment: done
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Installing pip dependencies: / Ran pip subprocess with arguments:
['/home/drr-18/miniconda3/envs/gmxMMPBSA/bin/python', '-m', 'pip', 'install', '-U', '-r', '/home/drr-18/Downloads/condaenv.dx_j942a.requirements.txt', '--exists-action=b']
Pip subprocess output:
WARNING: No ICDs were found. Either,
- Install a conda package providing a OpenCL implementation (pocl, oclgrind, intel-compute-runtime, beignet) or
- Make your system-wide implementation visible by installing ocl-icd-system conda package.
Collecting git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4 (from -r /home/drr-18/Downloads/condaenv.dx_j942a.requirements.txt (line 3))
Cloning https://github.com/Valdes-Tresanco-MS/ParmEd.git (to revision v3.4) to /tmp/pip-req-build-2gu4m69c
Pip subprocess error:
ERROR: Error [Errno 2] No such file or directory: 'git' while executing command git version
ERROR: Cannot find command 'git' - do you have 'git' installed and in your PATH?
failed
CondaEnvException: Pip failed
Thank you in advance.
Mario Sergio Valdes
Jan 7, 2023, 9:26:33 AM1/7/23
to gmx_MMPBSA
Please, install git
sudo apt install git
or
conda install -c anaconda git.
Lotfi Bourougaa
Jan 21, 2023, 8:17:51 PM1/21/23
to gmx_MMPBSA
Hi
I have the same error as you, did you find a solution?
I have the same error as you, did you find a solution?
Mario Sergio Valdes
Jan 21, 2023, 9:05:55 PM1/21/23
to gmx_MMPBSA
This problem seems to be a conda problem. Please check this thread (https://groups.google.com/g/gmx_mmpbsa/c/I5-lVPUcHts)
Sarthak Trivedi SVNIT
Jan 23, 2023, 1:05:45 AM1/23/23
to gmx_MMPBSA
Hello sir,
Hi bilal and mariosergio the error still persists even after the installation by yml file. The error is related with building wheels for mpi4py.
ERROR: - Building wheel for mpi4py (pyproject.toml) did not run successfully.
ERROR: Could not build wheels for mpi4py, which is required to install pyproject.toml-based projects
I also installed pyprojec.toml-based projects from pyproject-toml, but still it's not building wheels for mpi4py to execute the gmx_MMPBSA installation (Python 3.10.9)
Please help me with the installation
Mario Sergio Valdes
Jan 23, 2023, 2:24:04 AM1/23/23
to gmx_MMPBSA
Finally, I found out what the problem is. The compilers installed (v1.5.2) version is incompatible with the wheel generation. The solution, at least for me is to install version v1.2.0.
conda install -c conda-forge compilers=1.2.0
conda install -c conda-forge compilers=1.2.0
I will update everything related to the documentation. Let me know if it worked for you.
Mario S.
Sarthak Trivedi SVNIT
Jan 23, 2023, 5:34:06 AM1/23/23
to gmx_MMPBSA
Hi Sir,
Thank you so much for your support. The issue is resolved and i successfully installed gmx_MMPBSA by installing compilers 1.2.0 as you suggested. Thank you again.
Regards,
Sarthak.
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