On Fri, Oct 18, 2024, Andriy Kovalenko via AMBER wrote:
>
>At present, I have installed Ubuntu 24.04.1 LTS on my Dell Precision Tower
>5810 desktop from scratch, and have now been installing Amber24 and
>AmberTools24.
Hi Andriy: sorry to be so slow in replying. I'm hoping that someone with
access to Ubuntu 24.04 will be able to try to reproduce your problem. I
have a request out for volunteers, but maybe someon reading this on the
Amber mailing list will be able to chime in.
....dac
>Running *./run_cmake* (please see attached) succeeded in part.
>Running *make Install* (please see attached) ended up with:
>
> CMake Error at
>/home/andriy/amber24_src/cmake/Replace-function.cmake:32 (file):
> file failed to open for reading (No such file or directory):
>
>
>/home/andriy/amber24//miniconda/lib/python3.12/site-packages/conda_build/convert.py
> Call Stack (most recent call first):
>
>/home/andriy/amber24_src/cmake/FixCondaShebang/FixCondaShebang.cmake:48
>(configuretime_file_replace)
>
>Searching in amberarchives produced little.
>
>Could you please advise how to resolve this issue?
>
>Sincerely,
>
>
>Dr. Andriy Kovalenko
>
>Research Assistant
>Department of Biological Sciences
>University of Alberta
>CW 405, Biological Sciences Bldg.
>Edmonton, Alberta, Canada T6G 2E9
>
>Tel: 780-940-7477 (cell)
>e-mail: andriy.kovalenko.ualberta.ca
>andriy.andriy-Precision-Tower-5810:~/amber24_src/build$ ./run_cmake
>-- **************************************************************************
>-- Starting configuration of Amber version 24.0.0...
>-- CMake Version: 3.28.3
>-- For how to use this build system, please read this wiki:
>-- http://ambermd.org/pmwiki/pmwiki.php/Main/CMake
>-- For a list of important CMake variables, check here:
>-- http://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options
>-- **************************************************************************
>-- Amber source found, building AmberTools and Amber
>-- Miniconda is installed in the build directory!
>CMake Warning (dev) at cmake/PythonBuildConfig.cmake:13 (find_package):
> Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
> are removed. Run "cmake --help-policy CMP0148" for policy details. Use
> the cmake_policy command to set the policy and suppress this warning.
>
>Call Stack (most recent call first):
> CMakeLists.txt:121 (include)
>This warning is for project developers. Use -Wno-dev to suppress it.
>
>-- Found PythonLibs: /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/libpython3.12.so
>-- Found perl make: /usr/bin/make
>-- Perl modules well be installed to AMBERHOME/lib/perl
>-- Running updater...
>-- >>> Preparing to apply updates... please wait.
>-- >>> No new updates available for AmberTools 24
>-- >>> No new updates available for Amber 24
>-- Updater done. If you want to install updates, then set the APPLY_UPDATES variable to true.
>-- Checking whether to use built-in libraries...
>-- Unable to locate MKL_HOME for your system. To use MKL, set MKL_HOME to point to your MKL installation location.
>CMake Warning (dev) at /usr/share/cmake-3.28/Modules/FindPackageHandleStandardArgs.cmake:438 (message):
> The package name passed to `find_package_handle_standard_args` (OpenMP_C)
> does not match the name of the calling package (OpenMPFixed). This can
> lead to problems in calling code that expects `find_package` result
> variables (e.g., `_FOUND`) to follow a certain pattern.
>Call Stack (most recent call first):
> cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408 (find_package_handle_standard_args)
> cmake/hanjianwei/FindMKL.cmake:194 (find_package)
> cmake/3rdPartyTools.cmake:233 (find_package)
> CMakeLists.txt:218 (include)
>This warning is for project developers. Use -Wno-dev to suppress it.
>
>-- Could NOT find OpenMP_C (missing: OpenMP_pthread_LIBRARY)
>CMake Warning (dev) at /usr/share/cmake-3.28/Modules/FindPackageHandleStandardArgs.cmake:438 (message):
> The package name passed to `find_package_handle_standard_args` (OpenMP_CXX)
> does not match the name of the calling package (OpenMPFixed). This can
> lead to problems in calling code that expects `find_package` result
> variables (e.g., `_FOUND`) to follow a certain pattern.
>Call Stack (most recent call first):
> cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408 (find_package_handle_standard_args)
> cmake/hanjianwei/FindMKL.cmake:194 (find_package)
> cmake/3rdPartyTools.cmake:233 (find_package)
> CMakeLists.txt:218 (include)
>This warning is for project developers. Use -Wno-dev to suppress it.
>
>-- Could NOT find OpenMP_CXX (missing: OpenMP_pthread_LIBRARY)
>CMake Warning (dev) at /usr/share/cmake-3.28/Modules/FindPackageHandleStandardArgs.cmake:438 (message):
> The package name passed to `find_package_handle_standard_args`
> (OpenMP_Fortran) does not match the name of the calling package
> (OpenMPFixed). This can lead to problems in calling code that expects
> `find_package` result variables (e.g., `_FOUND`) to follow a certain
> pattern.
>Call Stack (most recent call first):
> cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408 (find_package_handle_standard_args)
> cmake/hanjianwei/FindMKL.cmake:194 (find_package)
> cmake/3rdPartyTools.cmake:233 (find_package)
> CMakeLists.txt:218 (include)
>This warning is for project developers. Use -Wno-dev to suppress it.
>
>-- Could NOT find OpenMP_Fortran (missing: OpenMP_pthread_LIBRARY)
>-- Could NOT find MKL (missing: MKL_INTERFACE_LIBRARY MKL_GFORTRAN_INTERFACE_LIBRARY MKL_GNU_THREADING_LIBRARY MKL_CORE_LIBRARY OpenMP_C_FOUND MKL_WORKS MKL_FORTRAN_WORKS)
>-- hints given to look for KMMD in DIR:
>-- found KMMD?: KMMD_LIB-NOTFOUND
>-- found INCLUDES?:
>-- Did not find an external KMMD library, should be able to use bundled. If you have a custom version then set the path with -DKMMD_DIR (missing: KMMD_LIB)
>-- Cannot search for FFTW Fortran headers because the serial headers were not found
>-- Could NOT find FFTW (missing: FFTW_LIBRARY_SERIAL FFTW_WORKS FFTW_INCLUDES_SERIAL FFTW_FORTRAN_WORKS)
>-- Failed to find NetCDF interface for F77 (NetCDF_INCLUDES_F77 = NetCDF_INCLUDES_F77-NOTFOUND, NetCDF_LIBRARIES_F77 = NetCDF_LIBRARIES_F77-NOTFOUND)
>-- Failed to find NetCDF interface for F90 (NetCDF_INCLUDES_F90 = NetCDF_INCLUDES_F90-NOTFOUND, NetCDF_LIBRARIES_F90 = NetCDF_LIBRARIES_F90-NOTFOUND)
>-- Could NOT find NetCDF (missing: NetCDF_C_WORKS NetCDF_LIBRARIES NetCDF_INCLUDES)
>-- Could NOT find Protobuf (missing: Protobuf_LIBRARIES Protobuf_INCLUDE_DIR)
>-- Could NOT find XBLAS (missing: XBLAS_LIBRARY XBLAS_C_WORKS XBLAS_FORTRAN_WORKS)
>-- A library with BLAS API not found. Please specify library location.
>-- LAPACK requires BLAS
>-- A library with LAPACK API not found. Please specify library location.
>-- The ARPACK library was not found. Please set ARPACK_LIBRARY to point to it. (missing: ARPACK_LIBRARY ARPACK_WORKS)
>-- Could not find some or all of the five main APBS libraries. Please set APBS_GENERIC_LIB, APBS_ROUTINES_LIB,
>APBS_PMGC_LIB, APBS_MG_LIB, APBS_MC_LIB, APBS_FEM_LIB, UMFPACK_LIB, and APBS_MALOC_LIB to point to the correct libraries (missing: APBS_API_LIB APBS_ROUTINES_LIB APBS_MG_LIB APBS_PMGC_LIB APBS_GENERIC_LIB APBS_FEM_LIB APBS_MC_LIB UMFPACK_LIB APBS_MALOC_LIB APBS_WORKS APBS_INCLUDES)
>-- Could NOT find JNI (missing: JAVA_INCLUDE_PATH JAVA_INCLUDE_PATH2 AWT JVM)
>-- Could NOT find PUPIL (missing: PUPIL_MAIN_LIB PUPIL_BLIND_LIB PUPIL_TIME_LIB JNI_FOUND PUPIL_WORKS)
>-- Could NOT find LIO (missing: LIO_G2G_LIBRARY LIO_AMBER_LIBRARY LIO_WORKS)
>-- Could NOT find PLUMED (missing: PLUMED_LIBRARY PLUMED_KERNEL_LIBRARY PLUMED_INCLUDES PLUMED_WORKS) (Required is at least version "2.5")
>-- Checking for perl module Chemistry::Mol
>-- Checking for perl module Chemistry::Mol - failed
>-- Failed to find Perl modules: Chemistry::Mol (missing: PERLMODULES_CHEMISTRY_MOL_MODULE)
>-- Could NOT find MBX (missing: MBX_DIR)
>-- Could not find MBX. To locate it, add its install dir to the prefix path.
>-- Could NOT find tng_io (missing: tng_io_DIR)
>-- Could not find tng_io. To locate it, add its install dir to the prefix path.
>-- The following libraries were found on your system, but are not being used: boost
>-- This is because the Amber devs have frequently seen broken installs of these libraries causing trouble.
>-- To tell Amber to link to these libraries, you can select individual ones using -DFORCE_EXTERNAL_LIBS=<names>.
>-- Alternatively, you can request that Amber link to all libraries it finds using -DTRUST_SYSTEM_LIBS=TRUE.
>-- KMMD not added to 3RDPARTY_SUBDIRS :
>-- : ucpp-1.3;fftw-3.3
>-- Cannot find PLUMED. You will still be able to load it at runtime. If you want to link it at build time, set PLUMED_ROOT to where you installed it.
>-- Generating amber source scripts
>-- Configuring subdirs...
>CMake Deprecation Warning at AmberTools/src/fftw-3.3/CMakeLists.txt:1 (cmake_minimum_required):
> Compatibility with CMake < 3.5 will be removed from a future version of
> CMake.
>
> Update the VERSION argument <min> value or use a ...<max> suffix to tell
> CMake that the project does not need compatibility with older versions.
>
>
>-- FFTW: compiler supports stack alignment: TRUE
>CMake Warning (dev) at AmberTools/src/netcdf-4.6.1/CMakeLists.txt:40 (exec_program):
> Policy CMP0153 is not set: The exec_program command should not be called.
> Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy
> command to set the policy and suppress this warning.
>
> Use execute_process() instead.
>Call Stack (most recent call first):
> AmberTools/src/netcdf-4.6.1/CMakeLists.txt:42 (getuname)
>This warning is for project developers. Use -Wno-dev to suppress it.
>
>CMake Warning (dev) at AmberTools/src/netcdf-4.6.1/CMakeLists.txt:40 (exec_program):
> Policy CMP0153 is not set: The exec_program command should not be called.
> Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy
> command to set the policy and suppress this warning.
>
> Use execute_process() instead.
>Call Stack (most recent call first):
> AmberTools/src/netcdf-4.6.1/CMakeLists.txt:43 (getuname)
>This warning is for project developers. Use -Wno-dev to suppress it.
>
>CMake Warning (dev) at AmberTools/src/netcdf-4.6.1/CMakeLists.txt:40 (exec_program):
> Policy CMP0153 is not set: The exec_program command should not be called.
> Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy
> command to set the policy and suppress this warning.
>
> Use execute_process() instead.
>Call Stack (most recent call first):
> AmberTools/src/netcdf-4.6.1/CMakeLists.txt:44 (getuname)
>This warning is for project developers. Use -Wno-dev to suppress it.
>
>-- Found bash: /usr/bin/bash
>CMake Warning (dev) at AmberTools/src/netcdf-fortran-4.4.4/CMakeLists.txt:37 (exec_program):
> Policy CMP0153 is not set: The exec_program command should not be called.
> Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy
> command to set the policy and suppress this warning.
>
> Use execute_process() instead.
>Call Stack (most recent call first):
> AmberTools/src/netcdf-fortran-4.4.4/CMakeLists.txt:39 (getuname)
>This warning is for project developers. Use -Wno-dev to suppress it.
>
>CMake Warning (dev) at AmberTools/src/netcdf-fortran-4.4.4/CMakeLists.txt:37 (exec_program):
> Policy CMP0153 is not set: The exec_program command should not be called.
> Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy
> command to set the policy and suppress this warning.
>
> Use execute_process() instead.
>Call Stack (most recent call first):
> AmberTools/src/netcdf-fortran-4.4.4/CMakeLists.txt:40 (getuname)
>This warning is for project developers. Use -Wno-dev to suppress it.
>
>CMake Warning (dev) at AmberTools/src/netcdf-fortran-4.4.4/CMakeLists.txt:37 (exec_program):
> Policy CMP0153 is not set: The exec_program command should not be called.
> Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy
> command to set the policy and suppress this warning.
>
> Use execute_process() instead.
>Call Stack (most recent call first):
> AmberTools/src/netcdf-fortran-4.4.4/CMakeLists.txt:41 (getuname)
>This warning is for project developers. Use -Wno-dev to suppress it.
>
>-- netcdf-fortran: Detected TS29113 support in Fortran compiler
>CMake Deprecation Warning at AmberTools/src/nlopt/CMakeLists.txt:15 (cmake_minimum_required):
> Compatibility with CMake < 3.5 will be removed from a future version of
> CMake.
>
> Update the VERSION argument <min> value or use a ...<max> suffix to tell
> CMake that the project does not need compatibility with older versions.
>
>
>-- NLopt version 2.7.1
>CMake Warning (dev) at AmberTools/src/nlopt/CMakeLists.txt:314 (find_package):
> Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
> are removed. Run "cmake --help-policy CMP0148" for policy details. Use
> the cmake_policy command to set the policy and suppress this warning.
>
>This warning is for project developers. Use -Wno-dev to suppress it.
>
>CMake Warning (dev) at AmberTools/src/nlopt/CMakeLists.txt:315 (find_package):
> Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
> are removed. Run "cmake --help-policy CMP0148" for policy details. Use
> the cmake_policy command to set the policy and suppress this warning.
>
>This warning is for project developers. Use -Wno-dev to suppress it.
>
>-- Found PythonLibs: /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/libpython3.12.so (Required is exact version "3.11.9")
>CMake Warning (dev) at AmberTools/src/nlopt/cmake/FindNumPy.cmake:45 (find_package):
> Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
> are removed. Run "cmake --help-policy CMP0148" for policy details. Use
> the cmake_policy command to set the policy and suppress this warning.
>
>Call Stack (most recent call first):
> AmberTools/src/nlopt/CMakeLists.txt:316 (find_package)
>This warning is for project developers. Use -Wno-dev to suppress it.
>
>-- Could NOT find Guile (missing: GUILE_EXECUTABLE GUILE_ROOT_DIR GUILE_INCLUDE_DIRS GUILE_LIBRARIES)
>-- Could NOT find SWIG (missing: SWIG_EXECUTABLE SWIG_DIR)
>-- Could NOT find Octave (missing: OCTAVE_EXECUTABLE OCTAVE_ROOT_DIR OCTAVE_INCLUDE_DIRS OCTAVE_LIBRARIES)
>-- Could NOT find Matlab (missing: Matlab_INCLUDE_DIRS Matlab_MEX_LIBRARY Matlab_MEX_EXTENSION Matlab_ROOT_DIR Matlab_MX_LIBRARY MX_LIBRARY MAIN_PROGRAM) (found version "NOTFOUND")
>CMake Warning at /usr/share/cmake-3.28/Modules/CPack.cmake:507 (message):
> CPack.cmake has already been included!!
>Call Stack (most recent call first):
> AmberTools/src/nlopt/CMakeLists.txt:368 (include)
>
>
>-- Reticulating splines...
>CMake Deprecation Warning at AmberTools/src/cpptraj/CMakeLists.txt:1 (cmake_minimum_required):
> Compatibility with CMake < 3.5 will be removed from a future version of
> CMake.
>
> Update the VERSION argument <min> value or use a ...<max> suffix to tell
> CMake that the project does not need compatibility with older versions.
>
>
>-- Found C++11 support: cxx_std_11
>CMake Deprecation Warning at AmberTools/src/cphstats/CMakeLists.txt:3 (cmake_minimum_required):
> Compatibility with CMake < 3.5 will be removed from a future version of
> CMake.
>
> Update the VERSION argument <min> value or use a ...<max> suffix to tell
> CMake that the project does not need compatibility with older versions.
>
>
>CMake Warning at src/pmemd/src/xray/CMakeLists.txt:25 (message):
> PMEMD_XRAY_CPU_FFT_BACKEND=NONE disables xray functionality of `pmemd`
> executable
>
>
>-- KMMD_LIB: kmmd
>If you can't see the following build report, then you need to turn off COLOR_CMAKE_MESSAGES
>-- **************************************************************************
>-- Build Report
>-- Compiler Flags:
>-- C No-Opt: -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -fcommon -O0
>-- C Optimized: -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -fcommon -O3 -mtune=native
>--
>-- CXX No-Opt: -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-local-typedefs -Wno-unused-variable -Wno-unused-but-set-variable -O0
>-- CXX Optimized: -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-local-typedefs -Wno-unused-variable -Wno-unused-but-set-variable -O3 -mtune=native
>--
>-- Fortran No-Opt: -Wall -Wno-tabs -Wno-unused-function -ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -fallow-argument-mismatch -fno-inline-arg-packing -O0
>-- Fortran Optimized: -Wall -Wno-tabs -Wno-unused-function -ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -fallow-argument-mismatch -fno-inline-arg-packing -O3 -mtune=native
>--
>-- 3rd Party Libraries
>-- ---building bundled: -----------------------------------------------------
>-- blas - for fundamental linear algebra calculations
>-- lapack - for fundamental linear algebra calculations
>-- arpack - for fundamental linear algebra calculations
>-- ucpp - used as a preprocessor for the NAB compiler
>-- netcdf - for creating trajectory data files
>-- netcdf-fortran - for creating trajectory data files from Fortran
>-- fftw - used to do Fourier transforms very quickly
>-- xblas - used for high-precision linear algebra calculations
>-- boost - C++ support library
>-- kmmd - Machine-learning molecular dynamics
>-- tng_io - enables GROMACS tng trajectory input in cpptraj
>-- nlopt - used to perform nonlinear optimizations
>-- perlmol - chemistry library used by FEW
>-- ---using installed: ------------------------------------------------------
>-- readline - enables an interactive terminal in cpptraj
>-- zlib - for various compression and decompression tasks
>-- libbz2 - for bzip2 compression in cpptraj
>-- libm - for fundamental math routines if they are not contained in the C library
>-- ---disabled: ------------------------------------------------
>-- c9x-complex - used as a support library on systems that do not have C99 complex.h support
>-- protobuf - protocol buffers library, used for communication with external software in QM/MM
>-- lio - used by Sander to run certain QM routines on the GPU
>-- apbs - used by Sander as an alternate Poisson-Boltzmann equation solver
>-- pupil - used by Sander as an alternate user interface
>-- plumed - used as an alternate MD backend for Sander
>-- mkl - alternate implementation of lapack and blas that is tuned for speed
>-- mbx - computes energies and forces for pmemd with the MB-pol model
>-- libtorch - enables libtorch C++ library for tensor computation and dynamic neural networks
>
>-- Features:
>-- MPI: OFF
>-- MVAPICH2-GDR for GPU-GPU comm.: OFF
>-- OpenMP: OFF
>-- CUDA: OFF
>-- Build Shared Libraries: ON
>-- Build GUI Interfaces: OFF
>-- Build Python Programs: ON
>-- -Python Interpreter: Internal Miniconda (version 3.11)
>-- Build Perl Programs: ON
>-- Build configuration: RELEASE
>-- Target Processor: x86_64
>-- Build Documentation: ON
>-- Sander Variants: normal LES API LES-API
>-- Install location: /home/andriy/amber24/
>-- Installation of Tests: ON
>
>-- Compilers:
>-- C: GNU 13.2.0 (/usr/bin/gcc)
>-- CXX: GNU 13.2.0 (/usr/bin/g++)
>-- Fortran: GNU 13.2.0 (/usr/bin/gfortran)
>
>-- Building Tools:
>-- addles ambpdb antechamber cew cifparse cphstats cpptraj emil etc fe-toolkit few gbnsr6 gem.pmemd kmmd leap lib mdgx mm_pbsa mmpbsa_py moft nabc ndiff-2.00 nfe-umbrella-slice nmode nmr_aux packmol_memgen paramfit parmed pbsa pdb4amber pmemd pymsmt pysander pytraj quick reduce rism sander saxs sebomd sff sqm xray xtalutil
>
>-- NOT Building Tools:
>-- tcpb-cpp - BUILD_TCPB is not enabled
>-- tcpb-cpp/pytcpb - BUILD_TCPB is not enabled
>-- reaxff_puremd - BUILD_REAXFF_PUREMD is not enabled
>-- gpu_utils - Requires CUDA
>-- **************************************************************************
>-- Environment resource files are provided to set the proper environment
>-- variables to use AMBER and AmberTools. This is required to run any Python
>-- programs (like MMPBSA.py, ParmEd, MCPB.py, and pytraj)
>--
>-- If you use a Bourne shell (e.g., bash, sh, zsh, etc.), source the
>-- /home/andriy/amber24//amber.sh file in your shell. Consider adding the line
>-- test -f /home/andriy/amber24//amber.sh && source /home/andriy/amber24//amber.sh
>-- to your startup file (e.g., ~/.bashrc)
>--
>-- If you use a C shell (e.g., csh, tcsh), source the
>-- /home/andriy/amber24//amber.csh file in your shell. Consider adding the line
>-- test -f /home/andriy/amber24//amber.csh && source /home/andriy/amber24//amber.csh
>-- to your startup file (e.g., ~/.cshrc)
>--
>-- Amber will be installed to /home/andriy/amber24/
>-- Configuring done (5.9s)
>-- Generating done (0.8s)
>-- Build files have been written to: /home/andriy/amber24_src/build
>
>If errors are reported, search for 'CMake Error' in the cmake.log file.
>
>If the cmake build report looks OK, you should now do the following:
>
> make install
> source /home/andriy/amber24/amber.sh
>
>Consider adding the last line to your login startup script, e.g. ~/.bashrc
>
>andriy.andriy-Precision-Tower-5810:~/amber24_src/build$ make install
>[ 0%] Built target ucpp
>[ 0%] Built target simd_support
>[ 2%] Built target fftw_api
>[ 3%] Built target dft
>[ 3%] Built target dft_scalar
>[ 4%] Built target dft_scalar_codelets
>[ 8%] Built target dft_sse2_codelets
>[ 8%] Built target rdft
>[ 8%] Built target rdft_scalar
>[ 10%] Built target rdft_scalar_r2cb
>[ 12%] Built target rdft_scalar_r2cf
>[ 12%] Built target rdft_scalar_r2r
>[ 13%] Built target rdft_sse2_codelets
>[ 14%] Built target fftw_kernel
>[ 14%] Built target reodft
>[ 14%] Built target fftw
>[ 15%] Built target libfftw_bench
>[ 15%] Built target fftw_benchmark_common_obj
>[ 15%] Built target fftw_benchmark
>[ 15%] Built target fftw_wisdom
>[ 15%] Built target dispatch
>[ 16%] Built target netcdf3
>[ 16%] Built target netcdf
>[ 16%] Built target ncgen
>[ 16%] Built target ncgen3
>[ 17%] Built target ncdump
>[ 17%] Built target nccopy
>[ 17%] Built target netcdff
>[ 17%] Built target xblas_build
>[ 19%] Built target blas
>[ 25%] Built target lapack
>[ 26%] Built target arpack
>[ 26%] Built target PerlMol
>[ 26%] Built target boost_build
>[ 26%] Built target tng_io
>[ 26%] Built target generate-cpp
>[ 26%] Built target generate-fortran
>[ 27%] Built target nlopt
>[ 27%] Built target amber_common
>[ 28%] Built target rism
>[ 28%] Built target sff_rism_interface
>[ 28%] Built target sff_lex
>[ 28%] Built target dsarpack_obj
>[ 28%] Built target sff
>[ 29%] Built target gbnsr6
>[ 29%] Built target cifparse
>[ 30%] Built target addles
>[ 30%] Built target libcew
>[ 31%] Built target sqm_common
>[ 31%] Built target libsqm
>[ 32%] Built target libpbsa
>[ 32%] Built target sff_fortran
>[ 32%] Built target sander_rism_interface
>[ 36%] Built target xc
>[ 36%] Built target octree
>[ 39%] Built target libquick
>[ 44%] Built target sander_base_obj
>[ 46%] Built target sebomd
>[ 46%] Built target emil
>[ 46%] Built target kmmd
>[ 46%] Built target pbsa_sander
>[ 46%] Built target sander
>[ 51%] Built target sander.LES
>[ 51%] Built target ambmask
>[ 56%] Built target libsander
>[ 61%] Built target libsanderles
>[ 61%] Built target makeDIST_RST
>[ 61%] Built target makeANG_RST
>[ 61%] Built target nef_to_RST
>[ 63%] Built target nmode
>[ 63%] Built target antechamber_eprintf_obj
>[ 63%] Built target am1bcc
>[ 63%] Built target atomtype
>[ 63%] Built target espgen
>[ 63%] Built target parmcal
>[ 63%] Built target parmchk2
>[ 63%] Built target prepgen
>[ 63%] Built target residuegen
>[ 63%] Built target respgen
>[ 63%] Built target match
>[ 64%] Built target match_atomname
>[ 64%] Built target antechamber
>[ 64%] Built target bondtype
>[ 64%] Built target test-penalties
>[ 64%] Built target test-int-part
>[ 65%] Built target test-combination
>[ 66%] Built target sqm
>[ 67%] Built target pdb++
>[ 67%] Built target toolclasses
>[ 67%] Built target reduce
>[ 67%] Built target ndiff
>[ 69%] Built target gem.pmemd
>[ 69%] Built target add_pdb
>[ 69%] Built target add_xray
>[ 79%] Built target cpptraj_common_obj
>[ 79%] Built target xdrfile
>[ 80%] Built target cpptraj
>[ 80%] Built target libcpptraj
>[ 81%] Built target cpptraj_core
>[ 81%] Built target cpptraj_file
>[ 81%] Built target cpptraj_traj
>[ 82%] Built target cpptraj_parm
>[ 82%] Built target ambpdb
>[ 84%] Built target pbsa
>[ 84%] Built target simplepbsa
>[ 84%] Built target hcp_getpdb
>[ 84%] Built target rism3d.snglpnt
>[ 84%] Built target rism1d
>[ 84%] Built target elsize
>[ 85%] Built target resp
>[ 85%] Built target gwh
>[ 85%] Built target tinker_to_amber
>[ 86%] Built target mdgx_common_obj
>[ 86%] Built target mdgx
>[ 86%] Built target libmdgx
>[ 86%] Built target Xtal
>[ 86%] Built target AddToBox
>[ 86%] Built target ChBox
>[ 86%] Built target PropPDB
>[ 86%] Built target UnitCell
>[ 86%] Built target saxs_common_obj
>[ 86%] Built target saxs_rism
>[ 86%] Built target saxs_md
>[ 86%] Built target libsaxs_rism
>[ 86%] Built target libsaxs_md
>[ 86%] Built target make_crd_hg
>[ 86%] Built target nabc
>[ 86%] Built target mm_pbsa_nabnmode
>[ 87%] Built target paramfit
>[ 87%] Built target draw_membrane2
>[ 87%] Built target cphstats
>[ 87%] Built target cestats
>[ 88%] Built target quick
>[ 88%] Built target test-api
>[ 88%] Built target nfe-umbrella-slice
>[ 88%] Built target leap_common_obj
>[ 88%] Built target leap_general_obj
>[ 89%] Built target leap_hierarchy_obj
>[ 90%] Built target utilMakeHelp
>[ 90%] Built target leap_leap_obj
>[ 90%] Built target leap_terminal_obj
>[ 90%] Built target teLeap
>[ 90%] Built target mmpbsa_py_energy
>[ 90%] Built target mmpbsa_py_nabnmode
>[ 90%] Building pysander native library
>Copying sander extension source to sanderles...
>running build
>running build_py
>copying sanderles/__init__.py -> /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-cpython-311/sanderles
>running build_ext
>building 'sanderles.pysander' extension
>gcc -pthread -B /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include -fPIC -DLES -I/home/andriy/amber24_src/AmberTools/src/include -I/home/andriy/amber24_src/AmberTools/src/sander -I/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include/python3.11 -c sanderles/src/pysandermodule.c -o /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/temp.linux-x86_64-cpython-311/sanderles/src/pysandermodule.o
>In file included from sanderles/src/pysandermodule.c:16:
>/home/andriy/amber24_src/AmberTools/src/sander/sander.h: In function ‘pysander_setup’:
>/home/andriy/amber24_src/AmberTools/src/sander/sander.h:342:5: warning: ‘__builtin_strncpy’ specified bound 256 equals destination size [-Wstringop-truncation]
> 342 | strncpy(prmtop, prmname, __MAX_FN_LEN);
> | ^
>gcc -pthread -B /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/compiler_compat -shared -Wl,-rpath,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -L/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -L/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/temp.linux-x86_64-cpython-311/sanderles/src/pysandermodule.o -L/home/andriy/amber24_src/build/AmberTools/src/sander -L/home/andriy/amber24_src/build/AmberTools/src/sander -lsanderles -o /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-cpython-311/sanderles/pysander.cpython-311-x86_64-linux-gnu.so
>[ 90%] Built target pysander
>[ 90%] Building pytraj native library
>sys.argv ['setup.py', 'build', '-b', '/home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build', '--disable-openmp']
>Original compiler envs
>CXX = /usr/bin/g++
>CC = /usr/bin/gcc
>COMPILER =
>use_pip = False, cpptraj_home =
>compile_c_extension = True
>2.0.6
>use_prebuilt_cythonized_files = False
>pytraj is inside AMBERHOME
>using environment: CC=/usr/bin/gcc, CXX=/usr/bin/g++
>using CC=/usr/bin/gcc, CXX=/usr/bin/g++
>Final compiler envs
>CXX = /usr/bin/g++
>CC = /usr/bin/gcc
>COMPILER =
>install = True
>set rpath to /home/andriy/amber24_src/build/AmberTools/src/cpptraj/src
>/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/dist.py:476: SetuptoolsDeprecationWarning: Invalid dash-separated options
>!!
>
> ********************************************************************************
> Usage of dash-separated 'description-file' will not be supported in future
> versions. Please use the underscore name 'description_file' instead.
>
> This deprecation is overdue, please update your project and remove deprecated
> calls to avoid build errors in the future.
>
> See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
> ********************************************************************************
>
>!!
> opt = self.warn_dash_deprecation(opt, section)
>running build
>running build_py
>copying pytraj/version.py -> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj
>running build_ext
>[ 90%] Built target pytraj
>[ 90%] Built target memembed
>[ 91%] Built target packmol
>[ 91%] Built target immers
>[ 91%] Built target metatwist
>[ 92%] Built target edgembar
>[ 93%] Built target ndfes
>[ 93%] Built target ndfes-path
>[ 93%] Built target pmemd_xray_contracts
>[ 94%] Built target xray_fft_interface
>[ 94%] Built target pmemd_xray_cpu
>[ 97%] Built target pmemd
>[100%] Built target pmemd.decomp
>Install the project...
>-- Install configuration: "RELEASE"
>-- Installing: /home/andriy/amber24/miniconda/bin/xzmore
>-- Installing: /home/andriy/amber24/miniconda/bin/ipython
>-- Installing: /home/andriy/amber24/miniconda/bin/mrcfile-validate
>-- Installing: /home/andriy/amber24/miniconda/bin/xzgrep
>-- Installing: /home/andriy/amber24/miniconda/bin/pyftsubset
>-- Installing: /home/andriy/amber24/miniconda/bin/jupyter
>-- Installing: /home/andriy/amber24/miniconda/bin/icu-config
>-- Installing: /home/andriy/amber24/miniconda/bin/pyftmerge
>-- Installing: /home/andriy/amber24/miniconda/bin/pdb2pqr
>-- Installing: /home/andriy/amber24/miniconda/bin/send2trash
>-- Installing: /home/andriy/amber24/miniconda/bin/deactivate
>-- Installing: /home/andriy/amber24/miniconda/bin/conda-env
>-- Installing: /home/andriy/amber24/miniconda/bin/conda-skeleton
>-- Installing: /home/andriy/amber24/miniconda/bin/conda-debug
>-- Installing: /home/andriy/amber24/miniconda/bin/jlpm
>-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-events
>-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-dejavu
>-- Installing: /home/andriy/amber24/miniconda/bin/2to3-3.11
>-- Installing: /home/andriy/amber24/miniconda/bin/conda-inspect
>-- Installing: /home/andriy/amber24/miniconda/bin/idle3.11
>-- Installing: /home/andriy/amber24/miniconda/bin/xzdiff
>-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-run
>-- Installing: /home/andriy/amber24/miniconda/bin/httpx
>-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-kernelspec
>-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-migrate
>-- Installing: /home/andriy/amber24/miniconda/bin/cygdb
>-- Installing: /home/andriy/amber24/miniconda/bin/normalizer
>-- Installing: /home/andriy/amber24/miniconda/bin/mrcfile-header
>-- Installing: /home/andriy/amber24/miniconda/bin/ipython3
>-- Installing: /home/andriy/amber24/miniconda/bin/wsdump
>-- Installing: /home/andriy/amber24/miniconda/bin/pydoc3.11
>-- Installing: /home/andriy/amber24/miniconda/bin/conda-content-trust
>-- Installing: /home/andriy/amber24/miniconda/bin/pyjson5
>-- Installing: /home/andriy/amber24/miniconda/bin/ncursesw6-config
>-- Installing: /home/andriy/amber24/miniconda/bin/distro
>-- Installing: /home/andriy/amber24/miniconda/bin/f2py
>-- Installing: /home/andriy/amber24/miniconda/bin/activate
>-- Installing: /home/andriy/amber24/miniconda/bin/c_rehash
>-- Installing: /home/andriy/amber24/miniconda/bin/archspec
>-- Installing: /home/andriy/amber24/miniconda/bin/sqlite3_analyzer
>-- Installing: /home/andriy/amber24/miniconda/bin/cython
>-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-trust
>-- Installing: /home/andriy/amber24/miniconda/bin/conda-develop
>-- Installing: /home/andriy/amber24/miniconda/bin/jsonpatch
>-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-nbconvert
>-- Installing: /home/andriy/amber24/miniconda/bin/fonttools
>-- Installing: /home/andriy/amber24/miniconda/bin/propka3
>-- Installing: /home/andriy/amber24/miniconda/bin/pcre2-config
>-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-server
>-- Installing: /home/andriy/amber24/miniconda/bin/wheel
>-- Installing: /home/andriy/amber24/miniconda/bin/conda-build
>-- Installing: /home/andriy/amber24/miniconda/bin/compile_et
>-- Installing: /home/andriy/amber24/miniconda/bin/dx2cube
>-- Installing: /home/andriy/amber24/miniconda/bin/curl-config
>-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-execute
>-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-labhub
>-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-troubleshoot
>-- Installing: /home/andriy/amber24/miniconda/bin/python3.11-config
>-- Installing: /home/andriy/amber24/miniconda/bin/pkginfo
>-- Installing: /home/andriy/amber24/miniconda/bin/pdb2pqr30
>-- Installing: /home/andriy/amber24/miniconda/bin/pygmentize
>-- Installing: /home/andriy/amber24/miniconda/bin/jsondiff
>-- Installing: /home/andriy/amber24/miniconda/bin/pybabel
>-- Installing: /home/andriy/amber24/miniconda/bin/jsonpointer
>-- Installing: /home/andriy/amber24/miniconda/bin/xml2-config
>-- Installing: /home/andriy/amber24/miniconda/bin/zstdless
>-- Installing: /home/andriy/amber24/miniconda/bin/pip3
>-- Installing: /home/andriy/amber24/miniconda/bin/pytest
>-- Installing: /home/andriy/amber24/miniconda/bin/pip3.11
>-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-labextension
>-- Installing: /home/andriy/amber24/miniconda/bin/bzdiff
>-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-lab
>-- Installing: /home/andriy/amber24/miniconda/bin/ttx
>-- Installing: /home/andriy/amber24/miniconda/bin/bzgrep
>-- Installing: /home/andriy/amber24/miniconda/bin/krb5-config
>-- Installing: /home/andriy/amber24/miniconda/bin/zstdgrep
>-- Installing: /home/andriy/amber24/miniconda/bin/conda
>-- Installing: /home/andriy/amber24/miniconda/bin/psize
>-- Installing: /home/andriy/amber24/miniconda/bin/cythonize
>-- Installing: /home/andriy/amber24/miniconda/bin/cph
>-- Installing: /home/andriy/amber24/miniconda/bin/conda-convert
>-- Installing: /home/andriy/amber24/miniconda/bin/conda-render
>-- Installing: /home/andriy/amber24/miniconda/bin/tqdm
>-- Installing: /home/andriy/amber24/miniconda/bin/xzless
>-- Installing: /home/andriy/amber24/miniconda/bin/jsonschema
>-- Installing: /home/andriy/amber24/miniconda/bin/pip
>-- Installing: /home/andriy/amber24/miniconda/bin/f90nml
>-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-kernel
>-- Installing: /home/andriy/amber24/miniconda/bin/py.test
>-- Installing: /home/andriy/amber24/miniconda/bin/conda-metapackage
>-- Installing: /home/andriy/amber24/miniconda/bin/chardetect
>-- Installing: /home/andriy/amber24/miniconda/bin/k5srvutil
>-- Installing: /home/andriy/amber24/miniconda/bin/inputgen
>-- Installing: /home/andriy/amber24/miniconda/bin/bzmore
>-- Installing: /home/andriy/amber24/miniconda/bin/jupyter-notebook
>-- Installing: /home/andriy/amber24/miniconda/share/jupyter/kernels/python3/kernel.json
>-- Installing: /home/andriy/amber24/bin/fftw-wisdom-to-conf
>-- Installing: /home/andriy/amber24/bin/nc-config
>-- Installing: /home/andriy/amber24/bin/nf-config
>-- Installing: /home/andriy/amber24/bin/senergy
>-- Installing: /home/andriy/amber24/bin/sviol
>-- Installing: /home/andriy/amber24/bin/sviol2
>-- Installing: /home/andriy/amber24/bin/makeCHIR_RST
>-- Installing: /home/andriy/amber24/bin/makeCSA_RST.na
>-- Installing: /home/andriy/amber24/bin/makeRIGID_RST
>-- Installing: /home/andriy/amber24/bin/makeDIP_RST.dna
>-- Installing: /home/andriy/amber24/bin/makeDIP_RST.protein
>-- Installing: /home/andriy/amber24/bin/am1bcc
>-- Installing: /home/andriy/amber24/bin/atomtype
>-- Installing: /home/andriy/amber24/bin/espgen
>-- Installing: /home/andriy/amber24/bin/parmcal
>-- Installing: /home/andriy/amber24/bin/parmchk2
>-- Installing: /home/andriy/amber24/bin/prepgen
>-- Installing: /home/andriy/amber24/bin/residuegen
>-- Installing: /home/andriy/amber24/bin/respgen
>-- Installing: /home/andriy/amber24/bin/match
>-- Installing: /home/andriy/amber24/bin/match_atomname
>-- Installing: /home/andriy/amber24/bin/antechamber
>-- Installing: /home/andriy/amber24/bin/bondtype
>-- Installing: /home/andriy/amber24/bin/reduce
>-- Installing: /home/andriy/amber24/bin/XrayPrep
>-- Installing: /home/andriy/amber24/bin/sgldinfo.sh
>-- Installing: /home/andriy/amber24/bin/sgldwt.sh
>-- Installing: /home/andriy/amber24/bin/process_mdout.perl
>-- Installing: /home/andriy/amber24/bin/process_minout.perl
>-- Installing: /home/andriy/amber24/bin/mdout2pymbar.pl
>running install
>/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
>!!
>
> ********************************************************************************
> Please avoid running ``setup.py`` directly.
> Instead, use pypa/build, pypa/installer or other
> standards-based tools.
>
> See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
> ********************************************************************************
>
>!!
> self.initialize_options()
>running build
>running build_py
>running build_scripts
>running install_lib
>copying build/lib/pyrespgen/constant.py -> /home/andriy/amber24//lib/python3.11/site-packages/pyrespgen
>copying build/lib/pyrespgen/prepin.py -> /home/andriy/amber24//lib/python3.11/site-packages/pyrespgen
>copying build/lib/pyrespgen/zmatrix.py -> /home/andriy/amber24//lib/python3.11/site-packages/pyrespgen
>copying build/lib/pyrespgen/constant_radii.py -> /home/andriy/amber24//lib/python3.11/site-packages/pyrespgen
>copying build/lib/mdoutanalyzer/windows.py -> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer
>copying build/lib/mdoutanalyzer/dataset.py -> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer
>copying build/lib/mdoutanalyzer/constants.py -> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer
>copying build/lib/mdoutanalyzer/toplevel_app.py -> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer
>copying build/lib/mdoutanalyzer/menus.py -> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer
>copying build/lib/mdoutanalyzer/graphproperties.py -> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer
>copying build/lib/mdoutanalyzer/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer
>copying build/lib/mdoutanalyzer/mdout.py -> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer
>copying build/lib/mdoutanalyzer/widgets.py -> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pyrespgen/constant.py to constant.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pyrespgen/prepin.py to prepin.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pyrespgen/zmatrix.py to zmatrix.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pyrespgen/constant_radii.py to constant_radii.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/windows.py to windows.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/dataset.py to dataset.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/constants.py to constants.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/toplevel_app.py to toplevel_app.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/menus.py to menus.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/graphproperties.py to graphproperties.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/mdout.py to mdout.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/widgets.py to widgets.cpython-311.pyc
>running install_egg_info
>running egg_info
>writing AmberUtils.egg-info/PKG-INFO
>writing dependency_links to AmberUtils.egg-info/dependency_links.txt
>writing top-level names to AmberUtils.egg-info/top_level.txt
>reading manifest file 'AmberUtils.egg-info/SOURCES.txt'
>writing manifest file 'AmberUtils.egg-info/SOURCES.txt'
>removing '/home/andriy/amber24//lib/python3.11/site-packages/AmberUtils-21.0-py3.11.egg-info' (and everything under it)
>Copying AmberUtils.egg-info to /home/andriy/amber24//lib/python3.11/site-packages/AmberUtils-21.0-py3.11.egg-info
>running install_scripts
>copying build/scripts-3.11/fitpkaeo.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/mdout_analyzer.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/cpeinutil.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/genremdinputs.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/fixremdcouts.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/charmmlipid2amber.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/cpinutil.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/softcore_setup.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/ceinutil.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/finddgref.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/pyresp_gen.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/py_resp.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/bar_pbsa.py -> /home/andriy/amber24//bin
>changing mode of /home/andriy/amber24//bin/fitpkaeo.py to 775
>changing mode of /home/andriy/amber24//bin/mdout_analyzer.py to 775
>changing mode of /home/andriy/amber24//bin/cpeinutil.py to 775
>changing mode of /home/andriy/amber24//bin/genremdinputs.py to 775
>changing mode of /home/andriy/amber24//bin/fixremdcouts.py to 775
>changing mode of /home/andriy/amber24//bin/charmmlipid2amber.py to 775
>changing mode of /home/andriy/amber24//bin/cpinutil.py to 775
>changing mode of /home/andriy/amber24//bin/softcore_setup.py to 775
>changing mode of /home/andriy/amber24//bin/ceinutil.py to 775
>changing mode of /home/andriy/amber24//bin/finddgref.py to 775
>changing mode of /home/andriy/amber24//bin/pyresp_gen.py to 775
>changing mode of /home/andriy/amber24//bin/py_resp.py to 775
>changing mode of /home/andriy/amber24//bin/bar_pbsa.py to 775
>-- Installing: /home/andriy/amber24/bin/mm_pbsa.pl
>-- Installing: /home/andriy/amber24/bin/mm_pbsa_statistics.pl
>-- Installing: /home/andriy/amber24/bin/FEW.pl
>-- Installing: /home/andriy/amber24/bin/tleap
>running install
>/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
>!!
>
> ********************************************************************************
> Please avoid running ``setup.py`` directly.
> Instead, use pypa/build, pypa/installer or other
> standards-based tools.
>
> See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
> ********************************************************************************
>
>!!
> self.initialize_options()
>running build
>running build_py
>UPDATING build/lib.linux-x86_64-cpython-311/parmed/_version.py
>set build/lib.linux-x86_64-cpython-311/parmed/_version.py to '0+unknown'
>running build_ext
>building 'parmed.amber._rdparm' extension
>gcc -pthread -B /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include -fPIC -I/home/andriy/amber24_src/AmberTools/src/parmed/src -I/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include/python3.11 -c src/_rdparm.cpp -o build/temp.linux-x86_64-cpython-311/src/_rdparm.o
>gcc -pthread -B /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include -fPIC -I/home/andriy/amber24_src/AmberTools/src/parmed/src -I/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include/python3.11 -c src/readparm.cpp -o build/temp.linux-x86_64-cpython-311/src/readparm.o
>src/readparm.cpp: In function ‘ExitStatus readparm(const std::string&, std::vector<std::__cxx11::basic_string<char> >&, ParmDataMap&, ParmStringMap&, ParmStringMap&, ParmFormatMap&, std::string&)’:
>src/readparm.cpp:143:28: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound 8 equals destination size [-Wstringop-truncation]
> 143 | strncpy(d.c, word.c_str(), MAX_HOLLERITH_SIZE);
> | ^
>g++ -pthread -B /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/compiler_compat -shared -Wl,-rpath,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -L/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -L/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib build/temp.linux-x86_64-cpython-311/src/_rdparm.o build/temp.linux-x86_64-cpython-311/src/readparm.o -o build/lib.linux-x86_64-cpython-311/parmed/amber/_rdparm.cpython-311-x86_64-linux-gnu.so
>UPDATING build/lib.linux-x86_64-cpython-311/parmed/_version.py
>set build/lib.linux-x86_64-cpython-311/parmed/_version.py to '0+unknown'
>running install_lib
>copying build/lib.linux-x86_64-cpython-311/parmed/rosetta/pose.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/rosetta
>copying build/lib.linux-x86_64-cpython-311/parmed/rosetta/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/rosetta
>copying build/lib.linux-x86_64-cpython-311/parmed/geometry.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed
>copying build/lib.linux-x86_64-cpython-311/parmed/_version.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed
>copying build/lib.linux-x86_64-cpython-311/parmed/openmm/reporters.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm
>copying build/lib.linux-x86_64-cpython-311/parmed/openmm/utils.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm
>copying build/lib.linux-x86_64-cpython-311/parmed/openmm/parameters.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm
>copying build/lib.linux-x86_64-cpython-311/parmed/openmm/topsystem.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm
>copying build/lib.linux-x86_64-cpython-311/parmed/openmm/xmlfile.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm
>copying build/lib.linux-x86_64-cpython-311/parmed/openmm/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm
>copying build/lib.linux-x86_64-cpython-311/parmed/constants.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed
>copying build/lib.linux-x86_64-cpython-311/parmed/rdkit/rdkit.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/rdkit
>copying build/lib.linux-x86_64-cpython-311/parmed/rdkit/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/rdkit
>copying build/lib.linux-x86_64-cpython-311/parmed/utils/netcdf.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils
>copying build/lib.linux-x86_64-cpython-311/parmed/utils/pandautils.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils
>copying build/lib.linux-x86_64-cpython-311/parmed/utils/decorators.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils
>copying build/lib.linux-x86_64-cpython-311/parmed/utils/timer.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils
>copying build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/_lexer.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat
>copying build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/_input.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat
>copying build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/FortranRecordWriter.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat
>copying build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/_misc.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat
>copying build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/_exceptions.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat
>copying build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/FortranRecordReader.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat
>copying build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/config.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat
>copying build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/_output.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat
>copying build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/_parser.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat
>copying build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/_edit_descriptors.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat
>copying build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat
>copying build/lib.linux-x86_64-cpython-311/parmed/utils/io.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils
>copying build/lib.linux-x86_64-cpython-311/parmed/utils/pairlist.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils
>copying build/lib.linux-x86_64-cpython-311/parmed/utils/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils
>copying build/lib.linux-x86_64-cpython-311/parmed/structure.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed
>copying build/lib.linux-x86_64-cpython-311/parmed/scripts.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed
>copying build/lib.linux-x86_64-cpython-311/parmed/tools/checkvalidity.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools
>copying build/lib.linux-x86_64-cpython-311/parmed/tools/addljtype.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools
>copying build/lib.linux-x86_64-cpython-311/parmed/tools/argumentlist.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools
>copying build/lib.linux-x86_64-cpython-311/parmed/tools/add1264.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools
>copying build/lib.linux-x86_64-cpython-311/parmed/tools/exceptions.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools
>copying build/lib.linux-x86_64-cpython-311/parmed/tools/parmlist.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools
>copying build/lib.linux-x86_64-cpython-311/parmed/tools/simulations/sanderapi.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/simulations
>copying build/lib.linux-x86_64-cpython-311/parmed/tools/simulations/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/simulations
>copying build/lib.linux-x86_64-cpython-311/parmed/tools/simulations/openmm.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/simulations
>copying build/lib.linux-x86_64-cpython-311/parmed/tools/parmed_cmd.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools
>copying build/lib.linux-x86_64-cpython-311/parmed/tools/logos.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools
>copying build/lib.linux-x86_64-cpython-311/parmed/tools/actions.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools
>copying build/lib.linux-x86_64-cpython-311/parmed/tools/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools
>copying build/lib.linux-x86_64-cpython-311/parmed/tools/changeradii.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools
>copying build/lib.linux-x86_64-cpython-311/parmed/symmetry.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed
>copying build/lib.linux-x86_64-cpython-311/parmed/exceptions.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed
>copying build/lib.linux-x86_64-cpython-311/parmed/gromacs/_cpp.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs
>copying build/lib.linux-x86_64-cpython-311/parmed/gromacs/gromacstop.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs
>copying build/lib.linux-x86_64-cpython-311/parmed/gromacs/gromacsgro.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs
>copying build/lib.linux-x86_64-cpython-311/parmed/gromacs/_gromacsfile.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs
>copying build/lib.linux-x86_64-cpython-311/parmed/gromacs/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs
>copying build/lib.linux-x86_64-cpython-311/parmed/topologyobjects.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed
>copying build/lib.linux-x86_64-cpython-311/parmed/parameters.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed
>copying build/lib.linux-x86_64-cpython-311/parmed/formats/pqr.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats
>copying build/lib.linux-x86_64-cpython-311/parmed/formats/psf.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats
>copying build/lib.linux-x86_64-cpython-311/parmed/formats/mol2.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats
>copying build/lib.linux-x86_64-cpython-311/parmed/formats/pdbx/PdbxContainers.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdbx
>copying build/lib.linux-x86_64-cpython-311/parmed/formats/pdbx/PdbxReader.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdbx
>copying build/lib.linux-x86_64-cpython-311/parmed/formats/pdbx/PdbxWriter.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdbx
>copying build/lib.linux-x86_64-cpython-311/parmed/formats/pdbx/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdbx
>copying build/lib.linux-x86_64-cpython-311/parmed/formats/pdb.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats
>copying build/lib.linux-x86_64-cpython-311/parmed/formats/registry.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats
>copying build/lib.linux-x86_64-cpython-311/parmed/formats/sdf.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats
>copying build/lib.linux-x86_64-cpython-311/parmed/formats/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats
>copying build/lib.linux-x86_64-cpython-311/parmed/tinker/system.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker
>copying build/lib.linux-x86_64-cpython-311/parmed/tinker/tinkerfiles.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker
>copying build/lib.linux-x86_64-cpython-311/parmed/tinker/topologyobjects.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker
>copying build/lib.linux-x86_64-cpython-311/parmed/tinker/parameterfile.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker
>copying build/lib.linux-x86_64-cpython-311/parmed/tinker/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker
>copying build/lib.linux-x86_64-cpython-311/parmed/periodic_table.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed
>copying build/lib.linux-x86_64-cpython-311/parmed/residue.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed
>copying build/lib.linux-x86_64-cpython-311/parmed/vec3.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed
>copying build/lib.linux-x86_64-cpython-311/parmed/namd/namdbinfiles.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/namd
>copying build/lib.linux-x86_64-cpython-311/parmed/namd/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/namd
>copying build/lib.linux-x86_64-cpython-311/parmed/modeller/data/standard_residues.lib -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller/data
>copying build/lib.linux-x86_64-cpython-311/parmed/modeller/data/nonstandard_ccd_residue_templates.json.gz -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller/data
>copying build/lib.linux-x86_64-cpython-311/parmed/modeller/data/ccd_residue_templates.json -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller/data
>copying build/lib.linux-x86_64-cpython-311/parmed/modeller/residue.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller
>copying build/lib.linux-x86_64-cpython-311/parmed/modeller/standardtemplates.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller
>copying build/lib.linux-x86_64-cpython-311/parmed/modeller/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller
>copying build/lib.linux-x86_64-cpython-311/parmed/entos/imports.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/entos
>copying build/lib.linux-x86_64-cpython-311/parmed/entos/converters.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/entos
>copying build/lib.linux-x86_64-cpython-311/parmed/entos/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/entos
>copying build/lib.linux-x86_64-cpython-311/parmed/dlpoly/dlpolyconfig.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/dlpoly
>copying build/lib.linux-x86_64-cpython-311/parmed/dlpoly/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/dlpoly
>copying build/lib.linux-x86_64-cpython-311/parmed/dlpoly/dlpolyfield.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/dlpoly
>copying build/lib.linux-x86_64-cpython-311/parmed/amber/amberformat.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
>copying build/lib.linux-x86_64-cpython-311/parmed/amber/_chamberparm.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
>copying build/lib.linux-x86_64-cpython-311/parmed/amber/netcdffiles.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
>copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/gbnsr6.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin
>copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/cntrl.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin
>copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/qmmm.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin
>copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/pb.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin
>copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/rism.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin
>copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/mdin.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin
>copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/ewald.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin
>copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/typing.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin
>copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin
>copying build/lib.linux-x86_64-cpython-311/parmed/amber/parameters.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
>copying build/lib.linux-x86_64-cpython-311/parmed/amber/_tinkerparm.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
>copying build/lib.linux-x86_64-cpython-311/parmed/amber/mask.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
>copying build/lib.linux-x86_64-cpython-311/parmed/amber/titratable_residues.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
>copying build/lib.linux-x86_64-cpython-311/parmed/amber/readparm.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
>copying build/lib.linux-x86_64-cpython-311/parmed/amber/_amberparm.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
>copying build/lib.linux-x86_64-cpython-311/parmed/amber/offlib.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
>copying build/lib.linux-x86_64-cpython-311/parmed/amber/_rdparm.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
>copying build/lib.linux-x86_64-cpython-311/parmed/amber/asciicrd.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
>copying build/lib.linux-x86_64-cpython-311/parmed/amber/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber
>copying build/lib.linux-x86_64-cpython-311/parmed/unit/unit_definitions.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit
>copying build/lib.linux-x86_64-cpython-311/parmed/unit/unit_math.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit
>copying build/lib.linux-x86_64-cpython-311/parmed/unit/constants.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit
>copying build/lib.linux-x86_64-cpython-311/parmed/unit/basedimension.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit
>copying build/lib.linux-x86_64-cpython-311/parmed/unit/prefix.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit
>copying build/lib.linux-x86_64-cpython-311/parmed/unit/unit_operators.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit
>copying build/lib.linux-x86_64-cpython-311/parmed/unit/quantity.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit
>copying build/lib.linux-x86_64-cpython-311/parmed/unit/unit.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit
>copying build/lib.linux-x86_64-cpython-311/parmed/unit/mymatrix.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit
>copying build/lib.linux-x86_64-cpython-311/parmed/unit/standard_dimensions.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit
>copying build/lib.linux-x86_64-cpython-311/parmed/unit/baseunit.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit
>copying build/lib.linux-x86_64-cpython-311/parmed/unit/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit
>copying build/lib.linux-x86_64-cpython-311/parmed/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed
>copying build/lib.linux-x86_64-cpython-311/parmed/charmm/psf.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm
>copying build/lib.linux-x86_64-cpython-311/parmed/charmm/charmmcrds.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm
>copying build/lib.linux-x86_64-cpython-311/parmed/charmm/parameters.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm
>copying build/lib.linux-x86_64-cpython-311/parmed/charmm/_charmmfile.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm
>copying build/lib.linux-x86_64-cpython-311/parmed/charmm/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/rosetta/pose.py to pose.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/rosetta/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/geometry.py to geometry.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/_version.py to _version.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm/reporters.py to reporters.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm/utils.py to utils.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm/parameters.py to parameters.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm/topsystem.py to topsystem.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm/xmlfile.py to xmlfile.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/constants.py to constants.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/rdkit/rdkit.py to rdkit.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/rdkit/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/netcdf.py to netcdf.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/pandautils.py to pandautils.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/decorators.py to decorators.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/timer.py to timer.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/_lexer.py to _lexer.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/_input.py to _input.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/FortranRecordWriter.py to FortranRecordWriter.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/_misc.py to _misc.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/_exceptions.py to _exceptions.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/FortranRecordReader.py to FortranRecordReader.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/config.py to config.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/_output.py to _output.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/_parser.py to _parser.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/_edit_descriptors.py to _edit_descriptors.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/io.py to io.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/pairlist.py to pairlist.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/structure.py to structure.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/scripts.py to scripts.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/checkvalidity.py to checkvalidity.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/addljtype.py to addljtype.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/argumentlist.py to argumentlist.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/add1264.py to add1264.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/exceptions.py to exceptions.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/parmlist.py to parmlist.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/simulations/sanderapi.py to sanderapi.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/simulations/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/simulations/openmm.py to openmm.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/parmed_cmd.py to parmed_cmd.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/logos.py to logos.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/actions.py to actions.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/changeradii.py to changeradii.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/symmetry.py to symmetry.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/exceptions.py to exceptions.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs/_cpp.py to _cpp.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs/gromacstop.py to gromacstop.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs/gromacsgro.py to gromacsgro.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs/_gromacsfile.py to _gromacsfile.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/topologyobjects.py to topologyobjects.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/parameters.py to parameters.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pqr.py to pqr.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/psf.py to psf.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/mol2.py to mol2.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdbx/PdbxContainers.py to PdbxContainers.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdbx/PdbxReader.py to PdbxReader.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdbx/PdbxWriter.py to PdbxWriter.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdbx/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdb.py to pdb.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/registry.py to registry.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/sdf.py to sdf.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker/system.py to system.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker/tinkerfiles.py to tinkerfiles.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker/topologyobjects.py to topologyobjects.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker/parameterfile.py to parameterfile.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/periodic_table.py to periodic_table.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/residue.py to residue.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/vec3.py to vec3.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/namd/namdbinfiles.py to namdbinfiles.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/namd/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller/residue.py to residue.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller/standardtemplates.py to standardtemplates.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/entos/imports.py to imports.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/entos/converters.py to converters.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/entos/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/dlpoly/dlpolyconfig.py to dlpolyconfig.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/dlpoly/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/dlpoly/dlpolyfield.py to dlpolyfield.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/amberformat.py to amberformat.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/_chamberparm.py to _chamberparm.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/netcdffiles.py to netcdffiles.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/gbnsr6.py to gbnsr6.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/cntrl.py to cntrl.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/qmmm.py to qmmm.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/pb.py to pb.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/rism.py to rism.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/mdin.py to mdin.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/ewald.py to ewald.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/typing.py to typing.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/parameters.py to parameters.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/_tinkerparm.py to _tinkerparm.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mask.py to mask.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/titratable_residues.py to titratable_residues.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/readparm.py to readparm.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/_amberparm.py to _amberparm.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/offlib.py to offlib.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/asciicrd.py to asciicrd.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/unit_definitions.py to unit_definitions.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/unit_math.py to unit_math.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/constants.py to constants.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/basedimension.py to basedimension.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/prefix.py to prefix.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/unit_operators.py to unit_operators.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/quantity.py to quantity.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/unit.py to unit.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/mymatrix.py to mymatrix.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/standard_dimensions.py to standard_dimensions.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/baseunit.py to baseunit.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm/psf.py to psf.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm/charmmcrds.py to charmmcrds.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm/parameters.py to parameters.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm/_charmmfile.py to _charmmfile.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm/__init__.py to __init__.cpython-311.pyc
>running install_egg_info
>running egg_info
>writing ParmEd.egg-info/PKG-INFO
>writing dependency_links to ParmEd.egg-info/dependency_links.txt
>writing entry points to ParmEd.egg-info/entry_points.txt
>writing top-level names to ParmEd.egg-info/top_level.txt
>dependency src/CompatabilityMacros.h won't be automatically included in the manifest: the path doesn't exist
>reading manifest file 'ParmEd.egg-info/SOURCES.txt'
>reading manifest template 'MANIFEST.in'
>writing manifest file 'ParmEd.egg-info/SOURCES.txt'
>removing '/home/andriy/amber24//lib/python3.11/site-packages/ParmEd-0+unknown-py3.11.egg-info' (and everything under it)
>Copying ParmEd.egg-info to /home/andriy/amber24//lib/python3.11/site-packages/ParmEd-0+unknown-py3.11.egg-info
>running install_scripts
>Installing parmed script to /home/andriy/amber24//bin
>running install
>/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
>!!
>
> ********************************************************************************
> Please avoid running ``setup.py`` directly.
> Instead, use pypa/build, pypa/installer or other
> standards-based tools.
>
> See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
> ********************************************************************************
>
>!!
> self.initialize_options()
>running build
>running build_py
>running build_scripts
>copying and adjusting MMPBSA.py.MPI -> build/scripts-3.11
>running install_lib
>copying build/lib/MMPBSA_mods/timer.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
>copying build/lib/MMPBSA_mods/input_parser.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
>copying build/lib/MMPBSA_mods/utils.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
>copying build/lib/MMPBSA_mods/output_file.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
>copying build/lib/MMPBSA_mods/API.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
>copying build/lib/MMPBSA_mods/exceptions.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
>copying build/lib/MMPBSA_mods/createinput.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
>copying build/lib/MMPBSA_mods/main.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
>copying build/lib/MMPBSA_mods/infofile.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
>copying build/lib/MMPBSA_mods/findprogs.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
>copying build/lib/MMPBSA_mods/alamdcrd.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
>copying build/lib/MMPBSA_mods/parm_setup.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
>copying build/lib/MMPBSA_mods/commandlineparser.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
>copying build/lib/MMPBSA_mods/fake_mpi.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
>copying build/lib/MMPBSA_mods/calculation.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
>copying build/lib/MMPBSA_mods/make_trajs.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
>copying build/lib/MMPBSA_mods/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
>copying build/lib/MMPBSA_mods/amber_outputs.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/timer.py to timer.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/input_parser.py to input_parser.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/utils.py to utils.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/output_file.py to output_file.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/API.py to API.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/exceptions.py to exceptions.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/createinput.py to createinput.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/main.py to main.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/infofile.py to infofile.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/findprogs.py to findprogs.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/alamdcrd.py to alamdcrd.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/parm_setup.py to parm_setup.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/commandlineparser.py to commandlineparser.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/fake_mpi.py to fake_mpi.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/calculation.py to calculation.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/make_trajs.py to make_trajs.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/amber_outputs.py to amber_outputs.cpython-311.pyc
>running install_egg_info
>running egg_info
>writing MMPBSA.py.egg-info/PKG-INFO
>writing dependency_links to MMPBSA.py.egg-info/dependency_links.txt
>writing top-level names to MMPBSA.py.egg-info/top_level.txt
>reading manifest file 'MMPBSA.py.egg-info/SOURCES.txt'
>writing manifest file 'MMPBSA.py.egg-info/SOURCES.txt'
>removing '/home/andriy/amber24//lib/python3.11/site-packages/MMPBSA.py-16.0-py3.11.egg-info' (and everything under it)
>Copying MMPBSA.py.egg-info to /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA.py-16.0-py3.11.egg-info
>running install_scripts
>copying build/scripts-3.11/MMPBSA.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/MMPBSA.py.MPI -> /home/andriy/amber24//bin
>copying build/scripts-3.11/ante-MMPBSA.py -> /home/andriy/amber24//bin
>changing mode of /home/andriy/amber24//bin/MMPBSA.py to 775
>changing mode of /home/andriy/amber24//bin/MMPBSA.py.MPI to 775
>changing mode of /home/andriy/amber24//bin/ante-MMPBSA.py to 775
>running install
>/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
>!!
>
> ********************************************************************************
> Please avoid running ``setup.py`` directly.
> Instead, use pypa/build, pypa/installer or other
> standards-based tools.
>
> See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
> ********************************************************************************
>
>!!
> self.initialize_options()
>running build
>running build_py
>running build_scripts
>running install_lib
>copying build/lib/pymsmt/mol/mol.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
>copying build/lib/pymsmt/mol/constants.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
>copying build/lib/pymsmt/mol/pdbio.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
>copying build/lib/pymsmt/mol/mol2io.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
>copying build/lib/pymsmt/mol/element.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
>copying build/lib/pymsmt/mol/getlist.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
>copying build/lib/pymsmt/mol/cal.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
>copying build/lib/pymsmt/mol/itfc_dict_table.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
>copying build/lib/pymsmt/mol/cario.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
>copying build/lib/pymsmt/mol/gmsio.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
>copying build/lib/pymsmt/mol/amb2chm_typ.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
>copying build/lib/pymsmt/mol/gauio.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
>copying build/lib/pymsmt/mol/rstio.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
>copying build/lib/pymsmt/mol/sqmio.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
>copying build/lib/pymsmt/mol/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol
>copying build/lib/pymsmt/ipmach/calhfe.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/ipmach
>copying build/lib/pymsmt/ipmach/tifiles.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/ipmach
>copying build/lib/pymsmt/ipmach/caliod.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/ipmach
>copying build/lib/pymsmt/ipmach/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/ipmach
>copying build/lib/pymsmt/title.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt
>copying build/lib/pymsmt/api/AmberParm.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/api
>copying build/lib/pymsmt/api/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/api
>copying build/lib/pymsmt/exp.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt
>copying build/lib/pymsmt/mcpb/rename_residues.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb
>copying build/lib/pymsmt/mcpb/gene_model_files.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb
>copying build/lib/pymsmt/mcpb/resp_fitting.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb
>copying build/lib/pymsmt/mcpb/amber_modeling.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb
>copying build/lib/pymsmt/mcpb/gene_pre_frcmod_file.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb
>copying build/lib/pymsmt/mcpb/gene_final_frcmod_file.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb
>copying build/lib/pymsmt/mcpb/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb
>copying build/lib/pymsmt/mcpb/fq_model.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb
>copying build/lib/pymsmt/lib.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt
>copying build/lib/pymsmt/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/mol.py to mol.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/constants.py to constants.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/pdbio.py to pdbio.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/mol2io.py to mol2io.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/element.py to element.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/getlist.py to getlist.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/cal.py to cal.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/itfc_dict_table.py to itfc_dict_table.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/cario.py to cario.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/gmsio.py to gmsio.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/amb2chm_typ.py to amb2chm_typ.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/gauio.py to gauio.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/rstio.py to rstio.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/sqmio.py to sqmio.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/ipmach/calhfe.py to calhfe.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/ipmach/tifiles.py to tifiles.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/ipmach/caliod.py to caliod.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/ipmach/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/title.py to title.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/api/AmberParm.py to AmberParm.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/api/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/exp.py to exp.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb/rename_residues.py to rename_residues.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb/gene_model_files.py to gene_model_files.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb/resp_fitting.py to resp_fitting.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb/amber_modeling.py to amber_modeling.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb/gene_pre_frcmod_file.py to gene_pre_frcmod_file.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb/gene_final_frcmod_file.py to gene_final_frcmod_file.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb/fq_model.py to fq_model.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/lib.py to lib.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/__init__.py to __init__.cpython-311.pyc
>running install_egg_info
>running egg_info
>writing pyMSMT.egg-info/PKG-INFO
>writing dependency_links to pyMSMT.egg-info/dependency_links.txt
>writing top-level names to pyMSMT.egg-info/top_level.txt
>reading manifest file 'pyMSMT.egg-info/SOURCES.txt'
>writing manifest file 'pyMSMT.egg-info/SOURCES.txt'
>removing '/home/andriy/amber24//lib/python3.11/site-packages/pyMSMT-22.0-py3.11.egg-info' (and everything under it)
>Copying pyMSMT.egg-info to /home/andriy/amber24//lib/python3.11/site-packages/pyMSMT-22.0-py3.11.egg-info
>running install_scripts
>copying build/scripts-3.11/metalpdb2mol2.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/amb2chm_psf_crd.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/espgen.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/PdbSearcher.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/amb2gro_top_gro.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/OptC4.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/mol2rtf.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/car_to_files.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/MCPB.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/amb2chm_par.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/IPMach.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/ProScrs.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/CartHess2FC.py -> /home/andriy/amber24//bin
>changing mode of /home/andriy/amber24//bin/metalpdb2mol2.py to 775
>changing mode of /home/andriy/amber24//bin/amb2chm_psf_crd.py to 775
>changing mode of /home/andriy/amber24//bin/espgen.py to 775
>changing mode of /home/andriy/amber24//bin/PdbSearcher.py to 775
>changing mode of /home/andriy/amber24//bin/amb2gro_top_gro.py to 775
>changing mode of /home/andriy/amber24//bin/OptC4.py to 775
>changing mode of /home/andriy/amber24//bin/mol2rtf.py to 775
>changing mode of /home/andriy/amber24//bin/car_to_files.py to 775
>changing mode of /home/andriy/amber24//bin/MCPB.py to 775
>changing mode of /home/andriy/amber24//bin/amb2chm_par.py to 775
>changing mode of /home/andriy/amber24//bin/IPMach.py to 775
>changing mode of /home/andriy/amber24//bin/ProScrs.py to 775
>changing mode of /home/andriy/amber24//bin/CartHess2FC.py to 775
>Copying sander extension source to sanderles...
>running build
>running build_py
>copying sanderles/__init__.py -> /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-cpython-311/sanderles
>running build_ext
>building 'sanderles.pysander' extension
>gcc -pthread -B /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include -fPIC -DLES -I/home/andriy/amber24_src/AmberTools/src/include -I/home/andriy/amber24_src/AmberTools/src/sander -I/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include/python3.11 -c sanderles/src/pysandermodule.c -o /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/temp.linux-x86_64-cpython-311/sanderles/src/pysandermodule.o
>In file included from sanderles/src/pysandermodule.c:16:
>/home/andriy/amber24_src/AmberTools/src/sander/sander.h: In function ‘pysander_setup’:
>/home/andriy/amber24_src/AmberTools/src/sander/sander.h:342:5: warning: ‘__builtin_strncpy’ specified bound 256 equals destination size [-Wstringop-truncation]
> 342 | strncpy(prmtop, prmname, __MAX_FN_LEN);
> | ^
>gcc -pthread -B /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/compiler_compat -shared -Wl,-rpath,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -L/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -L/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/temp.linux-x86_64-cpython-311/sanderles/src/pysandermodule.o -L/home/andriy/amber24//lib -lsanderles -o /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-cpython-311/sanderles/pysander.cpython-311-x86_64-linux-gnu.so
>running install
>/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
>!!
>
> ********************************************************************************
> Please avoid running ``setup.py`` directly.
> Instead, use pypa/build, pypa/installer or other
> standards-based tools.
>
> See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
> ********************************************************************************
>
>!!
> self.initialize_options()
>running install_lib
>copying /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-cpython-311/sanderles/pysander.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/sanderles
>copying /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-cpython-311/sanderles/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/sanderles
>copying /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-cpython-311/sander/pysander.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/sander
>copying /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-cpython-311/sander/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/sander
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/sanderles/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/sander/__init__.py to __init__.cpython-311.pyc
>running install_egg_info
>running egg_info
>writing sander.egg-info/PKG-INFO
>writing dependency_links to sander.egg-info/dependency_links.txt
>writing top-level names to sander.egg-info/top_level.txt
>reading manifest file 'sander.egg-info/SOURCES.txt'
>writing manifest file 'sander.egg-info/SOURCES.txt'
>removing '/home/andriy/amber24//lib/python3.11/site-packages/sander-22.0-py3.11.egg-info' (and everything under it)
>Copying sander.egg-info to /home/andriy/amber24//lib/python3.11/site-packages/sander-22.0-py3.11.egg-info
>running install_scripts
>/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/dist.py:476: SetuptoolsDeprecationWarning: Invalid dash-separated options
>!!
>
> ********************************************************************************
> Usage of dash-separated 'description-file' will not be supported in future
> versions. Please use the underscore name 'description_file' instead.
>
> This deprecation is overdue, please update your project and remove deprecated
> calls to avoid build errors in the future.
>
> See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
> ********************************************************************************
>
>!!
> opt = self.warn_dash_deprecation(opt, section)
>sys.argv ['./setup.py', 'build', '-b', '/home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build', '--disable-openmp', 'install', '-f', '--prefix=/home/andriy/amber24/', '--single-version-externally-managed', '--root', '/']
>Original compiler envs
>CXX = /usr/bin/g++
>CC = /usr/bin/gcc
>COMPILER =
>use_pip = False, cpptraj_home =
>compile_c_extension = True
>2.0.6
>use_prebuilt_cythonized_files = False
>pytraj is inside AMBERHOME
>using environment: CC=/usr/bin/gcc, CXX=/usr/bin/g++
>using CC=/usr/bin/gcc, CXX=/usr/bin/g++
>Final compiler envs
>CXX = /usr/bin/g++
>CC = /usr/bin/gcc
>COMPILER =
>install = True
>set rpath to /home/andriy/amber24_src/build/AmberTools/src/cpptraj/src
>running build
>running build_py
>copying pytraj/version.py -> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj
>running build_ext
>running install
>/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
>!!
>
> ********************************************************************************
> Please avoid running ``setup.py`` directly.
> Instead, use pypa/build, pypa/installer or other
> standards-based tools.
>
> See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
> ********************************************************************************
>
>!!
> self.initialize_options()
>running install_lib
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/externals/wurlitzer.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/externals
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/externals/magic.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/externals
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/externals/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/externals
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/version.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/cython_extra_header/cpp_algorithm.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/cython_extra_header
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/cython_extra_header/cpp_vector.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/cython_extra_header
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/topology_analysis.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/nmr.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/vector.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_analysis/c_analysis.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_analysis
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_analysis/analysis_dict.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_analysis
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_analysis/c_analysis.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_analysis
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_analysis/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_analysis
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/energy_analysis.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/dihedral_analysis.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/dssp_analysis.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/base_holder.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/matrix.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/water.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_action/c_action.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_action
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_action/actionlist.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_action
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_action/c_action.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_action
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_action/actionlist.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_action
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_action/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_action
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/rmsd.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/hbond_analysis.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/nucleic_acid_analysis.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/decorators.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/Timer.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/convert.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/progress-circle/progress-circle.js -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/progress-circle
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/progress-circle/css/circle.css -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/progress-circle/css
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/context.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/tools.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/get_common_objects.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/misc.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/cyutils.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/c_commands.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/progress.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/check_and_assert.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/css/oceans16.css -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/css
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/visualization/view.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/visualization
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/visualization/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/visualization
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/topology/topology.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/topology
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/topology/topology.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/topology
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/topology/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/topology
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/coordinfo.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/coordinfo.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/parameter_types.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/c_core.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/c_core.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/cpp_vector.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/topology_objects.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/c_options.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/parameter_types.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/c_dict.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/topology_objects.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/elements.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/box.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/box.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/c_dict.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datasets/cast_dataset.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datasets/c_datasetlist.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datasets/c_datasetlist.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datasets/c_datasets.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datasets/c_datasets.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datasets/datasetlist.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datasets/array.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datasets/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/math/cpp_math.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/math
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/math/cpp_math.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/math
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/math/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/math
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/testing/testing.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/testing
>copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/testing/run_tests.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/testing
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>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/sandbox/TrajectoryBaseIterator.py to TrajectoryBaseIterator.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/sandbox/lazy.py to lazy.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/sandbox/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/trajectory_iterator.py to trajectory_iterator.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/stripped_trajectory.py to stripped_trajectory.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/frameiter.py to frameiter.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/trajectory.py to trajectory.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/shared_methods.py to shared_methods.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/shared_trajectory.py to shared_trajectory.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/c_traj/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/io.py to io.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/parallel/dataset.py to dataset.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/parallel/base.py to base.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/parallel/multiprocess.py to multiprocess.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/parallel/mpi.py to mpi.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/parallel/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/trpcage/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/ala3/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/load_samples.py to load_samples.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/dpdp/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/remd_ala2/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/tz2/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/serialize/serialize.py to serialize.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/serialize/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/__init__.py to __init__.cpython-311.pyc
>running install_egg_info
>running egg_info
>writing pytraj.egg-info/PKG-INFO
>writing dependency_links to pytraj.egg-info/dependency_links.txt
>writing requirements to pytraj.egg-info/requires.txt
>writing top-level names to pytraj.egg-info/top_level.txt
>reading manifest file 'pytraj.egg-info/SOURCES.txt'
>reading manifest template 'MANIFEST.in'
>writing manifest file 'pytraj.egg-info/SOURCES.txt'
>removing '/home/andriy/amber24//lib/python3.11/site-packages/pytraj-2.0.6-py3.11.egg-info' (and everything under it)
>Copying pytraj.egg-info to /home/andriy/amber24//lib/python3.11/site-packages/pytraj-2.0.6-py3.11.egg-info
>running install_scripts
>running install
>/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
>!!
>
> ********************************************************************************
> Please avoid running ``setup.py`` directly.
> Instead, use pypa/build, pypa/installer or other
> standards-based tools.
>
> See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
> ********************************************************************************
>
>!!
> self.initialize_options()
>running build
>running build_py
>running install_lib
>copying build/lib/pdb4amber/utils.py -> /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber
>copying build/lib/pdb4amber/pdb4amber.py -> /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber
>copying build/lib/pdb4amber/leap_runner.py -> /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber
>copying build/lib/pdb4amber/residue.py -> /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber
>copying build/lib/pdb4amber/template.py -> /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber
>copying build/lib/pdb4amber/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber/utils.py to utils.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber/pdb4amber.py to pdb4amber.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber/leap_runner.py to leap_runner.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber/residue.py to residue.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber/template.py to template.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber/__init__.py to __init__.cpython-311.pyc
>running install_egg_info
>running egg_info
>writing pdb4amber.egg-info/PKG-INFO
>writing dependency_links to pdb4amber.egg-info/dependency_links.txt
>writing entry points to pdb4amber.egg-info/entry_points.txt
>writing top-level names to pdb4amber.egg-info/top_level.txt
>reading manifest file 'pdb4amber.egg-info/SOURCES.txt'
>adding license file 'LICENSE'
>writing manifest file 'pdb4amber.egg-info/SOURCES.txt'
>removing '/home/andriy/amber24//lib/python3.11/site-packages/pdb4amber-22.0-py3.11.egg-info' (and everything under it)
>Copying pdb4amber.egg-info to /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber-22.0-py3.11.egg-info
>running install_scripts
>Installing pdb4amber script to /home/andriy/amber24//bin
>Inside Amber CMake build system, skipping build of native executables
>running install
>/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
>!!
>
> ********************************************************************************
> Please avoid running ``setup.py`` directly.
> Instead, use pypa/build, pypa/installer or other
> standards-based tools.
>
> See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
> ********************************************************************************
>
>!!
> self.initialize_options()
>running build
>running build_py
>copying packmol_memgen/lib/utils.py -> build/lib/packmol_memgen/lib
>running egg_info
>writing packmol_memgen.egg-info/PKG-INFO
>writing dependency_links to packmol_memgen.egg-info/dependency_links.txt
>writing requirements to packmol_memgen.egg-info/requires.txt
>writing top-level names to packmol_memgen.egg-info/top_level.txt
>reading manifest file 'packmol_memgen.egg-info/SOURCES.txt'
>reading manifest template 'MANIFEST.in'
>adding license file 'LICENSE'
>writing manifest file 'packmol_memgen.egg-info/SOURCES.txt'
>/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'packmol_memgen.data' is absent from the `packages` configuration.
>!!
>
> ********************************************************************************
> ############################
> # Package would be ignored #
> ############################
> Python recognizes 'packmol_memgen.data' as an importable package[^1],
> but it is absent from setuptools' `packages` configuration.
>
> This leads to an ambiguous overall configuration. If you want to distribute this
> package, please make sure that 'packmol_memgen.data' is explicitly added
> to the `packages` configuration field.
>
> Alternatively, you can also rely on setuptools' discovery methods
> (for example by using `find_namespace_packages(...)`/`find_namespace:`
> instead of `find_packages(...)`/`find:`).
>
> You can read more about "package discovery" on setuptools documentation page:
>
> - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
>
> If you don't want 'packmol_memgen.data' to be distributed and are
> already explicitly excluding 'packmol_memgen.data' via
> `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
> you can try to use `exclude_package_data`, or `include-package-data=False` in
> combination with a more fine grained `package-data` configuration.
>
> You can read more about "package data files" on setuptools documentation page:
>
> - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
>
>
> [^1]: For Python, any directory (with suitable naming) can be imported,
> even if it does not contain any `.py` files.
> On the other hand, currently there is no concept of package data
> directory, all directories are treated like packages.
> ********************************************************************************
>
>!!
> check.warn(importable)
>/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'packmol_memgen.example' is absent from the `packages` configuration.
>!!
>
> ********************************************************************************
> ############################
> # Package would be ignored #
> ############################
> Python recognizes 'packmol_memgen.example' as an importable package[^1],
> but it is absent from setuptools' `packages` configuration.
>
> This leads to an ambiguous overall configuration. If you want to distribute this
> package, please make sure that 'packmol_memgen.example' is explicitly added
> to the `packages` configuration field.
>
> Alternatively, you can also rely on setuptools' discovery methods
> (for example by using `find_namespace_packages(...)`/`find_namespace:`
> instead of `find_packages(...)`/`find:`).
>
> You can read more about "package discovery" on setuptools documentation page:
>
> - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
>
> If you don't want 'packmol_memgen.example' to be distributed and are
> already explicitly excluding 'packmol_memgen.example' via
> `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
> you can try to use `exclude_package_data`, or `include-package-data=False` in
> combination with a more fine grained `package-data` configuration.
>
> You can read more about "package data files" on setuptools documentation page:
>
> - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
>
>
> [^1]: For Python, any directory (with suitable naming) can be imported,
> even if it does not contain any `.py` files.
> On the other hand, currently there is no concept of package data
> directory, all directories are treated like packages.
> ********************************************************************************
>
>!!
> check.warn(importable)
>/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'packmol_memgen.lib.memembed' is absent from the `packages` configuration.
>!!
>
> ********************************************************************************
> ############################
> # Package would be ignored #
> ############################
> Python recognizes 'packmol_memgen.lib.memembed' as an importable package[^1],
> but it is absent from setuptools' `packages` configuration.
>
> This leads to an ambiguous overall configuration. If you want to distribute this
> package, please make sure that 'packmol_memgen.lib.memembed' is explicitly added
> to the `packages` configuration field.
>
> Alternatively, you can also rely on setuptools' discovery methods
> (for example by using `find_namespace_packages(...)`/`find_namespace:`
> instead of `find_packages(...)`/`find:`).
>
> You can read more about "package discovery" on setuptools documentation page:
>
> - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
>
> If you don't want 'packmol_memgen.lib.memembed' to be distributed and are
> already explicitly excluding 'packmol_memgen.lib.memembed' via
> `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
> you can try to use `exclude_package_data`, or `include-package-data=False` in
> combination with a more fine grained `package-data` configuration.
>
> You can read more about "package data files" on setuptools documentation page:
>
> - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
>
>
> [^1]: For Python, any directory (with suitable naming) can be imported,
> even if it does not contain any `.py` files.
> On the other hand, currently there is no concept of package data
> directory, all directories are treated like packages.
> ********************************************************************************
>
>!!
> check.warn(importable)
>/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'packmol_memgen.lib.memembed.bin' is absent from the `packages` configuration.
>!!
>
> ********************************************************************************
> ############################
> # Package would be ignored #
> ############################
> Python recognizes 'packmol_memgen.lib.memembed.bin' as an importable package[^1],
> but it is absent from setuptools' `packages` configuration.
>
> This leads to an ambiguous overall configuration. If you want to distribute this
> package, please make sure that 'packmol_memgen.lib.memembed.bin' is explicitly added
> to the `packages` configuration field.
>
> Alternatively, you can also rely on setuptools' discovery methods
> (for example by using `find_namespace_packages(...)`/`find_namespace:`
> instead of `find_packages(...)`/`find:`).
>
> You can read more about "package discovery" on setuptools documentation page:
>
> - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
>
> If you don't want 'packmol_memgen.lib.memembed.bin' to be distributed and are
> already explicitly excluding 'packmol_memgen.lib.memembed.bin' via
> `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
> you can try to use `exclude_package_data`, or `include-package-data=False` in
> combination with a more fine grained `package-data` configuration.
>
> You can read more about "package data files" on setuptools documentation page:
>
> - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
>
>
> [^1]: For Python, any directory (with suitable naming) can be imported,
> even if it does not contain any `.py` files.
> On the other hand, currently there is no concept of package data
> directory, all directories are treated like packages.
> ********************************************************************************
>
>!!
> check.warn(importable)
>/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'packmol_memgen.lib.memembed.examples' is absent from the `packages` configuration.
>!!
>
> ********************************************************************************
> ############################
> # Package would be ignored #
> ############################
> Python recognizes 'packmol_memgen.lib.memembed.examples' as an importable package[^1],
> but it is absent from setuptools' `packages` configuration.
>
> This leads to an ambiguous overall configuration. If you want to distribute this
> package, please make sure that 'packmol_memgen.lib.memembed.examples' is explicitly added
> to the `packages` configuration field.
>
> Alternatively, you can also rely on setuptools' discovery methods
> (for example by using `find_namespace_packages(...)`/`find_namespace:`
> instead of `find_packages(...)`/`find:`).
>
> You can read more about "package discovery" on setuptools documentation page:
>
> - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
>
> If you don't want 'packmol_memgen.lib.memembed.examples' to be distributed and are
> already explicitly excluding 'packmol_memgen.lib.memembed.examples' via
> `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
> you can try to use `exclude_package_data`, or `include-package-data=False` in
> combination with a more fine grained `package-data` configuration.
>
> You can read more about "package data files" on setuptools documentation page:
>
> - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
>
>
> [^1]: For Python, any directory (with suitable naming) can be imported,
> even if it does not contain any `.py` files.
> On the other hand, currently there is no concept of package data
> directory, all directories are treated like packages.
> ********************************************************************************
>
>!!
> check.warn(importable)
>/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'packmol_memgen.lib.memembed.scripts' is absent from the `packages` configuration.
>!!
>
> ********************************************************************************
> ############################
> # Package would be ignored #
> ############################
> Python recognizes 'packmol_memgen.lib.memembed.scripts' as an importable package[^1],
> but it is absent from setuptools' `packages` configuration.
>
> This leads to an ambiguous overall configuration. If you want to distribute this
> package, please make sure that 'packmol_memgen.lib.memembed.scripts' is explicitly added
> to the `packages` configuration field.
>
> Alternatively, you can also rely on setuptools' discovery methods
> (for example by using `find_namespace_packages(...)`/`find_namespace:`
> instead of `find_packages(...)`/`find:`).
>
> You can read more about "package discovery" on setuptools documentation page:
>
> - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
>
> If you don't want 'packmol_memgen.lib.memembed.scripts' to be distributed and are
> already explicitly excluding 'packmol_memgen.lib.memembed.scripts' via
> `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
> you can try to use `exclude_package_data`, or `include-package-data=False` in
> combination with a more fine grained `package-data` configuration.
>
> You can read more about "package data files" on setuptools documentation page:
>
> - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
>
>
> [^1]: For Python, any directory (with suitable naming) can be imported,
> even if it does not contain any `.py` files.
> On the other hand, currently there is no concept of package data
> directory, all directories are treated like packages.
> ********************************************************************************
>
>!!
> check.warn(importable)
>/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'packmol_memgen.lib.memembed.src' is absent from the `packages` configuration.
>!!
>
> ********************************************************************************
> ############################
> # Package would be ignored #
> ############################
> Python recognizes 'packmol_memgen.lib.memembed.src' as an importable package[^1],
> but it is absent from setuptools' `packages` configuration.
>
> This leads to an ambiguous overall configuration. If you want to distribute this
> package, please make sure that 'packmol_memgen.lib.memembed.src' is explicitly added
> to the `packages` configuration field.
>
> Alternatively, you can also rely on setuptools' discovery methods
> (for example by using `find_namespace_packages(...)`/`find_namespace:`
> instead of `find_packages(...)`/`find:`).
>
> You can read more about "package discovery" on setuptools documentation page:
>
> - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
>
> If you don't want 'packmol_memgen.lib.memembed.src' to be distributed and are
> already explicitly excluding 'packmol_memgen.lib.memembed.src' via
> `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
> you can try to use `exclude_package_data`, or `include-package-data=False` in
> combination with a more fine grained `package-data` configuration.
>
> You can read more about "package data files" on setuptools documentation page:
>
> - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
>
>
> [^1]: For Python, any directory (with suitable naming) can be imported,
> even if it does not contain any `.py` files.
> On the other hand, currently there is no concept of package data
> directory, all directories are treated like packages.
> ********************************************************************************
>
>!!
> check.warn(importable)
>/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'packmol_memgen.lib.packmol' is absent from the `packages` configuration.
>!!
>
> ********************************************************************************
> ############################
> # Package would be ignored #
> ############################
> Python recognizes 'packmol_memgen.lib.packmol' as an importable package[^1],
> but it is absent from setuptools' `packages` configuration.
>
> This leads to an ambiguous overall configuration. If you want to distribute this
> package, please make sure that 'packmol_memgen.lib.packmol' is explicitly added
> to the `packages` configuration field.
>
> Alternatively, you can also rely on setuptools' discovery methods
> (for example by using `find_namespace_packages(...)`/`find_namespace:`
> instead of `find_packages(...)`/`find:`).
>
> You can read more about "package discovery" on setuptools documentation page:
>
> - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
>
> If you don't want 'packmol_memgen.lib.packmol' to be distributed and are
> already explicitly excluding 'packmol_memgen.lib.packmol' via
> `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
> you can try to use `exclude_package_data`, or `include-package-data=False` in
> combination with a more fine grained `package-data` configuration.
>
> You can read more about "package data files" on setuptools documentation page:
>
> - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
>
>
> [^1]: For Python, any directory (with suitable naming) can be imported,
> even if it does not contain any `.py` files.
> On the other hand, currently there is no concept of package data
> directory, all directories are treated like packages.
> ********************************************************************************
>
>!!
> check.warn(importable)
>/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'packmol_memgen.lib.packmol.docs' is absent from the `packages` configuration.
>!!
>
> ********************************************************************************
> ############################
> # Package would be ignored #
> ############################
> Python recognizes 'packmol_memgen.lib.packmol.docs' as an importable package[^1],
> but it is absent from setuptools' `packages` configuration.
>
> This leads to an ambiguous overall configuration. If you want to distribute this
> package, please make sure that 'packmol_memgen.lib.packmol.docs' is explicitly added
> to the `packages` configuration field.
>
> Alternatively, you can also rely on setuptools' discovery methods
> (for example by using `find_namespace_packages(...)`/`find_namespace:`
> instead of `find_packages(...)`/`find:`).
>
> You can read more about "package discovery" on setuptools documentation page:
>
> - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
>
> If you don't want 'packmol_memgen.lib.packmol.docs' to be distributed and are
> already explicitly excluding 'packmol_memgen.lib.packmol.docs' via
> `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
> you can try to use `exclude_package_data`, or `include-package-data=False` in
> combination with a more fine grained `package-data` configuration.
>
> You can read more about "package data files" on setuptools documentation page:
>
> - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
>
>
> [^1]: For Python, any directory (with suitable naming) can be imported,
> even if it does not contain any `.py` files.
> On the other hand, currently there is no concept of package data
> directory, all directories are treated like packages.
> ********************************************************************************
>
>!!
> check.warn(importable)
>/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'packmol_memgen.lib.packmol.docs.imgs' is absent from the `packages` configuration.
>!!
>
> ********************************************************************************
> ############################
> # Package would be ignored #
> ############################
> Python recognizes 'packmol_memgen.lib.packmol.docs.imgs' as an importable package[^1],
> but it is absent from setuptools' `packages` configuration.
>
> This leads to an ambiguous overall configuration. If you want to distribute this
> package, please make sure that 'packmol_memgen.lib.packmol.docs.imgs' is explicitly added
> to the `packages` configuration field.
>
> Alternatively, you can also rely on setuptools' discovery methods
> (for example by using `find_namespace_packages(...)`/`find_namespace:`
> instead of `find_packages(...)`/`find:`).
>
> You can read more about "package discovery" on setuptools documentation page:
>
> - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
>
> If you don't want 'packmol_memgen.lib.packmol.docs.imgs' to be distributed and are
> already explicitly excluding 'packmol_memgen.lib.packmol.docs.imgs' via
> `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
> you can try to use `exclude_package_data`, or `include-package-data=False` in
> combination with a more fine grained `package-data` configuration.
>
> You can read more about "package data files" on setuptools documentation page:
>
> - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
>
>
> [^1]: For Python, any directory (with suitable naming) can be imported,
> even if it does not contain any `.py` files.
> On the other hand, currently there is no concept of package data
> directory, all directories are treated like packages.
> ********************************************************************************
>
>!!
> check.warn(importable)
>/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'packmol_memgen.lib.pdbremix.data' is absent from the `packages` configuration.
>!!
>
> ********************************************************************************
> ############################
> # Package would be ignored #
> ############################
> Python recognizes 'packmol_memgen.lib.pdbremix.data' as an importable package[^1],
> but it is absent from setuptools' `packages` configuration.
>
> This leads to an ambiguous overall configuration. If you want to distribute this
> package, please make sure that 'packmol_memgen.lib.pdbremix.data' is explicitly added
> to the `packages` configuration field.
>
> Alternatively, you can also rely on setuptools' discovery methods
> (for example by using `find_namespace_packages(...)`/`find_namespace:`
> instead of `find_packages(...)`/`find:`).
>
> You can read more about "package discovery" on setuptools documentation page:
>
> - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
>
> If you don't want 'packmol_memgen.lib.pdbremix.data' to be distributed and are
> already explicitly excluding 'packmol_memgen.lib.pdbremix.data' via
> `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
> you can try to use `exclude_package_data`, or `include-package-data=False` in
> combination with a more fine grained `package-data` configuration.
>
> You can read more about "package data files" on setuptools documentation page:
>
> - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
>
>
> [^1]: For Python, any directory (with suitable naming) can be imported,
> even if it does not contain any `.py` files.
> On the other hand, currently there is no concept of package data
> directory, all directories are treated like packages.
> ********************************************************************************
>
>!!
> check.warn(importable)
>/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'packmol_memgen.lib.ppm3' is absent from the `packages` configuration.
>!!
>
> ********************************************************************************
> ############################
> # Package would be ignored #
> ############################
> Python recognizes 'packmol_memgen.lib.ppm3' as an importable package[^1],
> but it is absent from setuptools' `packages` configuration.
>
> This leads to an ambiguous overall configuration. If you want to distribute this
> package, please make sure that 'packmol_memgen.lib.ppm3' is explicitly added
> to the `packages` configuration field.
>
> Alternatively, you can also rely on setuptools' discovery methods
> (for example by using `find_namespace_packages(...)`/`find_namespace:`
> instead of `find_packages(...)`/`find:`).
>
> You can read more about "package discovery" on setuptools documentation page:
>
> - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
>
> If you don't want 'packmol_memgen.lib.ppm3' to be distributed and are
> already explicitly excluding 'packmol_memgen.lib.ppm3' via
> `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
> you can try to use `exclude_package_data`, or `include-package-data=False` in
> combination with a more fine grained `package-data` configuration.
>
> You can read more about "package data files" on setuptools documentation page:
>
> - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
>
>
> [^1]: For Python, any directory (with suitable naming) can be imported,
> even if it does not contain any `.py` files.
> On the other hand, currently there is no concept of package data
> directory, all directories are treated like packages.
> ********************************************************************************
>
>!!
> check.warn(importable)
>copying packmol_memgen/lib/memembed/bin/memembed -> build/lib/packmol_memgen/lib/memembed/bin
>running build_scripts
>running install_lib
>copying build/lib/packmol_memgen/data/memgen.parm -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data
>copying build/lib/packmol_memgen/data/leaprc.lipid_ext -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data
>copying build/lib/packmol_memgen/data/solvent.parm -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data
>copying build/lib/packmol_memgen/data/pdbs.tar.gz -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data
>copying build/lib/packmol_memgen/data/lipid_ext.lib -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data
>copying build/lib/packmol_memgen/data/frcmod.lipid_ext -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data
>copying build/lib/packmol_memgen/data/leaprc.extra_solvents -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data
>copying build/lib/packmol_memgen/data/extra_solvents.lib -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data
>copying build/lib/packmol_memgen/data/frcmod.solvents -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data
>copying build/lib/packmol_memgen/example/example.sh -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/example
>copying build/lib/packmol_memgen/main.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen
>copying build/lib/packmol_memgen/__version__.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen
>copying build/lib/packmol_memgen/Makefile -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen
>copying build/lib/packmol_memgen/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen
>copying build/lib/packmol_memgen/lib/utils.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib
>copying build/lib/packmol_memgen/lib/memembed/examples/2x2v.pdb -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/examples
>copying build/lib/packmol_memgen/lib/memembed/examples/2iahA.pdb -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/examples
>copying build/lib/packmol_memgen/lib/memembed/examples/2iahA.pot -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/examples
>copying build/lib/packmol_memgen/lib/memembed/examples/3o7qA.pdb -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/examples
>copying build/lib/packmol_memgen/lib/memembed/scripts/pymol_membrane_image.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/scripts
>copying build/lib/packmol_memgen/lib/memembed/scripts/pymol_rotate.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/scripts
>copying build/lib/packmol_memgen/lib/memembed/bin/memembed -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/bin
>copying build/lib/packmol_memgen/lib/memembed/bin/.gitignore -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/bin
>copying build/lib/packmol_memgen/lib/memembed/CMakeLists.txt -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed
>copying build/lib/packmol_memgen/lib/memembed/LICENSE -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed
>copying build/lib/packmol_memgen/lib/memembed/Makefile -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed
>copying build/lib/packmol_memgen/lib/memembed/src/pdb.cpp -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src
>copying build/lib/packmol_memgen/lib/memembed/src/pdb.hpp -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src
>copying build/lib/packmol_memgen/lib/memembed/src/direct.cpp -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src
>copying build/lib/packmol_memgen/lib/memembed/src/grid.cpp -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src
>copying build/lib/packmol_memgen/lib/memembed/src/main.cpp -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src
>copying build/lib/packmol_memgen/lib/memembed/src/direct.hpp -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src
>copying build/lib/packmol_memgen/lib/memembed/src/ga.hpp -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src
>copying build/lib/packmol_memgen/lib/memembed/src/grid.hpp -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src
>copying build/lib/packmol_memgen/lib/memembed/src/ga.cpp -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src
>copying build/lib/packmol_memgen/lib/memembed/README -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed
>copying build/lib/packmol_memgen/lib/charmmlipid2amber/charmmlipid2amber.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/charmmlipid2amber
>copying build/lib/packmol_memgen/lib/charmmlipid2amber/charmmlipid2amber.csv -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/charmmlipid2amber
>copying build/lib/packmol_memgen/lib/charmmlipid2amber/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/charmmlipid2amber
>copying build/lib/packmol_memgen/lib/packmol/title.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/data_types.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/gparc.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/computef.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/gencan.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/restmol.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/comprest.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/comparegrad.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/flashmod.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/fparc.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/setijk.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/release.sh -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/swaptype.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/README.md -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/configure -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/CMakeLists.txt -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/usegencan.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/ahestetic.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/sizes.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/LICENSE -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/output.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/writesuccess.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/strlength.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/compute_data.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/heuristics.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/tobar.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/swaptypemod.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/header -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/jacobi.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/cenmass.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/Makefile -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/gencan_ieee_signal_routines.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/packmol.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/flashsort.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/resetboxes.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/docs/README.md -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol/docs
>copying build/lib/packmol_memgen/lib/packmol/docs/imgs/img37.png -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol/docs/imgs
>copying build/lib/packmol_memgen/lib/packmol/docs/imgs/img38.png -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol/docs/imgs
>copying build/lib/packmol_memgen/lib/packmol/docs/imgs/img36.png -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol/docs/imgs
>copying build/lib/packmol_memgen/lib/packmol/docs/imgs/img39.png -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol/docs/imgs
>copying build/lib/packmol_memgen/lib/packmol/docs/imgs/img31.png -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol/docs/imgs
>copying build/lib/packmol_memgen/lib/packmol/docs/imgs/pbc.jpg -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol/docs/imgs
>copying build/lib/packmol_memgen/lib/packmol/docs/_config.yml -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol/docs
>copying build/lib/packmol_memgen/lib/packmol/AUTHORS -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/setsizes.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/gwalls.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/compile_cmake.sh -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/computeg.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/polartocart.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/input.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/exit_codes.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/getinp.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/setibox.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/pgencan.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/initial.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/random.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/checkpoint.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/packmol/solvate.tcl -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol
>copying build/lib/packmol_memgen/lib/ppm3/min.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
>copying build/lib/packmol_memgen/lib/ppm3/rmsd.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
>copying build/lib/packmol_memgen/lib/ppm3/watface.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
>copying build/lib/packmol_memgen/lib/ppm3/locate.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
>copying build/lib/packmol_memgen/lib/ppm3/tilting.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
>copying build/lib/packmol_memgen/lib/ppm3/opm.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
>copying build/lib/packmol_memgen/lib/ppm3/orient.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
>copying build/lib/packmol_memgen/lib/ppm3/CMakeLists.txt -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
>copying build/lib/packmol_memgen/lib/ppm3/ppm3_instructions.docx -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
>copying build/lib/packmol_memgen/lib/ppm3/hbcor.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
>copying build/lib/packmol_memgen/lib/ppm3/deftm.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
>copying build/lib/packmol_memgen/lib/ppm3/Makefile -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
>copying build/lib/packmol_memgen/lib/ppm3/res.lib -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
>copying build/lib/packmol_memgen/lib/ppm3/solva.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
>copying build/lib/packmol_memgen/lib/ppm3/license.txt -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
>copying build/lib/packmol_memgen/lib/ppm3/readpdb.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
>copying build/lib/packmol_memgen/lib/ppm3/read_small.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
>copying build/lib/packmol_memgen/lib/ppm3/profile.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
>copying build/lib/packmol_memgen/lib/ppm3/find_segm.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3
>copying build/lib/packmol_memgen/lib/amber.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib
>copying build/lib/packmol_memgen/lib/pdbremix/data/opls.parameter -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
>copying build/lib/packmol_memgen/lib/pdbremix/data/charmm22.parameter -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
>copying build/lib/packmol_memgen/lib/pdbremix/data/phd.frcmod -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
>copying build/lib/packmol_memgen/lib/pdbremix/data/phd.prepin -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
>copying build/lib/packmol_memgen/lib/pdbremix/data/color_b.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
>copying build/lib/packmol_memgen/lib/pdbremix/data/opls.topology -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
>copying build/lib/packmol_memgen/lib/pdbremix/data/binaries.json -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
>copying build/lib/packmol_memgen/lib/pdbremix/data/aminoacid.pdb -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
>copying build/lib/packmol_memgen/lib/pdbremix/data/template.pdb -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
>copying build/lib/packmol_memgen/lib/pdbremix/data/znb.leaprc -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
>copying build/lib/packmol_memgen/lib/pdbremix/data/hin.lib -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
>copying build/lib/packmol_memgen/lib/pdbremix/data/znb.frcmod -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
>copying build/lib/packmol_memgen/lib/pdbremix/data/hydroxide.lib -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
>copying build/lib/packmol_memgen/lib/pdbremix/data/charmm22.topology -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
>copying build/lib/packmol_memgen/lib/pdbremix/data/phd.leaprc -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
>copying build/lib/packmol_memgen/lib/pdbremix/data/znb.lib -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
>copying build/lib/packmol_memgen/lib/pdbremix/data/make_chi.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data
>copying build/lib/packmol_memgen/lib/pdbremix/namd.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
>copying build/lib/packmol_memgen/lib/pdbremix/pdbatoms.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
>copying build/lib/packmol_memgen/lib/pdbremix/spacehash.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
>copying build/lib/packmol_memgen/lib/pdbremix/_version.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
>copying build/lib/packmol_memgen/lib/pdbremix/data.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
>copying build/lib/packmol_memgen/lib/pdbremix/fetch.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
>copying build/lib/packmol_memgen/lib/pdbremix/v3.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
>copying build/lib/packmol_memgen/lib/pdbremix/force.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
>copying build/lib/packmol_memgen/lib/pdbremix/gromacs.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
>copying build/lib/packmol_memgen/lib/pdbremix/asa.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
>copying build/lib/packmol_memgen/lib/pdbremix/util.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
>copying build/lib/packmol_memgen/lib/pdbremix/simulate.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
>copying build/lib/packmol_memgen/lib/pdbremix/LICENSE -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
>copying build/lib/packmol_memgen/lib/pdbremix/trajectory.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
>copying build/lib/packmol_memgen/lib/pdbremix/pymol.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
>copying build/lib/packmol_memgen/lib/pdbremix/v3array.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
>copying build/lib/packmol_memgen/lib/pdbremix/pdbtext.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
>copying build/lib/packmol_memgen/lib/pdbremix/amber.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
>copying build/lib/packmol_memgen/lib/pdbremix/rmsd.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
>copying build/lib/packmol_memgen/lib/pdbremix/protein.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
>copying build/lib/packmol_memgen/lib/pdbremix/v3numpy.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
>copying build/lib/packmol_memgen/lib/pdbremix/volume.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
>copying build/lib/packmol_memgen/lib/pdbremix/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix
>copying build/lib/packmol_memgen/lib/pdbremix/lib/docopt.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/lib
>copying build/lib/packmol_memgen/lib/pdbremix/lib/pyqcprot.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/lib
>copying build/lib/packmol_memgen/lib/pdbremix/lib/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/lib
>copying build/lib/packmol_memgen/lib/tqdm/rich.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
>copying build/lib/packmol_memgen/lib/tqdm/std.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
>copying build/lib/packmol_memgen/lib/tqdm/version.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
>copying build/lib/packmol_memgen/lib/tqdm/dask.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
>copying build/lib/packmol_memgen/lib/tqdm/utils.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
>copying build/lib/packmol_memgen/lib/tqdm/_tqdm_gui.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
>copying build/lib/packmol_memgen/lib/tqdm/_utils.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
>copying build/lib/packmol_memgen/lib/tqdm/notebook.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
>copying build/lib/packmol_memgen/lib/tqdm/tk.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
>copying build/lib/packmol_memgen/lib/tqdm/asyncio.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
>copying build/lib/packmol_memgen/lib/tqdm/gui.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
>copying build/lib/packmol_memgen/lib/tqdm/auto.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
>copying build/lib/packmol_memgen/lib/tqdm/autonotebook.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
>copying build/lib/packmol_memgen/lib/tqdm/__main__.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
>copying build/lib/packmol_memgen/lib/tqdm/_tqdm_pandas.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
>copying build/lib/packmol_memgen/lib/tqdm/_monitor.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
>copying build/lib/packmol_memgen/lib/tqdm/_main.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
>copying build/lib/packmol_memgen/lib/tqdm/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
>copying build/lib/packmol_memgen/lib/tqdm/_tqdm.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
>copying build/lib/packmol_memgen/lib/tqdm/_tqdm_notebook.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
>copying build/lib/packmol_memgen/lib/tqdm/cli.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
>copying build/lib/packmol_memgen/lib/tqdm/tqdm.1 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm
>copying build/lib/packmol_memgen/lib/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/main.py to main.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/__version__.py to __version__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/utils.py to utils.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/scripts/pymol_membrane_image.py to pymol_membrane_image.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/scripts/pymol_rotate.py to pymol_rotate.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/charmmlipid2amber/charmmlipid2amber.py to charmmlipid2amber.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/charmmlipid2amber/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/amber.py to amber.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data/color_b.py to color_b.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data/make_chi.py to make_chi.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/namd.py to namd.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/pdbatoms.py to pdbatoms.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/spacehash.py to spacehash.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/_version.py to _version.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data.py to data.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/fetch.py to fetch.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/v3.py to v3.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/force.py to force.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/gromacs.py to gromacs.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/asa.py to asa.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/util.py to util.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/simulate.py to simulate.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/trajectory.py to trajectory.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/pymol.py to pymol.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/v3array.py to v3array.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/pdbtext.py to pdbtext.cpython-311.pyc
>home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/pdbtext.py:30: SyntaxWarning: "is" with a literal. Did you mean "=="?
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/amber.py to amber.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/rmsd.py to rmsd.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/protein.py to protein.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/v3numpy.py to v3numpy.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/volume.py to volume.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/lib/docopt.py to docopt.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/lib/pyqcprot.py to pyqcprot.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/lib/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/rich.py to rich.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/std.py to std.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/version.py to version.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/dask.py to dask.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/utils.py to utils.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/_tqdm_gui.py to _tqdm_gui.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/_utils.py to _utils.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/notebook.py to notebook.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/tk.py to tk.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/asyncio.py to asyncio.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/gui.py to gui.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/auto.py to auto.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/autonotebook.py to autonotebook.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/__main__.py to __main__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/_tqdm_pandas.py to _tqdm_pandas.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/_monitor.py to _monitor.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/_main.py to _main.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/_tqdm.py to _tqdm.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/_tqdm_notebook.py to _tqdm_notebook.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/cli.py to cli.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/__init__.py to __init__.cpython-311.pyc
>running install_egg_info
>removing '/home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen-2024.3.27-py3.11.egg-info' (and everything under it)
>Copying packmol_memgen.egg-info to /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen-2024.3.27-py3.11.egg-info
>running install_scripts
>copying build/scripts-3.11/packmol-memgen -> /home/andriy/amber24//bin
>changing mode of /home/andriy/amber24//bin/packmol-memgen to 775
>running install
>/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
>!!
>
> ********************************************************************************
> Please avoid running ``setup.py`` directly.
> Instead, use pypa/build, pypa/installer or other
> standards-based tools.
>
> See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
> ********************************************************************************
>
>!!
> self.initialize_options()
>running build
>running build_py
>running egg_info
>writing edgembar.egg-info/PKG-INFO
>writing dependency_links to edgembar.egg-info/dependency_links.txt
>writing requirements to edgembar.egg-info/requires.txt
>writing top-level names to edgembar.egg-info/top_level.txt
>reading manifest file 'edgembar.egg-info/SOURCES.txt'
>writing manifest file 'edgembar.egg-info/SOURCES.txt'
>running build_scripts
>running install_lib
>copying build/lib/edgembar/Splines.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
>copying build/lib/edgembar/Stage.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
>copying build/lib/edgembar/OptUtils.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
>copying build/lib/edgembar/Results.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
>copying build/lib/edgembar/DiscoverEdges.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
>copying build/lib/edgembar/AutoEquil.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
>copying build/lib/edgembar/TimeSeriesAnalysis.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
>copying build/lib/edgembar/CenteredCubic.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
>copying build/lib/edgembar/pkgdata/selerow.js -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata
>copying build/lib/edgembar/pkgdata/sorttable.js -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata
>copying build/lib/edgembar/pkgdata/edge.css -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata
>copying build/lib/edgembar/pkgdata/graph.css -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata
>copying build/lib/edgembar/pkgdata/tschart.js -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata
>copying build/lib/edgembar/pkgdata/vis-iface.js -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata
>copying build/lib/edgembar/pkgdata/vis-network.min.js -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata
>copying build/lib/edgembar/pkgdata/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata
>copying build/lib/edgembar/Trial.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
>copying build/lib/edgembar/Edge.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
>copying build/lib/edgembar/ImportEdge.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
>copying build/lib/edgembar/HtmlUtils.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
>copying build/lib/edgembar/Env.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
>copying build/lib/edgembar/Graph.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
>copying build/lib/edgembar/GraphSearch.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
>copying build/lib/edgembar/Names.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
>copying build/lib/edgembar/Cli.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
>copying build/lib/edgembar/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Splines.py to Splines.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Stage.py to Stage.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/OptUtils.py to OptUtils.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Results.py to Results.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/DiscoverEdges.py to DiscoverEdges.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/AutoEquil.py to AutoEquil.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/TimeSeriesAnalysis.py to TimeSeriesAnalysis.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/CenteredCubic.py to CenteredCubic.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Trial.py to Trial.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Edge.py to Edge.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/ImportEdge.py to ImportEdge.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/HtmlUtils.py to HtmlUtils.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Env.py to Env.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Graph.py to Graph.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/GraphSearch.py to GraphSearch.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Names.py to Names.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Cli.py to Cli.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/__init__.py to __init__.cpython-311.pyc
>running install_egg_info
>removing '/home/andriy/amber24//lib/python3.11/site-packages/edgembar-3.0-py3.11.egg-info' (and everything under it)
>Copying edgembar.egg-info to /home/andriy/amber24//lib/python3.11/site-packages/edgembar-3.0-py3.11.egg-info
>running install_scripts
>copying build/scripts-3.11/edgembar-WriteGraphHtml.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/edgembar-amber2dats.py -> /home/andriy/amber24//bin
>changing mode of /home/andriy/amber24//bin/edgembar-WriteGraphHtml.py to 775
>changing mode of /home/andriy/amber24//bin/edgembar-amber2dats.py to 775
>running install
>/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
>!!
>
> ********************************************************************************
> Please avoid running ``setup.py`` directly.
> Instead, use pypa/build, pypa/installer or other
> standards-based tools.
>
> See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
> ********************************************************************************
>
>!!
> self.initialize_options()
>running build
>running build_py
>running egg_info
>writing ndfes.egg-info/PKG-INFO
>writing dependency_links to ndfes.egg-info/dependency_links.txt
>writing requirements to ndfes.egg-info/requires.txt
>writing top-level names to ndfes.egg-info/top_level.txt
>reading manifest file 'ndfes.egg-info/SOURCES.txt'
>writing manifest file 'ndfes.egg-info/SOURCES.txt'
>running build_scripts
>running install_lib
>copying build/lib/ndfes/vFEP.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
>copying build/lib/ndfes/gaussian/GaussianOutput.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/gaussian
>copying build/lib/ndfes/gaussian/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/gaussian
>copying build/lib/ndfes/SpatialBin.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
>copying build/lib/ndfes/MBAR.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
>copying build/lib/ndfes/PCV.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
>copying build/lib/ndfes/PathData.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
>copying build/lib/ndfes/normalmode/normalmode.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/normalmode
>copying build/lib/ndfes/normalmode/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/normalmode
>copying build/lib/ndfes/normalmode/kie.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/normalmode
>copying build/lib/ndfes/EvalT.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
>copying build/lib/ndfes/PlotUtils.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
>copying build/lib/ndfes/AutoEquil.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
>copying build/lib/ndfes/WAVG.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
>copying build/lib/ndfes/GridUtils.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
>copying build/lib/ndfes/SpatialDim.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
>copying build/lib/ndfes/Trajectory.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
>copying build/lib/ndfes/ReadCheckpoint.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
>copying build/lib/ndfes/Bspline.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
>copying build/lib/ndfes/Metafile.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
>copying build/lib/ndfes/VirtualGrid.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
>copying build/lib/ndfes/deprecated/OptUtils.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/deprecated
>copying build/lib/ndfes/deprecated/DensityEst.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/deprecated
>copying build/lib/ndfes/deprecated/DensityString.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/deprecated
>copying build/lib/ndfes/deprecated/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/deprecated
>copying build/lib/ndfes/constants/Conversions.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/constants
>copying build/lib/ndfes/constants/PeriodicTable.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/constants
>copying build/lib/ndfes/constants/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/constants
>copying build/lib/ndfes/amber/Restraint.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber
>copying build/lib/ndfes/amber/Reader.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber
>copying build/lib/ndfes/amber/Geometry.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber
>copying build/lib/ndfes/amber/Disang.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber
>copying build/lib/ndfes/amber/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber
>copying build/lib/ndfes/SmoothCurve.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
>copying build/lib/ndfes/ScriptUtils.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
>copying build/lib/ndfes/PathUtils.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
>copying build/lib/ndfes/FTSM.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
>copying build/lib/ndfes/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
>copying build/lib/ndfes/RBF.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
>copying build/lib/ndfes/GPR.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
>copying build/lib/ndfes/FES.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/vFEP.py to vFEP.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/gaussian/GaussianOutput.py to GaussianOutput.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/gaussian/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/SpatialBin.py to SpatialBin.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/MBAR.py to MBAR.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/PCV.py to PCV.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/PathData.py to PathData.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/normalmode/normalmode.py to normalmode.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/normalmode/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/normalmode/kie.py to kie.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/EvalT.py to EvalT.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/PlotUtils.py to PlotUtils.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/AutoEquil.py to AutoEquil.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/WAVG.py to WAVG.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/GridUtils.py to GridUtils.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/SpatialDim.py to SpatialDim.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/Trajectory.py to Trajectory.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/ReadCheckpoint.py to ReadCheckpoint.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/Bspline.py to Bspline.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/Metafile.py to Metafile.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/VirtualGrid.py to VirtualGrid.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/deprecated/OptUtils.py to OptUtils.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/deprecated/DensityEst.py to DensityEst.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/deprecated/DensityString.py to DensityString.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/deprecated/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/constants/Conversions.py to Conversions.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/constants/PeriodicTable.py to PeriodicTable.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/constants/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber/Restraint.py to Restraint.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber/Reader.py to Reader.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber/Geometry.py to Geometry.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber/Disang.py to Disang.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/SmoothCurve.py to SmoothCurve.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/ScriptUtils.py to ScriptUtils.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/PathUtils.py to PathUtils.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/FTSM.py to FTSM.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/__init__.py to __init__.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/RBF.py to RBF.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/GPR.py to GPR.cpython-311.pyc
>byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/FES.py to FES.cpython-311.pyc
>running install_egg_info
>removing '/home/andriy/amber24//lib/python3.11/site-packages/ndfes-3.0-py3.11.egg-info' (and everything under it)
>Copying ndfes.egg-info to /home/andriy/amber24//lib/python3.11/site-packages/ndfes-3.0-py3.11.egg-info
>running install_scripts
>copying build/scripts-3.11/ndfes-AvgFESs.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/ndfes-path-analyzesims.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/ndfes-path-prepguess.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/ndfes-CombineMetafiles.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/ndfes-PrepareAmberData.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/ndfes-PrintFES.py -> /home/andriy/amber24//bin
>copying build/scripts-3.11/ndfes-CheckEquil.py -> /home/andriy/amber24//bin
>changing mode of /home/andriy/amber24//bin/ndfes-AvgFESs.py to 775
>changing mode of /home/andriy/amber24//bin/ndfes-path-analyzesims.py to 775
>changing mode of /home/andriy/amber24//bin/ndfes-path-prepguess.py to 775
>changing mode of /home/andriy/amber24//bin/ndfes-CombineMetafiles.py to 775
>changing mode of /home/andriy/amber24//bin/ndfes-PrepareAmberData.py to 775
>changing mode of /home/andriy/amber24//bin/ndfes-PrintFES.py to 775
>changing mode of /home/andriy/amber24//bin/ndfes-CheckEquil.py to 775
>-- Fixing Miniconda script shebangs
>CMake Error at /home/andriy/amber24_src/cmake/Replace-function.cmake:32 (file):
> file failed to open for reading (No such file or directory):
>
> /home/andriy/amber24//miniconda/lib/python3.12/site-packages/conda_build/convert.py
>Call Stack (most recent call first):
> /home/andriy/amber24_src/cmake/FixCondaShebang/FixCondaShebang.cmake:48 (configuretime_file_replace)
>
>
>
>
>
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
--
====================================================================
David A. Case | dacase1.gmail.com
Dept. of Chemistry & Chemical Biology |
Rutgers University | skype: dacase
PO Box 937 | cell: +1-609-751-8668
Arroyo Seco, NM 87514 USA | web: casegroup.rutgers.edu
====================================================================
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Nov 02 2024 - 10:00:02 PDT
