Linux binary installer fails when building wheel for pymatgen and wxpython

[kaarelmand]

The binary installer for Linux linked on the main website fails when installing the pymatgen and wxpython packages. As a consequence, the binary files for larch and related programs are not created.

I have these issues on my main Ubuntu 20.04 install, but it also happened when I tried it on a new Ubuntu 20.04 virtual machine with default settings.

Terminal log

``` Welcome to xraylarch 2021-07 In order to continue the installation process, please review the license agreement. Please, press ENTER to continue >>> BSD-2-CLAUSE LICENSE Copyright, Licensing, and Re-distribution ----------------------------------------- Unless otherwise stated, all files included here are copyrighted and distributed under the following license: Copyright (c) 2010-2020 Matthew Newville, The University of Chicago All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Do you accept the license terms? [yes|no] [no] >>> yes xraylarch will now be installed into this location: /home/test/xraylarch - Press ENTER to confirm the location - Press CTRL-C to abort the installation - Or specify a different location below [/home/test/xraylarch] >>> PREFIX=/home/test/xraylarch Unpacking payload ... Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/test/xraylarch added / updated specs: - _libgcc_mutex==0.1=main - _openmp_mutex==4.5=1_gnu - alabaster==0.7.12=pyhd3eb1b0_0 - attrs==21.2.0=pyhd3eb1b0_0 - babel==2.9.1=pyhd3eb1b0_0 - blas==1.0=mkl - blosc==1.21.0=h8c45485_0 - bottleneck==1.3.2=py39hdd57654_1 - brotli==1.0.9=he6710b0_2 - brotlipy==0.7.0=py39h27cfd23_1003 - brunsli==0.1=h2531618_0 - bzip2==1.0.8=h7b6447c_0 - ca-certificates==2021.5.25=h06a4308_1 - cached-property==1.5.2=py_0 - cairo==1.16.0=hf32fb01_1 - certifi==2021.5.30=py39h06a4308_0 - cffi==1.14.5=py39h261ae71_0 - cfitsio==3.470=hf0d0db6_5 - chardet==4.0.0=py39h06a4308_1003 - charls==2.2.0=h2531618_0 - cloudpickle==1.6.0=py_0 - conda-package-handling==1.7.3=py39h27cfd23_1 - conda==4.10.3=py39h06a4308_0 - cryptography==3.4.7=py39hd23ed53_0 - cycler==0.10.0=py39h06a4308_0 - cython==0.29.23=py39h2531618_0 - cytoolz==0.11.0=py39h27cfd23_0 - dask-core==2021.6.2=pyhd3eb1b0_0 - dbus==1.13.18=hb2f20db_0 - decorator==5.0.9=pyhd3eb1b0_0 - dill==0.3.4=pyhd3eb1b0_0 - docutils==0.17.1=py39h06a4308_1 - expat==2.4.1=h2531618_2 - fontconfig==2.13.1=h6c09931_0 - freetype==2.10.4=h5ab3b9f_0 - fribidi==1.0.10=h7b6447c_0 - fsspec==2021.6.0=pyhd3eb1b0_0 - giflib==5.1.4=h14c3975_1 - glib==2.68.2=h36276a3_0 - graphite2==1.3.14=h23475e2_0 - greenlet==1.1.0=py39h2531618_0 - gst-plugins-base==1.14.0=h8213a91_2 - gstreamer==1.14.0=h28cd5cc_2 - h5py==3.2.1=py39h6c542dc_0 - harfbuzz==2.8.1=h6f93f22_0 - hdf5==1.10.6=hb1b8bf9_0 - icu==58.2=he6710b0_3 - idna==2.10=pyhd3eb1b0_0 - imagecodecs==2021.6.8=py39h581e88b_0 - imageio==2.9.0=pyhd3eb1b0_0 - imagesize==1.2.0=pyhd3eb1b0_0 - iniconfig==1.1.1=pyhd3eb1b0_0 - intel-openmp==2021.2.0=h06a4308_610 - jinja2==3.0.1=pyhd3eb1b0_0 - joblib==1.0.1=pyhd3eb1b0_0 - jpeg==9b=h024ee3a_2 - jxrlib==1.1=h7b6447c_2 - kiwisolver==1.3.1=py39h2531618_0 - krb5==1.17.1=h173b8e3_0 - lcms2==2.12=h3be6417_0 - ld_impl_linux-64==2.35.1=h7274673_9 - lerc==2.2.1=h2531618_0 - libaec==1.0.4=he6710b0_1 - libcurl==7.69.1=h20c2e04_0 - libdeflate==1.7=h27cfd23_5 - libedit==3.1.20210216=h27cfd23_1 - libffi==3.3=he6710b0_2 - libgcc-ng==9.3.0=h5101ec6_17 - libgfortran-ng==7.5.0=ha8ba4b0_17 - libgfortran4==7.5.0=ha8ba4b0_17 - libgomp==9.3.0=h5101ec6_17 - libpng==1.6.37=hbc83047_0 - libpq==12.2=h20c2e04_0 - libssh2==1.9.0=h1ba5d50_1 - libstdcxx-ng==9.3.0=hd4cf53a_17 - libtiff==4.1.0=h2733197_1 - libuuid==1.0.3=h1bed415_2 - libwebp==1.0.1=h8e7db2f_0 - libxcb==1.14=h7b6447c_0 - libxml2==2.9.12=h03d6c58_0 - libzopfli==1.0.3=he6710b0_0 - locket==0.2.1=py39h06a4308_1 - lz4-c==1.9.3=h2531618_0 - markupsafe==2.0.1=py39h27cfd23_0 - matplotlib-base==3.3.4=py39h62a2d02_0 - matplotlib==3.3.4=py39h06a4308_0 - mkl-service==2.3.0=py39h27cfd23_1 - mkl==2021.2.0=h06a4308_296 - mkl_fft==1.3.0=py39h42c9631_2 - mkl_random==1.2.1=py39ha9443f7_2 - more-itertools==8.8.0=pyhd3eb1b0_0 - ncurses==6.2=he6710b0_1 - networkx==2.5=py_0 - nose==1.3.7=pyhd3eb1b0_1006 - numexpr==2.7.3=py39h22e1b3c_1 - numpy-base==1.20.2=py39hfae3a4d_0 - numpy==1.20.2=py39h2d18471_0 - olefile==0.46=py_0 - openjpeg==2.3.0=h05c96fa_1 - openssl==1.1.1k=h27cfd23_0 - packaging==20.9=pyhd3eb1b0_0 - pandas==1.2.5=py39h295c915_0 - pango==1.45.3=hd140c19_0 - partd==1.2.0=pyhd3eb1b0_0 - patchelf==0.12=h2531618_1 - pcre==8.45=h295c915_0 - pillow==8.2.0=py39he98fc37_0 - pip==21.1.3=py39h06a4308_0 - pixman==0.40.0=h7b6447c_0 - pluggy==0.13.1=py39h06a4308_0 - psutil==5.8.0=py39h27cfd23_1 - psycopg2==2.8.6=py39h3c74f83_1 - py==1.10.0=pyhd3eb1b0_0 - pycosat==0.6.3=py39h27cfd23_0 - pycparser==2.20=py_2 - pygments==2.9.0=pyhd3eb1b0_0 - pyopenssl==20.0.1=pyhd3eb1b0_1 - pyparsing==2.4.7=pyhd3eb1b0_0 - pyqt==5.9.2=py39h2531618_6 - pysocks==1.7.1=py39h06a4308_0 - pytest==6.2.4=py39h06a4308_2 - python-dateutil==2.8.1=pyhd3eb1b0_0 - python==3.9.5=h12debd9_4 - pytz==2021.1=pyhd3eb1b0_0 - pywavelets==1.1.1=py39h6323ea4_4 - pyyaml==5.4.1=py39h27cfd23_1 - qt==5.9.7=h5867ecd_1 - readline==8.1=h27cfd23_0 - requests==2.25.1=pyhd3eb1b0_0 - ruamel_yaml==0.15.100=py39h27cfd23_0 - scikit-image==0.18.1=py39ha9443f7_0 - scikit-learn==0.24.2=py39ha9443f7_0 - scipy==1.6.2=py39had2a1c9_1 - setuptools==52.0.0=py39h06a4308_0 - sip==4.19.13=py39h2531618_0 - six==1.16.0=pyhd3eb1b0_0 - snappy==1.1.8=he6710b0_0 - snowballstemmer==2.1.0=pyhd3eb1b0_0 - sphinx==4.0.2=pyhd3eb1b0_0 - sphinxcontrib-applehelp==1.0.2=pyhd3eb1b0_0 - sphinxcontrib-devhelp==1.0.2=pyhd3eb1b0_0 - sphinxcontrib-htmlhelp==2.0.0=pyhd3eb1b0_0 - sphinxcontrib-jsmath==1.0.1=pyhd3eb1b0_0 - sphinxcontrib-qthelp==1.0.3=pyhd3eb1b0_0 - sphinxcontrib-serializinghtml==1.1.5=pyhd3eb1b0_0 - sqlalchemy==1.4.19=py39h7f8727e_0 - sqlite==3.36.0=hc218d9a_0 - threadpoolctl==2.1.0=pyh5ca1d4c_0 - tifffile==2021.4.8=pyhd3eb1b0_2 - tk==8.6.10=hbc83047_0 - toml==0.10.2=pyhd3eb1b0_0 - toolz==0.11.1=pyhd3eb1b0_0 - tornado==6.1=py39h27cfd23_0 - tqdm==4.61.1=pyhd3eb1b0_1 - tzdata==2021a=h52ac0ba_0 - urllib3==1.26.6=pyhd3eb1b0_1 - wheel==0.36.2=pyhd3eb1b0_0 - xz==5.2.5=h7b6447c_0 - yaml==0.2.5=h7b6447c_0 - zfp==0.5.5=h2531618_6 - zlib==1.2.11=h7b6447c_3 - zstd==1.4.9=haebb681_0 The following NEW packages will be INSTALLED: _libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main _openmp_mutex pkgs/main/linux-64::_openmp_mutex-4.5-1_gnu alabaster pkgs/main/noarch::alabaster-0.7.12-pyhd3eb1b0_0 attrs pkgs/main/noarch::attrs-21.2.0-pyhd3eb1b0_0 babel pkgs/main/noarch::babel-2.9.1-pyhd3eb1b0_0 blas pkgs/main/linux-64::blas-1.0-mkl blosc pkgs/main/linux-64::blosc-1.21.0-h8c45485_0 bottleneck pkgs/main/linux-64::bottleneck-1.3.2-py39hdd57654_1 brotli pkgs/main/linux-64::brotli-1.0.9-he6710b0_2 brotlipy pkgs/main/linux-64::brotlipy-0.7.0-py39h27cfd23_1003 brunsli pkgs/main/linux-64::brunsli-0.1-h2531618_0 bzip2 pkgs/main/linux-64::bzip2-1.0.8-h7b6447c_0 ca-certificates pkgs/main/linux-64::ca-certificates-2021.5.25-h06a4308_1 cached-property pkgs/main/noarch::cached-property-1.5.2-py_0 cairo pkgs/main/linux-64::cairo-1.16.0-hf32fb01_1 certifi pkgs/main/linux-64::certifi-2021.5.30-py39h06a4308_0 cffi pkgs/main/linux-64::cffi-1.14.5-py39h261ae71_0 cfitsio pkgs/main/linux-64::cfitsio-3.470-hf0d0db6_5 chardet pkgs/main/linux-64::chardet-4.0.0-py39h06a4308_1003 charls pkgs/main/linux-64::charls-2.2.0-h2531618_0 cloudpickle pkgs/main/noarch::cloudpickle-1.6.0-py_0 conda pkgs/main/linux-64::conda-4.10.3-py39h06a4308_0 conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.7.3-py39h27cfd23_1 cryptography pkgs/main/linux-64::cryptography-3.4.7-py39hd23ed53_0 cycler pkgs/main/linux-64::cycler-0.10.0-py39h06a4308_0 cython pkgs/main/linux-64::cython-0.29.23-py39h2531618_0 cytoolz pkgs/main/linux-64::cytoolz-0.11.0-py39h27cfd23_0 dask-core pkgs/main/noarch::dask-core-2021.6.2-pyhd3eb1b0_0 dbus pkgs/main/linux-64::dbus-1.13.18-hb2f20db_0 decorator pkgs/main/noarch::decorator-5.0.9-pyhd3eb1b0_0 dill pkgs/main/noarch::dill-0.3.4-pyhd3eb1b0_0 docutils pkgs/main/linux-64::docutils-0.17.1-py39h06a4308_1 expat pkgs/main/linux-64::expat-2.4.1-h2531618_2 fontconfig pkgs/main/linux-64::fontconfig-2.13.1-h6c09931_0 freetype pkgs/main/linux-64::freetype-2.10.4-h5ab3b9f_0 fribidi pkgs/main/linux-64::fribidi-1.0.10-h7b6447c_0 fsspec pkgs/main/noarch::fsspec-2021.6.0-pyhd3eb1b0_0 giflib pkgs/main/linux-64::giflib-5.1.4-h14c3975_1 glib pkgs/main/linux-64::glib-2.68.2-h36276a3_0 graphite2 pkgs/main/linux-64::graphite2-1.3.14-h23475e2_0 greenlet pkgs/main/linux-64::greenlet-1.1.0-py39h2531618_0 gst-plugins-base pkgs/main/linux-64::gst-plugins-base-1.14.0-h8213a91_2 gstreamer pkgs/main/linux-64::gstreamer-1.14.0-h28cd5cc_2 h5py pkgs/main/linux-64::h5py-3.2.1-py39h6c542dc_0 harfbuzz pkgs/main/linux-64::harfbuzz-2.8.1-h6f93f22_0 hdf5 pkgs/main/linux-64::hdf5-1.10.6-hb1b8bf9_0 icu pkgs/main/linux-64::icu-58.2-he6710b0_3 idna pkgs/main/noarch::idna-2.10-pyhd3eb1b0_0 imagecodecs pkgs/main/linux-64::imagecodecs-2021.6.8-py39h581e88b_0 imageio pkgs/main/noarch::imageio-2.9.0-pyhd3eb1b0_0 imagesize pkgs/main/noarch::imagesize-1.2.0-pyhd3eb1b0_0 iniconfig pkgs/main/noarch::iniconfig-1.1.1-pyhd3eb1b0_0 intel-openmp pkgs/main/linux-64::intel-openmp-2021.2.0-h06a4308_610 jinja2 pkgs/main/noarch::jinja2-3.0.1-pyhd3eb1b0_0 joblib pkgs/main/noarch::joblib-1.0.1-pyhd3eb1b0_0 jpeg pkgs/main/linux-64::jpeg-9b-h024ee3a_2 jxrlib pkgs/main/linux-64::jxrlib-1.1-h7b6447c_2 kiwisolver pkgs/main/linux-64::kiwisolver-1.3.1-py39h2531618_0 krb5 pkgs/main/linux-64::krb5-1.17.1-h173b8e3_0 lcms2 pkgs/main/linux-64::lcms2-2.12-h3be6417_0 ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.35.1-h7274673_9 lerc pkgs/main/linux-64::lerc-2.2.1-h2531618_0 libaec pkgs/main/linux-64::libaec-1.0.4-he6710b0_1 libcurl pkgs/main/linux-64::libcurl-7.69.1-h20c2e04_0 libdeflate pkgs/main/linux-64::libdeflate-1.7-h27cfd23_5 libedit pkgs/main/linux-64::libedit-3.1.20210216-h27cfd23_1 libffi pkgs/main/linux-64::libffi-3.3-he6710b0_2 libgcc-ng pkgs/main/linux-64::libgcc-ng-9.3.0-h5101ec6_17 libgfortran-ng pkgs/main/linux-64::libgfortran-ng-7.5.0-ha8ba4b0_17 libgfortran4 pkgs/main/linux-64::libgfortran4-7.5.0-ha8ba4b0_17 libgomp pkgs/main/linux-64::libgomp-9.3.0-h5101ec6_17 libpng pkgs/main/linux-64::libpng-1.6.37-hbc83047_0 libpq pkgs/main/linux-64::libpq-12.2-h20c2e04_0 libssh2 pkgs/main/linux-64::libssh2-1.9.0-h1ba5d50_1 libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.3.0-hd4cf53a_17 libtiff pkgs/main/linux-64::libtiff-4.1.0-h2733197_1 libuuid pkgs/main/linux-64::libuuid-1.0.3-h1bed415_2 libwebp pkgs/main/linux-64::libwebp-1.0.1-h8e7db2f_0 libxcb pkgs/main/linux-64::libxcb-1.14-h7b6447c_0 libxml2 pkgs/main/linux-64::libxml2-2.9.12-h03d6c58_0 libzopfli pkgs/main/linux-64::libzopfli-1.0.3-he6710b0_0 locket pkgs/main/linux-64::locket-0.2.1-py39h06a4308_1 lz4-c pkgs/main/linux-64::lz4-c-1.9.3-h2531618_0 markupsafe pkgs/main/linux-64::markupsafe-2.0.1-py39h27cfd23_0 matplotlib pkgs/main/linux-64::matplotlib-3.3.4-py39h06a4308_0 matplotlib-base pkgs/main/linux-64::matplotlib-base-3.3.4-py39h62a2d02_0 mkl pkgs/main/linux-64::mkl-2021.2.0-h06a4308_296 mkl-service pkgs/main/linux-64::mkl-service-2.3.0-py39h27cfd23_1 mkl_fft pkgs/main/linux-64::mkl_fft-1.3.0-py39h42c9631_2 mkl_random pkgs/main/linux-64::mkl_random-1.2.1-py39ha9443f7_2 more-itertools pkgs/main/noarch::more-itertools-8.8.0-pyhd3eb1b0_0 ncurses pkgs/main/linux-64::ncurses-6.2-he6710b0_1 networkx pkgs/main/noarch::networkx-2.5-py_0 nose pkgs/main/noarch::nose-1.3.7-pyhd3eb1b0_1006 numexpr pkgs/main/linux-64::numexpr-2.7.3-py39h22e1b3c_1 numpy pkgs/main/linux-64::numpy-1.20.2-py39h2d18471_0 numpy-base pkgs/main/linux-64::numpy-base-1.20.2-py39hfae3a4d_0 olefile pkgs/main/noarch::olefile-0.46-py_0 openjpeg pkgs/main/linux-64::openjpeg-2.3.0-h05c96fa_1 openssl pkgs/main/linux-64::openssl-1.1.1k-h27cfd23_0 packaging pkgs/main/noarch::packaging-20.9-pyhd3eb1b0_0 pandas pkgs/main/linux-64::pandas-1.2.5-py39h295c915_0 pango pkgs/main/linux-64::pango-1.45.3-hd140c19_0 partd pkgs/main/noarch::partd-1.2.0-pyhd3eb1b0_0 patchelf pkgs/main/linux-64::patchelf-0.12-h2531618_1 pcre pkgs/main/linux-64::pcre-8.45-h295c915_0 pillow pkgs/main/linux-64::pillow-8.2.0-py39he98fc37_0 pip pkgs/main/linux-64::pip-21.1.3-py39h06a4308_0 pixman pkgs/main/linux-64::pixman-0.40.0-h7b6447c_0 pluggy pkgs/main/linux-64::pluggy-0.13.1-py39h06a4308_0 psutil pkgs/main/linux-64::psutil-5.8.0-py39h27cfd23_1 psycopg2 pkgs/main/linux-64::psycopg2-2.8.6-py39h3c74f83_1 py pkgs/main/noarch::py-1.10.0-pyhd3eb1b0_0 pycosat pkgs/main/linux-64::pycosat-0.6.3-py39h27cfd23_0 pycparser pkgs/main/noarch::pycparser-2.20-py_2 pygments pkgs/main/noarch::pygments-2.9.0-pyhd3eb1b0_0 pyopenssl pkgs/main/noarch::pyopenssl-20.0.1-pyhd3eb1b0_1 pyparsing pkgs/main/noarch::pyparsing-2.4.7-pyhd3eb1b0_0 pyqt pkgs/main/linux-64::pyqt-5.9.2-py39h2531618_6 pysocks pkgs/main/linux-64::pysocks-1.7.1-py39h06a4308_0 pytest pkgs/main/linux-64::pytest-6.2.4-py39h06a4308_2 python pkgs/main/linux-64::python-3.9.5-h12debd9_4 python-dateutil pkgs/main/noarch::python-dateutil-2.8.1-pyhd3eb1b0_0 pytz pkgs/main/noarch::pytz-2021.1-pyhd3eb1b0_0 pywavelets pkgs/main/linux-64::pywavelets-1.1.1-py39h6323ea4_4 pyyaml pkgs/main/linux-64::pyyaml-5.4.1-py39h27cfd23_1 qt pkgs/main/linux-64::qt-5.9.7-h5867ecd_1 readline pkgs/main/linux-64::readline-8.1-h27cfd23_0 requests pkgs/main/noarch::requests-2.25.1-pyhd3eb1b0_0 ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.100-py39h27cfd23_0 scikit-image pkgs/main/linux-64::scikit-image-0.18.1-py39ha9443f7_0 scikit-learn pkgs/main/linux-64::scikit-learn-0.24.2-py39ha9443f7_0 scipy pkgs/main/linux-64::scipy-1.6.2-py39had2a1c9_1 setuptools pkgs/main/linux-64::setuptools-52.0.0-py39h06a4308_0 sip pkgs/main/linux-64::sip-4.19.13-py39h2531618_0 six pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_0 snappy pkgs/main/linux-64::snappy-1.1.8-he6710b0_0 snowballstemmer pkgs/main/noarch::snowballstemmer-2.1.0-pyhd3eb1b0_0 sphinx pkgs/main/noarch::sphinx-4.0.2-pyhd3eb1b0_0 sphinxcontrib-app~ pkgs/main/noarch::sphinxcontrib-applehelp-1.0.2-pyhd3eb1b0_0 sphinxcontrib-dev~ pkgs/main/noarch::sphinxcontrib-devhelp-1.0.2-pyhd3eb1b0_0 sphinxcontrib-htm~ pkgs/main/noarch::sphinxcontrib-htmlhelp-2.0.0-pyhd3eb1b0_0 sphinxcontrib-jsm~ pkgs/main/noarch::sphinxcontrib-jsmath-1.0.1-pyhd3eb1b0_0 sphinxcontrib-qth~ pkgs/main/noarch::sphinxcontrib-qthelp-1.0.3-pyhd3eb1b0_0 sphinxcontrib-ser~ pkgs/main/noarch::sphinxcontrib-serializinghtml-1.1.5-pyhd3eb1b0_0 sqlalchemy pkgs/main/linux-64::sqlalchemy-1.4.19-py39h7f8727e_0 sqlite pkgs/main/linux-64::sqlite-3.36.0-hc218d9a_0 threadpoolctl pkgs/main/noarch::threadpoolctl-2.1.0-pyh5ca1d4c_0 tifffile pkgs/main/noarch::tifffile-2021.4.8-pyhd3eb1b0_2 tk pkgs/main/linux-64::tk-8.6.10-hbc83047_0 toml pkgs/main/noarch::toml-0.10.2-pyhd3eb1b0_0 toolz pkgs/main/noarch::toolz-0.11.1-pyhd3eb1b0_0 tornado pkgs/main/linux-64::tornado-6.1-py39h27cfd23_0 tqdm pkgs/main/noarch::tqdm-4.61.1-pyhd3eb1b0_1 tzdata pkgs/main/noarch::tzdata-2021a-h52ac0ba_0 urllib3 pkgs/main/noarch::urllib3-1.26.6-pyhd3eb1b0_1 wheel pkgs/main/noarch::wheel-0.36.2-pyhd3eb1b0_0 xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0 yaml pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0 zfp pkgs/main/linux-64::zfp-0.5.5-h2531618_6 zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3 zstd pkgs/main/linux-64::zstd-1.4.9-haebb681_0 Preparing transaction: done Executing transaction: | Installed package of scikit-learn can be accelerated using scikit-learn-intelex. More details are available here: https://intel.github.io/scikit-learn-intelex For example: $ conda install scikit-learn-intelex $ python -m sklearnex my_application.py done THIS IS POST INSTALL LINUX PREFIX /home/test/xraylarch ### /home/test/xraylarch/bin/conda install -yc conda-forge wxpython tomopy Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): / /home/test/xraylarch/pkgs/post_install.sh: line 12: 3303 Killed $PREFIX/bin/conda install --force-reinstall -yc conda-forge wxpython tomopy pymatgen pycifrw Collecting xraylarch Downloading xraylarch-0.9.55.tar.gz (36.7 MB) |████████████████████████████████| 36.7 MB 8.9 MB/s Collecting pyepics Downloading pyepics-3.5.0.tar.gz (5.8 MB) |████████████████████████████████| 5.8 MB 11.5 MB/s Collecting epicsapps Downloading epicsapps-0.9.1.tar.gz (380 kB) |████████████████████████████████| 380 kB 13.9 MB/s Collecting psycopg2-binary Downloading psycopg2_binary-2.9.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.4 MB) |████████████████████████████████| 3.4 MB 12.8 MB/s Collecting pyFAI Downloading pyFAI-0.20.0-cp39-cp39-manylinux2014_x86_64.whl (19.9 MB) |████████████████████████████████| 19.9 MB 11.4 MB/s Collecting numdifftools Downloading numdifftools-0.9.40-py2.py3-none-any.whl (99 kB) |████████████████████████████████| 99 kB 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pillow in ./lib/python3.9/site-packages (from xraylarch) (8.2.0) Collecting peakutils Downloading PeakUtils-1.3.3-py3-none-any.whl (7.7 kB) Requirement already satisfied: requests in ./lib/python3.9/site-packages (from xraylarch) (2.25.1) Requirement already satisfied: scikit-image in ./lib/python3.9/site-packages (from xraylarch) (0.18.1) Requirement already satisfied: scikit-learn in ./lib/python3.9/site-packages (from xraylarch) (0.24.2) Collecting asteval>=0.9.22 Downloading asteval-0.9.25.tar.gz (39 kB) Collecting lmfit>=1.0.2 Downloading lmfit-1.0.3.tar.gz (292 kB) |████████████████████████████████| 292 kB 24.1 MB/s Collecting uncertainties>=3.1 Downloading uncertainties-3.1.6-py2.py3-none-any.whl (98 kB) |████████████████████████████████| 98 kB 4.6 MB/s Collecting pyshortcuts>=1.7.2 Downloading pyshortcuts-1.8.0.tar.gz (933 kB) |████████████████████████████████| 933 kB 12.2 MB/s Collecting xraydb>=4.4 Downloading xraydb-4.4.7.tar.gz (3.9 MB) |████████████████████████████████| 3.9 MB 15.5 MB/s Collecting silx>=0.15.2 Downloading silx-0.15.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (13.8 MB) |████████████████████████████████| 13.8 MB 11.5 MB/s Collecting hdf5plugin Downloading hdf5plugin-3.2.0-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (9.3 MB) |████████████████████████████████| 9.3 MB 8.9 MB/s Requirement already satisfied: psutil in ./lib/python3.9/site-packages (from xraylarch) (5.8.0) Collecting pymatgen Downloading pymatgen-2022.0.14.tar.gz (3.3 MB) |████████████████████████████████| 3.3 MB 14.3 MB/s Installing build dependencies ... done Getting requirements to build wheel ... done Installing backend dependencies ... done Preparing wheel metadata ... done Collecting importlib_metadata Downloading importlib_metadata-4.8.1-py3-none-any.whl (17 kB) Requirement already satisfied: kiwisolver>=1.0.1 in ./lib/python3.9/site-packages (from matplotlib>=3.0->xraylarch) (1.3.1) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in ./lib/python3.9/site-packages (from matplotlib>=3.0->xraylarch) (2.4.7) Requirement already satisfied: cycler>=0.10 in ./lib/python3.9/site-packages (from matplotlib>=3.0->xraylarch) (0.10.0) Requirement already satisfied: python-dateutil>=2.1 in ./lib/python3.9/site-packages (from matplotlib>=3.0->xraylarch) (2.8.1) Requirement already satisfied: six in ./lib/python3.9/site-packages (from cycler>=0.10->matplotlib>=3.0->xraylarch) (1.16.0) Collecting fabio>=0.9 Downloading fabio-0.12.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.8 MB) |████████████████████████████████| 3.8 MB 4.1 MB/s Requirement already satisfied: setuptools in ./lib/python3.9/site-packages (from silx>=0.15.2->xraylarch) (52.0.0.post20210125) Requirement already satisfied: greenlet!=0.4.17 in ./lib/python3.9/site-packages (from sqlalchemy>=1.0->xraylarch) (1.1.0) Collecting future Downloading future-0.18.2.tar.gz (829 kB) |████████████████████████████████| 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tabulate-0.8.9-py3-none-any.whl (25 kB) Collecting ruamel.yaml>=0.15.6 Downloading ruamel.yaml-0.17.16-py3-none-any.whl (109 kB) |████████████████████████████████| 109 kB 10.2 MB/s Requirement already satisfied: decorator>=4.3.0 in ./lib/python3.9/site-packages (from networkx>=2.2->pymatgen->xraylarch) (5.0.9) Collecting tenacity>=6.2.0 Downloading tenacity-8.0.1-py3-none-any.whl (24 kB) Collecting ruamel.yaml.clib>=0.1.2 Downloading ruamel.yaml.clib-0.2.6-cp39-cp39-manylinux1_x86_64.whl (539 kB) |████████████████████████████████| 539 kB 26.1 MB/s Requirement already satisfied: attrs>=19.2.0 in ./lib/python3.9/site-packages (from pytest->xraylarch) (21.2.0) Requirement already satisfied: iniconfig in ./lib/python3.9/site-packages (from pytest->xraylarch) (1.1.1) Requirement already satisfied: pluggy<1.0.0a1,>=0.12 in ./lib/python3.9/site-packages (from pytest->xraylarch) (0.13.1) Requirement already satisfied: py>=1.8.2 in ./lib/python3.9/site-packages (from pytest->xraylarch) (1.10.0) Requirement already satisfied: toml in ./lib/python3.9/site-packages (from pytest->xraylarch) (0.10.2) Requirement already satisfied: certifi>=2017.4.17 in ./lib/python3.9/site-packages (from requests->xraylarch) (2021.5.30) Requirement already satisfied: chardet<5,>=3.0.2 in ./lib/python3.9/site-packages (from requests->xraylarch) (4.0.0) Requirement already satisfied: idna<3,>=2.5 in ./lib/python3.9/site-packages (from requests->xraylarch) (2.10) Requirement already satisfied: urllib3<1.27,>=1.21.1 in ./lib/python3.9/site-packages (from requests->xraylarch) (1.26.6) Requirement already satisfied: imageio>=2.3.0 in ./lib/python3.9/site-packages (from scikit-image->xraylarch) (2.9.0) Requirement already satisfied: tifffile>=2019.7.26 in ./lib/python3.9/site-packages (from scikit-image->xraylarch) (2021.4.8) Requirement already satisfied: PyWavelets>=1.1.1 in ./lib/python3.9/site-packages (from scikit-image->xraylarch) (1.1.1) Requirement already satisfied: joblib>=0.11 in ./lib/python3.9/site-packages (from scikit-learn->xraylarch) (1.0.1) Requirement already satisfied: threadpoolctl>=2.0.0 in ./lib/python3.9/site-packages (from scikit-learn->xraylarch) (2.1.0) Collecting mpmath>=0.19 Downloading mpmath-1.2.1-py3-none-any.whl (532 kB) |████████████████████████████████| 532 kB 12.2 MB/s Building wheels for collected packages: xraylarch, asteval, lmfit, pyshortcuts, xraydb, pyepics, epicsapps, algopy, future, pymatgen, termcolor, wxmplot, wxpython, wxutils Building wheel for xraylarch (setup.py) ... done Created wheel for xraylarch: filename=xraylarch-0.9.55-py3-none-any.whl size=25148908 sha256=5f68e26e9a2ef982fef47186ef70b271145d605f80c58244aa4ed418c8dbd25f Stored in directory: /home/test/.cache/pip/wheels/e8/9b/60/4f57fc43ce53a923c969ddf125532bafd38ff4e737354f61b3 Building wheel for asteval (setup.py) ... done Created wheel for asteval: filename=asteval-0.9.25-py3-none-any.whl size=17287 sha256=6143cd60b769c7ad87be6e8e5f9f2691978a965670377a3dbc1b932bd5ad9b33 Stored in directory: /home/test/.cache/pip/wheels/72/43/66/4c430ea3af2af8ed7ba85e6636fdbc3bfef47ea49aa617659e Building wheel for lmfit (setup.py) ... done Created wheel for lmfit: filename=lmfit-1.0.3-py3-none-any.whl size=84390 sha256=a030efca0a5551effc178812a731d0d5f8a18d947fd393a3dd79c06c74b5e806 Stored in directory: /home/test/.cache/pip/wheels/76/f4/32/c336957bfd694c7746f4df19b74e08d918ada688fe1349cca2 Building wheel for pyshortcuts (setup.py) ... done Created wheel for pyshortcuts: filename=pyshortcuts-1.8.0-py3-none-any.whl size=157230 sha256=ca70bfc3cf897a0d6afcc64a241463ad68307595a5902ce7e1d6b97e3cdca8a6 Stored in directory: /home/test/.cache/pip/wheels/3c/9e/f8/2e1b9a3b6d96adbe99cd76b50ae3009a75c656325635740aae Building wheel for xraydb (setup.py) ... done Created wheel for xraydb: filename=xraydb-4.4.7-py3-none-any.whl size=3850536 sha256=728c6c9b83125c5d7b757d3b937464c9f7190e4eab582e2e61749d6e06eaee91 Stored in directory: /home/test/.cache/pip/wheels/28/b1/42/ad3a6529c38bc11007c631865402be853c2ccef01947e3fac9 Building wheel for pyepics (setup.py) ... done Created wheel for pyepics: filename=pyepics-3.5.0-py3-none-any.whl size=4993847 sha256=76cd6daa593fd0bf093a2557953570223a2db1862d5f465863b6086e6ac22552 Stored in directory: /home/test/.cache/pip/wheels/0a/f7/71/e89c277dad2905421ae88ef278026f224f809db2ecfa14594d Building wheel for epicsapps (setup.py) ... done Created wheel for epicsapps: filename=epicsapps-0.9.1-py3-none-any.whl size=321758 sha256=e6b20e7711a9dced4a9795692c272458c2a899800d35c83a5f05f5afa1fcd4b5 Stored in directory: /home/test/.cache/pip/wheels/2a/8a/d0/e2c946b4fd7c3c328e8c6ead0c1564db5b05aa4336cdee4c19 Building wheel for algopy (setup.py) ... done Created wheel for algopy: filename=algopy-0.5.7-py3-none-any.whl size=107609 sha256=12ab06c227775f2289abae1c6c48ef8103435143bfd6c3790c320aed83f8ba72 Stored in directory: /home/test/.cache/pip/wheels/84/94/f7/79486786a473bd5e841b49908d5b0cf816ddf78c962ade3cbf Building wheel for future (setup.py) ... done Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491059 sha256=91adcc295abbd9ef48ba8b208fadb0d1a9fa3ac2097230c61531185feef93d81 Stored in directory: /home/test/.cache/pip/wheels/2f/a0/d3/4030d9f80e6b3be787f19fc911b8e7aa462986a40ab1e4bb94 Building wheel for pymatgen (PEP 517) ... error ERROR: Command errored out with exit status 1: command: /home/test/xraylarch/bin/python /home/test/xraylarch/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmp6q93u45k cwd: /tmp/pip-install-jhbcot45/pymatgen_823a2e18abd9404f87cf0c5d00beb160 Complete output (498 lines): running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-3.9 creating build/lib.linux-x86_64-3.9/pymatgen creating build/lib.linux-x86_64-3.9/pymatgen/command_line copying pymatgen/command_line/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/command_line copying pymatgen/command_line/enumlib_caller.py -> build/lib.linux-x86_64-3.9/pymatgen/command_line copying pymatgen/command_line/vampire_caller.py -> build/lib.linux-x86_64-3.9/pymatgen/command_line copying pymatgen/command_line/critic2_caller.py -> build/lib.linux-x86_64-3.9/pymatgen/command_line copying pymatgen/command_line/gulp_caller.py -> build/lib.linux-x86_64-3.9/pymatgen/command_line copying pymatgen/command_line/mcsqs_caller.py -> build/lib.linux-x86_64-3.9/pymatgen/command_line copying pymatgen/command_line/bader_caller.py -> build/lib.linux-x86_64-3.9/pymatgen/command_line creating build/lib.linux-x86_64-3.9/pymatgen/apps copying pymatgen/apps/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/apps creating build/lib.linux-x86_64-3.9/pymatgen/symmetry copying pymatgen/symmetry/analyzer.py -> build/lib.linux-x86_64-3.9/pymatgen/symmetry copying pymatgen/symmetry/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/symmetry copying pymatgen/symmetry/structure.py -> build/lib.linux-x86_64-3.9/pymatgen/symmetry copying pymatgen/symmetry/kpath.py -> build/lib.linux-x86_64-3.9/pymatgen/symmetry copying pymatgen/symmetry/maggroups.py -> build/lib.linux-x86_64-3.9/pymatgen/symmetry copying pymatgen/symmetry/settings.py -> build/lib.linux-x86_64-3.9/pymatgen/symmetry copying pymatgen/symmetry/groups.py -> build/lib.linux-x86_64-3.9/pymatgen/symmetry copying pymatgen/symmetry/bandstructure.py -> build/lib.linux-x86_64-3.9/pymatgen/symmetry copying pymatgen/symmetry/site_symmetries.py -> build/lib.linux-x86_64-3.9/pymatgen/symmetry creating build/lib.linux-x86_64-3.9/pymatgen/vis copying pymatgen/vis/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/vis copying pymatgen/vis/structure_chemview.py -> build/lib.linux-x86_64-3.9/pymatgen/vis copying pymatgen/vis/plotters.py -> build/lib.linux-x86_64-3.9/pymatgen/vis copying pymatgen/vis/structure_vtk.py -> build/lib.linux-x86_64-3.9/pymatgen/vis creating build/lib.linux-x86_64-3.9/pymatgen/alchemy copying pymatgen/alchemy/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/alchemy copying pymatgen/alchemy/materials.py -> build/lib.linux-x86_64-3.9/pymatgen/alchemy copying pymatgen/alchemy/filters.py -> build/lib.linux-x86_64-3.9/pymatgen/alchemy copying pymatgen/alchemy/transmuters.py -> build/lib.linux-x86_64-3.9/pymatgen/alchemy creating build/lib.linux-x86_64-3.9/pymatgen/util copying pymatgen/util/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/util copying pymatgen/util/io_utils.py -> build/lib.linux-x86_64-3.9/pymatgen/util copying pymatgen/util/provenance.py -> build/lib.linux-x86_64-3.9/pymatgen/util copying pymatgen/util/sequence.py -> build/lib.linux-x86_64-3.9/pymatgen/util copying pymatgen/util/serialization.py -> build/lib.linux-x86_64-3.9/pymatgen/util copying pymatgen/util/testing.py -> build/lib.linux-x86_64-3.9/pymatgen/util copying pymatgen/util/convergence.py -> build/lib.linux-x86_64-3.9/pymatgen/util copying pymatgen/util/plotting.py -> build/lib.linux-x86_64-3.9/pymatgen/util copying pymatgen/util/coord.py -> build/lib.linux-x86_64-3.9/pymatgen/util copying pymatgen/util/string.py -> build/lib.linux-x86_64-3.9/pymatgen/util copying pymatgen/util/typing.py -> build/lib.linux-x86_64-3.9/pymatgen/util copying pymatgen/util/num.py -> build/lib.linux-x86_64-3.9/pymatgen/util creating build/lib.linux-x86_64-3.9/pymatgen/transformations copying pymatgen/transformations/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/transformations copying pymatgen/transformations/standard_transformations.py -> build/lib.linux-x86_64-3.9/pymatgen/transformations copying pymatgen/transformations/advanced_transformations.py -> build/lib.linux-x86_64-3.9/pymatgen/transformations copying pymatgen/transformations/defect_transformations.py -> build/lib.linux-x86_64-3.9/pymatgen/transformations copying pymatgen/transformations/site_transformations.py -> build/lib.linux-x86_64-3.9/pymatgen/transformations copying pymatgen/transformations/transformation_abc.py -> build/lib.linux-x86_64-3.9/pymatgen/transformations creating build/lib.linux-x86_64-3.9/pymatgen/entries copying pymatgen/entries/entry_tools.py -> build/lib.linux-x86_64-3.9/pymatgen/entries copying pymatgen/entries/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/entries copying pymatgen/entries/exp_entries.py -> build/lib.linux-x86_64-3.9/pymatgen/entries copying pymatgen/entries/correction_calculator.py -> build/lib.linux-x86_64-3.9/pymatgen/entries copying pymatgen/entries/computed_entries.py -> build/lib.linux-x86_64-3.9/pymatgen/entries copying pymatgen/entries/compatibility.py -> build/lib.linux-x86_64-3.9/pymatgen/entries creating build/lib.linux-x86_64-3.9/pymatgen/core copying pymatgen/core/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/core copying pymatgen/core/structure.py -> build/lib.linux-x86_64-3.9/pymatgen/core copying pymatgen/core/xcfunc.py -> build/lib.linux-x86_64-3.9/pymatgen/core copying pymatgen/core/trajectory.py -> build/lib.linux-x86_64-3.9/pymatgen/core copying pymatgen/core/composition.py -> build/lib.linux-x86_64-3.9/pymatgen/core copying pymatgen/core/tensors.py -> build/lib.linux-x86_64-3.9/pymatgen/core copying pymatgen/core/surface.py -> build/lib.linux-x86_64-3.9/pymatgen/core copying pymatgen/core/operations.py -> build/lib.linux-x86_64-3.9/pymatgen/core copying pymatgen/core/units.py -> build/lib.linux-x86_64-3.9/pymatgen/core copying pymatgen/core/spectrum.py -> build/lib.linux-x86_64-3.9/pymatgen/core copying pymatgen/core/sites.py -> build/lib.linux-x86_64-3.9/pymatgen/core copying pymatgen/core/bonds.py -> build/lib.linux-x86_64-3.9/pymatgen/core copying pymatgen/core/molecular_orbitals.py -> build/lib.linux-x86_64-3.9/pymatgen/core copying pymatgen/core/libxcfunc.py -> build/lib.linux-x86_64-3.9/pymatgen/core copying pymatgen/core/periodic_table.py -> build/lib.linux-x86_64-3.9/pymatgen/core copying pymatgen/core/lattice.py -> build/lib.linux-x86_64-3.9/pymatgen/core copying pymatgen/core/ion.py -> build/lib.linux-x86_64-3.9/pymatgen/core copying pymatgen/core/interface.py -> build/lib.linux-x86_64-3.9/pymatgen/core creating build/lib.linux-x86_64-3.9/pymatgen/optimization copying pymatgen/optimization/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/optimization copying pymatgen/optimization/linear_assignment_numpy.py -> build/lib.linux-x86_64-3.9/pymatgen/optimization creating build/lib.linux-x86_64-3.9/pymatgen/electronic_structure copying pymatgen/electronic_structure/cohp.py -> build/lib.linux-x86_64-3.9/pymatgen/electronic_structure copying pymatgen/electronic_structure/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/electronic_structure copying pymatgen/electronic_structure/boltztrap.py -> build/lib.linux-x86_64-3.9/pymatgen/electronic_structure copying pymatgen/electronic_structure/bandstructure.py -> build/lib.linux-x86_64-3.9/pymatgen/electronic_structure copying pymatgen/electronic_structure/dos.py -> build/lib.linux-x86_64-3.9/pymatgen/electronic_structure copying pymatgen/electronic_structure/plotter.py -> build/lib.linux-x86_64-3.9/pymatgen/electronic_structure copying pymatgen/electronic_structure/core.py -> build/lib.linux-x86_64-3.9/pymatgen/electronic_structure copying pymatgen/electronic_structure/boltztrap2.py -> build/lib.linux-x86_64-3.9/pymatgen/electronic_structure package init file 'pymatgen/ext/__init__.py' not found (or not a regular file) creating build/lib.linux-x86_64-3.9/pymatgen/ext copying pymatgen/ext/optimade.py -> build/lib.linux-x86_64-3.9/pymatgen/ext copying pymatgen/ext/jhu.py -> build/lib.linux-x86_64-3.9/pymatgen/ext copying pymatgen/ext/crystalsai.py -> build/lib.linux-x86_64-3.9/pymatgen/ext copying pymatgen/ext/matproj.py -> build/lib.linux-x86_64-3.9/pymatgen/ext copying pymatgen/ext/cod.py -> build/lib.linux-x86_64-3.9/pymatgen/ext creating build/lib.linux-x86_64-3.9/pymatgen/cli copying pymatgen/cli/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/cli copying pymatgen/cli/gaussian_analyzer.py -> build/lib.linux-x86_64-3.9/pymatgen/cli copying pymatgen/cli/feff_plot_dos.py -> build/lib.linux-x86_64-3.9/pymatgen/cli copying pymatgen/cli/pmg_plot.py -> build/lib.linux-x86_64-3.9/pymatgen/cli copying pymatgen/cli/pmg.py -> build/lib.linux-x86_64-3.9/pymatgen/cli copying pymatgen/cli/pmg_structure.py -> build/lib.linux-x86_64-3.9/pymatgen/cli copying pymatgen/cli/pmg_analyze.py -> build/lib.linux-x86_64-3.9/pymatgen/cli copying pymatgen/cli/feff_plot_cross_section.py -> build/lib.linux-x86_64-3.9/pymatgen/cli copying pymatgen/cli/pmg_query.py -> build/lib.linux-x86_64-3.9/pymatgen/cli copying pymatgen/cli/get_environment.py -> build/lib.linux-x86_64-3.9/pymatgen/cli copying pymatgen/cli/pmg_config.py -> build/lib.linux-x86_64-3.9/pymatgen/cli copying pymatgen/cli/pmg_potcar.py -> build/lib.linux-x86_64-3.9/pymatgen/cli package init file 'pymatgen/analysis/__init__.py' not found (or not a regular file) creating build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/adsorption.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/bond_valence.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/prototypes.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/interface_reactions.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/path_finder.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/hhi.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/ewald.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/xps.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/find_dimension.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/phase_diagram.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/nmr.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/diffusion_analyzer.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/reaction_calculator.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/structure_analyzer.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/chempot_diagram.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/eos.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/substrate_analyzer.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/energy_models.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/thermochemistry.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/piezo.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/bond_dissociation.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/local_env.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/transition_state.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/quasiharmonic.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/fragmenter.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/molecule_matcher.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/piezo_sensitivity.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/molecule_structure_comparator.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/excitation.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/cost.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/structure_matcher.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/pourbaix_diagram.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/wulff.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/dimensionality.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/functional_groups.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/graphs.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/interface.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/surface_analysis.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis package init file 'pymatgen/io/__init__.py' not found (or not a regular file) creating build/lib.linux-x86_64-3.9/pymatgen/io copying pymatgen/io/gaussian.py -> build/lib.linux-x86_64-3.9/pymatgen/io copying pymatgen/io/aiida.py -> build/lib.linux-x86_64-3.9/pymatgen/io copying pymatgen/io/cssr.py -> build/lib.linux-x86_64-3.9/pymatgen/io copying pymatgen/io/ase.py -> build/lib.linux-x86_64-3.9/pymatgen/io copying pymatgen/io/lmto.py -> build/lib.linux-x86_64-3.9/pymatgen/io copying pymatgen/io/xcrysden.py -> build/lib.linux-x86_64-3.9/pymatgen/io copying pymatgen/io/fiesta.py -> build/lib.linux-x86_64-3.9/pymatgen/io copying pymatgen/io/xr.py -> build/lib.linux-x86_64-3.9/pymatgen/io copying pymatgen/io/adf.py -> build/lib.linux-x86_64-3.9/pymatgen/io copying pymatgen/io/shengbte.py -> build/lib.linux-x86_64-3.9/pymatgen/io copying pymatgen/io/nwchem.py -> build/lib.linux-x86_64-3.9/pymatgen/io copying pymatgen/io/zeopp.py -> build/lib.linux-x86_64-3.9/pymatgen/io copying pymatgen/io/phonopy.py -> build/lib.linux-x86_64-3.9/pymatgen/io copying pymatgen/io/prismatic.py -> build/lib.linux-x86_64-3.9/pymatgen/io copying pymatgen/io/cif.py -> build/lib.linux-x86_64-3.9/pymatgen/io copying pymatgen/io/wannier90.py -> build/lib.linux-x86_64-3.9/pymatgen/io copying pymatgen/io/atat.py -> build/lib.linux-x86_64-3.9/pymatgen/io copying pymatgen/io/pwscf.py -> build/lib.linux-x86_64-3.9/pymatgen/io copying pymatgen/io/cube.py -> build/lib.linux-x86_64-3.9/pymatgen/io copying pymatgen/io/babel.py -> build/lib.linux-x86_64-3.9/pymatgen/io copying pymatgen/io/xyz.py -> build/lib.linux-x86_64-3.9/pymatgen/io copying pymatgen/io/jarvis.py -> build/lib.linux-x86_64-3.9/pymatgen/io creating build/lib.linux-x86_64-3.9/pymatgen/phonon copying pymatgen/phonon/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/phonon copying pymatgen/phonon/gruneisen.py -> build/lib.linux-x86_64-3.9/pymatgen/phonon copying pymatgen/phonon/bandstructure.py -> build/lib.linux-x86_64-3.9/pymatgen/phonon copying pymatgen/phonon/ir_spectra.py -> build/lib.linux-x86_64-3.9/pymatgen/phonon copying pymatgen/phonon/dos.py -> build/lib.linux-x86_64-3.9/pymatgen/phonon copying pymatgen/phonon/plotter.py -> build/lib.linux-x86_64-3.9/pymatgen/phonon creating build/lib.linux-x86_64-3.9/pymatgen/apps/borg copying pymatgen/apps/borg/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/apps/borg copying pymatgen/apps/borg/hive.py -> build/lib.linux-x86_64-3.9/pymatgen/apps/borg copying pymatgen/apps/borg/queen.py -> build/lib.linux-x86_64-3.9/pymatgen/apps/borg creating build/lib.linux-x86_64-3.9/pymatgen/apps/battery copying pymatgen/apps/battery/conversion_battery.py -> build/lib.linux-x86_64-3.9/pymatgen/apps/battery copying pymatgen/apps/battery/analyzer.py -> build/lib.linux-x86_64-3.9/pymatgen/apps/battery copying pymatgen/apps/battery/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/apps/battery copying pymatgen/apps/battery/battery_abc.py -> build/lib.linux-x86_64-3.9/pymatgen/apps/battery copying pymatgen/apps/battery/plotter.py -> build/lib.linux-x86_64-3.9/pymatgen/apps/battery copying pymatgen/apps/battery/insertion_battery.py -> build/lib.linux-x86_64-3.9/pymatgen/apps/battery package init file 'pymatgen/util/structures/__init__.py' not found (or not a regular file) package init file 'pymatgen/entries/data/__init__.py' not found (or not a regular file) creating build/lib.linux-x86_64-3.9/pymatgen/analysis/diffraction copying pymatgen/analysis/diffraction/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/diffraction copying pymatgen/analysis/diffraction/xrd.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/diffraction copying pymatgen/analysis/diffraction/tem.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/diffraction copying pymatgen/analysis/diffraction/neutron.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/diffraction copying pymatgen/analysis/diffraction/core.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/diffraction creating build/lib.linux-x86_64-3.9/pymatgen/analysis/ferroelectricity copying pymatgen/analysis/ferroelectricity/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/ferroelectricity copying pymatgen/analysis/ferroelectricity/polarization.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/ferroelectricity creating build/lib.linux-x86_64-3.9/pymatgen/analysis/elasticity copying pymatgen/analysis/elasticity/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/elasticity copying pymatgen/analysis/elasticity/elastic.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/elasticity copying pymatgen/analysis/elasticity/strain.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/elasticity copying pymatgen/analysis/elasticity/stress.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/elasticity creating build/lib.linux-x86_64-3.9/pymatgen/analysis/interfaces copying pymatgen/analysis/interfaces/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/interfaces copying pymatgen/analysis/interfaces/zsl.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/interfaces copying pymatgen/analysis/interfaces/substrate_analyzer.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/interfaces copying pymatgen/analysis/interfaces/coherent_interfaces.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/interfaces creating build/lib.linux-x86_64-3.9/pymatgen/analysis/defects copying pymatgen/analysis/defects/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/defects copying pymatgen/analysis/defects/corrections.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/defects copying pymatgen/analysis/defects/generators.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/defects copying pymatgen/analysis/defects/dilute_solution_model.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/defects copying pymatgen/analysis/defects/thermodynamics.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/defects copying pymatgen/analysis/defects/core.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/defects copying pymatgen/analysis/defects/defect_compatibility.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/defects copying pymatgen/analysis/defects/utils.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/defects creating build/lib.linux-x86_64-3.9/pymatgen/analysis/xas copying pymatgen/analysis/xas/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/xas copying pymatgen/analysis/xas/spectrum.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/xas creating build/lib.linux-x86_64-3.9/pymatgen/analysis/magnetism copying pymatgen/analysis/magnetism/analyzer.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/magnetism copying pymatgen/analysis/magnetism/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/magnetism copying pymatgen/analysis/magnetism/heisenberg.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/magnetism copying pymatgen/analysis/magnetism/jahnteller.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/magnetism creating build/lib.linux-x86_64-3.9/pymatgen/analysis/gb copying pymatgen/analysis/gb/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/gb copying pymatgen/analysis/gb/grain.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/gb creating build/lib.linux-x86_64-3.9/pymatgen/analysis/solar copying pymatgen/analysis/solar/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/solar copying pymatgen/analysis/solar/slme.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/solar creating build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv copying pymatgen/analysis/chemenv/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv creating build/lib.linux-x86_64-3.9/pymatgen/analysis/structure_prediction copying pymatgen/analysis/structure_prediction/volume_predictor.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/structure_prediction copying pymatgen/analysis/structure_prediction/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/structure_prediction copying pymatgen/analysis/structure_prediction/dopant_predictor.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/structure_prediction copying pymatgen/analysis/structure_prediction/substitutor.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/structure_prediction copying pymatgen/analysis/structure_prediction/substitution_probability.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/structure_prediction creating build/lib.linux-x86_64-3.9/pymatgen/analysis/topological copying pymatgen/analysis/topological/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/topological copying pymatgen/analysis/topological/spillage.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/topological creating build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments copying pymatgen/analysis/chemenv/coordination_environments/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments copying pymatgen/analysis/chemenv/coordination_environments/structure_environments.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments copying pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments copying pymatgen/analysis/chemenv/coordination_environments/voronoi.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments creating build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/utils copying pymatgen/analysis/chemenv/utils/chemenv_config.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/utils copying pymatgen/analysis/chemenv/utils/func_utils.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/utils copying pymatgen/analysis/chemenv/utils/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/utils copying pymatgen/analysis/chemenv/utils/defs_utils.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/utils copying pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/utils copying pymatgen/analysis/chemenv/utils/math_utils.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/utils copying pymatgen/analysis/chemenv/utils/chemenv_errors.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/utils copying pymatgen/analysis/chemenv/utils/scripts_utils.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/utils copying pymatgen/analysis/chemenv/utils/graph_utils.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/utils creating build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/connectivity copying pymatgen/analysis/chemenv/connectivity/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/connectivity copying pymatgen/analysis/chemenv/connectivity/structure_connectivity.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/connectivity copying pymatgen/analysis/chemenv/connectivity/environment_nodes.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/connectivity copying pymatgen/analysis/chemenv/connectivity/connected_components.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/connectivity copying pymatgen/analysis/chemenv/connectivity/connectivity_finder.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/connectivity creating build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files package init file 'pymatgen/analysis/chemenv/coordination_environments/strategy_files/__init__.py' not found (or not a regular file) package init file 'pymatgen/analysis/structure_prediction/data/__init__.py' not found (or not a regular file) creating build/lib.linux-x86_64-3.9/pymatgen/io/xtb copying pymatgen/io/xtb/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/io/xtb copying pymatgen/io/xtb/outputs.py -> build/lib.linux-x86_64-3.9/pymatgen/io/xtb copying pymatgen/io/xtb/inputs.py -> build/lib.linux-x86_64-3.9/pymatgen/io/xtb creating build/lib.linux-x86_64-3.9/pymatgen/io/cp2k copying pymatgen/io/cp2k/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/io/cp2k copying pymatgen/io/cp2k/sets.py -> build/lib.linux-x86_64-3.9/pymatgen/io/cp2k copying pymatgen/io/cp2k/outputs.py -> build/lib.linux-x86_64-3.9/pymatgen/io/cp2k copying pymatgen/io/cp2k/utils.py -> build/lib.linux-x86_64-3.9/pymatgen/io/cp2k copying pymatgen/io/cp2k/inputs.py -> build/lib.linux-x86_64-3.9/pymatgen/io/cp2k creating build/lib.linux-x86_64-3.9/pymatgen/io/exciting copying pymatgen/io/exciting/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/io/exciting copying pymatgen/io/exciting/inputs.py -> build/lib.linux-x86_64-3.9/pymatgen/io/exciting creating build/lib.linux-x86_64-3.9/pymatgen/io/lobster copying pymatgen/io/lobster/lobsterenv.py -> build/lib.linux-x86_64-3.9/pymatgen/io/lobster copying pymatgen/io/lobster/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/io/lobster copying pymatgen/io/lobster/outputs.py -> build/lib.linux-x86_64-3.9/pymatgen/io/lobster copying pymatgen/io/lobster/inputs.py -> build/lib.linux-x86_64-3.9/pymatgen/io/lobster creating build/lib.linux-x86_64-3.9/pymatgen/io/lammps copying pymatgen/io/lammps/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/io/lammps copying pymatgen/io/lammps/data.py -> build/lib.linux-x86_64-3.9/pymatgen/io/lammps copying pymatgen/io/lammps/outputs.py -> build/lib.linux-x86_64-3.9/pymatgen/io/lammps copying pymatgen/io/lammps/utils.py -> build/lib.linux-x86_64-3.9/pymatgen/io/lammps copying pymatgen/io/lammps/inputs.py -> build/lib.linux-x86_64-3.9/pymatgen/io/lammps creating build/lib.linux-x86_64-3.9/pymatgen/io/feff copying pymatgen/io/feff/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/io/feff copying pymatgen/io/feff/sets.py -> build/lib.linux-x86_64-3.9/pymatgen/io/feff copying pymatgen/io/feff/outputs.py -> build/lib.linux-x86_64-3.9/pymatgen/io/feff copying pymatgen/io/feff/inputs.py -> build/lib.linux-x86_64-3.9/pymatgen/io/feff creating build/lib.linux-x86_64-3.9/pymatgen/io/abinit copying pymatgen/io/abinit/pseudos.py -> build/lib.linux-x86_64-3.9/pymatgen/io/abinit copying pymatgen/io/abinit/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/io/abinit copying pymatgen/io/abinit/abiobjects.py -> build/lib.linux-x86_64-3.9/pymatgen/io/abinit copying pymatgen/io/abinit/variable.py -> build/lib.linux-x86_64-3.9/pymatgen/io/abinit copying pymatgen/io/abinit/abitimer.py -> build/lib.linux-x86_64-3.9/pymatgen/io/abinit copying pymatgen/io/abinit/netcdf.py -> build/lib.linux-x86_64-3.9/pymatgen/io/abinit copying pymatgen/io/abinit/inputs.py -> build/lib.linux-x86_64-3.9/pymatgen/io/abinit creating build/lib.linux-x86_64-3.9/pymatgen/io/qchem copying pymatgen/io/qchem/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/io/qchem copying pymatgen/io/qchem/sets.py -> build/lib.linux-x86_64-3.9/pymatgen/io/qchem copying pymatgen/io/qchem/outputs.py -> build/lib.linux-x86_64-3.9/pymatgen/io/qchem copying pymatgen/io/qchem/utils.py -> build/lib.linux-x86_64-3.9/pymatgen/io/qchem copying pymatgen/io/qchem/inputs.py -> build/lib.linux-x86_64-3.9/pymatgen/io/qchem creating build/lib.linux-x86_64-3.9/pymatgen/io/vasp copying pymatgen/io/vasp/__init__.py -> build/lib.linux-x86_64-3.9/pymatgen/io/vasp copying pymatgen/io/vasp/sets.py -> build/lib.linux-x86_64-3.9/pymatgen/io/vasp copying pymatgen/io/vasp/help.py -> build/lib.linux-x86_64-3.9/pymatgen/io/vasp copying pymatgen/io/vasp/outputs.py -> build/lib.linux-x86_64-3.9/pymatgen/io/vasp copying pymatgen/io/vasp/inputs.py -> build/lib.linux-x86_64-3.9/pymatgen/io/vasp package init file 'pymatgen/io/lobster/lobster_basis/__init__.py' not found (or not a regular file) package init file 'pymatgen/io/lammps/templates/__init__.py' not found (or not a regular file) copying pymatgen/command_line/OxideTersoffPotentials -> build/lib.linux-x86_64-3.9/pymatgen/command_line copying pymatgen/symmetry/symm_data.yaml -> build/lib.linux-x86_64-3.9/pymatgen/symmetry copying pymatgen/symmetry/symm_ops.yaml -> build/lib.linux-x86_64-3.9/pymatgen/symmetry copying pymatgen/symmetry/symm_data.json -> build/lib.linux-x86_64-3.9/pymatgen/symmetry copying pymatgen/symmetry/symm_ops.json -> build/lib.linux-x86_64-3.9/pymatgen/symmetry copying pymatgen/symmetry/symm_data_magnetic.sqlite -> build/lib.linux-x86_64-3.9/pymatgen/symmetry copying pymatgen/vis/ElementColorSchemes.yaml -> build/lib.linux-x86_64-3.9/pymatgen/vis creating build/lib.linux-x86_64-3.9/pymatgen/util/structures copying pymatgen/util/structures/Sn.json -> build/lib.linux-x86_64-3.9/pymatgen/util/structures copying pymatgen/util/structures/SiO2.json -> build/lib.linux-x86_64-3.9/pymatgen/util/structures copying pymatgen/util/structures/VO2.json -> build/lib.linux-x86_64-3.9/pymatgen/util/structures copying pymatgen/util/structures/K2O2.json -> build/lib.linux-x86_64-3.9/pymatgen/util/structures copying pymatgen/util/structures/Li2O2.json -> build/lib.linux-x86_64-3.9/pymatgen/util/structures copying pymatgen/util/structures/SrTiO3.json -> build/lib.linux-x86_64-3.9/pymatgen/util/structures copying pymatgen/util/structures/CsCl.json -> build/lib.linux-x86_64-3.9/pymatgen/util/structures copying pymatgen/util/structures/He_BCC.json -> build/lib.linux-x86_64-3.9/pymatgen/util/structures copying pymatgen/util/structures/Li3V2(PO4)3.json -> build/lib.linux-x86_64-3.9/pymatgen/util/structures copying pymatgen/util/structures/TiO2.json -> build/lib.linux-x86_64-3.9/pymatgen/util/structures copying pymatgen/util/structures/Graphite.json -> build/lib.linux-x86_64-3.9/pymatgen/util/structures copying pymatgen/util/structures/Si_SiO2_Interface.json -> build/lib.linux-x86_64-3.9/pymatgen/util/structures copying pymatgen/util/structures/Pb2TiZrO6.json -> build/lib.linux-x86_64-3.9/pymatgen/util/structures copying pymatgen/util/structures/Li2O.json -> build/lib.linux-x86_64-3.9/pymatgen/util/structures copying pymatgen/util/structures/LiFePO4.json -> build/lib.linux-x86_64-3.9/pymatgen/util/structures copying pymatgen/util/structures/TlBiSe2.json -> build/lib.linux-x86_64-3.9/pymatgen/util/structures copying pymatgen/util/structures/Li10GeP2S12.json -> build/lib.linux-x86_64-3.9/pymatgen/util/structures copying pymatgen/util/structures/NaFePO4.json -> build/lib.linux-x86_64-3.9/pymatgen/util/structures copying pymatgen/util/structures/BaNiO3.json -> build/lib.linux-x86_64-3.9/pymatgen/util/structures copying pymatgen/util/structures/Si.json -> build/lib.linux-x86_64-3.9/pymatgen/util/structures copying pymatgen/util/plotly_pd_layouts.json -> build/lib.linux-x86_64-3.9/pymatgen/util copying pymatgen/util/plotly_chempot_layouts.json -> build/lib.linux-x86_64-3.9/pymatgen/util copying pymatgen/entries/exp_compounds.json.gz -> build/lib.linux-x86_64-3.9/pymatgen/entries copying pymatgen/entries/calc_compounds.json.gz -> build/lib.linux-x86_64-3.9/pymatgen/entries copying pymatgen/entries/MP2020Compatibility.yaml -> build/lib.linux-x86_64-3.9/pymatgen/entries copying pymatgen/entries/MPCompatibility.yaml -> build/lib.linux-x86_64-3.9/pymatgen/entries copying pymatgen/entries/MITCompatibility.yaml -> build/lib.linux-x86_64-3.9/pymatgen/entries creating build/lib.linux-x86_64-3.9/pymatgen/entries/data copying pymatgen/entries/data/nist_gas_gf.json -> build/lib.linux-x86_64-3.9/pymatgen/entries/data copying pymatgen/entries/data/g_els.json -> build/lib.linux-x86_64-3.9/pymatgen/entries/data copying pymatgen/core/py.typed -> build/lib.linux-x86_64-3.9/pymatgen/core copying pymatgen/core/func_groups.json -> build/lib.linux-x86_64-3.9/pymatgen/core copying pymatgen/core/quad_data.json -> build/lib.linux-x86_64-3.9/pymatgen/core copying pymatgen/core/periodic_table.json -> build/lib.linux-x86_64-3.9/pymatgen/core copying pymatgen/core/libxc_docs.json -> build/lib.linux-x86_64-3.9/pymatgen/core copying pymatgen/core/bond_lengths.json -> build/lib.linux-x86_64-3.9/pymatgen/core copying pymatgen/core/reconstructions_archive.json -> build/lib.linux-x86_64-3.9/pymatgen/core copying pymatgen/analysis/vesta_cutoffs.yaml -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/bonds_jmol_ob.yaml -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/icsd_bv.yaml -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/op_params.yaml -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/bvparam_1991.yaml -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/cn_opt_params.yaml -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/aflow_prototypes.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/ionic_radii.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/hhi_data.csv -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/costdb_elements.csv -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/atomic_subshell_photoionization_cross_sections.csv -> build/lib.linux-x86_64-3.9/pymatgen/analysis copying pymatgen/analysis/diffraction/neutron_scattering_length.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/diffraction copying pymatgen/analysis/diffraction/atomic_scattering_params.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/diffraction copying pymatgen/analysis/magnetism/default_magmoms.yaml -> build/lib.linux-x86_64-3.9/pymatgen/analysis/magnetism copying pymatgen/analysis/solar/am1.5G.dat -> build/lib.linux-x86_64-3.9/pymatgen/analysis/solar copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SMA#9.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/PBP#12.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/HB#8.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TI#9.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/PP#6.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/HA#12.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SBT#8.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/DD#8.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/C#8.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/FO#7.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/I#12.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/PP#10.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/S#1.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/L#2.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SH#13.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/PP#5.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TO_2#9.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TC#9.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SC#12.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TO_3#9.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/DI#11.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/MI#10.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/S#5.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/HP#12.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SBSA#10.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/O#6_explicit.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TBT#8.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/H#10.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/BO_3#8.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/ET#7.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SS#4.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/CO#11.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TT_2#9.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TT#12.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/BS_2#10.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/S#4.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/DD#20.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TT_3#9.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/T#6.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/S#10.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/C#12.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/S#12.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/T#4.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/PA#10.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SA#8.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/BO_1#8.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/BO_2#8.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TY#3.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/PB#7.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TBSA#10.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/HD#9.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/O#6.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/ST#7.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/T#5.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TS#3.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TO_1#9.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/DDPN#8.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/AC#12.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SY#4.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/PCPA#11.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/BS_1#10.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/A#2.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SS#9.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/SH#11.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TT_1#9.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/H#11.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/TL#3.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files copying pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/allcg.txt -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files creating build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/strategy_files copying pymatgen/analysis/chemenv/coordination_environments/strategy_files/ImprovedConfidenceCutoffDefaultParameters.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/chemenv/coordination_environments/strategy_files copying pymatgen/analysis/structure_prediction/DLS_bond_params.yaml -> build/lib.linux-x86_64-3.9/pymatgen/analysis/structure_prediction creating build/lib.linux-x86_64-3.9/pymatgen/analysis/structure_prediction/data copying pymatgen/analysis/structure_prediction/data/pair_correlation.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/structure_prediction/data copying pymatgen/analysis/structure_prediction/data/lambda.json -> build/lib.linux-x86_64-3.9/pymatgen/analysis/structure_prediction/data copying pymatgen/io/cp2k/gth_potentials.yaml -> build/lib.linux-x86_64-3.9/pymatgen/io/cp2k copying pymatgen/io/cp2k/aux_basis.yaml -> build/lib.linux-x86_64-3.9/pymatgen/io/cp2k copying pymatgen/io/cp2k/NLCC_POTENTIALS.yaml -> build/lib.linux-x86_64-3.9/pymatgen/io/cp2k copying pymatgen/io/cp2k/basis_molopt.yaml -> build/lib.linux-x86_64-3.9/pymatgen/io/cp2k creating build/lib.linux-x86_64-3.9/pymatgen/io/lobster/lobster_basis copying pymatgen/io/lobster/lobster_basis/BASIS_PBE_54_standard.yaml -> build/lib.linux-x86_64-3.9/pymatgen/io/lobster/lobster_basis copying pymatgen/io/lobster/lobster_basis/BASIS_PBE_54_max.yaml -> build/lib.linux-x86_64-3.9/pymatgen/io/lobster/lobster_basis copying pymatgen/io/lobster/lobster_basis/BASIS_PBE_54_min.yaml -> build/lib.linux-x86_64-3.9/pymatgen/io/lobster/lobster_basis copying pymatgen/io/lammps/CoeffsDataType.yaml -> build/lib.linux-x86_64-3.9/pymatgen/io/lammps creating build/lib.linux-x86_64-3.9/pymatgen/io/lammps/templates copying pymatgen/io/lammps/templates/md.txt -> build/lib.linux-x86_64-3.9/pymatgen/io/lammps/templates copying pymatgen/io/feff/MPEXAFSSet.yaml -> build/lib.linux-x86_64-3.9/pymatgen/io/feff copying pymatgen/io/feff/MPELNESSet.yaml -> build/lib.linux-x86_64-3.9/pymatgen/io/feff copying pymatgen/io/feff/MPEXELFSSet.yaml -> build/lib.linux-x86_64-3.9/pymatgen/io/feff copying pymatgen/io/feff/MPXANESSet.yaml -> build/lib.linux-x86_64-3.9/pymatgen/io/feff copying pymatgen/io/vasp/MPSCANRelaxSet.yaml -> build/lib.linux-x86_64-3.9/pymatgen/io/vasp copying pymatgen/io/vasp/MVLRelax52Set.yaml -> build/lib.linux-x86_64-3.9/pymatgen/io/vasp copying pymatgen/io/vasp/MPHSERelaxSet.yaml -> build/lib.linux-x86_64-3.9/pymatgen/io/vasp copying pymatgen/io/vasp/vdW_parameters.yaml -> build/lib.linux-x86_64-3.9/pymatgen/io/vasp copying pymatgen/io/vasp/MVLGWSet.yaml -> build/lib.linux-x86_64-3.9/pymatgen/io/vasp copying pymatgen/io/vasp/MITRelaxSet.yaml -> build/lib.linux-x86_64-3.9/pymatgen/io/vasp copying pymatgen/io/vasp/MPRelaxSet.yaml -> build/lib.linux-x86_64-3.9/pymatgen/io/vasp copying pymatgen/io/vasp/VASPIncarBase.yaml -> build/lib.linux-x86_64-3.9/pymatgen/io/vasp copying pymatgen/io/vasp/vasp_potcar_pymatgen_hashes.json -> build/lib.linux-x86_64-3.9/pymatgen/io/vasp copying pymatgen/io/vasp/incar_parameters.json -> build/lib.linux-x86_64-3.9/pymatgen/io/vasp copying pymatgen/io/vasp/vasp_potcar_file_hashes.json -> build/lib.linux-x86_64-3.9/pymatgen/io/vasp running build_ext /home/test/xraylarch/lib/python3.9/importlib/__init__.py:169: UserWarning: The NumPy module was reloaded (imported a second time). This can in some cases result in small but subtle issues and is discouraged. _bootstrap._exec(spec, module) building 'pymatgen.optimization.linear_assignment' extension creating build/temp.linux-x86_64-3.9 creating build/temp.linux-x86_64-3.9/pymatgen creating build/temp.linux-x86_64-3.9/pymatgen/optimization gcc -pthread -B /home/test/xraylarch/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/test/xraylarch/include -fPIC -O2 -isystem /home/test/xraylarch/include -fPIC -I/home/test/xraylarch/include/python3.9 -I/tmp/pip-build-env-oojhyzgx/overlay/lib/python3.9/site-packages/numpy/core/include -c pymatgen/optimization/linear_assignment.c -o build/temp.linux-x86_64-3.9/pymatgen/optimization/linear_assignment.o error: command 'gcc' failed: No such file or directory ---------------------------------------- ERROR: Failed building wheel for pymatgen Building wheel for termcolor (setup.py) ... done Created wheel for termcolor: filename=termcolor-1.1.0-py3-none-any.whl size=4829 sha256=3a8968b817fb5cddb03b741a1eb28372e4f57576e145dff7e1a3680d7a77b5c1 Stored in directory: /home/test/.cache/pip/wheels/b6/0d/90/0d1bbd99855f99cb2f6c2e5ff96f8023fad8ec367695f7d72d Building wheel for wxmplot (setup.py) ... done Created wheel for wxmplot: filename=wxmplot-0.9.45-py3-none-any.whl size=92082 sha256=215680d083c28de54dab7938eb023270f7997b63b0ddc4854ba47be4b6f11420 Stored in directory: /home/test/.cache/pip/wheels/04/69/c0/0462329c325e43d9ab222a38a438706440c1720a965f3a2855 Building wheel for wxpython (setup.py) ... error ERROR: Command errored out with exit status 1: command: /home/test/xraylarch/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-jhbcot45/wxpython_5b052486bf574f31a014074a51dfb0d1/setup.py'"'"'; __file__='"'"'/tmp/pip-install-jhbcot45/wxpython_5b052486bf574f31a014074a51dfb0d1/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-o7koh0ww cwd: /tmp/pip-install-jhbcot45/wxpython_5b052486bf574f31a014074a51dfb0d1/ Complete output (42 lines): running bdist_wheel running build WARNING: Building this way assumes that all generated files have been generated already. If that is not the case then use build.py directly to generate the source and perform the build stage. You can use --skip-build with the bdist_* or install commands to avoid this message and the wxWidgets and Phoenix build steps in the future. "/home/test/xraylarch/bin/python" -u build.py build Will build using: "/home/test/xraylarch/bin/python" 3.9.5 (default, Jun 4 2021, 12:28:51) [GCC 7.5.0] Python's architecture is 64bit cfg.VERSION: 4.1.1 Running command: build Running command: build_wx wxWidgets build options: ['--wxpython', '--unicode', '--gtk3'] Configure options: ['--enable-unicode', '--with-gtk=3', '--enable-sound', '--enable-graphics_ctx', '--enable-display', '--enable-geometry', '--enable-debug_flag', '--enable-optimise', '--disable-debugreport', '--enable-uiactionsim', '--enable-autoidman', '--with-sdl'] /tmp/pip-install-jhbcot45/wxpython_5b052486bf574f31a014074a51dfb0d1/ext/wxWidgets/configure --enable-unicode --with-gtk=3 --enable-sound --enable-graphics_ctx --enable-display --enable-geometry --enable-debug_flag --enable-optimise --disable-debugreport --enable-uiactionsim --enable-autoidman --with-sdl checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for toolkit... gtk checking for gcc... no checking for cc... no checking for cl.exe... no configure: error: in `/tmp/pip-install-jhbcot45/wxpython_5b052486bf574f31a014074a51dfb0d1/build/wxbld/gtk3': configure: error: no acceptable C compiler found in $PATH See `config.log' for more details Error running configure ERROR: failed building wxWidgets Traceback (most recent call last): File "/tmp/pip-install-jhbcot45/wxpython_5b052486bf574f31a014074a51dfb0d1/build.py", line 1510, in cmd_build_wx wxbuild.main(wxDir(), build_options) File "/tmp/pip-install-jhbcot45/wxpython_5b052486bf574f31a014074a51dfb0d1/buildtools/build_wxwidgets.py", line 372, in main exitIfError(wxBuilder.configure(dir=wxRootDir, options=configure_opts), File "/tmp/pip-install-jhbcot45/wxpython_5b052486bf574f31a014074a51dfb0d1/buildtools/build_wxwidgets.py", line 85, in exitIfError raise builder.BuildError(msg) buildtools.builder.BuildError: Error running configure Finished command: build_wx (0.821s) Finished command: build (0.821s) Command '"/home/test/xraylarch/bin/python" -u build.py build' failed with exit code 1. ---------------------------------------- ERROR: Failed building wheel for wxpython Running setup.py clean for wxpython Building wheel for wxutils (setup.py) ... done Created wheel for wxutils: filename=wxutils-0.2.4-py3-none-any.whl size=37044 sha256=30c4fd42a7169d4ab034ee56fc77ba4a138ad3aa60e06c30790ec31b1b22b312 Stored in directory: /home/test/.cache/pip/wheels/b8/3a/48/8c3a474db0af35cfbd8d81cee05394d81548b27cf78832aa18 Successfully built xraylarch asteval lmfit pyshortcuts xraydb pyepics epicsapps algopy future termcolor wxmplot wxutils Failed to build pymatgen wxpython ERROR: Could not build wheels for pymatgen which use PEP 517 and cannot be installed directly /home/test/xraylarch/bin/python: can't open file '/home/test/xraylarch/bin/larch': [Errno 2] No such file or directory # Larch post install done! installation finished. Do you wish the installer to initialize xraylarch by running conda init? [yes|no] [no] >>> yes no change /home/test/xraylarch/condabin/conda no change /home/test/xraylarch/bin/conda no change /home/test/xraylarch/bin/conda-env no change /home/test/xraylarch/bin/activate no change /home/test/xraylarch/bin/deactivate no change /home/test/xraylarch/etc/profile.d/conda.sh no change /home/test/xraylarch/etc/fish/conf.d/conda.fish no change /home/test/xraylarch/shell/condabin/Conda.psm1 no change /home/test/xraylarch/shell/condabin/conda-hook.ps1 no change /home/test/xraylarch/lib/python3.9/site-packages/xontrib/conda.xsh no change /home/test/xraylarch/etc/profile.d/conda.csh modified /home/test/.bashrc ==> For changes to take effect, close and re-open your current shell. <== If you'd prefer that conda's base environment not be activated on startup, set the auto_activate_base parameter to false: conda config --set auto_activate_base false Thank you for installing xraylarch! ```

[newville]

@kaarelmand Sorry for the trouble. That looks to me that pymatgen failed to build. Is that correct? If you install a miniconda environment on Ubuntu 20.04, can you install pymatgen and/or wxPython?

For sure, getting the various linux binaries for all of these packages is challenging, and the error messages don't give much detail on missing packages needed for those libraries to build from source. I know that wxPython will need many gtk and other libraries (and the "dev" versions of those) to be installed when building from source.

[kaarelmand]

No trouble at all; I'm just looking through your summer school lectures (they're great!) and trying to finally get to analyzing the data I procured at APS with your help in 2018. Earlier I got Larch working through pip, but it began giving me errors when starting up, so I uninstalled and tried the binary route.

I already have pymatgen and wxypthon installed through the anaconda distribution on my main machine. I tried installing them with miniconda on the virtual machine. While wxpython installed easily through conda-forge, pymatgen for some reason didn't. It didn't even give an error message; just stopped at some point:

> conda install -c conda-forge pymatgen
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): -

[kaarelmand]

By the way, installing larch through pip (where I have wxpython and pymatgen installed) and launching it on the terminal gives me this error message:

> larch
Traceback (most recent call last):
  File "/home/kaarel/anaconda3/bin/larch", line 5, in <module>
    from larch.apps import run_larch
  File "/home/kaarel/anaconda3/lib/python3.8/site-packages/larch/__init__.py", line 52, in <module>
    from . import builtins
  File "/home/kaarel/anaconda3/lib/python3.8/site-packages/larch/builtins.py", line 46, in <module>
    from . import wxlib
  File "/home/kaarel/anaconda3/lib/python3.8/site-packages/larch/wxlib/__init__.py", line 39, in <module>
    from . import larchframe
  File "/home/kaarel/anaconda3/lib/python3.8/site-packages/larch/wxlib/larchframe.py", line 18, in <module>
    from .columnframe import ColumnDataFileFrame
  File "/home/kaarel/anaconda3/lib/python3.8/site-packages/larch/wxlib/columnframe.py", line 15, in <module>
    from wxmplot import PlotPanel
  File "/home/kaarel/anaconda3/lib/python3.8/site-packages/wxmplot/__init__.py", line 41, in <module>
    from .imagepanel import ImagePanel
  File "/home/kaarel/anaconda3/lib/python3.8/site-packages/wxmplot/imagepanel.py", line 20, in <module>
    from .imageconf import ImageConfig, RGB_COLORS
  File "/home/kaarel/anaconda3/lib/python3.8/site-packages/wxmplot/imageconf.py", line 24, in <module>
    cm_names = register_custom_colormaps()
  File "/home/kaarel/anaconda3/lib/python3.8/site-packages/wxmplot/colors.py", line 432, in register_custom_colormaps
    register_cmap(name=nam1, cmap=makemap(nam1, cm1, 256), lut=256)
TypeError: register_cmap() got an unexpected keyword argument 'lut'

[newville]

@kaarelmand Thanks - that did get fixed earlier this year, and released with wxmplot version 0.9.45. Running pip install --upgrade wxmplot

should fix that.

.. I'm still trying to figure out what's going on with pymatgen...

[maurov]

@newville this issue is related to #333: I confirm that the linux binary installer fails, so I propose for Linux to remove it from the documentation page and point to the GetLarch.sh script only.

[maurov]

@kaarelmand I am closing this issue because I think it is fixed with the current release or at least it is not relevant anymore. Please, follow the updated installation instructions and let us know if something goes wrong.

@newville I have updated the list of tasks for the next release accordingly.