sbuild (Debian sbuild) 0.85.11~bpo12+1 (31 August 2024) on debusine-worker-arm64-demeter-07.freexian.com
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| mdanalysis 2.7.0-5+bd1 (arm64) Thu, 24 Oct 2024 16:31:28 +0000 |
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Package: mdanalysis
Version: 2.7.0-5+bd1
Source Version: 2.7.0-5
Distribution: sid
Machine Architecture: arm64
Host Architecture: arm64
Build Architecture: arm64
Build Type: any
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Merged Build-Depends: debhelper-compat (= 13), cython3, dh-sequence-python3, pybuild-plugin-pyproject, python3-all-dev, python3-setuptools, python3-numpy, python3-biopython (>= 1.80), python3-networkx, python3-griddataformats, python3-mmtf, python3-joblib, python3-scipy, python3-matplotlib, python3-mda-xdrlib, python3-tqdm, python3-threadpoolctl, python3-packaging, python3-fasteners, python3-gsd (>= 3.0.1~), python3-netcdf4, python3-h5py, python3-seaborn, python3-sklearn, python3-duecredit, python3-hypothesis, python3-pytest, python3-sphinx, build-essential, fakeroot, dumb-init
Filtered Build-Depends: debhelper-compat (= 13), cython3, dh-sequence-python3, pybuild-plugin-pyproject, python3-all-dev, python3-setuptools, python3-numpy, python3-biopython (>= 1.80), python3-networkx, python3-griddataformats, python3-mmtf, python3-joblib, python3-scipy, python3-matplotlib, python3-mda-xdrlib, python3-tqdm, python3-threadpoolctl, python3-packaging, python3-fasteners, python3-gsd (>= 3.0.1~), python3-netcdf4, python3-h5py, python3-seaborn, python3-sklearn, python3-duecredit, python3-hypothesis, python3-pytest, python3-sphinx, build-essential, fakeroot, dumb-init
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
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The following additional packages will be installed:
autoconf automake autopoint autotools-dev blt build-essential cpp cpp-14
cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu cython3 debhelper
dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dumb-init
dwz fakeroot fontconfig-config fonts-dejavu-core fonts-dejavu-mono
fonts-font-awesome fonts-lato fonts-lyx fonts-urw-base35 g++ g++-14
g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14
gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu libaec0 libasan8 libblas3
libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libcurl4t64
libdebhelper-perl libdeflate0 libelf1t64 libexpat1 libexpat1-dev libfakeroot
libfile-stripnondeterminism-perl libfontconfig1 libfontenc1 libfreetype6
libfribidi0 libgcc-14-dev libgfortran5 libgraphite2-3 libharfbuzz0b
libhdf5-103-1t64 libhdf5-hl-100t64 libhwasan0 libimagequant0 libisl23
libitm1 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui
libjs-sphinxdoc libjs-underscore libjson-perl liblapack3 liblbfgsb0
liblcms2-2 liblerc4 liblsan0 liblzf1 libmpc3 libmpfr6 libncursesw6
libnetcdf19t64 libnsl2 libopenjp2-7 libpixman-1-0 libpng16-16t64 libproc2-0
libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.12-dev
libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libpython3.13
libpython3.13-dev libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0
libraqm0 libsharpyuv0 libstdc++-14-dev libsz2 libtcl8.6 libtiff6
libtirpc-common libtirpc3t64 libtk8.6 libtool libtsan2 libubsan1 libwebp7
libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0
libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxrender1 libxslt1.1
libxss1 linux-libc-dev m4 media-types po-debconf procps
pybuild-plugin-pyproject python-babel-localedata python-matplotlib-data
python3 python3-alabaster python3-all python3-all-dev python3-appdirs
python3-attr python3-autocommand python3-babel python3-biopython
python3-brotli python3-build python3-cairo python3-certifi python3-cftime
python3-chardet python3-charset-normalizer python3-citeproc
python3-contourpy python3-cycler python3-dateutil python3-decorator
python3-defusedxml python3-dev python3-docutils python3-duecredit
python3-fasteners python3-fonttools python3-freetype python3-fs
python3-griddataformats python3-gsd python3-h5py python3-h5py-serial
python3-hypothesis python3-idna python3-imagesize python3-inflect
python3-iniconfig python3-installer python3-jaraco.context
python3-jaraco.functools python3-jaraco.text python3-jinja2 python3-joblib
python3-kiwisolver python3-looseversion python3-lxml python3-lz4
python3-markupsafe python3-matplotlib python3-mda-xdrlib python3-minimal
python3-mmtf python3-monotonic python3-more-itertools python3-mpmath
python3-mrcfile python3-msgpack python3-netcdf4 python3-networkx
python3-numpy python3-packaging python3-pandas python3-pandas-lib
python3-pil python3-pil.imagetk python3-pkg-resources python3-pluggy
python3-pygments python3-pyparsing python3-pyproject-hooks python3-pytest
python3-reportlab python3-requests python3-rlpycairo python3-roman
python3-scipy python3-seaborn python3-setuptools python3-six python3-sklearn
python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers
python3-sphinx python3-sympy python3-threadpoolctl python3-tk python3-toml
python3-tqdm python3-typeguard python3-typing-extensions python3-tz
python3-ufolib2 python3-urllib3 python3-wheel python3-zipp python3.12
python3.12-dev python3.12-minimal python3.12-tk python3.13 python3.13-dev
python3.13-minimal python3.13-tk rpcsvc-proto sgml-base sphinx-common
sphinx-rtd-theme-common tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common
xfonts-encodings xfonts-utils xml-core zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc blt-demo cpp-doc gcc-14-locales
cpp-14-doc cython-doc dh-make flit fonts-freefont-otf | fonts-freefont-ttf
fonts-texgyre gcc-14-doc gcc-multilib manpages-dev flex bison gdb gcc-doc
gdb-aarch64-linux-gnu libc-devtools glibc-doc libjs-jquery-ui-docs
liblcms2-utils libstdc++-14-doc tcl8.6 tk8.6 libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc libmail-box-perl python3-doc
python3-venv python-attr-doc bwa clustalo clustalw dialign dssp emboss
fasttree mafft muscle3 phylip phyml prank probcons python3-mysqldb
python3-rdflib python3-psycopg2 raxml samtools t-coffee wise python3-pip
python-build-doc python-charset-normalizer-doc python-cycler-doc
docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french
texlive-latex-base texlive-latex-recommended python-gsd-doc python-h5py-doc
python-hypothesis-doc python-installer-doc python-jinja2-doc
python-joblib-doc python-lxml-doc cm-super-minimal dvipng ffmpeg
fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common
python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo
python3-gobject python3-pyqt5 python3-sip python3-tornado
texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2
gfortran python-numpy-doc python-pandas-doc python3-statsmodels
python-pil-doc python-pygments-doc ttf-bitstream-vera python-pyparsing-doc
pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel
rl-renderpm python3-cryptography python3-openssl python3-socks
python-requests-doc python-scipy-doc python-setuptools-doc python3-dap
python-sklearn-doc python3-stemmer python-sortedcontainers-doc dvisvgm
fonts-freefont-otf imagemagick-6.q16 latexmk libjs-mathjax
python3-sphinx-rtd-theme sphinx-doc tex-gyre texlive-fonts-extra
texlive-fonts-recommended texlive-plain-generic python-sympy-doc tix
python3-tk-dbg python3.12-venv python3.12-doc binfmt-support python3.13-venv
python3.13-doc sgml-base-doc
Recommended packages:
manpages manpages-dev libarchive-cpio-perl javascript-common libjson-xs-perl
libgpm2 libltdl-dev libmail-sendmail-perl psmisc linux-sysctl-defaults
python-biopython-doc ncbi-blast+ libpaper-utils python3-click
python3-simplejson python3-psutil python3-bs4 python3-cssselect
python3-html5lib python3-gdal python3-pydot python3-pygraphviz python3-yaml
python3-bottleneck python3-numexpr python3-odf python3-openpyxl
python3-tables python3-olefile fonts-dejavu-extra isympy-common
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev blt build-essential cpp cpp-14
cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu cython3 debhelper
dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dumb-init
dwz fakeroot fontconfig-config fonts-dejavu-core fonts-dejavu-mono
fonts-font-awesome fonts-lato fonts-lyx fonts-urw-base35 g++ g++-14
g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14
gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu libaec0 libasan8 libblas3
libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libcurl4t64
libdebhelper-perl libdeflate0 libelf1t64 libexpat1 libexpat1-dev libfakeroot
libfile-stripnondeterminism-perl libfontconfig1 libfontenc1 libfreetype6
libfribidi0 libgcc-14-dev libgfortran5 libgraphite2-3 libharfbuzz0b
libhdf5-103-1t64 libhdf5-hl-100t64 libhwasan0 libimagequant0 libisl23
libitm1 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui
libjs-sphinxdoc libjs-underscore libjson-perl liblapack3 liblbfgsb0
liblcms2-2 liblerc4 liblsan0 liblzf1 libmpc3 libmpfr6 libncursesw6
libnetcdf19t64 libnsl2 libopenjp2-7 libpixman-1-0 libpng16-16t64 libproc2-0
libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.12-dev
libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libpython3.13
libpython3.13-dev libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0
libraqm0 libsharpyuv0 libstdc++-14-dev libsz2 libtcl8.6 libtiff6
libtirpc-common libtirpc3t64 libtk8.6 libtool libtsan2 libubsan1 libwebp7
libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0
libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxrender1 libxslt1.1
libxss1 linux-libc-dev m4 media-types po-debconf procps
pybuild-plugin-pyproject python-babel-localedata python-matplotlib-data
python3 python3-alabaster python3-all python3-all-dev python3-appdirs
python3-attr python3-autocommand python3-babel python3-biopython
python3-brotli python3-build python3-cairo python3-certifi python3-cftime
python3-chardet python3-charset-normalizer python3-citeproc
python3-contourpy python3-cycler python3-dateutil python3-decorator
python3-defusedxml python3-dev python3-docutils python3-duecredit
python3-fasteners python3-fonttools python3-freetype python3-fs
python3-griddataformats python3-gsd python3-h5py python3-h5py-serial
python3-hypothesis python3-idna python3-imagesize python3-inflect
python3-iniconfig python3-installer python3-jaraco.context
python3-jaraco.functools python3-jaraco.text python3-jinja2 python3-joblib
python3-kiwisolver python3-looseversion python3-lxml python3-lz4
python3-markupsafe python3-matplotlib python3-mda-xdrlib python3-minimal
python3-mmtf python3-monotonic python3-more-itertools python3-mpmath
python3-mrcfile python3-msgpack python3-netcdf4 python3-networkx
python3-numpy python3-packaging python3-pandas python3-pandas-lib
python3-pil python3-pil.imagetk python3-pkg-resources python3-pluggy
python3-pygments python3-pyparsing python3-pyproject-hooks python3-pytest
python3-reportlab python3-requests python3-rlpycairo python3-roman
python3-scipy python3-seaborn python3-setuptools python3-six python3-sklearn
python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers
python3-sphinx python3-sympy python3-threadpoolctl python3-tk python3-toml
python3-tqdm python3-typeguard python3-typing-extensions python3-tz
python3-ufolib2 python3-urllib3 python3-wheel python3-zipp python3.12
python3.12-dev python3.12-minimal python3.12-tk python3.13 python3.13-dev
python3.13-minimal python3.13-tk rpcsvc-proto
sbuild-build-depends-main-dummy sgml-base sphinx-common
sphinx-rtd-theme-common tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common
xfonts-encodings xfonts-utils xml-core zlib1g-dev
0 upgraded, 251 newly installed, 0 to remove and 0 not upgraded.
Need to get 177 MB/219 MB of archives.
After this operation, 993 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [1100 B]
Get:2 file:/<<BUILDDIR>>/resolver-aWEMlD/apt_archive ./ python3-minimal 3.12.6-1+debusine1 [26.8 kB]
Get:3 file:/<<BUILDDIR>>/resolver-aWEMlD/apt_archive ./ libpython3-stdlib 3.12.6-1+debusine1 [9732 B]
Get:4 file:/<<BUILDDIR>>/resolver-aWEMlD/apt_archive ./ python3 3.12.6-1+debusine1 [27.8 kB]
Get:5 http://deb.debian.org/debian sid/main arm64 fonts-lato all 2.015-1 [2780 kB]
Get:6 file:/<<BUILDDIR>>/resolver-aWEMlD/apt_archive ./ cython3 3.0.11+dfsg-1+debusine1 [2724 kB]
Get:7 file:/<<BUILDDIR>>/resolver-aWEMlD/apt_archive ./ libpython3-dev 3.12.6-1+debusine1 [9992 B]
Get:8 file:/<<BUILDDIR>>/resolver-aWEMlD/apt_archive ./ libpython3-all-dev 3.12.6-1+debusine1 [1084 B]
Get:9 file:/<<BUILDDIR>>/resolver-aWEMlD/apt_archive ./ python-matplotlib-data 3.8.3-3+bootstrap1 [2731 kB]
Get:10 file:/<<BUILDDIR>>/resolver-aWEMlD/apt_archive ./ python3-all 3.12.6-1+debusine1 [1056 B]
Get:11 file:/<<BUILDDIR>>/resolver-aWEMlD/apt_archive ./ python3-dev 3.12.6-1+debusine1 [26.1 kB]
Get:12 file:/<<BUILDDIR>>/resolver-aWEMlD/apt_archive ./ python3-all-dev 3.12.6-1+debusine1 [1084 B]
Get:13 http://deb.debian.org/debian sid/main arm64 libpython3.12-minimal arm64 3.12.7-1 [807 kB]
Get:14 file:/<<BUILDDIR>>/resolver-aWEMlD/apt_archive ./ python3-numpy 1:1.26.4+ds-11+bootstrap1 [3815 kB]
Get:15 http://deb.debian.org/debian sid/main arm64 libexpat1 arm64 2.6.3-1 [90.2 kB]
Get:16 http://deb.debian.org/debian sid/main arm64 python3.12-minimal arm64 3.12.7-1 [1941 kB]
Get:17 file:/<<BUILDDIR>>/resolver-aWEMlD/apt_archive ./ python3-biopython 1.84+dfsg-3+bd1 [1643 kB]
Get:18 http://deb.debian.org/debian sid/main arm64 media-types all 10.1.0 [26.9 kB]
Get:19 http://deb.debian.org/debian sid/main arm64 libncursesw6 arm64 6.5-2 [124 kB]
Get:20 http://deb.debian.org/debian sid/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get:21 http://deb.debian.org/debian sid/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3 [78.4 kB]
Get:22 http://deb.debian.org/debian sid/main arm64 libnsl2 arm64 1.3.0-3+b2 [37.7 kB]
Get:23 http://deb.debian.org/debian sid/main arm64 libpython3.12-stdlib arm64 3.12.7-1 [1901 kB]
Get:24 http://deb.debian.org/debian sid/main arm64 python3.12 arm64 3.12.7-1 [671 kB]
Get:25 http://deb.debian.org/debian sid/main arm64 libpython3.13-minimal arm64 3.13.0-1 [849 kB]
Get:26 http://deb.debian.org/debian sid/main arm64 python3.13-minimal arm64 3.13.0-1 [1835 kB]
Get:27 file:/<<BUILDDIR>>/resolver-aWEMlD/apt_archive ./ python3-scipy 1.13.1-5+nocheck1 [18.1 MB]
Get:28 file:/<<BUILDDIR>>/resolver-aWEMlD/apt_archive ./ python3-gsd 3.3.0-1+bd1 [212 kB]
Get:29 file:/<<BUILDDIR>>/resolver-aWEMlD/apt_archive ./ python3-h5py-serial 3.11.0-7+bd1 [1241 kB]
Get:30 http://deb.debian.org/debian sid/main arm64 sgml-base all 1.31 [15.4 kB]
Get:31 http://deb.debian.org/debian sid/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB]
Get:32 http://deb.debian.org/debian sid/main arm64 procps arm64 2:4.0.4-6 [872 kB]
Get:33 http://deb.debian.org/debian sid/main arm64 m4 arm64 1.4.19-4 [277 kB]
Get:34 http://deb.debian.org/debian sid/main arm64 autoconf all 2.72-3 [493 kB]
Get:35 http://deb.debian.org/debian sid/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get:36 http://deb.debian.org/debian sid/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get:37 file:/<<BUILDDIR>>/resolver-aWEMlD/apt_archive ./ python3-matplotlib 3.8.3-3+bootstrap1 [5583 kB]
Get:38 http://deb.debian.org/debian sid/main arm64 autopoint all 0.22.5-2 [723 kB]
Get:39 file:/<<BUILDDIR>>/resolver-aWEMlD/apt_archive ./ python3-netcdf4 1.7.2-1+bd1 [724 kB]
Get:40 http://deb.debian.org/debian sid/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [982 kB]
Get:41 http://deb.debian.org/debian sid/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB]
Get:42 http://deb.debian.org/debian sid/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB]
Get:43 http://deb.debian.org/debian sid/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get:44 http://deb.debian.org/debian sid/main arm64 fonts-dejavu-core all 2.37-8 [840 kB]
Get:45 file:/<<BUILDDIR>>/resolver-aWEMlD/apt_archive ./ python3-sklearn-lib 1.4.2+dfsg-6+debusine1 [5386 kB]
Get:46 http://deb.debian.org/debian sid/main arm64 libfontenc1 arm64 1:1.1.8-1 [22.2 kB]
Get:47 http://deb.debian.org/debian sid/main arm64 x11-common all 1:7.7+23.1 [216 kB]
Get:48 http://deb.debian.org/debian sid/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB]
Get:49 http://deb.debian.org/debian sid/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB]
Get:50 http://deb.debian.org/debian sid/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB]
Get:51 http://deb.debian.org/debian sid/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB]
Get:52 http://deb.debian.org/debian sid/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB]
Get:53 http://deb.debian.org/debian sid/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB]
Get:54 http://deb.debian.org/debian sid/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB]
Get:55 http://deb.debian.org/debian sid/main arm64 libxcb1 arm64 1.17.0-2 [143 kB]
Get:56 http://deb.debian.org/debian sid/main arm64 libx11-data all 2:1.8.7-1 [328 kB]
Get:57 http://deb.debian.org/debian sid/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB]
Get:58 http://deb.debian.org/debian sid/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB]
Get:59 http://deb.debian.org/debian sid/main arm64 libxft2 arm64 2.3.6-1+b1 [51.0 kB]
Get:60 http://deb.debian.org/debian sid/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB]
Get:61 http://deb.debian.org/debian sid/main arm64 libxss1 arm64 1:1.2.3-1+b1 [17.0 kB]
Get:62 http://deb.debian.org/debian sid/main arm64 libtk8.6 arm64 8.6.15-1 [738 kB]
Get:63 http://deb.debian.org/debian sid/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7 [533 kB]
Get:64 http://deb.debian.org/debian sid/main arm64 blt arm64 2.5.3+dfsg-7 [6024 B]
Get:65 http://deb.debian.org/debian sid/main arm64 libc-dev-bin arm64 2.40-3 [50.9 kB]
Get:66 http://deb.debian.org/debian sid/main arm64 linux-libc-dev all 6.11.4-1 [2440 kB]
Get:67 http://deb.debian.org/debian sid/main arm64 libcrypt-dev arm64 1:4.4.36-5 [122 kB]
Get:68 http://deb.debian.org/debian sid/main arm64 rpcsvc-proto arm64 1.4.3-1 [59.7 kB]
Get:69 http://deb.debian.org/debian sid/main arm64 libc6-dev arm64 2.40-3 [1591 kB]
Get:70 http://deb.debian.org/debian sid/main arm64 libisl23 arm64 0.27-1 [601 kB]
Get:71 http://deb.debian.org/debian sid/main arm64 libmpfr6 arm64 4.2.1-1+b1 [674 kB]
Get:72 http://deb.debian.org/debian sid/main arm64 libmpc3 arm64 1.3.1-1+b2 [50.2 kB]
Get:73 http://deb.debian.org/debian sid/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-7 [9164 kB]
Get:74 http://deb.debian.org/debian sid/main arm64 cpp-14 arm64 14.2.0-7 [1280 B]
Get:75 http://deb.debian.org/debian sid/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1 [4832 B]
Get:76 http://deb.debian.org/debian sid/main arm64 cpp arm64 4:14.2.0-1 [1568 B]
Get:77 http://deb.debian.org/debian sid/main arm64 libcc1-0 arm64 14.2.0-7 [42.2 kB]
Get:78 http://deb.debian.org/debian sid/main arm64 libitm1 arm64 14.2.0-7 [24.2 kB]
Get:79 http://deb.debian.org/debian sid/main arm64 libasan8 arm64 14.2.0-7 [2578 kB]
Get:80 http://deb.debian.org/debian sid/main arm64 liblsan0 arm64 14.2.0-7 [1162 kB]
Get:81 http://deb.debian.org/debian sid/main arm64 libtsan2 arm64 14.2.0-7 [2386 kB]
Get:82 http://deb.debian.org/debian sid/main arm64 libubsan1 arm64 14.2.0-7 [1040 kB]
Get:83 http://deb.debian.org/debian sid/main arm64 libhwasan0 arm64 14.2.0-7 [1442 kB]
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Get:85 http://deb.debian.org/debian sid/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-7 [17.7 MB]
Get:86 http://deb.debian.org/debian sid/main arm64 gcc-14 arm64 14.2.0-7 [517 kB]
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Get:89 http://deb.debian.org/debian sid/main arm64 libstdc++-14-dev arm64 14.2.0-7 [2265 kB]
Get:90 http://deb.debian.org/debian sid/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-7 [10.1 MB]
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Get:94 http://deb.debian.org/debian sid/main arm64 build-essential arm64 12.12 [4624 B]
Get:95 http://deb.debian.org/debian sid/main arm64 libdebhelper-perl all 13.20 [89.7 kB]
Get:96 http://deb.debian.org/debian sid/main arm64 libtool all 2.4.7-7 [517 kB]
Get:97 http://deb.debian.org/debian sid/main arm64 dh-autoreconf all 20 [17.1 kB]
Get:98 http://deb.debian.org/debian sid/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get:99 http://deb.debian.org/debian sid/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get:100 http://deb.debian.org/debian sid/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get:101 http://deb.debian.org/debian sid/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get:102 http://deb.debian.org/debian sid/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:103 http://deb.debian.org/debian sid/main arm64 debhelper all 13.20 [915 kB]
Get:104 http://deb.debian.org/debian sid/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get:105 http://deb.debian.org/debian sid/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB]
Get:106 http://deb.debian.org/debian sid/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get:107 http://deb.debian.org/debian sid/main arm64 python3-typeguard all 4.3.0-1 [36.5 kB]
Get:108 http://deb.debian.org/debian sid/main arm64 python3-inflect all 7.3.1-2 [32.4 kB]
Get:109 http://deb.debian.org/debian sid/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B]
Get:110 http://deb.debian.org/debian sid/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get:111 http://deb.debian.org/debian sid/main arm64 python3-pkg-resources all 75.2.0-1 [213 kB]
Get:112 http://deb.debian.org/debian sid/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get:113 http://deb.debian.org/debian sid/main arm64 python3-zipp all 3.20.2-1 [10.3 kB]
Get:114 http://deb.debian.org/debian sid/main arm64 python3-setuptools all 75.2.0-1 [731 kB]
Get:115 http://deb.debian.org/debian sid/main arm64 dh-python all 6.20240824 [109 kB]
Get:116 http://deb.debian.org/debian sid/main arm64 xml-core all 0.19 [20.1 kB]
Get:117 http://deb.debian.org/debian sid/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB]
Get:118 http://deb.debian.org/debian sid/main arm64 dumb-init arm64 1.2.5-3 [13.4 kB]
Get:119 http://deb.debian.org/debian sid/main arm64 libfakeroot arm64 1.36-1 [29.1 kB]
Get:120 http://deb.debian.org/debian sid/main arm64 fakeroot arm64 1.36-1 [74.4 kB]
Get:121 http://deb.debian.org/debian sid/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB]
Get:122 http://deb.debian.org/debian sid/main arm64 fonts-lyx all 2.4.2.1-1 [190 kB]
Get:123 http://deb.debian.org/debian sid/main arm64 libaec0 arm64 1.1.3-1 [22.1 kB]
Get:124 http://deb.debian.org/debian sid/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB]
Get:125 http://deb.debian.org/debian sid/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB]
Get:126 http://deb.debian.org/debian sid/main arm64 libxcb-render0 arm64 1.17.0-2 [115 kB]
Get:127 http://deb.debian.org/debian sid/main arm64 libxcb-shm0 arm64 1.17.0-2 [105 kB]
Get:128 http://deb.debian.org/debian sid/main arm64 libcairo2 arm64 1.18.2-2 [483 kB]
Get:129 http://deb.debian.org/debian sid/main arm64 libcurl4t64 arm64 8.10.1-2 [322 kB]
Get:130 http://deb.debian.org/debian sid/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB]
Get:131 http://deb.debian.org/debian sid/main arm64 libexpat1-dev arm64 2.6.3-1 [142 kB]
Get:132 http://deb.debian.org/debian sid/main arm64 libfribidi0 arm64 1.0.15-1 [71.8 kB]
Get:133 http://deb.debian.org/debian sid/main arm64 libgfortran5 arm64 14.2.0-7 [361 kB]
Get:134 http://deb.debian.org/debian sid/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB]
Get:135 http://deb.debian.org/debian sid/main arm64 libharfbuzz0b arm64 10.0.1-1 [441 kB]
Get:136 http://deb.debian.org/debian sid/main arm64 libsz2 arm64 1.1.3-1 [7664 B]
Get:137 http://deb.debian.org/debian sid/main arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4 [1050 kB]
Get:138 http://deb.debian.org/debian sid/main arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-4 [60.9 kB]
Get:139 http://deb.debian.org/debian sid/main arm64 libimagequant0 arm64 2.18.0-1+b1 [34.6 kB]
Get:140 http://deb.debian.org/debian sid/main arm64 libjbig0 arm64 2.1-6.1+b1 [30.4 kB]
Get:141 http://deb.debian.org/debian sid/main arm64 libjpeg62-turbo arm64 1:2.1.5-3 [172 kB]
Get:142 http://deb.debian.org/debian sid/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:143 http://deb.debian.org/debian sid/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get:144 http://deb.debian.org/debian sid/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get:145 http://deb.debian.org/debian sid/main arm64 libjs-sphinxdoc all 7.4.7-3 [158 kB]
Get:146 http://deb.debian.org/debian sid/main arm64 libjson-perl all 4.10000-1 [87.5 kB]
Get:147 http://deb.debian.org/debian sid/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB]
Get:148 http://deb.debian.org/debian sid/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b1 [25.0 kB]
Get:149 http://deb.debian.org/debian sid/main arm64 liblcms2-2 arm64 2.16-2 [151 kB]
Get:150 http://deb.debian.org/debian sid/main arm64 liblerc4 arm64 4.0.0+ds-4+b1 [142 kB]
Get:151 http://deb.debian.org/debian sid/main arm64 liblzf1 arm64 3.6-4+b1 [10.3 kB]
Get:152 http://deb.debian.org/debian sid/main arm64 libnetcdf19t64 arm64 1:4.9.2-7 [444 kB]
Get:153 http://deb.debian.org/debian sid/main arm64 libopenjp2-7 arm64 2.5.0-2+b3 [177 kB]
Get:154 http://deb.debian.org/debian sid/main arm64 libpython3.12t64 arm64 3.12.7-1 [1982 kB]
Get:155 http://deb.debian.org/debian sid/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB]
Get:156 http://deb.debian.org/debian sid/main arm64 libpython3.12-dev arm64 3.12.7-1 [4793 kB]
Get:157 http://deb.debian.org/debian sid/main arm64 libpython3.13-stdlib arm64 3.13.0-1 [1920 kB]
Get:158 http://deb.debian.org/debian sid/main arm64 libpython3.13 arm64 3.13.0-1 [1960 kB]
Get:159 http://deb.debian.org/debian sid/main arm64 libpython3.13-dev arm64 3.13.0-1 [4668 kB]
Get:160 http://deb.debian.org/debian sid/main arm64 libqhull-r8.0 arm64 2020.2-6+b1 [226 kB]
Get:161 http://deb.debian.org/debian sid/main arm64 libraqm0 arm64 0.10.1-1+b1 [13.7 kB]
Get:162 http://deb.debian.org/debian sid/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [111 kB]
Get:163 http://deb.debian.org/debian sid/main arm64 libwebp7 arm64 1.4.0-0.1 [267 kB]
Get:164 http://deb.debian.org/debian sid/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB]
Get:165 http://deb.debian.org/debian sid/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [110 kB]
Get:166 http://deb.debian.org/debian sid/main arm64 libwebpmux3 arm64 1.4.0-0.1 [122 kB]
Get:167 http://deb.debian.org/debian sid/main arm64 libxslt1.1 arm64 1.1.35-1.1 [221 kB]
Get:168 http://deb.debian.org/debian sid/main arm64 python3-packaging all 24.1-1 [45.8 kB]
Get:169 http://deb.debian.org/debian sid/main arm64 python3-pyproject-hooks all 1.1.0-2 [11.3 kB]
Get:170 http://deb.debian.org/debian sid/main arm64 python3-toml all 0.10.2-1 [16.2 kB]
Get:171 http://deb.debian.org/debian sid/main arm64 python3-wheel all 0.44.0-2 [53.4 kB]
Get:172 http://deb.debian.org/debian sid/main arm64 python3-build all 1.2.2-1 [36.0 kB]
Get:173 http://deb.debian.org/debian sid/main arm64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB]
Get:174 http://deb.debian.org/debian sid/main arm64 pybuild-plugin-pyproject all 6.20240824 [11.2 kB]
Get:175 http://deb.debian.org/debian sid/main arm64 python-babel-localedata all 2.14.0-1 [5701 kB]
Get:176 http://deb.debian.org/debian sid/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB]
Get:177 http://deb.debian.org/debian sid/main arm64 python3.13 arm64 3.13.0-1 [730 kB]
Get:178 http://deb.debian.org/debian sid/main arm64 python3.12-dev arm64 3.12.7-1 [505 kB]
Get:179 http://deb.debian.org/debian sid/main arm64 python3.13-dev arm64 3.13.0-1 [504 kB]
Get:180 http://deb.debian.org/debian sid/main arm64 python3-appdirs all 1.4.4-4 [12.5 kB]
Get:181 http://deb.debian.org/debian sid/main arm64 python3-attr all 24.2.0-1 [68.4 kB]
Get:182 http://deb.debian.org/debian sid/main arm64 python3-tz all 2024.1-2 [30.9 kB]
Get:183 http://deb.debian.org/debian sid/main arm64 python3-babel all 2.14.0-1 [111 kB]
Get:184 http://deb.debian.org/debian sid/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB]
Get:185 http://deb.debian.org/debian sid/main arm64 python3.12-tk arm64 3.12.7-1 [110 kB]
Get:186 http://deb.debian.org/debian sid/main arm64 python3.13-tk arm64 3.13.0-1 [101 kB]
Get:187 http://deb.debian.org/debian sid/main arm64 python3-tk arm64 3.12.6-1 [9428 B]
Get:188 http://deb.debian.org/debian sid/main arm64 python3-pil.imagetk arm64 10.4.0-1 [79.4 kB]
Get:189 http://deb.debian.org/debian sid/main arm64 python3-pil arm64 10.4.0-1 [480 kB]
Get:190 http://deb.debian.org/debian sid/main arm64 python3-cairo arm64 1.26.1-2 [113 kB]
Get:191 http://deb.debian.org/debian sid/main arm64 python3-freetype all 2.5.1-1 [89.3 kB]
Get:192 http://deb.debian.org/debian sid/main arm64 python3-rlpycairo all 0.3.0-3 [9904 B]
Get:193 http://deb.debian.org/debian sid/main arm64 python3-reportlab all 4.2.5-1 [1117 kB]
Get:194 http://deb.debian.org/debian sid/main arm64 w3c-sgml-lib all 1.3-3 [273 kB]
Get:195 http://deb.debian.org/debian sid/main arm64 python3-brotli arm64 1.1.0-2+b4 [301 kB]
Get:196 http://deb.debian.org/debian sid/main arm64 python3-certifi all 2024.8.30+dfsg-1 [9576 B]
Get:197 http://deb.debian.org/debian sid/main arm64 python3-cftime arm64 1.6.4-1+b1 [173 kB]
Get:198 http://deb.debian.org/debian sid/main arm64 python3-charset-normalizer arm64 3.4.0-1 [112 kB]
Get:199 http://deb.debian.org/debian sid/main arm64 python3-lxml arm64 5.3.0-1 [1096 kB]
Get:200 http://deb.debian.org/debian sid/main arm64 python3-citeproc all 0.6.0-3 [96.7 kB]
Get:201 http://deb.debian.org/debian sid/main arm64 python3-contourpy arm64 1.3.0-2 [191 kB]
Get:202 http://deb.debian.org/debian sid/main arm64 python3-cycler all 0.12.1-1 [9496 B]
Get:203 http://deb.debian.org/debian sid/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB]
Get:204 http://deb.debian.org/debian sid/main arm64 python3-decorator all 5.1.1-5 [15.1 kB]
Get:205 http://deb.debian.org/debian sid/main arm64 python3-defusedxml all 0.7.1-2 [43.3 kB]
Get:206 http://deb.debian.org/debian sid/main arm64 python3-roman all 4.2-1 [10.4 kB]
Get:207 http://deb.debian.org/debian sid/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB]
Get:208 http://deb.debian.org/debian sid/main arm64 python3-looseversion all 1.3.0-3 [8964 B]
Get:209 http://deb.debian.org/debian sid/main arm64 python3-idna all 3.8-2 [41.6 kB]
Get:210 http://deb.debian.org/debian sid/main arm64 python3-urllib3 all 2.0.7-2 [111 kB]
Get:211 http://deb.debian.org/debian sid/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB]
Get:212 http://deb.debian.org/debian sid/main arm64 python3-duecredit all 0.10.2-2 [70.6 kB]
Get:213 http://deb.debian.org/debian sid/main arm64 python3-monotonic all 1.6-2 [5728 B]
Get:214 http://deb.debian.org/debian sid/main arm64 python3-fasteners all 0.18-2 [14.0 kB]
Get:215 http://deb.debian.org/debian sid/main arm64 python3-six all 1.16.0-7 [16.4 kB]
Get:216 http://deb.debian.org/debian sid/main arm64 python3-fs all 2.4.16-4 [95.4 kB]
Get:217 http://deb.debian.org/debian sid/main arm64 python3-lz4 arm64 4.0.2+dfsg-1+b4 [25.1 kB]
Get:218 http://deb.debian.org/debian sid/main arm64 python3-mpmath all 1.3.0-1 [419 kB]
Get:219 http://deb.debian.org/debian sid/main arm64 python3-sympy all 1.13.3-1 [4147 kB]
Get:220 http://deb.debian.org/debian sid/main arm64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB]
Get:221 http://deb.debian.org/debian sid/main arm64 unicode-data all 15.1.0-1 [8547 kB]
Get:222 http://deb.debian.org/debian sid/main arm64 python3-fonttools arm64 4.54.1-4 [1356 kB]
Get:223 http://deb.debian.org/debian sid/main arm64 sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1022 kB]
Get:224 http://deb.debian.org/debian sid/main arm64 python3-mrcfile all 1.5.3-3 [119 kB]
Get:225 http://deb.debian.org/debian sid/main arm64 python3-griddataformats all 1.0.2-2 [2048 kB]
Get:226 http://deb.debian.org/debian sid/main arm64 python3-h5py all 3.11.0-7 [14.8 kB]
Get:227 http://deb.debian.org/debian sid/main arm64 python3-sortedcontainers all 2.4.0-2 [31.9 kB]
Get:228 http://deb.debian.org/debian sid/main arm64 python3-hypothesis all 6.115.3-1 [321 kB]
Get:229 http://deb.debian.org/debian sid/main arm64 python3-imagesize all 1.4.1-1 [6688 B]
Get:230 http://deb.debian.org/debian sid/main arm64 python3-iniconfig all 1.1.1-2 [6396 B]
Get:231 http://deb.debian.org/debian sid/main arm64 python3-markupsafe arm64 2.1.5-1+b1 [13.7 kB]
Get:232 http://deb.debian.org/debian sid/main arm64 python3-jinja2 all 3.1.3-1 [119 kB]
Get:233 http://deb.debian.org/debian sid/main arm64 python3-joblib all 1.3.2-4 [216 kB]
Get:234 http://deb.debian.org/debian sid/main arm64 python3-kiwisolver arm64 1.4.7-2 [56.7 kB]
Get:235 http://deb.debian.org/debian sid/main arm64 python3-pyparsing all 3.1.2-1 [146 kB]
Get:236 http://deb.debian.org/debian sid/main arm64 python3-mda-xdrlib all 0.2.0-3 [11.6 kB]
Get:237 http://deb.debian.org/debian sid/main arm64 python3-msgpack arm64 1.0.3-3+b2 [73.8 kB]
Get:238 http://deb.debian.org/debian sid/main arm64 python3-mmtf all 1.1.3-1 [17.0 kB]
Get:239 http://deb.debian.org/debian sid/main arm64 python3-networkx all 3.2.1-4 [14.2 MB]
Get:240 http://deb.debian.org/debian sid/main arm64 python3-pandas-lib arm64 2.2.3+dfsg-4 [3746 kB]
Get:241 http://deb.debian.org/debian sid/main arm64 python3-pandas all 2.2.3+dfsg-4 [3096 kB]
Get:242 http://deb.debian.org/debian sid/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB]
Get:243 http://deb.debian.org/debian sid/main arm64 python3-pygments all 2.18.0+dfsg-1 [836 kB]
Get:244 http://deb.debian.org/debian sid/main arm64 python3-pytest all 8.3.3-1 [249 kB]
Get:245 http://deb.debian.org/debian sid/main arm64 python3-seaborn all 0.13.2-4 [215 kB]
Get:246 http://deb.debian.org/debian sid/main arm64 python3-threadpoolctl all 3.1.0-1 [21.2 kB]
Get:247 http://deb.debian.org/debian sid/main arm64 python3-sklearn all 1.4.2+dfsg-6 [2248 kB]
Get:248 http://deb.debian.org/debian sid/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB]
Get:249 http://deb.debian.org/debian sid/main arm64 sphinx-common all 7.4.7-3 [731 kB]
Get:250 http://deb.debian.org/debian sid/main arm64 python3-sphinx all 7.4.7-3 [588 kB]
Get:251 http://deb.debian.org/debian sid/main arm64 python3-tqdm all 4.66.5-1 [90.1 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking libpython3.12-minimal:arm64 (3.12.7-1) ...
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Setting up libpython3.12-minimal:arm64 (3.12.7-1) ...
Setting up libexpat1:arm64 (2.6.3-1) ...
Setting up python3.12-minimal (3.12.7-1) ...
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Unpacking python3-minimal (3.12.6-1+debusine1) ...
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Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3) ...
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Unpacking libnsl2:arm64 (1.3.0-3+b2) ...
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Unpacking libpython3.12-stdlib:arm64 (3.12.7-1) ...
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Unpacking python3.12 (3.12.7-1) ...
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Unpacking libpython3-stdlib:arm64 (3.12.6-1+debusine1) ...
Setting up python3-minimal (3.12.6-1+debusine1) ...
Selecting previously unselected package python3.
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Unpacking python3 (3.12.6-1+debusine1) ...
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Unpacking libpython3.13-minimal:arm64 (3.13.0-1) ...
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Unpacking python3.13-minimal (3.13.0-1) ...
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Unpacking sgml-base (1.31) ...
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Unpacking procps (2:4.0.4-6) ...
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Unpacking m4 (1.4.19-4) ...
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Unpacking autoconf (2.72-3) ...
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Selecting previously unselected package libtcl8.6:arm64.
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Unpacking libtcl8.6:arm64 (8.6.15+dfsg-2) ...
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Unpacking libfreetype6:arm64 (2.13.3+dfsg-1) ...
Selecting previously unselected package fonts-dejavu-mono.
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Unpacking fonts-dejavu-mono (2.37-8) ...
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Unpacking libfontenc1:arm64 (1:1.1.8-1) ...
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Unpacking libxau6:arm64 (1:1.0.9-1+b1) ...
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Unpacking libxext6:arm64 (2:1.3.4-1+b2) ...
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Unpacking libxss1:arm64 (1:1.2.3-1+b1) ...
Selecting previously unselected package libtk8.6:arm64.
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update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode
Setting up debhelper (13.20) ...
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Setting up w3c-sgml-lib (1.3-3) ...
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Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (arm64 included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 6.1.0-26-cloud-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) arm64 (aarch64)
Toolchain package versions: binutils_2.43.1-5 dpkg-dev_1.22.11 g++-14_14.2.0-7 gcc-14_14.2.0-7 libc6-dev_2.40-3 libstdc++-14-dev_14.2.0-7 libstdc++6_14.2.0-7 linux-libc-dev_6.11.4-1
Package versions: appstream_1.0.3-1 apt_2.9.10 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.5 base-passwd_3.6.5 bash_5.2.32-1+b2 binutils_2.43.1-5 binutils-aarch64-linux-gnu_2.43.1-5 binutils-common_2.43.1-5 blt_2.5.3+dfsg-7 bsdextrautils_2.40.2-9 bsdutils_1:2.40.2-9 build-essential_12.12 bzip2_1.0.8-6 ca-certificates_20240203 coreutils_9.5-1 cpp_4:14.2.0-1 cpp-14_14.2.0-7 cpp-14-aarch64-linux-gnu_14.2.0-7 cpp-aarch64-linux-gnu_4:14.2.0-1 cython3_3.0.11+dfsg-1+debusine1 dash_0.5.12-9 debconf_1.5.87 debhelper_13.20 debian-archive-keyring_2023.4 debianutils_5.20 dh-autoreconf_20 dh-python_6.20240824 dh-strip-nondeterminism_1.14.0-1 diffstat_1.66-1 diffutils_1:3.10-1 docutils-common_0.21.2+dfsg-2 dpkg_1.22.11 dpkg-dev_1.22.11 dumb-init_1.2.5-3 dwz_0.15-1+b1 e2fsprogs_1.47.1-1 fakeroot_1.36-1 file_1:5.45-3 findutils_4.10.0-3 fontconfig-config_2.15.0-1.1 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 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python3-pyproject-hooks_1.1.0-2 python3-pytest_8.3.3-1 python3-reportlab_4.2.5-1 python3-requests_2.32.3+dfsg-1 python3-rlpycairo_0.3.0-3 python3-roman_4.2-1 python3-scipy_1.13.1-5+nocheck1 python3-seaborn_0.13.2-4 python3-setuptools_75.2.0-1 python3-six_1.16.0-7 python3-sklearn_1.4.2+dfsg-6 python3-sklearn-lib_1.4.2+dfsg-6+debusine1 python3-snowballstemmer_2.2.0-4 python3-sortedcontainers_2.4.0-2 python3-sphinx_7.4.7-3 python3-sympy_1.13.3-1 python3-threadpoolctl_3.1.0-1 python3-tk_3.12.6-1 python3-toml_0.10.2-1 python3-tqdm_4.66.5-1 python3-typeguard_4.3.0-1 python3-typing-extensions_4.12.2-2 python3-tz_2024.1-2 python3-ufolib2_0.16.0+dfsg1-1 python3-urllib3_2.0.7-2 python3-wheel_0.44.0-2 python3-zipp_3.20.2-1 python3.12_3.12.7-1 python3.12-dev_3.12.7-1 python3.12-minimal_3.12.7-1 python3.12-tk_3.12.7-1 python3.13_3.13.0-1 python3.13-dev_3.13.0-1 python3.13-minimal_3.13.0-1 python3.13-tk_3.13.0-1 readline-common_8.2-5 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 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+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: mdanalysis
Binary: python3-mdanalysis, python-mdanalysis-doc
Architecture: any all
Version: 2.7.0-5
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Uploaders: Drew Parsons <dparsons@debian.org>
Homepage: https://www.mdanalysis.org/
Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/debichem-team/mdanalysis
Vcs-Git: https://salsa.debian.org/debichem-team/mdanalysis.git
Testsuite: autopkgtest
Testsuite-Triggers: @builddeps@, python3-all, python3-hypothesis, python3-pytest, python3-sklearn
Build-Depends: debhelper-compat (= 13), cython3, dh-sequence-python3, pybuild-plugin-pyproject, python3-all-dev, python3-setuptools, python3-numpy, python3-biopython (>= 1.80), python3-networkx, python3-griddataformats, python3-mmtf, python3-joblib, python3-scipy, python3-matplotlib, python3-mda-xdrlib, python3-tqdm, python3-threadpoolctl, python3-packaging, python3-fasteners, python3-gsd (>= 3.0.1~) [!s390x !hppa !m68k !powerpc !ppc64 !sparc64], python3-netcdf4, python3-h5py, python3-seaborn, python3-sklearn, python3-duecredit, python3-hypothesis <!nocheck>, python3-pytest <!nocheck>, python3-sphinx
Build-Depends-Indep: python3-msmb-theme, python3-pybtex, python3-sphinx-rtd-theme, python3-sphinx-sitemap, python3-sphinxcontrib.bibtex, libjs-mathjax
Package-List:
python-mdanalysis-doc deb doc optional arch=all
python3-mdanalysis deb python optional arch=any
Checksums-Sha1:
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Files:
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ec117204a55a900b4f6d49d5de1ed486 10864 mdanalysis_2.7.0-5.debian.tar.xz
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gpgv: Signature made Sat Aug 10 17:37:57 2024 UTC
gpgv: using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA
gpgv: issuer "dparsons@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.7.0-5.dsc: no acceptable signature found
dpkg-source: info: extracting mdanalysis in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking mdanalysis_2.7.0.orig.tar.xz
dpkg-source: info: unpacking mdanalysis_2.7.0-5.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying docs_use_built_module.patch
dpkg-source: info: applying docs_sphinx_warnings_are_not_errors.patch
dpkg-source: info: applying docs_local_mathjax.patch
dpkg-source: info: applying xdr_type_PR4408.patch
dpkg-source: info: applying doc_no_mdanalysis_sphinx.patch
Check disk space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 2.7.0-5+bd1
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
HOME=/sbuild-nonexistent
LANG=en_US.UTF-8
LC_ALL=C.UTF-8
LOGNAME=debusine-worker
OLDPWD=/
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/<<PKGBUILDDIR>>
SHELL=/bin/sh
USER=debusine-worker
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -us -uc -mDebusine Rebuild <debusine@example.net> -B -rfakeroot
dpkg-buildpackage: info: source package mdanalysis
dpkg-buildpackage: info: source version 2.7.0-5+bd1
dpkg-buildpackage: info: source distribution sid
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
dpkg-source: info: using options from mdanalysis-2.7.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/
debian/rules clean
dh clean --with sphinxdoc --buildsystem=pybuild
dh_auto_clean -O--buildsystem=pybuild
debian/rules execute_after_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f .duecredit.p
rm -f package/MDAnalysis/authors.py
rm -f package/MDAnalysis/analysis/encore/clustering/affinityprop.c \
package/MDAnalysis/analysis/encore/cutils.c \
package/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c \
package/MDAnalysis/coordinates/timestep.cpp \
package/MDAnalysis/lib/_augment.cpp \
package/MDAnalysis/lib/_cutil.cpp \
package/MDAnalysis/lib/c_distances.c \
package/MDAnalysis/lib/c_distances_openmp.c \
package/MDAnalysis/lib/formats/cython_util.c \
package/MDAnalysis/lib/formats/libdcd.c \
package/MDAnalysis/lib/formats/libmdaxdr.c \
package/MDAnalysis/lib/nsgrid.cpp \
package/MDAnalysis/lib/qcprot.c
rm -rf package/MDAnalysis.egg-info
rm -f testsuite/MDAnalysisTests/data/.*_offsets.npz testsuite/MDAnalysisTests/data/*/.*_offsets.npz
rm -rf testsuite/.pytest_cache
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules binary-arch
dh binary-arch --with sphinxdoc --buildsystem=pybuild
dh_update_autotools_config -a -O--buildsystem=pybuild
dh_autoreconf -a -O--buildsystem=pybuild
dh_auto_configure -a -O--buildsystem=pybuild
dh_auto_build -a -O--buildsystem=pybuild
I: pybuild plugin_pyproject:129: Building wheel for python3.13 with "build" module
I: pybuild base:311: python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_mdanalysis
* Building wheel...
performance hint: MDAnalysis/lib/c_distances.pyx:275:5: Exception check on '_minimum_image_orthogonal' will always require the GIL to be acquired.
Possible solutions:
1. Declare '_minimum_image_orthogonal' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on '_minimum_image_orthogonal' to allow an error code to be returned.
performance hint: MDAnalysis/lib/c_distances.pyx:302:5: Exception check on '_minimum_image_triclinic' will always require the GIL to be acquired.
Possible solutions:
1. Declare '_minimum_image_triclinic' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on '_minimum_image_triclinic' to allow an error code to be returned.
performance hint: MDAnalysis/lib/c_distances.pyx:390:37: Exception check after calling '__pyx_fuse_0_minimum_image_orthogonal' will always require the GIL to be acquired.
Possible solutions:
1. Declare '__pyx_fuse_0_minimum_image_orthogonal' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on '__pyx_fuse_0_minimum_image_orthogonal' to allow an error code to be returned.
performance hint: MDAnalysis/lib/c_distances.pyx:390:37: Exception check after calling '__pyx_fuse_1_minimum_image_orthogonal' will always require the GIL to be acquired.
Possible solutions:
1. Declare '__pyx_fuse_1_minimum_image_orthogonal' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on '__pyx_fuse_1_minimum_image_orthogonal' to allow an error code to be returned.
performance hint: MDAnalysis/lib/c_distances.pyx:414:36: Exception check after calling '__pyx_fuse_0_minimum_image_triclinic' will always require the GIL to be acquired.
Possible solutions:
1. Declare '__pyx_fuse_0_minimum_image_triclinic' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on '__pyx_fuse_0_minimum_image_triclinic' to allow an error code to be returned.
performance hint: MDAnalysis/lib/c_distances.pyx:414:36: Exception check after calling '__pyx_fuse_1_minimum_image_triclinic' will always require the GIL to be acquired.
Possible solutions:
1. Declare '__pyx_fuse_1_minimum_image_triclinic' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on '__pyx_fuse_1_minimum_image_triclinic' to allow an error code to be returned.
performance hint: MDAnalysis/lib/nsgrid.pyx:417:37: Exception check after calling 'coord2cellid' will always require the GIL to be acquired. Declare 'coord2cellid' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: MDAnalysis/lib/nsgrid.pyx:431:26: Exception check after calling 'coord2cellxyz' will always require the GIL to be acquired.
Possible solutions:
1. Declare 'coord2cellxyz' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on 'coord2cellxyz' to allow an error code to be returned.
performance hint: MDAnalysis/lib/nsgrid.pyx:559:34: Exception check after calling 'coord2cellxyz' will always require the GIL to be acquired.
Possible solutions:
1. Declare 'coord2cellxyz' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on 'coord2cellxyz' to allow an error code to be returned.
performance hint: MDAnalysis/lib/nsgrid.pyx:567:56: Exception check after calling 'cellxyz2cellid' will always require the GIL to be acquired. Declare 'cellxyz2cellid' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: MDAnalysis/lib/nsgrid.pyx:574:53: Exception check after calling 'calc_distsq' will always require the GIL to be acquired. Declare 'calc_distsq' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
performance hint: MDAnalysis/lib/nsgrid.pyx:578:57: Exception check after calling 'add_neighbors' will always require the GIL to be acquired.
Possible solutions:
1. Declare 'add_neighbors' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on 'add_neighbors' to allow an error code to be returned.
Attempting to autodetect OpenMP support... Compiler supports OpenMP
Will attempt to use Cython.
Compiling MDAnalysis/lib/formats/libdcd.pyx because it changed.
Compiling MDAnalysis/lib/c_distances.pyx because it changed.
Compiling MDAnalysis/lib/c_distances_openmp.pyx because it changed.
Compiling MDAnalysis/lib/qcprot.pyx because it changed.
Compiling MDAnalysis/lib/formats/libmdaxdr.pyx because it changed.
Compiling MDAnalysis/lib/formats/cython_util.pyx because it changed.
Compiling MDAnalysis/analysis/encore/cutils.pyx because it changed.
Compiling MDAnalysis/analysis/encore/clustering/affinityprop.pyx because it changed.
Compiling MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx because it changed.
Compiling MDAnalysis/lib/_cutil.pyx because it changed.
Compiling MDAnalysis/lib/_augment.pyx because it changed.
Compiling MDAnalysis/lib/nsgrid.pyx because it changed.
Compiling MDAnalysis/coordinates/timestep.pyx because it changed.
[ 1/13] Cythonizing MDAnalysis/analysis/encore/clustering/affinityprop.pyx
[ 2/13] Cythonizing MDAnalysis/analysis/encore/cutils.pyx
[ 3/13] Cythonizing MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx
[ 4/13] Cythonizing MDAnalysis/coordinates/timestep.pyx
[ 5/13] Cythonizing MDAnalysis/lib/_augment.pyx
[ 6/13] Cythonizing MDAnalysis/lib/_cutil.pyx
[ 7/13] Cythonizing MDAnalysis/lib/c_distances.pyx
[ 8/13] Cythonizing MDAnalysis/lib/c_distances_openmp.pyx
[ 9/13] Cythonizing MDAnalysis/lib/formats/cython_util.pyx
[10/13] Cythonizing MDAnalysis/lib/formats/libdcd.pyx
[11/13] Cythonizing MDAnalysis/lib/formats/libmdaxdr.pyx
[12/13] Cythonizing MDAnalysis/lib/nsgrid.pyx
[13/13] Cythonizing MDAnalysis/lib/qcprot.pyx
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite'
warnings.warn(msg)
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require'
warnings.warn(msg)
/usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:78: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies)
corresp(dist, value, root_dir)
running bdist_wheel
running build
running build_py
creating build/lib.linux-aarch64-cpython-313/MDAnalysis
copying MDAnalysis/version.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis
copying MDAnalysis/due.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis
copying MDAnalysis/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis
copying MDAnalysis/exceptions.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis
copying MDAnalysis/units.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis
copying MDAnalysis/authors.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/ITPParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/tables.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/guessers.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/GROParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/core.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/ParmEdParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/base.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
copying MDAnalysis/lib/transformations.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
copying MDAnalysis/lib/picklable_file_io.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
copying MDAnalysis/lib/mdamath.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
copying MDAnalysis/lib/_distopia.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
copying MDAnalysis/lib/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
copying MDAnalysis/lib/distances.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
copying MDAnalysis/lib/correlations.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
copying MDAnalysis/lib/log.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
copying MDAnalysis/lib/util.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/auxiliary
copying MDAnalysis/auxiliary/EDR.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/auxiliary
copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/auxiliary
copying MDAnalysis/auxiliary/core.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/auxiliary
copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/auxiliary
copying MDAnalysis/auxiliary/base.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/auxiliary
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/core
copying MDAnalysis/core/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/core
copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/core
copying MDAnalysis/core/selection.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/core
copying MDAnalysis/core/groups.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/core
copying MDAnalysis/core/_get_readers.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/core
copying MDAnalysis/core/topology.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/core
copying MDAnalysis/core/accessors.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/core
copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/core
copying MDAnalysis/core/universe.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/core
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/tests
copying MDAnalysis/tests/datafiles.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/tests
copying MDAnalysis/tests/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/tests
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis
copying MDAnalysis/analysis/polymer.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis
copying MDAnalysis/analysis/atomicdistances.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis
copying MDAnalysis/analysis/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis
copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis
copying MDAnalysis/analysis/distances.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis
copying MDAnalysis/analysis/dielectric.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis
copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis
copying MDAnalysis/analysis/align.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis
copying MDAnalysis/analysis/rdf.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis
copying MDAnalysis/analysis/gnm.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis
copying MDAnalysis/analysis/rms.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis
copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis
copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis
copying MDAnalysis/analysis/contacts.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis
copying MDAnalysis/analysis/density.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis
copying MDAnalysis/analysis/msd.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis
copying MDAnalysis/analysis/helix_analysis.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis
copying MDAnalysis/analysis/pca.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis
copying MDAnalysis/analysis/bat.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis
copying MDAnalysis/analysis/base.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis
copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis
copying MDAnalysis/analysis/psa.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis
copying MDAnalysis/analysis/nucleicacids.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis
copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/selections
copying MDAnalysis/selections/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/selections
copying MDAnalysis/selections/charmm.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/selections
copying MDAnalysis/selections/vmd.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/selections
copying MDAnalysis/selections/pymol.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/selections
copying MDAnalysis/selections/gromacs.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/selections
copying MDAnalysis/selections/base.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/selections
copying MDAnalysis/selections/jmol.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/selections
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations
copying MDAnalysis/transformations/wrap.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations
copying MDAnalysis/transformations/translate.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations
copying MDAnalysis/transformations/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations
copying MDAnalysis/transformations/positionaveraging.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations
copying MDAnalysis/transformations/rotate.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations
copying MDAnalysis/transformations/boxdimensions.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations
copying MDAnalysis/transformations/nojump.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations
copying MDAnalysis/transformations/base.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations
copying MDAnalysis/transformations/fit.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/visualization
copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/visualization
copying MDAnalysis/visualization/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/visualization
copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/visualization
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/converters
copying MDAnalysis/converters/OpenMMParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/converters
copying MDAnalysis/converters/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/converters
copying MDAnalysis/converters/OpenMM.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/converters
copying MDAnalysis/converters/RDKit.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/converters
copying MDAnalysis/converters/RDKitParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/converters
copying MDAnalysis/converters/ParmEdParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/converters
copying MDAnalysis/converters/base.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/converters
copying MDAnalysis/converters/ParmEd.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/converters
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TNG.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRC.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/H5MD.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/chain.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/core.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/chemfiles.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/base.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/ParmEd.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/null.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/memory.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/tpr
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats
copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/legacy
copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/legacy
copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/legacy
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/covariance.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/similarity.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hydrogenbonds
copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hydrogenbonds
copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hydrogenbonds
copying MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hydrogenbonds
copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hydrogenbonds
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/data
copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/data
copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/data
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hole2
copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hole2
copying MDAnalysis/analysis/hole2/templates.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hole2
copying MDAnalysis/analysis/hole2/utils.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hole2
copying MDAnalysis/analysis/hole2/hole.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hole2
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hbonds
copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hbonds
copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hbonds
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction
copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction
copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction
copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering
copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering
copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering
copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering
copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering
running egg_info
creating MDAnalysis.egg-info
writing MDAnalysis.egg-info/PKG-INFO
writing dependency_links to MDAnalysis.egg-info/dependency_links.txt
writing requirements to MDAnalysis.egg-info/requires.txt
writing top-level names to MDAnalysis.egg-info/top_level.txt
writing manifest file 'MDAnalysis.egg-info/SOURCES.txt'
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /<<PKGBUILDDIR>>/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /<<PKGBUILDDIR>>/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /<<PKGBUILDDIR>>/package/MDAnalysis/analysis/encore/clustering/include/ap.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /<<PKGBUILDDIR>>/package/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /<<PKGBUILDDIR>>/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /<<PKGBUILDDIR>>/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
reading manifest file 'MDAnalysis.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching 'doc/html/html' found anywhere in distribution
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '*.pyd' found anywhere in distribution
warning: no previously-included files matching '*~' found anywhere in distribution
warning: no previously-included files matching '.git' found anywhere in distribution
adding license file 'LICENSE'
adding license file 'AUTHORS'
writing manifest file 'MDAnalysis.egg-info/SOURCES.txt'
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'MDAnalysis.analysis.encore.clustering.include' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'MDAnalysis.analysis.encore.clustering.include' 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 'MDAnalysis.analysis.encore.clustering.include' 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 'MDAnalysis.analysis.encore.clustering.include' to be distributed and are
already explicitly excluding 'MDAnalysis.analysis.encore.clustering.include' 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)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'MDAnalysis.analysis.encore.clustering.src' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'MDAnalysis.analysis.encore.clustering.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 'MDAnalysis.analysis.encore.clustering.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 'MDAnalysis.analysis.encore.clustering.src' to be distributed and are
already explicitly excluding 'MDAnalysis.analysis.encore.clustering.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)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'MDAnalysis.analysis.encore.dimensionality_reduction.include' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'MDAnalysis.analysis.encore.dimensionality_reduction.include' 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 'MDAnalysis.analysis.encore.dimensionality_reduction.include' 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 'MDAnalysis.analysis.encore.dimensionality_reduction.include' to be distributed and are
already explicitly excluding 'MDAnalysis.analysis.encore.dimensionality_reduction.include' 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)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'MDAnalysis.analysis.encore.dimensionality_reduction.src' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'MDAnalysis.analysis.encore.dimensionality_reduction.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 'MDAnalysis.analysis.encore.dimensionality_reduction.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 'MDAnalysis.analysis.encore.dimensionality_reduction.src' to be distributed and are
already explicitly excluding 'MDAnalysis.analysis.encore.dimensionality_reduction.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)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'MDAnalysis.lib.formats.include' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'MDAnalysis.lib.formats.include' 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 'MDAnalysis.lib.formats.include' 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 'MDAnalysis.lib.formats.include' to be distributed and are
already explicitly excluding 'MDAnalysis.lib.formats.include' 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)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'MDAnalysis.lib.formats.src' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'MDAnalysis.lib.formats.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 'MDAnalysis.lib.formats.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 'MDAnalysis.lib.formats.src' to be distributed and are
already explicitly excluding 'MDAnalysis.lib.formats.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)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'MDAnalysis.lib.include' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'MDAnalysis.lib.include' 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 'MDAnalysis.lib.include' 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 'MDAnalysis.lib.include' to be distributed and are
already explicitly excluding 'MDAnalysis.lib.include' 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)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'MDAnalysis.lib.libmdanalysis' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'MDAnalysis.lib.libmdanalysis' 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 'MDAnalysis.lib.libmdanalysis' 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 'MDAnalysis.lib.libmdanalysis' to be distributed and are
already explicitly excluding 'MDAnalysis.lib.libmdanalysis' 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)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'MDAnalysis.lib.src.transformations' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'MDAnalysis.lib.src.transformations' 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 'MDAnalysis.lib.src.transformations' 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 'MDAnalysis.lib.src.transformations' to be distributed and are
already explicitly excluding 'MDAnalysis.lib.src.transformations' 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 MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/data
copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/data
copying MDAnalysis/lib/_augment.cpp -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
copying MDAnalysis/lib/_augment.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
copying MDAnalysis/lib/_cutil.cpp -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
copying MDAnalysis/lib/_cutil.pxd -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
copying MDAnalysis/lib/_cutil.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
copying MDAnalysis/lib/c_distances.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
copying MDAnalysis/lib/c_distances.pxd -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
copying MDAnalysis/lib/c_distances.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
copying MDAnalysis/lib/c_distances_openmp.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
copying MDAnalysis/lib/c_distances_openmp.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
copying MDAnalysis/lib/nsgrid.cpp -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
copying MDAnalysis/lib/nsgrid.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
copying MDAnalysis/lib/qcprot.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
copying MDAnalysis/lib/qcprot.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/include
copying MDAnalysis/lib/include/calc_distances.h -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/include
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/libmdanalysis
copying MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/libmdanalysis
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/src/transformations
copying MDAnalysis/lib/src/transformations/AUTHOR -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/src/transformations
copying MDAnalysis/lib/src/transformations/LICENCE -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/src/transformations
copying MDAnalysis/lib/src/transformations/transformations.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/src/transformations
copying MDAnalysis/coordinates/timestep.cpp -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/timestep.pxd -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/coordinates/timestep.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates
copying MDAnalysis/lib/formats/cython_util.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats
copying MDAnalysis/lib/formats/cython_util.pxd -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats
copying MDAnalysis/lib/formats/cython_util.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats
copying MDAnalysis/lib/formats/libdcd.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats
copying MDAnalysis/lib/formats/libdcd.pxd -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats
copying MDAnalysis/lib/formats/libdcd.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats
copying MDAnalysis/lib/formats/libmdaxdr.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats
copying MDAnalysis/lib/formats/libmdaxdr.pxd -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats
copying MDAnalysis/lib/formats/libmdaxdr.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include
copying MDAnalysis/lib/formats/include/endianswap.h -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include
copying MDAnalysis/lib/formats/include/fastio.h -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include
copying MDAnalysis/lib/formats/include/readdcd.h -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include
copying MDAnalysis/lib/formats/include/trr_seek.h -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include
copying MDAnalysis/lib/formats/include/xdrfile.h -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include
copying MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include
copying MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include
copying MDAnalysis/lib/formats/include/xtc_seek.h -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src
copying MDAnalysis/lib/formats/src/trr_seek.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src
copying MDAnalysis/lib/formats/src/xdrfile.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src
copying MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src
copying MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src
copying MDAnalysis/lib/formats/src/xtc_seek.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src
copying MDAnalysis/analysis/encore/cutils.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/cutils.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction
copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include
copying MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src
copying MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src
copying MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering
copying MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/include
copying MDAnalysis/analysis/encore/clustering/include/ap.h -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/include
creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/src
copying MDAnalysis/analysis/encore/clustering/src/ap.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/src
running build_ext
building 'MDAnalysis.lib.formats.libdcd' extension
creating build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include -I/usr/include/python3.13 -c MDAnalysis/lib/formats/libdcd.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libdcd.o -std=c99 -O3 -funroll-loops -fsigned-zeros
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/lib/formats/libdcd.c:1261:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
In file included from MDAnalysis/lib/formats/libdcd.c:1268:
MDAnalysis/lib/formats/include/readdcd.h: In function ‘read_dcdstep’:
MDAnalysis/lib/formats/include/readdcd.h:549:17: warning: comparison of integer expressions of different signedness: ‘fio_size_t’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare]
549 | if (readlen != (6*sizeof(int) + 3*N*sizeof(float)))
| ^~
MDAnalysis/lib/formats/include/readdcd.h:562:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
562 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT;
| ^~
MDAnalysis/lib/formats/include/readdcd.h: In function ‘write_dcdheader’:
MDAnalysis/lib/formats/include/readdcd.h:698:14: warning: unused variable ‘tmbuf’ [-Wunused-variable]
698 | struct tm *tmbuf;
| ^~~~~
MDAnalysis/lib/formats/include/readdcd.h:697:10: warning: unused variable ‘cur_time’ [-Wunused-variable]
697 | time_t cur_time;
| ^~~~~~~~
In file included from MDAnalysis/lib/formats/include/readdcd.h:25:
MDAnalysis/lib/formats/include/endianswap.h: At top level:
MDAnalysis/lib/formats/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function]
96 | static void swap2_aligned(void *v, long ndata) {
| ^~~~~~~~~~~~~
MDAnalysis/lib/formats/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function]
32 | static void swap2_unaligned(void *v, long ndata) {
| ^~~~~~~~~~~~~~~
In file included from MDAnalysis/lib/formats/libdcd.c:1267:
MDAnalysis/lib/formats/include/fastio.h:453:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function]
453 | static int fio_write_str(fio_fd fd, const char *str) {
| ^~~~~~~~~~~~~
MDAnalysis/lib/formats/include/fastio.h:449:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function]
449 | static int fio_read_int32(fio_fd fd, int *i) {
| ^~~~~~~~~~~~~~
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libdcd.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libdcd.cpython-313-aarch64-linux-gnu.so
building 'MDAnalysis.lib.c_distances' extension
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/include -I/usr/include/python3.13 -c MDAnalysis/lib/c_distances.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances.o -std=c99 -O3 -funroll-loops -fsigned-zeros
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/lib/c_distances.c:1263:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances.o -L/usr/lib/aarch64-linux-gnu -lm -o build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances.cpython-313-aarch64-linux-gnu.so
building 'MDAnalysis.lib.c_distances_openmp' extension
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPARALLEL -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/include -I/usr/include/python3.13 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c99 -O3 -funroll-loops -fsigned-zeros
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/lib/c_distances_openmp.c:1272:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances_openmp.o -L/usr/lib/aarch64-linux-gnu -lm -lgomp -o build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances_openmp.cpython-313-aarch64-linux-gnu.so -fopenmp
building 'MDAnalysis.lib.qcprot' extension
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c MDAnalysis/lib/qcprot.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/qcprot.o -std=c99 -O3 -funroll-loops -fsigned-zeros
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/lib/qcprot.c:1255:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
MDAnalysis/lib/qcprot.c: In function ‘__pyx_fuse_0__pyx_f_10MDAnalysis_3lib_6qcprot_InnerProduct’:
MDAnalysis/lib/qcprot.c:21123:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
21123 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
| ^
MDAnalysis/lib/qcprot.c:21331:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
21331 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
| ^
MDAnalysis/lib/qcprot.c: In function ‘__pyx_fuse_1__pyx_f_10MDAnalysis_3lib_6qcprot_InnerProduct’:
MDAnalysis/lib/qcprot.c:21801:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
21801 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
| ^
MDAnalysis/lib/qcprot.c:22009:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
22009 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
| ^
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/qcprot.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/qcprot.cpython-313-aarch64-linux-gnu.so
building 'MDAnalysis.lib._transformations' extension
creating build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/src/transformations
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/src/transformations/transformations.o -std=c99 -O3 -funroll-loops -fsigned-zeros
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/lib/src/transformations/transformations.c:73:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_superimposition_matrix’:
MDAnalysis/lib/src/transformations/transformations.c:1837: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
1837 | #pragma vector always
MDAnalysis/lib/src/transformations/transformations.c:1954: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
1954 | #pragma vector always
MDAnalysis/lib/src/transformations/transformations.c:1978: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
1978 | #pragma vector always
MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_vector_norm’:
MDAnalysis/lib/src/transformations/transformations.c:3414: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
3414 | #pragma vector always
MDAnalysis/lib/src/transformations/transformations.c:3495: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
3495 | #pragma vector always
MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_unit_vector’:
MDAnalysis/lib/src/transformations/transformations.c:3597: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
3597 | #pragma vector always
MDAnalysis/lib/src/transformations/transformations.c:3602: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
3602 | #pragma vector always
MDAnalysis/lib/src/transformations/transformations.c:3666: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
3666 | #pragma vector always
MDAnalysis/lib/src/transformations/transformations.c:3671: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
3671 | #pragma vector always
MDAnalysis/lib/src/transformations/transformations.c: At top level:
MDAnalysis/lib/src/transformations/transformations.c:910:1: warning: ‘PyConverter_DoubleVector4Copy’ defined but not used [-Wunused-function]
910 | PyConverter_DoubleVector4Copy(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MDAnalysis/lib/src/transformations/transformations.c:804:1: warning: ‘PyConverter_DoubleArrayOrNone’ defined but not used [-Wunused-function]
804 | PyConverter_DoubleArrayOrNone(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MDAnalysis/lib/src/transformations/transformations.c:774:1: warning: ‘PyConverter_DoubleArray’ defined but not used [-Wunused-function]
774 | PyConverter_DoubleArray(
| ^~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/src/transformations/transformations.o -L/usr/lib/aarch64-linux-gnu -lm -o build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/_transformations.cpython-313-aarch64-linux-gnu.so
building 'MDAnalysis.lib.formats.libmdaxdr' extension
creating build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.o -std=c99 -O3 -funroll-loops -fsigned-zeros
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/lib/formats/libmdaxdr.c:1282:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
In file included from MDAnalysis/lib/formats/libmdaxdr.c:1288:
MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
In file included from MDAnalysis/lib/formats/libmdaxdr.c:1289:
MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
In file included from MDAnalysis/lib/formats/include/xdrfile_xtc.h:43:
MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
In file included from MDAnalysis/lib/formats/libmdaxdr.c:1290:
MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/trr_seek.o -std=c99 -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/formats/src/trr_seek.c:30:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
In file included from MDAnalysis/lib/formats/src/trr_seek.c:31:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
In file included from /<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile_trr.h:42:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
MDAnalysis/lib/formats/src/trr_seek.c: In function ‘read_trr_n_frames’:
MDAnalysis/lib/formats/src/trr_seek.c:39:27: warning: unused variable ‘totalframebytes’ [-Wunused-variable]
39 | int result, framebytes, totalframebytes;
| ^~~~~~~~~~~~~~~
MDAnalysis/lib/formats/src/trr_seek.c:38:15: warning: unused variable ‘lambda’ [-Wunused-variable]
38 | float time, lambda;
| ^~~~~~
MDAnalysis/lib/formats/src/trr_seek.c:38:9: warning: unused variable ‘time’ [-Wunused-variable]
38 | float time, lambda;
| ^~~~
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/xdrfile.o -std=c99 -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/formats/src/xdrfile.c:62:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
MDAnalysis/lib/formats/src/xdrfile.c: In function ‘sizeofint’:
MDAnalysis/lib/formats/src/xdrfile.c:501:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
501 | while (size >= num && num_of_bits < 32)
| ^~
MDAnalysis/lib/formats/src/xdrfile.c: In function ‘sizeofints’:
MDAnalysis/lib/formats/src/xdrfile.c:547:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
547 | while (bytes[num_of_bytes] >= num)
| ^~
MDAnalysis/lib/formats/src/xdrfile.c: In function ‘encodeints’:
MDAnalysis/lib/formats/src/xdrfile.c:656:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
656 | if (num_of_bits >= num_of_bytes * 8)
| ^~
MDAnalysis/lib/formats/src/xdrfile.c:658:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
658 | for (i = 0; i < num_of_bytes; i++)
| ^
MDAnalysis/lib/formats/src/xdrfile.c:666:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
666 | for (i = 0; i < num_of_bytes-1; i++)
| ^
MDAnalysis/lib/formats/src/xdrfile.c: In function ‘decodebits’:
MDAnalysis/lib/formats/src/xdrfile.c:706:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
706 | if (lastbits < num_of_bits)
| ^
MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’:
MDAnalysis/lib/formats/src/xdrfile.c:816:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
816 | if(size3>xfp->buf1size)
| ^
MDAnalysis/lib/formats/src/xdrfile.c:868:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
868 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
| ^
MDAnalysis/lib/formats/src/xdrfile.c:868:44: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare]
868 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
| ^~~
MDAnalysis/lib/formats/src/xdrfile.c:794:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
794 | int smallnum, smaller, larger, i, is_smaller, run;
| ^~~~~~
MDAnalysis/lib/formats/src/xdrfile.c:791:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
791 | int smallidx, minidx, maxidx;
| ^~~~~~
MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’:
MDAnalysis/lib/formats/src/xdrfile.c:1012:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
1012 | if(size3>xfp->buf1size)
| ^
MDAnalysis/lib/formats/src/xdrfile.c:1135:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
1135 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff)
| ^
MDAnalysis/lib/formats/src/xdrfile.c:1141:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
1141 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
| ^
MDAnalysis/lib/formats/src/xdrfile.c:1141:44: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare]
1141 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
| ^~~
MDAnalysis/lib/formats/src/xdrfile.c:1273:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
1273 | if(tmp==(unsigned int)buf2[0])
| ^~
MDAnalysis/lib/formats/src/xdrfile.c:1001:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
1001 | int errval=1;
| ^~~~~~
MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’:
MDAnalysis/lib/formats/src/xdrfile.c:1313:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
1313 | if(size3>xfp->buf1size)
| ^
MDAnalysis/lib/formats/src/xdrfile.c:1368:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
1368 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
| ^
MDAnalysis/lib/formats/src/xdrfile.c:1368:44: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare]
1368 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
| ^~~
MDAnalysis/lib/formats/src/xdrfile.c:1290:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
1290 | int smallnum, smaller, larger, i, is_smaller, run;
| ^~~~~~
MDAnalysis/lib/formats/src/xdrfile.c:1287:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
1287 | int smallidx, minidx, maxidx;
| ^~~~~~
MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’:
MDAnalysis/lib/formats/src/xdrfile.c:1504:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
1504 | if(size3>xfp->buf1size) {
| ^
MDAnalysis/lib/formats/src/xdrfile.c:1619:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
1619 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) {
| ^
MDAnalysis/lib/formats/src/xdrfile.c:1624:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
1624 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
| ^
MDAnalysis/lib/formats/src/xdrfile.c:1624:44: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare]
1624 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
| ^~~
MDAnalysis/lib/formats/src/xdrfile.c:1734:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
1734 | if(tmp==(unsigned int)buf2[0])
| ^~
MDAnalysis/lib/formats/src/xdrfile.c:1494:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
1494 | int errval=1;
| ^~~~~~
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/src/xdrfile_trr.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_trr.o -std=c99 -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:38:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:39:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
In file included from /<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile_trr.h:42:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
MDAnalysis/lib/formats/src/xdrfile_trr.c: In function ‘do_trnheader’:
MDAnalysis/lib/formats/src/xdrfile_trr.c:78:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
78 | if (slen != strlen(version) + 1)
| ^~
MDAnalysis/lib/formats/src/xdrfile_trr.c:86:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
86 | if (xdrfile_write_string(version, xd) != (strlen(version) + 1))
| ^~
MDAnalysis/lib/formats/src/xdrfile_trr.c: In function ‘write_trr’:
MDAnalysis/lib/formats/src/xdrfile_trr.c:408:10: warning: ‘plcholder’ is used uninitialized [-Wuninitialized]
408 | return do_trn(xd, 0, &step, &t, &lambda, box, &natoms, x, v, f, plcholder);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MDAnalysis/lib/formats/src/xdrfile_trr.c:407:8: note: ‘plcholder’ was declared here
407 | int *plcholder;
| ^~~~~~~~~
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/src/xdrfile_xtc.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_xtc.o -std=c99 -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:30:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:31:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
In file included from /<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile_xtc.h:43:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/src/xtc_seek.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/xtc_seek.o -std=c99 -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/formats/src/xtc_seek.c:25:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
In file included from MDAnalysis/lib/formats/src/xtc_seek.c:26:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
In file included from /<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile_xtc.h:43:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/trr_seek.o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/xdrfile.o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_trr.o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_xtc.o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/xtc_seek.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.cpython-313-aarch64-linux-gnu.so
building 'MDAnalysis.lib.formats.cython_util' extension
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c MDAnalysis/lib/formats/cython_util.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/cython_util.o -std=c99 -O3 -funroll-loops -fsigned-zeros
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/lib/formats/cython_util.c:1272:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/cython_util.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/cython_util.cpython-313-aarch64-linux-gnu.so
building 'MDAnalysis.analysis.encore.cutils' extension
creating build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c MDAnalysis/analysis/encore/cutils.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/cutils.o -std=c99 -funroll-loops -fsigned-zeros -O1
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/analysis/encore/cutils.c:1255:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/cutils.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/cutils.cpython-313-aarch64-linux-gnu.so
building 'MDAnalysis.analysis.encore.clustering.affinityprop' extension
creating build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering
creating build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/src
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.13 -c MDAnalysis/analysis/encore/clustering/affinityprop.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.o -std=c99 -funroll-loops -fsigned-zeros -O1
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/analysis/encore/clustering/affinityprop.c:1261:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.13 -c MDAnalysis/analysis/encore/clustering/src/ap.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/src/ap.o -std=c99 -funroll-loops -fsigned-zeros -O1
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.o build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/src/ap.o -L/usr/lib/aarch64-linux-gnu -lm -o build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-313-aarch64-linux-gnu.so
building 'MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed' extension
creating build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.13 -c MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -std=c99 -funroll-loops -fsigned-zeros -O1
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.13 -c MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -std=c99 -funroll-loops -fsigned-zeros -O1
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:1261:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -L/usr/lib/aarch64-linux-gnu -lm -o build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-313-aarch64-linux-gnu.so
building 'MDAnalysis.lib._cutil' extension
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/include -I/usr/include/python3.13 -c MDAnalysis/lib/_cutil.cpp -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/_cutil.o -O3 -funroll-loops -fsigned-zeros -std=c++11
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/lib/_cutil.cpp:1273:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/_cutil.o -L/usr/lib/aarch64-linux-gnu -lm -o build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/_cutil.cpython-313-aarch64-linux-gnu.so
building 'MDAnalysis.lib._augment' extension
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c MDAnalysis/lib/_augment.cpp -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/_augment.o -O3 -funroll-loops -fsigned-zeros -std=c++11
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/lib/_augment.cpp:1268:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/_augment.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/_augment.cpython-313-aarch64-linux-gnu.so
building 'MDAnalysis.lib.nsgrid' extension
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/include -I/usr/include/python3.13 -c MDAnalysis/lib/nsgrid.cpp -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/nsgrid.o -O3 -funroll-loops -fsigned-zeros -std=c++11
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/nsgrid.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/nsgrid.cpython-313-aarch64-linux-gnu.so
building 'MDAnalysis.coordinates.timestep' extension
creating build/temp.linux-aarch64-cpython-313/MDAnalysis/coordinates
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c MDAnalysis/coordinates/timestep.cpp -o build/temp.linux-aarch64-cpython-313/MDAnalysis/coordinates/timestep.o -O3 -funroll-loops -fsigned-zeros -std=c++11
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/coordinates/timestep.cpp:1269:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/coordinates/timestep.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/timestep.cpython-313-aarch64-linux-gnu.so
installing to build/bdist.linux-aarch64/wheel
running install
running install_lib
creating build/bdist.linux-aarch64/wheel
creating build/bdist.linux-aarch64/wheel/MDAnalysis
creating build/bdist.linux-aarch64/wheel/MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/FHIAIMSParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/DLPolyParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/PSFParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/MOL2Parser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/XYZParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/PQRParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/ITPParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/tables.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/DMSParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/HoomdXMLParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/GSDParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/TPRParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/CRDParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/LAMMPSParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
creating build/bdist.linux-aarch64/wheel/MDAnalysis/topology/tpr
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/tpr/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology/tpr
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/tpr/utils.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology/tpr
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/tpr/setting.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology/tpr
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/tpr/obj.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology/tpr
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/MinimalParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/PDBQTParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/guessers.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/TOPParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/GROParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/GMSParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/MMTFParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/TXYZParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/PDBParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/core.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/ParmEdParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/ExtendedPDBParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/version.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/due.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis
creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/transformations.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/picklable_file_io.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/mdamath.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances_openmp.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/_augment.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/NeighborSearch.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/_distopia.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/distances.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/include
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/include/calc_distances.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/include
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/_cutil.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/_cutil.cpp -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/pkdtree.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/formats
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libdcd.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/formats/include
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include/xdrfile.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include/readdcd.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include/fastio.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include/xtc_seek.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include/endianswap.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include/trr_seek.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/cython_util.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/cython_util.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/cython_util.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libdcd.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libdcd.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/formats/src
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/trr_seek.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/src
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/xtc_seek.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/src
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/xdrfile.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/src
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/src
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/src
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/cython_util.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libdcd.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances_openmp.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/nsgrid.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/qcprot.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances_openmp.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/correlations.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/libmdanalysis
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/libmdanalysis
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/log.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/_cutil.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/_cutil.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/util.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/qcprot.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/_transformations.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/nsgrid.cpp -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/src
creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/src/transformations
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/src/transformations/AUTHOR -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/src/transformations
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/src/transformations/LICENCE -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/src/transformations
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/src/transformations/transformations.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/src/transformations
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/_augment.cpp -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/qcprot.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/_augment.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/nsgrid.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
creating build/bdist.linux-aarch64/wheel/MDAnalysis/auxiliary
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copying build/lib.linux-aarch64-cpython-313/MDAnalysis/auxiliary/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/auxiliary
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/auxiliary/core.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/auxiliary
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/auxiliary/XVG.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/auxiliary
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/auxiliary/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/auxiliary
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis
creating build/bdist.linux-aarch64/wheel/MDAnalysis/core
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/core/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/core/topologyattrs.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/core/selection.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/core/groups.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/core/_get_readers.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/core/topology.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/core/accessors.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/core/topologyobjects.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/core/universe.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core
creating build/bdist.linux-aarch64/wheel/MDAnalysis/tests
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/tests/datafiles.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/tests
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/tests/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/tests
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/legacy
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/legacy/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/legacy
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/legacy/x3dna.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/legacy
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/polymer.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/atomicdistances.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/lineardensity.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/distances.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/dielectric.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/nuclinfo.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/align.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/rdf.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/gnm.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/encore
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/include
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction/include
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/src
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction/src
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/cutils.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/utils.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/confdistmatrix.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/covariance.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/encore/clustering
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/cluster.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/encore/clustering/include
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/include/ap.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering/include
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/encore/clustering/src
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/src/ap.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering/src
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/similarity.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/bootstrap.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/cutils.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/cutils.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/rms.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/leaflet.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/hydrogenbonds
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hydrogenbonds
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hydrogenbonds
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hydrogenbonds
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hydrogenbonds
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/diffusionmap.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/contacts.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/density.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/msd.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/data
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/data/rama_ref_data.npy -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/data
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/data/janin_ref_data.npy -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/data
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/data/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/data
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/data/filenames.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/data
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/hole2
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hole2/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hole2
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hole2/templates.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hole2
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hole2/utils.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hole2
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hole2/hole.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hole2
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/helix_analysis.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/hbonds
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hbonds/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hbonds
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hbonds
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/pca.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/bat.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/waterdynamics.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/psa.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/nucleicacids.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/dihedrals.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/exceptions.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis
creating build/bdist.linux-aarch64/wheel/MDAnalysis/selections
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/selections/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/selections/charmm.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/selections/vmd.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/selections/pymol.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/selections/gromacs.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/selections/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/selections/jmol.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections
creating build/bdist.linux-aarch64/wheel/MDAnalysis/transformations
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copying build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations/translate.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations/positionaveraging.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations/rotate.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations/boxdimensions.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations/nojump.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations/fit.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations
creating build/bdist.linux-aarch64/wheel/MDAnalysis/visualization
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/visualization/streamlines.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/visualization
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/visualization/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/visualization
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/visualization/streamlines_3D.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/visualization
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/units.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis
creating build/bdist.linux-aarch64/wheel/MDAnalysis/converters
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/converters/OpenMMParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/converters/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/converters/OpenMM.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/converters/RDKit.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/converters/RDKitParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/converters/ParmEdParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/converters/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/converters/ParmEd.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/authors.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis
creating build/bdist.linux-aarch64/wheel/MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/TNG.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/timestep.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/timestep.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/TRZ.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/XDR.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/CRD.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/PQR.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/XYZ.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/TRC.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/DCD.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/H5MD.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/timestep.cpp -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/chain.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/NAMDBIN.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/GRO.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/timestep.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/DLPoly.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/PDB.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/MMTF.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/GSD.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/FHIAIMS.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/INPCRD.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/XTC.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/TRR.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/MOL2.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/LAMMPS.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/TXYZ.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/PDBQT.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/core.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/chemfiles.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/GMS.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/TRJ.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/ParmEd.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/DMS.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/null.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/memory.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
running install_egg_info
Copying MDAnalysis.egg-info to build/bdist.linux-aarch64/wheel/./MDAnalysis-2.7.0.egg-info
running install_scripts
creating build/bdist.linux-aarch64/wheel/MDAnalysis-2.7.0.dist-info/WHEEL
creating '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_mdanalysis/.tmp-pl0eprse/MDAnalysis-2.7.0-cp313-cp313-linux_aarch64.whl' and adding 'build/bdist.linux-aarch64/wheel' to it
adding 'MDAnalysis/__init__.py'
adding 'MDAnalysis/authors.py'
adding 'MDAnalysis/due.py'
adding 'MDAnalysis/exceptions.py'
adding 'MDAnalysis/units.py'
adding 'MDAnalysis/version.py'
adding 'MDAnalysis/analysis/__init__.py'
adding 'MDAnalysis/analysis/align.py'
adding 'MDAnalysis/analysis/atomicdistances.py'
adding 'MDAnalysis/analysis/base.py'
adding 'MDAnalysis/analysis/bat.py'
adding 'MDAnalysis/analysis/contacts.py'
adding 'MDAnalysis/analysis/density.py'
adding 'MDAnalysis/analysis/dielectric.py'
adding 'MDAnalysis/analysis/diffusionmap.py'
adding 'MDAnalysis/analysis/dihedrals.py'
adding 'MDAnalysis/analysis/distances.py'
adding 'MDAnalysis/analysis/gnm.py'
adding 'MDAnalysis/analysis/helix_analysis.py'
adding 'MDAnalysis/analysis/leaflet.py'
adding 'MDAnalysis/analysis/lineardensity.py'
adding 'MDAnalysis/analysis/msd.py'
adding 'MDAnalysis/analysis/nucleicacids.py'
adding 'MDAnalysis/analysis/nuclinfo.py'
adding 'MDAnalysis/analysis/pca.py'
adding 'MDAnalysis/analysis/polymer.py'
adding 'MDAnalysis/analysis/psa.py'
adding 'MDAnalysis/analysis/rdf.py'
adding 'MDAnalysis/analysis/rms.py'
adding 'MDAnalysis/analysis/waterdynamics.py'
adding 'MDAnalysis/analysis/data/__init__.py'
adding 'MDAnalysis/analysis/data/filenames.py'
adding 'MDAnalysis/analysis/data/janin_ref_data.npy'
adding 'MDAnalysis/analysis/data/rama_ref_data.npy'
adding 'MDAnalysis/analysis/encore/__init__.py'
adding 'MDAnalysis/analysis/encore/bootstrap.py'
adding 'MDAnalysis/analysis/encore/confdistmatrix.py'
adding 'MDAnalysis/analysis/encore/covariance.py'
adding 'MDAnalysis/analysis/encore/cutils.c'
adding 'MDAnalysis/analysis/encore/cutils.cpython-313-aarch64-linux-gnu.so'
adding 'MDAnalysis/analysis/encore/cutils.pyx'
adding 'MDAnalysis/analysis/encore/similarity.py'
adding 'MDAnalysis/analysis/encore/utils.py'
adding 'MDAnalysis/analysis/encore/clustering/ClusterCollection.py'
adding 'MDAnalysis/analysis/encore/clustering/ClusteringMethod.py'
adding 'MDAnalysis/analysis/encore/clustering/__init__.py'
adding 'MDAnalysis/analysis/encore/clustering/affinityprop.c'
adding 'MDAnalysis/analysis/encore/clustering/affinityprop.cpython-313-aarch64-linux-gnu.so'
adding 'MDAnalysis/analysis/encore/clustering/affinityprop.pyx'
adding 'MDAnalysis/analysis/encore/clustering/cluster.py'
adding 'MDAnalysis/analysis/encore/clustering/include/ap.h'
adding 'MDAnalysis/analysis/encore/clustering/src/ap.c'
adding 'MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py'
adding 'MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py'
adding 'MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py'
adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c'
adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-313-aarch64-linux-gnu.so'
adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx'
adding 'MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h'
adding 'MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c'
adding 'MDAnalysis/analysis/hbonds/__init__.py'
adding 'MDAnalysis/analysis/hbonds/hbond_autocorrel.py'
adding 'MDAnalysis/analysis/hole2/__init__.py'
adding 'MDAnalysis/analysis/hole2/hole.py'
adding 'MDAnalysis/analysis/hole2/templates.py'
adding 'MDAnalysis/analysis/hole2/utils.py'
adding 'MDAnalysis/analysis/hydrogenbonds/__init__.py'
adding 'MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py'
adding 'MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py'
adding 'MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py'
adding 'MDAnalysis/analysis/legacy/__init__.py'
adding 'MDAnalysis/analysis/legacy/x3dna.py'
adding 'MDAnalysis/auxiliary/EDR.py'
adding 'MDAnalysis/auxiliary/XVG.py'
adding 'MDAnalysis/auxiliary/__init__.py'
adding 'MDAnalysis/auxiliary/base.py'
adding 'MDAnalysis/auxiliary/core.py'
adding 'MDAnalysis/converters/OpenMM.py'
adding 'MDAnalysis/converters/OpenMMParser.py'
adding 'MDAnalysis/converters/ParmEd.py'
adding 'MDAnalysis/converters/ParmEdParser.py'
adding 'MDAnalysis/converters/RDKit.py'
adding 'MDAnalysis/converters/RDKitParser.py'
adding 'MDAnalysis/converters/__init__.py'
adding 'MDAnalysis/converters/base.py'
adding 'MDAnalysis/coordinates/CRD.py'
adding 'MDAnalysis/coordinates/DCD.py'
adding 'MDAnalysis/coordinates/DLPoly.py'
adding 'MDAnalysis/coordinates/DMS.py'
adding 'MDAnalysis/coordinates/FHIAIMS.py'
adding 'MDAnalysis/coordinates/GMS.py'
adding 'MDAnalysis/coordinates/GRO.py'
adding 'MDAnalysis/coordinates/GSD.py'
adding 'MDAnalysis/coordinates/H5MD.py'
adding 'MDAnalysis/coordinates/INPCRD.py'
adding 'MDAnalysis/coordinates/LAMMPS.py'
adding 'MDAnalysis/coordinates/MMTF.py'
adding 'MDAnalysis/coordinates/MOL2.py'
adding 'MDAnalysis/coordinates/NAMDBIN.py'
adding 'MDAnalysis/coordinates/PDB.py'
adding 'MDAnalysis/coordinates/PDBQT.py'
adding 'MDAnalysis/coordinates/PQR.py'
adding 'MDAnalysis/coordinates/ParmEd.py'
adding 'MDAnalysis/coordinates/TNG.py'
adding 'MDAnalysis/coordinates/TRC.py'
adding 'MDAnalysis/coordinates/TRJ.py'
adding 'MDAnalysis/coordinates/TRR.py'
adding 'MDAnalysis/coordinates/TRZ.py'
adding 'MDAnalysis/coordinates/TXYZ.py'
adding 'MDAnalysis/coordinates/XDR.py'
adding 'MDAnalysis/coordinates/XTC.py'
adding 'MDAnalysis/coordinates/XYZ.py'
adding 'MDAnalysis/coordinates/__init__.py'
adding 'MDAnalysis/coordinates/base.py'
adding 'MDAnalysis/coordinates/chain.py'
adding 'MDAnalysis/coordinates/chemfiles.py'
adding 'MDAnalysis/coordinates/core.py'
adding 'MDAnalysis/coordinates/memory.py'
adding 'MDAnalysis/coordinates/null.py'
adding 'MDAnalysis/coordinates/timestep.cpp'
adding 'MDAnalysis/coordinates/timestep.cpython-313-aarch64-linux-gnu.so'
adding 'MDAnalysis/coordinates/timestep.pxd'
adding 'MDAnalysis/coordinates/timestep.pyx'
adding 'MDAnalysis/core/__init__.py'
adding 'MDAnalysis/core/_get_readers.py'
adding 'MDAnalysis/core/accessors.py'
adding 'MDAnalysis/core/groups.py'
adding 'MDAnalysis/core/selection.py'
adding 'MDAnalysis/core/topology.py'
adding 'MDAnalysis/core/topologyattrs.py'
adding 'MDAnalysis/core/topologyobjects.py'
adding 'MDAnalysis/core/universe.py'
adding 'MDAnalysis/lib/NeighborSearch.py'
adding 'MDAnalysis/lib/__init__.py'
adding 'MDAnalysis/lib/_augment.cpp'
adding 'MDAnalysis/lib/_augment.cpython-313-aarch64-linux-gnu.so'
adding 'MDAnalysis/lib/_augment.pyx'
adding 'MDAnalysis/lib/_cutil.cpp'
adding 'MDAnalysis/lib/_cutil.cpython-313-aarch64-linux-gnu.so'
adding 'MDAnalysis/lib/_cutil.pxd'
adding 'MDAnalysis/lib/_cutil.pyx'
adding 'MDAnalysis/lib/_distopia.py'
adding 'MDAnalysis/lib/_transformations.cpython-313-aarch64-linux-gnu.so'
adding 'MDAnalysis/lib/c_distances.c'
adding 'MDAnalysis/lib/c_distances.cpython-313-aarch64-linux-gnu.so'
adding 'MDAnalysis/lib/c_distances.pxd'
adding 'MDAnalysis/lib/c_distances.pyx'
adding 'MDAnalysis/lib/c_distances_openmp.c'
adding 'MDAnalysis/lib/c_distances_openmp.cpython-313-aarch64-linux-gnu.so'
adding 'MDAnalysis/lib/c_distances_openmp.pyx'
adding 'MDAnalysis/lib/correlations.py'
adding 'MDAnalysis/lib/distances.py'
adding 'MDAnalysis/lib/log.py'
adding 'MDAnalysis/lib/mdamath.py'
adding 'MDAnalysis/lib/nsgrid.cpp'
adding 'MDAnalysis/lib/nsgrid.cpython-313-aarch64-linux-gnu.so'
adding 'MDAnalysis/lib/nsgrid.pyx'
adding 'MDAnalysis/lib/picklable_file_io.py'
adding 'MDAnalysis/lib/pkdtree.py'
adding 'MDAnalysis/lib/qcprot.c'
adding 'MDAnalysis/lib/qcprot.cpython-313-aarch64-linux-gnu.so'
adding 'MDAnalysis/lib/qcprot.pyx'
adding 'MDAnalysis/lib/transformations.py'
adding 'MDAnalysis/lib/util.py'
adding 'MDAnalysis/lib/formats/__init__.py'
adding 'MDAnalysis/lib/formats/cython_util.c'
adding 'MDAnalysis/lib/formats/cython_util.cpython-313-aarch64-linux-gnu.so'
adding 'MDAnalysis/lib/formats/cython_util.pxd'
adding 'MDAnalysis/lib/formats/cython_util.pyx'
adding 'MDAnalysis/lib/formats/libdcd.c'
adding 'MDAnalysis/lib/formats/libdcd.cpython-313-aarch64-linux-gnu.so'
adding 'MDAnalysis/lib/formats/libdcd.pxd'
adding 'MDAnalysis/lib/formats/libdcd.pyx'
adding 'MDAnalysis/lib/formats/libmdaxdr.c'
adding 'MDAnalysis/lib/formats/libmdaxdr.cpython-313-aarch64-linux-gnu.so'
adding 'MDAnalysis/lib/formats/libmdaxdr.pxd'
adding 'MDAnalysis/lib/formats/libmdaxdr.pyx'
adding 'MDAnalysis/lib/formats/include/endianswap.h'
adding 'MDAnalysis/lib/formats/include/fastio.h'
adding 'MDAnalysis/lib/formats/include/readdcd.h'
adding 'MDAnalysis/lib/formats/include/trr_seek.h'
adding 'MDAnalysis/lib/formats/include/xdrfile.h'
adding 'MDAnalysis/lib/formats/include/xdrfile_trr.h'
adding 'MDAnalysis/lib/formats/include/xdrfile_xtc.h'
adding 'MDAnalysis/lib/formats/include/xtc_seek.h'
adding 'MDAnalysis/lib/formats/src/trr_seek.c'
adding 'MDAnalysis/lib/formats/src/xdrfile.c'
adding 'MDAnalysis/lib/formats/src/xdrfile_trr.c'
adding 'MDAnalysis/lib/formats/src/xdrfile_xtc.c'
adding 'MDAnalysis/lib/formats/src/xtc_seek.c'
adding 'MDAnalysis/lib/include/calc_distances.h'
adding 'MDAnalysis/lib/libmdanalysis/__init__.pxd'
adding 'MDAnalysis/lib/src/transformations/AUTHOR'
adding 'MDAnalysis/lib/src/transformations/LICENCE'
adding 'MDAnalysis/lib/src/transformations/transformations.c'
adding 'MDAnalysis/selections/__init__.py'
adding 'MDAnalysis/selections/base.py'
adding 'MDAnalysis/selections/charmm.py'
adding 'MDAnalysis/selections/gromacs.py'
adding 'MDAnalysis/selections/jmol.py'
adding 'MDAnalysis/selections/pymol.py'
adding 'MDAnalysis/selections/vmd.py'
adding 'MDAnalysis/tests/__init__.py'
adding 'MDAnalysis/tests/datafiles.py'
adding 'MDAnalysis/topology/CRDParser.py'
adding 'MDAnalysis/topology/DLPolyParser.py'
adding 'MDAnalysis/topology/DMSParser.py'
adding 'MDAnalysis/topology/ExtendedPDBParser.py'
adding 'MDAnalysis/topology/FHIAIMSParser.py'
adding 'MDAnalysis/topology/GMSParser.py'
adding 'MDAnalysis/topology/GROParser.py'
adding 'MDAnalysis/topology/GSDParser.py'
adding 'MDAnalysis/topology/HoomdXMLParser.py'
adding 'MDAnalysis/topology/ITPParser.py'
adding 'MDAnalysis/topology/LAMMPSParser.py'
adding 'MDAnalysis/topology/MMTFParser.py'
adding 'MDAnalysis/topology/MOL2Parser.py'
adding 'MDAnalysis/topology/MinimalParser.py'
adding 'MDAnalysis/topology/PDBParser.py'
adding 'MDAnalysis/topology/PDBQTParser.py'
adding 'MDAnalysis/topology/PQRParser.py'
adding 'MDAnalysis/topology/PSFParser.py'
adding 'MDAnalysis/topology/ParmEdParser.py'
adding 'MDAnalysis/topology/TOPParser.py'
adding 'MDAnalysis/topology/TPRParser.py'
adding 'MDAnalysis/topology/TXYZParser.py'
adding 'MDAnalysis/topology/XYZParser.py'
adding 'MDAnalysis/topology/__init__.py'
adding 'MDAnalysis/topology/base.py'
adding 'MDAnalysis/topology/core.py'
adding 'MDAnalysis/topology/guessers.py'
adding 'MDAnalysis/topology/tables.py'
adding 'MDAnalysis/topology/tpr/__init__.py'
adding 'MDAnalysis/topology/tpr/obj.py'
adding 'MDAnalysis/topology/tpr/setting.py'
adding 'MDAnalysis/topology/tpr/utils.py'
adding 'MDAnalysis/transformations/__init__.py'
adding 'MDAnalysis/transformations/base.py'
adding 'MDAnalysis/transformations/boxdimensions.py'
adding 'MDAnalysis/transformations/fit.py'
adding 'MDAnalysis/transformations/nojump.py'
adding 'MDAnalysis/transformations/positionaveraging.py'
adding 'MDAnalysis/transformations/rotate.py'
adding 'MDAnalysis/transformations/translate.py'
adding 'MDAnalysis/transformations/wrap.py'
adding 'MDAnalysis/visualization/__init__.py'
adding 'MDAnalysis/visualization/streamlines.py'
adding 'MDAnalysis/visualization/streamlines_3D.py'
adding 'MDAnalysis-2.7.0.dist-info/AUTHORS'
adding 'MDAnalysis-2.7.0.dist-info/LICENSE'
adding 'MDAnalysis-2.7.0.dist-info/METADATA'
adding 'MDAnalysis-2.7.0.dist-info/WHEEL'
adding 'MDAnalysis-2.7.0.dist-info/top_level.txt'
adding 'MDAnalysis-2.7.0.dist-info/RECORD'
removing build/bdist.linux-aarch64/wheel
Successfully built MDAnalysis-2.7.0-cp313-cp313-linux_aarch64.whl
I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.13 with "installer" module
I: pybuild plugin_pyproject:129: Building wheel for python3.12 with "build" module
I: pybuild base:311: python3.12 -m build --skip-dependency-check --no-isolation --wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis
* Building wheel...
Attempting to autodetect OpenMP support... Compiler supports OpenMP
Will attempt to use Cython.
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite'
warnings.warn(msg)
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require'
warnings.warn(msg)
/usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:78: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies)
corresp(dist, value, root_dir)
running bdist_wheel
running build
running build_py
creating build/lib.linux-aarch64-cpython-312/MDAnalysis
copying MDAnalysis/version.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis
copying MDAnalysis/due.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis
copying MDAnalysis/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis
copying MDAnalysis/exceptions.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis
copying MDAnalysis/units.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis
copying MDAnalysis/authors.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/ITPParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/tables.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/guessers.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/GROParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/core.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/ParmEdParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/base.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
copying MDAnalysis/lib/transformations.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
copying MDAnalysis/lib/picklable_file_io.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
copying MDAnalysis/lib/mdamath.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
copying MDAnalysis/lib/_distopia.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
copying MDAnalysis/lib/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
copying MDAnalysis/lib/distances.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
copying MDAnalysis/lib/correlations.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
copying MDAnalysis/lib/log.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
copying MDAnalysis/lib/util.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/auxiliary
copying MDAnalysis/auxiliary/EDR.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/auxiliary
copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/auxiliary
copying MDAnalysis/auxiliary/core.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/auxiliary
copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/auxiliary
copying MDAnalysis/auxiliary/base.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/auxiliary
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/core
copying MDAnalysis/core/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/core
copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/core
copying MDAnalysis/core/selection.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/core
copying MDAnalysis/core/groups.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/core
copying MDAnalysis/core/_get_readers.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/core
copying MDAnalysis/core/topology.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/core
copying MDAnalysis/core/accessors.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/core
copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/core
copying MDAnalysis/core/universe.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/core
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/tests
copying MDAnalysis/tests/datafiles.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/tests
copying MDAnalysis/tests/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/tests
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis
copying MDAnalysis/analysis/polymer.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis
copying MDAnalysis/analysis/atomicdistances.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis
copying MDAnalysis/analysis/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis
copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis
copying MDAnalysis/analysis/distances.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis
copying MDAnalysis/analysis/dielectric.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis
copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis
copying MDAnalysis/analysis/align.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis
copying MDAnalysis/analysis/rdf.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis
copying MDAnalysis/analysis/gnm.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis
copying MDAnalysis/analysis/rms.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis
copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis
copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis
copying MDAnalysis/analysis/contacts.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis
copying MDAnalysis/analysis/density.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis
copying MDAnalysis/analysis/msd.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis
copying MDAnalysis/analysis/helix_analysis.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis
copying MDAnalysis/analysis/pca.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis
copying MDAnalysis/analysis/bat.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis
copying MDAnalysis/analysis/base.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis
copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis
copying MDAnalysis/analysis/psa.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis
copying MDAnalysis/analysis/nucleicacids.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis
copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/selections
copying MDAnalysis/selections/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/selections
copying MDAnalysis/selections/charmm.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/selections
copying MDAnalysis/selections/vmd.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/selections
copying MDAnalysis/selections/pymol.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/selections
copying MDAnalysis/selections/gromacs.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/selections
copying MDAnalysis/selections/base.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/selections
copying MDAnalysis/selections/jmol.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/selections
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations
copying MDAnalysis/transformations/wrap.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations
copying MDAnalysis/transformations/translate.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations
copying MDAnalysis/transformations/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations
copying MDAnalysis/transformations/positionaveraging.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations
copying MDAnalysis/transformations/rotate.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations
copying MDAnalysis/transformations/boxdimensions.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations
copying MDAnalysis/transformations/nojump.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations
copying MDAnalysis/transformations/base.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations
copying MDAnalysis/transformations/fit.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/visualization
copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/visualization
copying MDAnalysis/visualization/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/visualization
copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/visualization
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/converters
copying MDAnalysis/converters/OpenMMParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/converters
copying MDAnalysis/converters/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/converters
copying MDAnalysis/converters/OpenMM.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/converters
copying MDAnalysis/converters/RDKit.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/converters
copying MDAnalysis/converters/RDKitParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/converters
copying MDAnalysis/converters/ParmEdParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/converters
copying MDAnalysis/converters/base.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/converters
copying MDAnalysis/converters/ParmEd.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/converters
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TNG.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRC.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/H5MD.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/chain.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/core.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/chemfiles.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/base.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/ParmEd.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/null.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/memory.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/tpr
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats
copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/legacy
copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/legacy
copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/legacy
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/covariance.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/similarity.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hydrogenbonds
copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hydrogenbonds
copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hydrogenbonds
copying MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hydrogenbonds
copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hydrogenbonds
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/data
copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/data
copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/data
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hole2
copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hole2
copying MDAnalysis/analysis/hole2/templates.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hole2
copying MDAnalysis/analysis/hole2/utils.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hole2
copying MDAnalysis/analysis/hole2/hole.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hole2
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hbonds
copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hbonds
copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hbonds
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction
copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction
copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction
copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering
copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering
copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering
copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering
copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering
running egg_info
writing MDAnalysis.egg-info/PKG-INFO
writing dependency_links to MDAnalysis.egg-info/dependency_links.txt
writing requirements to MDAnalysis.egg-info/requires.txt
writing top-level names to MDAnalysis.egg-info/top_level.txt
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dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
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dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
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dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /<<PKGBUILDDIR>>/package/MDAnalysis/analysis/encore/clustering/include/ap.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
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dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /<<PKGBUILDDIR>>/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /<<PKGBUILDDIR>>/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
reading manifest file 'MDAnalysis.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching 'doc/html/html' found anywhere in distribution
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '*.pyd' found anywhere in distribution
warning: no previously-included files matching '*~' found anywhere in distribution
warning: no previously-included files matching '.git' found anywhere in distribution
adding license file 'LICENSE'
adding license file 'AUTHORS'
writing manifest file 'MDAnalysis.egg-info/SOURCES.txt'
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'MDAnalysis.analysis.encore.clustering.include' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'MDAnalysis.analysis.encore.clustering.include' 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 'MDAnalysis.analysis.encore.clustering.include' 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 'MDAnalysis.analysis.encore.clustering.include' to be distributed and are
already explicitly excluding 'MDAnalysis.analysis.encore.clustering.include' 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)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'MDAnalysis.analysis.encore.clustering.src' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'MDAnalysis.analysis.encore.clustering.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 'MDAnalysis.analysis.encore.clustering.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 'MDAnalysis.analysis.encore.clustering.src' to be distributed and are
already explicitly excluding 'MDAnalysis.analysis.encore.clustering.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)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'MDAnalysis.analysis.encore.dimensionality_reduction.include' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'MDAnalysis.analysis.encore.dimensionality_reduction.include' 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 'MDAnalysis.analysis.encore.dimensionality_reduction.include' 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 'MDAnalysis.analysis.encore.dimensionality_reduction.include' to be distributed and are
already explicitly excluding 'MDAnalysis.analysis.encore.dimensionality_reduction.include' 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)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'MDAnalysis.analysis.encore.dimensionality_reduction.src' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'MDAnalysis.analysis.encore.dimensionality_reduction.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 'MDAnalysis.analysis.encore.dimensionality_reduction.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 'MDAnalysis.analysis.encore.dimensionality_reduction.src' to be distributed and are
already explicitly excluding 'MDAnalysis.analysis.encore.dimensionality_reduction.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)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'MDAnalysis.lib.formats.include' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'MDAnalysis.lib.formats.include' 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 'MDAnalysis.lib.formats.include' 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 'MDAnalysis.lib.formats.include' to be distributed and are
already explicitly excluding 'MDAnalysis.lib.formats.include' 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)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'MDAnalysis.lib.formats.src' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'MDAnalysis.lib.formats.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 'MDAnalysis.lib.formats.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 'MDAnalysis.lib.formats.src' to be distributed and are
already explicitly excluding 'MDAnalysis.lib.formats.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)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'MDAnalysis.lib.include' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'MDAnalysis.lib.include' 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 'MDAnalysis.lib.include' 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 'MDAnalysis.lib.include' to be distributed and are
already explicitly excluding 'MDAnalysis.lib.include' 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)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'MDAnalysis.lib.libmdanalysis' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'MDAnalysis.lib.libmdanalysis' 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 'MDAnalysis.lib.libmdanalysis' 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 'MDAnalysis.lib.libmdanalysis' to be distributed and are
already explicitly excluding 'MDAnalysis.lib.libmdanalysis' 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)
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'MDAnalysis.lib.src.transformations' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'MDAnalysis.lib.src.transformations' 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 'MDAnalysis.lib.src.transformations' 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 'MDAnalysis.lib.src.transformations' to be distributed and are
already explicitly excluding 'MDAnalysis.lib.src.transformations' 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 MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/data
copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/data
copying MDAnalysis/lib/_augment.cpp -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
copying MDAnalysis/lib/_augment.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
copying MDAnalysis/lib/_cutil.cpp -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
copying MDAnalysis/lib/_cutil.pxd -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
copying MDAnalysis/lib/_cutil.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
copying MDAnalysis/lib/c_distances.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
copying MDAnalysis/lib/c_distances.pxd -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
copying MDAnalysis/lib/c_distances.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
copying MDAnalysis/lib/c_distances_openmp.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
copying MDAnalysis/lib/c_distances_openmp.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
copying MDAnalysis/lib/nsgrid.cpp -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
copying MDAnalysis/lib/nsgrid.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
copying MDAnalysis/lib/qcprot.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
copying MDAnalysis/lib/qcprot.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/include
copying MDAnalysis/lib/include/calc_distances.h -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/include
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/libmdanalysis
copying MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/libmdanalysis
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/src/transformations
copying MDAnalysis/lib/src/transformations/AUTHOR -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/src/transformations
copying MDAnalysis/lib/src/transformations/LICENCE -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/src/transformations
copying MDAnalysis/lib/src/transformations/transformations.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/src/transformations
copying MDAnalysis/coordinates/timestep.cpp -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/timestep.pxd -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/coordinates/timestep.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates
copying MDAnalysis/lib/formats/cython_util.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats
copying MDAnalysis/lib/formats/cython_util.pxd -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats
copying MDAnalysis/lib/formats/cython_util.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats
copying MDAnalysis/lib/formats/libdcd.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats
copying MDAnalysis/lib/formats/libdcd.pxd -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats
copying MDAnalysis/lib/formats/libdcd.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats
copying MDAnalysis/lib/formats/libmdaxdr.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats
copying MDAnalysis/lib/formats/libmdaxdr.pxd -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats
copying MDAnalysis/lib/formats/libmdaxdr.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include
copying MDAnalysis/lib/formats/include/endianswap.h -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include
copying MDAnalysis/lib/formats/include/fastio.h -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include
copying MDAnalysis/lib/formats/include/readdcd.h -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include
copying MDAnalysis/lib/formats/include/trr_seek.h -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include
copying MDAnalysis/lib/formats/include/xdrfile.h -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include
copying MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include
copying MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include
copying MDAnalysis/lib/formats/include/xtc_seek.h -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src
copying MDAnalysis/lib/formats/src/trr_seek.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src
copying MDAnalysis/lib/formats/src/xdrfile.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src
copying MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src
copying MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src
copying MDAnalysis/lib/formats/src/xtc_seek.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src
copying MDAnalysis/analysis/encore/cutils.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/cutils.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore
copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction
copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/include
copying MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/include
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/src
copying MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/src
copying MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering
copying MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/include
copying MDAnalysis/analysis/encore/clustering/include/ap.h -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/include
creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/src
copying MDAnalysis/analysis/encore/clustering/src/ap.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/src
running build_ext
building 'MDAnalysis.lib.formats.libdcd' extension
creating build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/formats
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include -I/usr/include/python3.12 -c MDAnalysis/lib/formats/libdcd.c -o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libdcd.o -std=c99 -O3 -funroll-loops -fsigned-zeros
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/lib/formats/libdcd.c:1261:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
In file included from MDAnalysis/lib/formats/libdcd.c:1268:
MDAnalysis/lib/formats/include/readdcd.h: In function ‘read_dcdstep’:
MDAnalysis/lib/formats/include/readdcd.h:549:17: warning: comparison of integer expressions of different signedness: ‘fio_size_t’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare]
549 | if (readlen != (6*sizeof(int) + 3*N*sizeof(float)))
| ^~
MDAnalysis/lib/formats/include/readdcd.h:562:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
562 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT;
| ^~
MDAnalysis/lib/formats/include/readdcd.h: In function ‘write_dcdheader’:
MDAnalysis/lib/formats/include/readdcd.h:698:14: warning: unused variable ‘tmbuf’ [-Wunused-variable]
698 | struct tm *tmbuf;
| ^~~~~
MDAnalysis/lib/formats/include/readdcd.h:697:10: warning: unused variable ‘cur_time’ [-Wunused-variable]
697 | time_t cur_time;
| ^~~~~~~~
In file included from MDAnalysis/lib/formats/include/readdcd.h:25:
MDAnalysis/lib/formats/include/endianswap.h: At top level:
MDAnalysis/lib/formats/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function]
96 | static void swap2_aligned(void *v, long ndata) {
| ^~~~~~~~~~~~~
MDAnalysis/lib/formats/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function]
32 | static void swap2_unaligned(void *v, long ndata) {
| ^~~~~~~~~~~~~~~
In file included from MDAnalysis/lib/formats/libdcd.c:1267:
MDAnalysis/lib/formats/include/fastio.h:453:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function]
453 | static int fio_write_str(fio_fd fd, const char *str) {
| ^~~~~~~~~~~~~
MDAnalysis/lib/formats/include/fastio.h:449:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function]
449 | static int fio_read_int32(fio_fd fd, int *i) {
| ^~~~~~~~~~~~~~
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libdcd.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libdcd.cpython-312-aarch64-linux-gnu.so
building 'MDAnalysis.lib.c_distances' extension
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/include -I/usr/include/python3.12 -c MDAnalysis/lib/c_distances.c -o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances.o -std=c99 -O3 -funroll-loops -fsigned-zeros
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/lib/c_distances.c:1263:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances.o -L/usr/lib/aarch64-linux-gnu -lm -o build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances.cpython-312-aarch64-linux-gnu.so
building 'MDAnalysis.lib.c_distances_openmp' extension
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPARALLEL -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/include -I/usr/include/python3.12 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c99 -O3 -funroll-loops -fsigned-zeros
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/lib/c_distances_openmp.c:1272:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances_openmp.o -L/usr/lib/aarch64-linux-gnu -lm -lgomp -o build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances_openmp.cpython-312-aarch64-linux-gnu.so -fopenmp
building 'MDAnalysis.lib.qcprot' extension
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c MDAnalysis/lib/qcprot.c -o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/qcprot.o -std=c99 -O3 -funroll-loops -fsigned-zeros
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/lib/qcprot.c:1255:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
MDAnalysis/lib/qcprot.c: In function ‘__pyx_fuse_0__pyx_f_10MDAnalysis_3lib_6qcprot_InnerProduct’:
MDAnalysis/lib/qcprot.c:21123:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
21123 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
| ^
MDAnalysis/lib/qcprot.c:21331:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
21331 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
| ^
MDAnalysis/lib/qcprot.c: In function ‘__pyx_fuse_1__pyx_f_10MDAnalysis_3lib_6qcprot_InnerProduct’:
MDAnalysis/lib/qcprot.c:21801:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
21801 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
| ^
MDAnalysis/lib/qcprot.c:22009:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
22009 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
| ^
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/qcprot.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/qcprot.cpython-312-aarch64-linux-gnu.so
building 'MDAnalysis.lib._transformations' extension
creating build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/src/transformations
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/src/transformations/transformations.o -std=c99 -O3 -funroll-loops -fsigned-zeros
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/lib/src/transformations/transformations.c:73:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_superimposition_matrix’:
MDAnalysis/lib/src/transformations/transformations.c:1837: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
1837 | #pragma vector always
MDAnalysis/lib/src/transformations/transformations.c:1954: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
1954 | #pragma vector always
MDAnalysis/lib/src/transformations/transformations.c:1978: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
1978 | #pragma vector always
MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_vector_norm’:
MDAnalysis/lib/src/transformations/transformations.c:3414: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
3414 | #pragma vector always
MDAnalysis/lib/src/transformations/transformations.c:3495: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
3495 | #pragma vector always
MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_unit_vector’:
MDAnalysis/lib/src/transformations/transformations.c:3597: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
3597 | #pragma vector always
MDAnalysis/lib/src/transformations/transformations.c:3602: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
3602 | #pragma vector always
MDAnalysis/lib/src/transformations/transformations.c:3666: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
3666 | #pragma vector always
MDAnalysis/lib/src/transformations/transformations.c:3671: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
3671 | #pragma vector always
MDAnalysis/lib/src/transformations/transformations.c: At top level:
MDAnalysis/lib/src/transformations/transformations.c:910:1: warning: ‘PyConverter_DoubleVector4Copy’ defined but not used [-Wunused-function]
910 | PyConverter_DoubleVector4Copy(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MDAnalysis/lib/src/transformations/transformations.c:804:1: warning: ‘PyConverter_DoubleArrayOrNone’ defined but not used [-Wunused-function]
804 | PyConverter_DoubleArrayOrNone(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MDAnalysis/lib/src/transformations/transformations.c:774:1: warning: ‘PyConverter_DoubleArray’ defined but not used [-Wunused-function]
774 | PyConverter_DoubleArray(
| ^~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/src/transformations/transformations.o -L/usr/lib/aarch64-linux-gnu -lm -o build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/_transformations.cpython-312-aarch64-linux-gnu.so
building 'MDAnalysis.lib.formats.libmdaxdr' extension
creating build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/include/python3.12 -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libmdaxdr.o -std=c99 -O3 -funroll-loops -fsigned-zeros
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/lib/formats/libmdaxdr.c:1282:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
In file included from MDAnalysis/lib/formats/libmdaxdr.c:1288:
MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
In file included from MDAnalysis/lib/formats/libmdaxdr.c:1289:
MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
In file included from MDAnalysis/lib/formats/include/xdrfile_xtc.h:43:
MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
In file included from MDAnalysis/lib/formats/libmdaxdr.c:1290:
MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/include/python3.12 -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src/trr_seek.o -std=c99 -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/formats/src/trr_seek.c:30:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
In file included from MDAnalysis/lib/formats/src/trr_seek.c:31:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
In file included from /<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile_trr.h:42:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
MDAnalysis/lib/formats/src/trr_seek.c: In function ‘read_trr_n_frames’:
MDAnalysis/lib/formats/src/trr_seek.c:39:27: warning: unused variable ‘totalframebytes’ [-Wunused-variable]
39 | int result, framebytes, totalframebytes;
| ^~~~~~~~~~~~~~~
MDAnalysis/lib/formats/src/trr_seek.c:38:15: warning: unused variable ‘lambda’ [-Wunused-variable]
38 | float time, lambda;
| ^~~~~~
MDAnalysis/lib/formats/src/trr_seek.c:38:9: warning: unused variable ‘time’ [-Wunused-variable]
38 | float time, lambda;
| ^~~~
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/include/python3.12 -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src/xdrfile.o -std=c99 -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/formats/src/xdrfile.c:62:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
MDAnalysis/lib/formats/src/xdrfile.c: In function ‘sizeofint’:
MDAnalysis/lib/formats/src/xdrfile.c:501:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
501 | while (size >= num && num_of_bits < 32)
| ^~
MDAnalysis/lib/formats/src/xdrfile.c: In function ‘sizeofints’:
MDAnalysis/lib/formats/src/xdrfile.c:547:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
547 | while (bytes[num_of_bytes] >= num)
| ^~
MDAnalysis/lib/formats/src/xdrfile.c: In function ‘encodeints’:
MDAnalysis/lib/formats/src/xdrfile.c:656:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
656 | if (num_of_bits >= num_of_bytes * 8)
| ^~
MDAnalysis/lib/formats/src/xdrfile.c:658:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
658 | for (i = 0; i < num_of_bytes; i++)
| ^
MDAnalysis/lib/formats/src/xdrfile.c:666:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
666 | for (i = 0; i < num_of_bytes-1; i++)
| ^
MDAnalysis/lib/formats/src/xdrfile.c: In function ‘decodebits’:
MDAnalysis/lib/formats/src/xdrfile.c:706:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
706 | if (lastbits < num_of_bits)
| ^
MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’:
MDAnalysis/lib/formats/src/xdrfile.c:816:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
816 | if(size3>xfp->buf1size)
| ^
MDAnalysis/lib/formats/src/xdrfile.c:868:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
868 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
| ^
MDAnalysis/lib/formats/src/xdrfile.c:868:44: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare]
868 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
| ^~~
MDAnalysis/lib/formats/src/xdrfile.c:794:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
794 | int smallnum, smaller, larger, i, is_smaller, run;
| ^~~~~~
MDAnalysis/lib/formats/src/xdrfile.c:791:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
791 | int smallidx, minidx, maxidx;
| ^~~~~~
MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’:
MDAnalysis/lib/formats/src/xdrfile.c:1012:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
1012 | if(size3>xfp->buf1size)
| ^
MDAnalysis/lib/formats/src/xdrfile.c:1135:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
1135 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff)
| ^
MDAnalysis/lib/formats/src/xdrfile.c:1141:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
1141 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
| ^
MDAnalysis/lib/formats/src/xdrfile.c:1141:44: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare]
1141 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
| ^~~
MDAnalysis/lib/formats/src/xdrfile.c:1273:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
1273 | if(tmp==(unsigned int)buf2[0])
| ^~
MDAnalysis/lib/formats/src/xdrfile.c:1001:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
1001 | int errval=1;
| ^~~~~~
MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’:
MDAnalysis/lib/formats/src/xdrfile.c:1313:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
1313 | if(size3>xfp->buf1size)
| ^
MDAnalysis/lib/formats/src/xdrfile.c:1368:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
1368 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
| ^
MDAnalysis/lib/formats/src/xdrfile.c:1368:44: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare]
1368 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
| ^~~
MDAnalysis/lib/formats/src/xdrfile.c:1290:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
1290 | int smallnum, smaller, larger, i, is_smaller, run;
| ^~~~~~
MDAnalysis/lib/formats/src/xdrfile.c:1287:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
1287 | int smallidx, minidx, maxidx;
| ^~~~~~
MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’:
MDAnalysis/lib/formats/src/xdrfile.c:1504:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
1504 | if(size3>xfp->buf1size) {
| ^
MDAnalysis/lib/formats/src/xdrfile.c:1619:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
1619 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) {
| ^
MDAnalysis/lib/formats/src/xdrfile.c:1624:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
1624 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
| ^
MDAnalysis/lib/formats/src/xdrfile.c:1624:44: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare]
1624 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
| ^~~
MDAnalysis/lib/formats/src/xdrfile.c:1734:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
1734 | if(tmp==(unsigned int)buf2[0])
| ^~
MDAnalysis/lib/formats/src/xdrfile.c:1494:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
1494 | int errval=1;
| ^~~~~~
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/include/python3.12 -c MDAnalysis/lib/formats/src/xdrfile_trr.c -o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src/xdrfile_trr.o -std=c99 -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:38:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:39:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
In file included from /<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile_trr.h:42:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
MDAnalysis/lib/formats/src/xdrfile_trr.c: In function ‘do_trnheader’:
MDAnalysis/lib/formats/src/xdrfile_trr.c:78:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
78 | if (slen != strlen(version) + 1)
| ^~
MDAnalysis/lib/formats/src/xdrfile_trr.c:86:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
86 | if (xdrfile_write_string(version, xd) != (strlen(version) + 1))
| ^~
MDAnalysis/lib/formats/src/xdrfile_trr.c: In function ‘write_trr’:
MDAnalysis/lib/formats/src/xdrfile_trr.c:408:10: warning: ‘plcholder’ is used uninitialized [-Wuninitialized]
408 | return do_trn(xd, 0, &step, &t, &lambda, box, &natoms, x, v, f, plcholder);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MDAnalysis/lib/formats/src/xdrfile_trr.c:407:8: note: ‘plcholder’ was declared here
407 | int *plcholder;
| ^~~~~~~~~
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/include/python3.12 -c MDAnalysis/lib/formats/src/xdrfile_xtc.c -o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src/xdrfile_xtc.o -std=c99 -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:30:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:31:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
In file included from /<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile_xtc.h:43:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats -I/usr/include/python3.12 -c MDAnalysis/lib/formats/src/xtc_seek.c -o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src/xtc_seek.o -std=c99 -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/formats/src/xtc_seek.c:25:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
In file included from MDAnalysis/lib/formats/src/xtc_seek.c:26:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
In file included from /<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile_xtc.h:43:
/<<PKGBUILDDIR>>/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libmdaxdr.o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src/trr_seek.o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src/xdrfile.o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src/xdrfile_trr.o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src/xdrfile_xtc.o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src/xtc_seek.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libmdaxdr.cpython-312-aarch64-linux-gnu.so
building 'MDAnalysis.lib.formats.cython_util' extension
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c MDAnalysis/lib/formats/cython_util.c -o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/formats/cython_util.o -std=c99 -O3 -funroll-loops -fsigned-zeros
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/lib/formats/cython_util.c:1272:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/formats/cython_util.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/cython_util.cpython-312-aarch64-linux-gnu.so
building 'MDAnalysis.analysis.encore.cutils' extension
creating build/temp.linux-aarch64-cpython-312/MDAnalysis/analysis/encore
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c MDAnalysis/analysis/encore/cutils.c -o build/temp.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/cutils.o -std=c99 -funroll-loops -fsigned-zeros -O1
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/analysis/encore/cutils.c:1255:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/cutils.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/cutils.cpython-312-aarch64-linux-gnu.so
building 'MDAnalysis.analysis.encore.clustering.affinityprop' extension
creating build/temp.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering
creating build/temp.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/src
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.12 -c MDAnalysis/analysis/encore/clustering/affinityprop.c -o build/temp.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/affinityprop.o -std=c99 -funroll-loops -fsigned-zeros -O1
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/analysis/encore/clustering/affinityprop.c:1261:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.12 -c MDAnalysis/analysis/encore/clustering/src/ap.c -o build/temp.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/src/ap.o -std=c99 -funroll-loops -fsigned-zeros -O1
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/affinityprop.o build/temp.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/src/ap.o -L/usr/lib/aarch64-linux-gnu -lm -o build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-312-aarch64-linux-gnu.so
building 'MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed' extension
creating build/temp.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/src
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.12 -c MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -o build/temp.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -std=c99 -funroll-loops -fsigned-zeros -O1
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.12 -c MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -o build/temp.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -std=c99 -funroll-loops -fsigned-zeros -O1
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:1261:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o build/temp.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -L/usr/lib/aarch64-linux-gnu -lm -o build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-312-aarch64-linux-gnu.so
building 'MDAnalysis.lib._cutil' extension
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/include -I/usr/include/python3.12 -c MDAnalysis/lib/_cutil.cpp -o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/_cutil.o -O3 -funroll-loops -fsigned-zeros -std=c++11
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/lib/_cutil.cpp:1273:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/_cutil.o -L/usr/lib/aarch64-linux-gnu -lm -o build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/_cutil.cpython-312-aarch64-linux-gnu.so
building 'MDAnalysis.lib._augment' extension
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c MDAnalysis/lib/_augment.cpp -o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/_augment.o -O3 -funroll-loops -fsigned-zeros -std=c++11
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/lib/_augment.cpp:1268:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/_augment.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/_augment.cpython-312-aarch64-linux-gnu.so
building 'MDAnalysis.lib.nsgrid' extension
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/package/MDAnalysis/lib/include -I/usr/include/python3.12 -c MDAnalysis/lib/nsgrid.cpp -o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/nsgrid.o -O3 -funroll-loops -fsigned-zeros -std=c++11
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/nsgrid.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/nsgrid.cpython-312-aarch64-linux-gnu.so
building 'MDAnalysis.coordinates.timestep' extension
creating build/temp.linux-aarch64-cpython-312/MDAnalysis/coordinates
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c MDAnalysis/coordinates/timestep.cpp -o build/temp.linux-aarch64-cpython-312/MDAnalysis/coordinates/timestep.o -O3 -funroll-loops -fsigned-zeros -std=c++11
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from MDAnalysis/coordinates/timestep.cpp:1269:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/MDAnalysis/coordinates/timestep.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/timestep.cpython-312-aarch64-linux-gnu.so
installing to build/bdist.linux-aarch64/wheel
running install
running install_lib
creating build/bdist.linux-aarch64/wheel
creating build/bdist.linux-aarch64/wheel/MDAnalysis
creating build/bdist.linux-aarch64/wheel/MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/FHIAIMSParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/DLPolyParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/PSFParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/MOL2Parser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/XYZParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/PQRParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/ITPParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/tables.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/DMSParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/HoomdXMLParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/GSDParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/TPRParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/CRDParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/LAMMPSParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
creating build/bdist.linux-aarch64/wheel/MDAnalysis/topology/tpr
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/tpr/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology/tpr
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/tpr/utils.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology/tpr
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/tpr/setting.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology/tpr
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/tpr/obj.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology/tpr
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/MinimalParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/PDBQTParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/guessers.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/TOPParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/GROParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/GMSParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/MMTFParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/TXYZParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/PDBParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/core.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/ParmEdParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/ExtendedPDBParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/version.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/due.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis
creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/nsgrid.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/_transformations.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/transformations.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/picklable_file_io.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/mdamath.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances_openmp.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances_openmp.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/NeighborSearch.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/_distopia.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/distances.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/include
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/include/calc_distances.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/include
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/_cutil.cpp -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/pkdtree.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/formats
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/cython_util.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libmdaxdr.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/formats/include
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include/xdrfile.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include/readdcd.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include/fastio.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include/xtc_seek.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include/endianswap.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include/trr_seek.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libmdaxdr.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/cython_util.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libmdaxdr.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/cython_util.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libdcd.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libdcd.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libdcd.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/formats/src
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src/trr_seek.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/src
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src/xtc_seek.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/src
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src/xdrfile.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/src
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/src
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/src
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/cython_util.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libmdaxdr.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libdcd.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/nsgrid.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/qcprot.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances_openmp.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/correlations.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/libmdanalysis
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/libmdanalysis
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/log.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/_cutil.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/_cutil.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/_cutil.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/qcprot.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/util.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/nsgrid.cpp -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/src
creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/src/transformations
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/src/transformations/AUTHOR -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/src/transformations
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/src/transformations/LICENCE -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/src/transformations
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/src/transformations/transformations.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/src/transformations
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/_augment.cpp -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/qcprot.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/_augment.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/_augment.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib
creating build/bdist.linux-aarch64/wheel/MDAnalysis/auxiliary
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/auxiliary/EDR.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/auxiliary
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/auxiliary/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/auxiliary
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/auxiliary/core.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/auxiliary
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/auxiliary/XVG.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/auxiliary
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/auxiliary/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/auxiliary
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis
creating build/bdist.linux-aarch64/wheel/MDAnalysis/core
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/core/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/core/topologyattrs.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/core/selection.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/core/groups.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/core/_get_readers.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/core/topology.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/core/accessors.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/core/topologyobjects.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/core/universe.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core
creating build/bdist.linux-aarch64/wheel/MDAnalysis/tests
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copying build/lib.linux-aarch64-cpython-312/MDAnalysis/tests/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/tests
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/legacy
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/legacy/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/legacy
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/legacy/x3dna.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/legacy
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/polymer.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/atomicdistances.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/lineardensity.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/distances.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/dielectric.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/nuclinfo.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/align.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/rdf.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/gnm.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/encore
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/include
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction/include
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/src
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction/src
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/cutils.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/utils.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/confdistmatrix.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/covariance.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/encore/clustering
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/cluster.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/encore/clustering/include
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/include/ap.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering/include
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/encore/clustering/src
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/src/ap.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering/src
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/similarity.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/cutils.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/bootstrap.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/cutils.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/rms.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/leaflet.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/hydrogenbonds
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hydrogenbonds
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hydrogenbonds
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hydrogenbonds
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hydrogenbonds
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/diffusionmap.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/contacts.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/density.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/msd.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/data
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/data/rama_ref_data.npy -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/data
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/data/janin_ref_data.npy -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/data
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/data/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/data
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/data/filenames.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/data
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/hole2
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hole2/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hole2
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hole2/templates.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hole2
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hole2/utils.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hole2
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hole2/hole.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hole2
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/helix_analysis.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/hbonds
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hbonds/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hbonds
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hbonds
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/pca.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/bat.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/waterdynamics.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/psa.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/nucleicacids.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/dihedrals.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/exceptions.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis
creating build/bdist.linux-aarch64/wheel/MDAnalysis/selections
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/selections/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/selections/charmm.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/selections/vmd.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/selections/pymol.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/selections/gromacs.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/selections/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/selections/jmol.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections
creating build/bdist.linux-aarch64/wheel/MDAnalysis/transformations
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copying build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations/translate.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations/positionaveraging.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations/rotate.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations/boxdimensions.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations/nojump.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations/fit.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations
creating build/bdist.linux-aarch64/wheel/MDAnalysis/visualization
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copying build/lib.linux-aarch64-cpython-312/MDAnalysis/visualization/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/visualization
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/visualization/streamlines_3D.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/visualization
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/units.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis
creating build/bdist.linux-aarch64/wheel/MDAnalysis/converters
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/converters/OpenMMParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/converters/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/converters/OpenMM.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/converters/RDKit.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/converters/RDKitParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/converters/ParmEdParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/converters/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/converters/ParmEd.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/authors.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis
creating build/bdist.linux-aarch64/wheel/MDAnalysis/coordinates
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copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/timestep.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/timestep.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/TRZ.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/XDR.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/CRD.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/PQR.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/timestep.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/XYZ.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/TRC.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/DCD.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/H5MD.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/timestep.cpp -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/chain.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/NAMDBIN.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/GRO.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/DLPoly.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/PDB.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/MMTF.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/GSD.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/FHIAIMS.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/INPCRD.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/XTC.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/TRR.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/MOL2.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/LAMMPS.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/TXYZ.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/PDBQT.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/core.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/chemfiles.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/GMS.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/TRJ.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/ParmEd.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/DMS.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/null.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/memory.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates
running install_egg_info
Copying MDAnalysis.egg-info to build/bdist.linux-aarch64/wheel/./MDAnalysis-2.7.0.egg-info
running install_scripts
creating build/bdist.linux-aarch64/wheel/MDAnalysis-2.7.0.dist-info/WHEEL
creating '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/.tmp-1get3phb/MDAnalysis-2.7.0-cp312-cp312-linux_aarch64.whl' and adding 'build/bdist.linux-aarch64/wheel' to it
adding 'MDAnalysis/__init__.py'
adding 'MDAnalysis/authors.py'
adding 'MDAnalysis/due.py'
adding 'MDAnalysis/exceptions.py'
adding 'MDAnalysis/units.py'
adding 'MDAnalysis/version.py'
adding 'MDAnalysis/analysis/__init__.py'
adding 'MDAnalysis/analysis/align.py'
adding 'MDAnalysis/analysis/atomicdistances.py'
adding 'MDAnalysis/analysis/base.py'
adding 'MDAnalysis/analysis/bat.py'
adding 'MDAnalysis/analysis/contacts.py'
adding 'MDAnalysis/analysis/density.py'
adding 'MDAnalysis/analysis/dielectric.py'
adding 'MDAnalysis/analysis/diffusionmap.py'
adding 'MDAnalysis/analysis/dihedrals.py'
adding 'MDAnalysis/analysis/distances.py'
adding 'MDAnalysis/analysis/gnm.py'
adding 'MDAnalysis/analysis/helix_analysis.py'
adding 'MDAnalysis/analysis/leaflet.py'
adding 'MDAnalysis/analysis/lineardensity.py'
adding 'MDAnalysis/analysis/msd.py'
adding 'MDAnalysis/analysis/nucleicacids.py'
adding 'MDAnalysis/analysis/nuclinfo.py'
adding 'MDAnalysis/analysis/pca.py'
adding 'MDAnalysis/analysis/polymer.py'
adding 'MDAnalysis/analysis/psa.py'
adding 'MDAnalysis/analysis/rdf.py'
adding 'MDAnalysis/analysis/rms.py'
adding 'MDAnalysis/analysis/waterdynamics.py'
adding 'MDAnalysis/analysis/data/__init__.py'
adding 'MDAnalysis/analysis/data/filenames.py'
adding 'MDAnalysis/analysis/data/janin_ref_data.npy'
adding 'MDAnalysis/analysis/data/rama_ref_data.npy'
adding 'MDAnalysis/analysis/encore/__init__.py'
adding 'MDAnalysis/analysis/encore/bootstrap.py'
adding 'MDAnalysis/analysis/encore/confdistmatrix.py'
adding 'MDAnalysis/analysis/encore/covariance.py'
adding 'MDAnalysis/analysis/encore/cutils.c'
adding 'MDAnalysis/analysis/encore/cutils.cpython-312-aarch64-linux-gnu.so'
adding 'MDAnalysis/analysis/encore/cutils.pyx'
adding 'MDAnalysis/analysis/encore/similarity.py'
adding 'MDAnalysis/analysis/encore/utils.py'
adding 'MDAnalysis/analysis/encore/clustering/ClusterCollection.py'
adding 'MDAnalysis/analysis/encore/clustering/ClusteringMethod.py'
adding 'MDAnalysis/analysis/encore/clustering/__init__.py'
adding 'MDAnalysis/analysis/encore/clustering/affinityprop.c'
adding 'MDAnalysis/analysis/encore/clustering/affinityprop.cpython-312-aarch64-linux-gnu.so'
adding 'MDAnalysis/analysis/encore/clustering/affinityprop.pyx'
adding 'MDAnalysis/analysis/encore/clustering/cluster.py'
adding 'MDAnalysis/analysis/encore/clustering/include/ap.h'
adding 'MDAnalysis/analysis/encore/clustering/src/ap.c'
adding 'MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py'
adding 'MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py'
adding 'MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py'
adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c'
adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-312-aarch64-linux-gnu.so'
adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx'
adding 'MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h'
adding 'MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c'
adding 'MDAnalysis/analysis/hbonds/__init__.py'
adding 'MDAnalysis/analysis/hbonds/hbond_autocorrel.py'
adding 'MDAnalysis/analysis/hole2/__init__.py'
adding 'MDAnalysis/analysis/hole2/hole.py'
adding 'MDAnalysis/analysis/hole2/templates.py'
adding 'MDAnalysis/analysis/hole2/utils.py'
adding 'MDAnalysis/analysis/hydrogenbonds/__init__.py'
adding 'MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py'
adding 'MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py'
adding 'MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py'
adding 'MDAnalysis/analysis/legacy/__init__.py'
adding 'MDAnalysis/analysis/legacy/x3dna.py'
adding 'MDAnalysis/auxiliary/EDR.py'
adding 'MDAnalysis/auxiliary/XVG.py'
adding 'MDAnalysis/auxiliary/__init__.py'
adding 'MDAnalysis/auxiliary/base.py'
adding 'MDAnalysis/auxiliary/core.py'
adding 'MDAnalysis/converters/OpenMM.py'
adding 'MDAnalysis/converters/OpenMMParser.py'
adding 'MDAnalysis/converters/ParmEd.py'
adding 'MDAnalysis/converters/ParmEdParser.py'
adding 'MDAnalysis/converters/RDKit.py'
adding 'MDAnalysis/converters/RDKitParser.py'
adding 'MDAnalysis/converters/__init__.py'
adding 'MDAnalysis/converters/base.py'
adding 'MDAnalysis/coordinates/CRD.py'
adding 'MDAnalysis/coordinates/DCD.py'
adding 'MDAnalysis/coordinates/DLPoly.py'
adding 'MDAnalysis/coordinates/DMS.py'
adding 'MDAnalysis/coordinates/FHIAIMS.py'
adding 'MDAnalysis/coordinates/GMS.py'
adding 'MDAnalysis/coordinates/GRO.py'
adding 'MDAnalysis/coordinates/GSD.py'
adding 'MDAnalysis/coordinates/H5MD.py'
adding 'MDAnalysis/coordinates/INPCRD.py'
adding 'MDAnalysis/coordinates/LAMMPS.py'
adding 'MDAnalysis/coordinates/MMTF.py'
adding 'MDAnalysis/coordinates/MOL2.py'
adding 'MDAnalysis/coordinates/NAMDBIN.py'
adding 'MDAnalysis/coordinates/PDB.py'
adding 'MDAnalysis/coordinates/PDBQT.py'
adding 'MDAnalysis/coordinates/PQR.py'
adding 'MDAnalysis/coordinates/ParmEd.py'
adding 'MDAnalysis/coordinates/TNG.py'
adding 'MDAnalysis/coordinates/TRC.py'
adding 'MDAnalysis/coordinates/TRJ.py'
adding 'MDAnalysis/coordinates/TRR.py'
adding 'MDAnalysis/coordinates/TRZ.py'
adding 'MDAnalysis/coordinates/TXYZ.py'
adding 'MDAnalysis/coordinates/XDR.py'
adding 'MDAnalysis/coordinates/XTC.py'
adding 'MDAnalysis/coordinates/XYZ.py'
adding 'MDAnalysis/coordinates/__init__.py'
adding 'MDAnalysis/coordinates/base.py'
adding 'MDAnalysis/coordinates/chain.py'
adding 'MDAnalysis/coordinates/chemfiles.py'
adding 'MDAnalysis/coordinates/core.py'
adding 'MDAnalysis/coordinates/memory.py'
adding 'MDAnalysis/coordinates/null.py'
adding 'MDAnalysis/coordinates/timestep.cpp'
adding 'MDAnalysis/coordinates/timestep.cpython-312-aarch64-linux-gnu.so'
adding 'MDAnalysis/coordinates/timestep.pxd'
adding 'MDAnalysis/coordinates/timestep.pyx'
adding 'MDAnalysis/core/__init__.py'
adding 'MDAnalysis/core/_get_readers.py'
adding 'MDAnalysis/core/accessors.py'
adding 'MDAnalysis/core/groups.py'
adding 'MDAnalysis/core/selection.py'
adding 'MDAnalysis/core/topology.py'
adding 'MDAnalysis/core/topologyattrs.py'
adding 'MDAnalysis/core/topologyobjects.py'
adding 'MDAnalysis/core/universe.py'
adding 'MDAnalysis/lib/NeighborSearch.py'
adding 'MDAnalysis/lib/__init__.py'
adding 'MDAnalysis/lib/_augment.cpp'
adding 'MDAnalysis/lib/_augment.cpython-312-aarch64-linux-gnu.so'
adding 'MDAnalysis/lib/_augment.pyx'
adding 'MDAnalysis/lib/_cutil.cpp'
adding 'MDAnalysis/lib/_cutil.cpython-312-aarch64-linux-gnu.so'
adding 'MDAnalysis/lib/_cutil.pxd'
adding 'MDAnalysis/lib/_cutil.pyx'
adding 'MDAnalysis/lib/_distopia.py'
adding 'MDAnalysis/lib/_transformations.cpython-312-aarch64-linux-gnu.so'
adding 'MDAnalysis/lib/c_distances.c'
adding 'MDAnalysis/lib/c_distances.cpython-312-aarch64-linux-gnu.so'
adding 'MDAnalysis/lib/c_distances.pxd'
adding 'MDAnalysis/lib/c_distances.pyx'
adding 'MDAnalysis/lib/c_distances_openmp.c'
adding 'MDAnalysis/lib/c_distances_openmp.cpython-312-aarch64-linux-gnu.so'
adding 'MDAnalysis/lib/c_distances_openmp.pyx'
adding 'MDAnalysis/lib/correlations.py'
adding 'MDAnalysis/lib/distances.py'
adding 'MDAnalysis/lib/log.py'
adding 'MDAnalysis/lib/mdamath.py'
adding 'MDAnalysis/lib/nsgrid.cpp'
adding 'MDAnalysis/lib/nsgrid.cpython-312-aarch64-linux-gnu.so'
adding 'MDAnalysis/lib/nsgrid.pyx'
adding 'MDAnalysis/lib/picklable_file_io.py'
adding 'MDAnalysis/lib/pkdtree.py'
adding 'MDAnalysis/lib/qcprot.c'
adding 'MDAnalysis/lib/qcprot.cpython-312-aarch64-linux-gnu.so'
adding 'MDAnalysis/lib/qcprot.pyx'
adding 'MDAnalysis/lib/transformations.py'
adding 'MDAnalysis/lib/util.py'
adding 'MDAnalysis/lib/formats/__init__.py'
adding 'MDAnalysis/lib/formats/cython_util.c'
adding 'MDAnalysis/lib/formats/cython_util.cpython-312-aarch64-linux-gnu.so'
adding 'MDAnalysis/lib/formats/cython_util.pxd'
adding 'MDAnalysis/lib/formats/cython_util.pyx'
adding 'MDAnalysis/lib/formats/libdcd.c'
adding 'MDAnalysis/lib/formats/libdcd.cpython-312-aarch64-linux-gnu.so'
adding 'MDAnalysis/lib/formats/libdcd.pxd'
adding 'MDAnalysis/lib/formats/libdcd.pyx'
adding 'MDAnalysis/lib/formats/libmdaxdr.c'
adding 'MDAnalysis/lib/formats/libmdaxdr.cpython-312-aarch64-linux-gnu.so'
adding 'MDAnalysis/lib/formats/libmdaxdr.pxd'
adding 'MDAnalysis/lib/formats/libmdaxdr.pyx'
adding 'MDAnalysis/lib/formats/include/endianswap.h'
adding 'MDAnalysis/lib/formats/include/fastio.h'
adding 'MDAnalysis/lib/formats/include/readdcd.h'
adding 'MDAnalysis/lib/formats/include/trr_seek.h'
adding 'MDAnalysis/lib/formats/include/xdrfile.h'
adding 'MDAnalysis/lib/formats/include/xdrfile_trr.h'
adding 'MDAnalysis/lib/formats/include/xdrfile_xtc.h'
adding 'MDAnalysis/lib/formats/include/xtc_seek.h'
adding 'MDAnalysis/lib/formats/src/trr_seek.c'
adding 'MDAnalysis/lib/formats/src/xdrfile.c'
adding 'MDAnalysis/lib/formats/src/xdrfile_trr.c'
adding 'MDAnalysis/lib/formats/src/xdrfile_xtc.c'
adding 'MDAnalysis/lib/formats/src/xtc_seek.c'
adding 'MDAnalysis/lib/include/calc_distances.h'
adding 'MDAnalysis/lib/libmdanalysis/__init__.pxd'
adding 'MDAnalysis/lib/src/transformations/AUTHOR'
adding 'MDAnalysis/lib/src/transformations/LICENCE'
adding 'MDAnalysis/lib/src/transformations/transformations.c'
adding 'MDAnalysis/selections/__init__.py'
adding 'MDAnalysis/selections/base.py'
adding 'MDAnalysis/selections/charmm.py'
adding 'MDAnalysis/selections/gromacs.py'
adding 'MDAnalysis/selections/jmol.py'
adding 'MDAnalysis/selections/pymol.py'
adding 'MDAnalysis/selections/vmd.py'
adding 'MDAnalysis/tests/__init__.py'
adding 'MDAnalysis/tests/datafiles.py'
adding 'MDAnalysis/topology/CRDParser.py'
adding 'MDAnalysis/topology/DLPolyParser.py'
adding 'MDAnalysis/topology/DMSParser.py'
adding 'MDAnalysis/topology/ExtendedPDBParser.py'
adding 'MDAnalysis/topology/FHIAIMSParser.py'
adding 'MDAnalysis/topology/GMSParser.py'
adding 'MDAnalysis/topology/GROParser.py'
adding 'MDAnalysis/topology/GSDParser.py'
adding 'MDAnalysis/topology/HoomdXMLParser.py'
adding 'MDAnalysis/topology/ITPParser.py'
adding 'MDAnalysis/topology/LAMMPSParser.py'
adding 'MDAnalysis/topology/MMTFParser.py'
adding 'MDAnalysis/topology/MOL2Parser.py'
adding 'MDAnalysis/topology/MinimalParser.py'
adding 'MDAnalysis/topology/PDBParser.py'
adding 'MDAnalysis/topology/PDBQTParser.py'
adding 'MDAnalysis/topology/PQRParser.py'
adding 'MDAnalysis/topology/PSFParser.py'
adding 'MDAnalysis/topology/ParmEdParser.py'
adding 'MDAnalysis/topology/TOPParser.py'
adding 'MDAnalysis/topology/TPRParser.py'
adding 'MDAnalysis/topology/TXYZParser.py'
adding 'MDAnalysis/topology/XYZParser.py'
adding 'MDAnalysis/topology/__init__.py'
adding 'MDAnalysis/topology/base.py'
adding 'MDAnalysis/topology/core.py'
adding 'MDAnalysis/topology/guessers.py'
adding 'MDAnalysis/topology/tables.py'
adding 'MDAnalysis/topology/tpr/__init__.py'
adding 'MDAnalysis/topology/tpr/obj.py'
adding 'MDAnalysis/topology/tpr/setting.py'
adding 'MDAnalysis/topology/tpr/utils.py'
adding 'MDAnalysis/transformations/__init__.py'
adding 'MDAnalysis/transformations/base.py'
adding 'MDAnalysis/transformations/boxdimensions.py'
adding 'MDAnalysis/transformations/fit.py'
adding 'MDAnalysis/transformations/nojump.py'
adding 'MDAnalysis/transformations/positionaveraging.py'
adding 'MDAnalysis/transformations/rotate.py'
adding 'MDAnalysis/transformations/translate.py'
adding 'MDAnalysis/transformations/wrap.py'
adding 'MDAnalysis/visualization/__init__.py'
adding 'MDAnalysis/visualization/streamlines.py'
adding 'MDAnalysis/visualization/streamlines_3D.py'
adding 'MDAnalysis-2.7.0.dist-info/AUTHORS'
adding 'MDAnalysis-2.7.0.dist-info/LICENSE'
adding 'MDAnalysis-2.7.0.dist-info/METADATA'
adding 'MDAnalysis-2.7.0.dist-info/WHEEL'
adding 'MDAnalysis-2.7.0.dist-info/top_level.txt'
adding 'MDAnalysis-2.7.0.dist-info/RECORD'
removing build/bdist.linux-aarch64/wheel
Successfully built MDAnalysis-2.7.0-cp312-cp312-linux_aarch64.whl
I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.12 with "installer" module
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
py3versions: no X-Python3-Version in control file, using supported versions
for py in 3.13 3.12; do \
echo "=== testing with python$py ==="; \
pydir=`pybuild -p $py --system=distutils --print {build_dir}`; \
MPLBACKEND=agg PYTHONPATH=$pydir python$py -mpytest testsuite; \
rm -rf $pydir/MDAnalysis/.hypothesis; \
done
=== testing with python3.13 ===
============================= test session starts ==============================
platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0
rootdir: /<<PKGBUILDDIR>>/testsuite
configfile: setup.cfg
plugins: typeguard-4.3.0, hypothesis-6.115.3
collected 19089 items / 5 errors / 6 skipped
==================================== ERRORS ====================================
_________ ERROR collecting MDAnalysisTests/analysis/test_dihedrals.py __________
ImportError while importing test module '/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/analysis/test_dihedrals.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
testsuite/MDAnalysisTests/analysis/test_dihedrals.py:25: in <module>
import matplotlib
/usr/lib/python3/dist-packages/duecredit/injections/injector.py:342: in __import
mod = self._orig_import(name, *args, **kwargs)
/usr/lib/python3/dist-packages/matplotlib/__init__.py:161: in <module>
from . import _api, _version, cbook, _docstring, rcsetup
/usr/lib/python3/dist-packages/duecredit/injections/injector.py:342: in __import
mod = self._orig_import(name, *args, **kwargs)
/usr/lib/python3/dist-packages/matplotlib/rcsetup.py:27: in <module>
from matplotlib.colors import Colormap, is_color_like
/usr/lib/python3/dist-packages/duecredit/injections/injector.py:342: in __import
mod = self._orig_import(name, *args, **kwargs)
/usr/lib/python3/dist-packages/matplotlib/colors.py:52: in <module>
from PIL import Image
/usr/lib/python3/dist-packages/duecredit/injections/injector.py:342: in __import
mod = self._orig_import(name, *args, **kwargs)
/usr/lib/python3/dist-packages/PIL/Image.py:100: in <module>
from . import _imaging as core
E ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py)
------------------------------- Captured stderr --------------------------------
2024-10-24 16:40:35,508 [WARNING] Failed to access module matplotlib among sys.modules (injector.py:230)
___________ ERROR collecting MDAnalysisTests/analysis/test_hole2.py ____________
ImportError while importing test module '/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/analysis/test_hole2.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
testsuite/MDAnalysisTests/analysis/test_hole2.py:31: in <module>
import matplotlib
/usr/lib/python3/dist-packages/duecredit/injections/injector.py:315: in __import
return _very_orig_import(name, *args, **kwargs)
/usr/lib/python3/dist-packages/matplotlib/__init__.py:161: in <module>
from . import _api, _version, cbook, _docstring, rcsetup
/usr/lib/python3/dist-packages/duecredit/injections/injector.py:342: in __import
mod = self._orig_import(name, *args, **kwargs)
/usr/lib/python3/dist-packages/matplotlib/rcsetup.py:27: in <module>
from matplotlib.colors import Colormap, is_color_like
/usr/lib/python3/dist-packages/duecredit/injections/injector.py:315: in __import
return _very_orig_import(name, *args, **kwargs)
/usr/lib/python3/dist-packages/matplotlib/colors.py:52: in <module>
from PIL import Image
/usr/lib/python3/dist-packages/duecredit/injections/injector.py:315: in __import
return _very_orig_import(name, *args, **kwargs)
/usr/lib/python3/dist-packages/PIL/Image.py:100: in <module>
from . import _imaging as core
E ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py)
_____ ERROR collecting MDAnalysisTests/analysis/test_persistencelength.py ______
ImportError while importing test module '/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/analysis/test_persistencelength.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
testsuite/MDAnalysisTests/analysis/test_persistencelength.py:31: in <module>
import matplotlib
/usr/lib/python3/dist-packages/duecredit/injections/injector.py:315: in __import
return _very_orig_import(name, *args, **kwargs)
/usr/lib/python3/dist-packages/matplotlib/__init__.py:161: in <module>
from . import _api, _version, cbook, _docstring, rcsetup
/usr/lib/python3/dist-packages/duecredit/injections/injector.py:342: in __import
mod = self._orig_import(name, *args, **kwargs)
/usr/lib/python3/dist-packages/matplotlib/rcsetup.py:27: in <module>
from matplotlib.colors import Colormap, is_color_like
/usr/lib/python3/dist-packages/duecredit/injections/injector.py:315: in __import
return _very_orig_import(name, *args, **kwargs)
/usr/lib/python3/dist-packages/matplotlib/colors.py:52: in <module>
from PIL import Image
/usr/lib/python3/dist-packages/duecredit/injections/injector.py:315: in __import
return _very_orig_import(name, *args, **kwargs)
/usr/lib/python3/dist-packages/PIL/Image.py:100: in <module>
from . import _imaging as core
E ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py)
____________ ERROR collecting MDAnalysisTests/analysis/test_psa.py _____________
ImportError while importing test module '/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/analysis/test_psa.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
testsuite/MDAnalysisTests/analysis/test_psa.py:26: in <module>
import MDAnalysis.analysis.psa as PSA
/usr/lib/python3/dist-packages/duecredit/injections/injector.py:342: in __import
mod = self._orig_import(name, *args, **kwargs)
.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/analysis/psa.py:210: in <module>
import matplotlib
/usr/lib/python3/dist-packages/duecredit/injections/injector.py:315: in __import
return _very_orig_import(name, *args, **kwargs)
/usr/lib/python3/dist-packages/matplotlib/__init__.py:161: in <module>
from . import _api, _version, cbook, _docstring, rcsetup
/usr/lib/python3/dist-packages/duecredit/injections/injector.py:342: in __import
mod = self._orig_import(name, *args, **kwargs)
/usr/lib/python3/dist-packages/matplotlib/rcsetup.py:27: in <module>
from matplotlib.colors import Colormap, is_color_like
/usr/lib/python3/dist-packages/duecredit/injections/injector.py:315: in __import
return _very_orig_import(name, *args, **kwargs)
/usr/lib/python3/dist-packages/matplotlib/colors.py:52: in <module>
from PIL import Image
/usr/lib/python3/dist-packages/duecredit/injections/injector.py:315: in __import
return _very_orig_import(name, *args, **kwargs)
/usr/lib/python3/dist-packages/PIL/Image.py:100: in <module>
from . import _imaging as core
E ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py)
______ ERROR collecting MDAnalysisTests/visualization/test_streamlines.py ______
ImportError while importing test module '/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/visualization/test_streamlines.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
../../../../testsuite/MDAnalysisTests/visualization/test_streamlines.py:26: in <module>
from MDAnalysis.visualization import (streamlines,
/usr/lib/python3/dist-packages/duecredit/injections/injector.py:342: in __import
mod = self._orig_import(name, *args, **kwargs)
visualization/__init__.py:24: in <module>
from . import streamlines
/usr/lib/python3/dist-packages/duecredit/injections/injector.py:342: in __import
mod = self._orig_import(name, *args, **kwargs)
visualization/streamlines.py:54: in <module>
raise ImportError(
E ImportError: 2d streamplot module requires: matplotlib.path for its path.Path.contains_points method. The installation instructions for the matplotlib module can be found here: http://matplotlib.org/faq/installing_faq.html?highlight=install
=============================== warnings summary ===============================
../../../usr/lib/python3/dist-packages/Bio/Application/__init__.py:39
/usr/lib/python3/dist-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.
Due to the on going maintenance burden of keeping command line application
wrappers up to date, we have decided to deprecate and eventually remove these
modules.
We instead now recommend building your command line and invoking it directly
with the subprocess module.
warnings.warn(
.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/coordinates/DCD.py:165
.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/coordinates/DCD.py:165
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/coordinates/DCD.py:165: DeprecationWarning: DCDReader currently makes independent timesteps by copying self.ts while other readers update self.ts inplace. This behavior will be changed in 3.0 to be the same as other readers. Read more at https://github.com/MDAnalysis/mdanalysis/issues/3889 to learn if this change in behavior might affect you.
warnings.warn("DCDReader currently makes independent timesteps"
.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52: DeprecationWarning: This module was moved to MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel; hbonds.hbond_autocorrel will be removed in 3.0.0.
warnings.warn(wmsg, category=DeprecationWarning)
.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/coordinates/chemfiles.py:122
.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/coordinates/chemfiles.py:122
.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/coordinates/chemfiles.py:122
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/coordinates/chemfiles.py:122: UserWarning: chemfiles package not found, try installing it with 'pip install chemfiles'
warnings.warn(
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
ERROR testsuite/MDAnalysisTests/analysis/test_dihedrals.py
ERROR testsuite/MDAnalysisTests/analysis/test_hole2.py
ERROR testsuite/MDAnalysisTests/analysis/test_persistencelength.py
ERROR testsuite/MDAnalysisTests/analysis/test_psa.py
ERROR testsuite/MDAnalysisTests/visualization/test_streamlines.py
!!!!!!!!!!!!!!!!!!! Interrupted: 5 errors during collection !!!!!!!!!!!!!!!!!!!!
=================== 6 skipped, 7 warnings, 5 errors in 7.21s ===================
--- Logging error ---
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/duecredit/utils.py", line 209, in wrapped_func
return f(*args, **kwargs)
File "/usr/lib/python3/dist-packages/duecredit/dueswitch.py", line 102, in dump
due_summary.dump()
~~~~~~~~~~~~~~~~^^
File "/usr/lib/python3/dist-packages/duecredit/collector.py", line 499, in dump
output.dump()
~~~~~~~~~~~^^
File "/usr/lib/python3/dist-packages/duecredit/io.py", line 247, in dump
self.fd.write(get_text_rendering(cit.entry, style=self.style))
~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/duecredit/io.py", line 254, in get_text_rendering
return format_bibtex(get_bibtex_rendering(entry), style=style)
~~~~~~~~~~~~~~~~~~~~^^^^^^^
File "/usr/lib/python3/dist-packages/duecredit/io.py", line 267, in get_bibtex_rendering
return BibTeX(import_doi(entry.doi))
~~~~~~~~~~^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/duecredit/io.py", line 50, in import_doi
cached = get_doi_cache_file(doi)
File "/usr/lib/python3/dist-packages/duecredit/io.py", line 43, in get_doi_cache_file
os.makedirs(CACHE_DIR)
~~~~~~~~~~~^^^^^^^^^^^
File "<frozen os>", line 217, in makedirs
File "<frozen os>", line 217, in makedirs
File "<frozen os>", line 217, in makedirs
File "<frozen os>", line 227, in makedirs
PermissionError: [Errno 13] Permission denied: '/sbuild-nonexistent'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3.13/logging/__init__.py", line 1153, in emit
stream.write(msg + self.terminator)
~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
ValueError: I/O operation on closed file.
Call stack:
File "/usr/lib/python3/dist-packages/duecredit/utils.py", line 211, in wrapped_func
lgr.warning(
Message: "DueCredit internal failure while running <function DueSwitch.dump at 0xffffa4f3c720>: PermissionError(13, 'Permission denied'). Please report to developers at https://github.com/duecredit/duecredit/issues"
Arguments: ()
DueCredit Report:
- Molecular simulation analysis library / MDAnalysis (v 2.7.0) [1, 2]
- Dielectric analysis / MDAnalysis.analysis.dielectric (v 2.7.0) [3]
- ENCORE Ensemble Comparison / MDAnalysis.analysis.encore (v 2.7.0) [4]
- Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.7.0) [5]
- Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel (v 2.7.0) [6]
- LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.7.0) [2]
- FCA fast correlation algorithm, Mean Squared Displacements with tidynamics / MDAnalysis.analysis.msd (v 2.7.0) [7, 8]
- QCProt implementation / MDAnalysis.lib.qcprot (v 2.7.0) [9, 10]
- Scientific tools library / numpy (v 1.26.4) [11]
2 packages cited
7 modules cited
0 functions cited
References
----------
[1] === testing with python3.12 ===
============================= test session starts ==============================
platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0
rootdir: /<<PKGBUILDDIR>>/testsuite
configfile: setup.cfg
plugins: typeguard-4.3.0, hypothesis-6.115.3
collected 19229 items / 6 skipped
testsuite/MDAnalysisTests/analysis/test_align.py ....................... [ 0%]
....................s.ss.s... [ 0%]
testsuite/MDAnalysisTests/analysis/test_atomicdistances.py ... [ 0%]
testsuite/MDAnalysisTests/analysis/test_base.py ........................ [ 0%]
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testsuite/MDAnalysisTests/analysis/test_bat.py ............ [ 1%]
testsuite/MDAnalysisTests/analysis/test_contacts.py .................... [ 1%]
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testsuite/MDAnalysisTests/analysis/test_data.py . [ 1%]
testsuite/MDAnalysisTests/analysis/test_density.py ..................... [ 1%]
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testsuite/MDAnalysisTests/analysis/test_dielectric.py ...... [ 1%]
testsuite/MDAnalysisTests/analysis/test_diffusionmap.py .......... [ 1%]
testsuite/MDAnalysisTests/analysis/test_dihedrals.py ................... [ 1%]
.... [ 1%]
testsuite/MDAnalysisTests/analysis/test_distances.py ............ [ 1%]
testsuite/MDAnalysisTests/analysis/test_encore.py .................X..X. [ 2%]
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testsuite/MDAnalysisTests/analysis/test_gnm.py ...... [ 2%]
testsuite/MDAnalysisTests/analysis/test_helix_analysis.py .............. [ 2%]
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testsuite/MDAnalysisTests/analysis/test_hole2.py ....sssssssssssssssssss [ 2%]
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testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py ...... [ 2%]
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testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py . [ 2%]
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testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py ...... [ 2%]
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testsuite/MDAnalysisTests/analysis/test_leaflet.py s............ [ 3%]
testsuite/MDAnalysisTests/analysis/test_lineardensity.py ........ [ 3%]
testsuite/MDAnalysisTests/analysis/test_msd.py .......................ss [ 3%]
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testsuite/MDAnalysisTests/analysis/test_nucleicacids.py ................ [ 3%]
[ 3%]
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testsuite/MDAnalysisTests/analysis/test_pca.py ......................... [ 3%]
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testsuite/MDAnalysisTests/analysis/test_persistencelength.py ........... [ 4%]
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testsuite/MDAnalysisTests/analysis/test_psa.py ......................... [ 4%]
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testsuite/MDAnalysisTests/analysis/test_rdf.py .................... [ 4%]
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testsuite/MDAnalysisTests/analysis/test_wbridge.py ..................... [ 5%]
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testsuite/MDAnalysisTests/auxiliary/test_core.py ..... [ 5%]
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testsuite/MDAnalysisTests/converters/test_base.py .. [ 6%]
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testsuite/MDAnalysisTests/coordinates/test_copying.py .................. [ 7%]
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testsuite/MDAnalysisTests/coordinates/test_gms.py .................. [ 9%]
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testsuite/MDAnalysisTests/core/test_group_traj_access.py ............... [ 27%]
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testsuite/MDAnalysisTests/core/test_residue.py .... [ 30%]
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testsuite/MDAnalysisTests/core/test_segment.py ....... [ 31%]
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testsuite/MDAnalysisTests/core/test_topology.py ........................ [ 31%]
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testsuite/MDAnalysisTests/core/test_topologyattrs.py ................... [ 31%]
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testsuite/MDAnalysisTests/core/test_topologyobjects.py ................. [ 32%]
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testsuite/MDAnalysisTests/lib/test_pkdtree.py ................. [ 54%]
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testsuite/MDAnalysisTests/transformations/test_translate.py ............ [ 97%]
............ [ 97%]
testsuite/MDAnalysisTests/transformations/test_wrap.py ................. [ 97%]
....... [ 97%]
testsuite/MDAnalysisTests/utils/test_authors.py . [ 97%]
testsuite/MDAnalysisTests/utils/test_datafiles.py .... [ 97%]
testsuite/MDAnalysisTests/utils/test_duecredit.py .............. [ 97%]
testsuite/MDAnalysisTests/utils/test_failure.py . [ 97%]
testsuite/MDAnalysisTests/utils/test_imports.py ........................ [ 97%]
........................................................................ [ 97%]
........................................................................ [ 98%]
................... [ 98%]
testsuite/MDAnalysisTests/utils/test_log.py . [ 98%]
testsuite/MDAnalysisTests/utils/test_meta.py .... [ 98%]
testsuite/MDAnalysisTests/utils/test_modelling.py ............. [ 98%]
testsuite/MDAnalysisTests/utils/test_persistence.py ....... [ 98%]
testsuite/MDAnalysisTests/utils/test_pickleio.py ....................... [ 98%]
..............ss.. [ 98%]
testsuite/MDAnalysisTests/utils/test_qcprot.py ...... [ 98%]
testsuite/MDAnalysisTests/utils/test_selections.py ..................... [ 98%]
[ 98%]
testsuite/MDAnalysisTests/utils/test_streamio.py ....................... [ 98%]
............... [ 99%]
testsuite/MDAnalysisTests/utils/test_transformations.py ................ [ 99%]
........................................................................ [ 99%]
........................................................ [ 99%]
testsuite/MDAnalysisTests/utils/test_units.py .......................... [ 99%]
....... [ 99%]
testsuite/MDAnalysisTests/visualization/test_streamlines.py ... [100%]
=============================== warnings summary ===============================
../../../usr/lib/python3/dist-packages/Bio/Application/__init__.py:39
/usr/lib/python3/dist-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.
Due to the on going maintenance burden of keeping command line application
wrappers up to date, we have decided to deprecate and eventually remove these
modules.
We instead now recommend building your command line and invoking it directly
with the subprocess module.
warnings.warn(
.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/DCD.py:165: 2 warnings
MDAnalysisTests/analysis/test_align.py: 77 warnings
MDAnalysisTests/analysis/test_base.py: 3 warnings
MDAnalysisTests/analysis/test_bat.py: 2 warnings
MDAnalysisTests/analysis/test_contacts.py: 21 warnings
MDAnalysisTests/analysis/test_dielectric.py: 6 warnings
MDAnalysisTests/analysis/test_encore.py: 10 warnings
MDAnalysisTests/analysis/test_helix_analysis.py: 7 warnings
MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning
MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning
MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 6 warnings
MDAnalysisTests/analysis/test_lineardensity.py: 6 warnings
MDAnalysisTests/analysis/test_msd.py: 2 warnings
MDAnalysisTests/analysis/test_pca.py: 12 warnings
MDAnalysisTests/analysis/test_psa.py: 124 warnings
MDAnalysisTests/analysis/test_rms.py: 38 warnings
MDAnalysisTests/analysis/test_waterdynamics.py: 1 warning
MDAnalysisTests/coordinates/test_chainreader.py: 72 warnings
MDAnalysisTests/coordinates/test_copying.py: 18 warnings
MDAnalysisTests/coordinates/test_dcd.py: 112 warnings
MDAnalysisTests/coordinates/test_lammps.py: 5 warnings
MDAnalysisTests/coordinates/test_memory.py: 88 warnings
MDAnalysisTests/coordinates/test_pdb.py: 7 warnings
MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings
MDAnalysisTests/core/test_accumulate.py: 48 warnings
MDAnalysisTests/core/test_atom.py: 15 warnings
MDAnalysisTests/core/test_atomgroup.py: 170 warnings
MDAnalysisTests/core/test_atomselections.py: 4 warnings
MDAnalysisTests/core/test_copying.py: 6 warnings
MDAnalysisTests/core/test_groups.py: 11 warnings
MDAnalysisTests/core/test_residue.py: 4 warnings
MDAnalysisTests/core/test_residuegroup.py: 23 warnings
MDAnalysisTests/core/test_segmentgroup.py: 9 warnings
MDAnalysisTests/core/test_topologyattrs.py: 8 warnings
MDAnalysisTests/core/test_topologyobjects.py: 4 warnings
MDAnalysisTests/core/test_universe.py: 31 warnings
MDAnalysisTests/lib/test_distances.py: 46 warnings
MDAnalysisTests/lib/test_neighborsearch.py: 2 warnings
MDAnalysisTests/lib/test_qcprot.py: 2 warnings
MDAnalysisTests/lib/test_util.py: 67 warnings
MDAnalysisTests/parallelism/test_multiprocessing.py: 3 warnings
MDAnalysisTests/parallelism/test_pickle_transformation.py: 8 warnings
MDAnalysisTests/topology/test_guessers.py: 1 warning
MDAnalysisTests/topology/test_minimal.py: 2 warnings
MDAnalysisTests/transformations/test_base.py: 1 warning
MDAnalysisTests/transformations/test_nojump.py: 3 warnings
MDAnalysisTests/utils/test_modelling.py: 3 warnings
MDAnalysisTests/utils/test_selections.py: 20 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/DCD.py:165: DeprecationWarning: DCDReader currently makes independent timesteps by copying self.ts while other readers update self.ts inplace. This behavior will be changed in 3.0 to be the same as other readers. Read more at https://github.com/MDAnalysis/mdanalysis/issues/3889 to learn if this change in behavior might affect you.
warnings.warn("DCDReader currently makes independent timesteps"
.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52: DeprecationWarning: This module was moved to MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel; hbonds.hbond_autocorrel will be removed in 3.0.0.
warnings.warn(wmsg, category=DeprecationWarning)
.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/chemfiles.py:122
.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/chemfiles.py:122
.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/chemfiles.py:122
MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[ChemfilesWriter]
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[ChemfilesWriter]
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[ChemfilesWriter]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/chemfiles.py:122: UserWarning: chemfiles package not found, try installing it with 'pip install chemfiles'
warnings.warn(
MDAnalysisTests/analysis/test_align.py: 699 warnings
MDAnalysisTests/analysis/test_psa.py: 5960 warnings
MDAnalysisTests/coordinates/test_chainreader.py: 298 warnings
MDAnalysisTests/coordinates/test_dcd.py: 687 warnings
MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
MDAnalysisTests/core/test_atomgroup.py: 318 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/DCD.py:463: UserWarning: No dimensions set for current frame, zeroed unitcell will be written
warnings.warn(wmsg)
MDAnalysisTests/analysis/test_align.py: 5 warnings
MDAnalysisTests/analysis/test_encore.py: 203 warnings
MDAnalysisTests/coordinates/test_memory.py: 9 warnings
MDAnalysisTests/core/test_universe.py: 17 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/memory.py:535: DeprecationWarning: asel argument to timeseries will be renamed to'atomgroup' in 3.0, see #3911
warnings.warn(
MDAnalysisTests/analysis/test_bat.py: 9 warnings
MDAnalysisTests/coordinates/test_mol2.py: 3 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/topology/MOL2Parser.py:234: UserWarning: Unknown elements found for some atoms: {'c3', 'hc', 'oh', 'h1', 'ho'}. These have been given an empty element record.
warnings.warn("Unknown elements found for some "
MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox
MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape
MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_shape
MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_type
MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_missing
MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_type
MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_nanvalue
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/density.py:423: UserWarning: Box padding (currently set at 2.0) is not used in user defined grids.
warnings.warn(msg)
MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox
MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape
MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_warn_userdefn_padding
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/density.py:556: UserWarning: Atom selection does not fit grid --- you may want to define a larger box
warnings.warn(msg)
MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran
MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_single_frame
MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_residue_selections
MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_attr_warning
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/dihedrals.py:400: UserWarning: Cannot determine phi and psi angles for the first or last residues
warnings.warn("Cannot determine phi and psi angles for the first "
MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin
MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_tpr
MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_single_frame
MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_plot
MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_attr_warning
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/dihedrals.py:582: UserWarning: All residues selected with 'resname ALA CYS* GLY PRO SER THR VAL' have been removed from the selection.
warnings.warn(f"All residues selected with '{select_remove}' "
MDAnalysisTests/analysis/test_encore.py: 5 warnings
MDAnalysisTests/parallelism/test_multiprocessing.py: 34 warnings
MDAnalysisTests/visualization/test_streamlines.py: 3 warnings
/usr/lib/python3.12/multiprocessing/popen_fork.py:66: DeprecationWarning: This process (pid=352) is multi-threaded, use of fork() may lead to deadlocks in the child.
self.pid = os.fork()
MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_plane_circle
MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_ortho_circle
MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_parallel_axes
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/helix_analysis.py:181: RuntimeWarning: invalid value encountered in divide
cos = cos_perp, cos_ortho = np.matmul(refs, proj_plane.T)/norms
MDAnalysisTests/analysis/test_helix_analysis.py: 30 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/helix_analysis.py:262: RuntimeWarning: invalid value encountered in divide
local_axes = (cross_bi.T / mdamath.pnorm(cross_bi)).T # (n_res-3, 3)
MDAnalysisTests/analysis/test_helix_analysis.py: 176 warnings
/usr/lib/python3/dist-packages/numpy/core/_methods.py:206: RuntimeWarning: Degrees of freedom <= 0 for slice
ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof,
MDAnalysisTests/analysis/test_helix_analysis.py: 160 warnings
/usr/lib/python3/dist-packages/numpy/core/_methods.py:195: RuntimeWarning: invalid value encountered in divide
ret = um.true_divide(
MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings
/usr/lib/python3/dist-packages/numpy/core/_methods.py:198: RuntimeWarning: invalid value encountered in scalar divide
ret = ret.dtype.type(ret / rcount)
MDAnalysisTests/analysis/test_hole2.py: 1 warning
MDAnalysisTests/coordinates/test_pdb.py: 16 warnings
MDAnalysisTests/core/test_atomgroup.py: 26 warnings
MDAnalysisTests/core/test_atomselections.py: 1 warning
MDAnalysisTests/core/test_topologyattrs.py: 1 warning
MDAnalysisTests/topology/test_pdb.py: 1 warning
MDAnalysisTests/utils/test_modelling.py: 1 warning
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:453: UserWarning: 1 A^3 CRYST1 record, this is usually a placeholder. Unit cell dimensions will be set to None.
warnings.warn("1 A^3 CRYST1 record,"
MDAnalysisTests/analysis/test_hole2.py: 1 warning
MDAnalysisTests/coordinates/test_pdb.py: 23 warnings
MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
MDAnalysisTests/core/test_atomgroup.py: 15 warnings
MDAnalysisTests/utils/test_modelling.py: 1 warning
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:777: UserWarning: Unit cell dimensions not found. CRYST1 record set to unitary values.
warnings.warn("Unit cell dimensions not found. "
MDAnalysisTests/analysis/test_hole2.py: 1 warning
MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
MDAnalysisTests/coordinates/test_pdb.py: 22 warnings
MDAnalysisTests/coordinates/test_trz.py: 1 warning
MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
MDAnalysisTests/core/test_atomgroup.py: 15 warnings
MDAnalysisTests/transformations/test_nojump.py: 1 warning
MDAnalysisTests/utils/test_modelling.py: 2 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'elements' Using default value of ' '
warnings.warn("Found no information for attr: '{}'"
MDAnalysisTests/analysis/test_hole2.py: 1 warning
MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
MDAnalysisTests/coordinates/test_pdb.py: 32 warnings
MDAnalysisTests/coordinates/test_trz.py: 1 warning
MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
MDAnalysisTests/core/test_atomgroup.py: 15 warnings
MDAnalysisTests/topology/test_altloc.py: 1 warning
MDAnalysisTests/transformations/test_nojump.py: 1 warning
MDAnalysisTests/utils/test_modelling.py: 3 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'formalcharges' Using default value of '0'
warnings.warn("Found no information for attr: '{}'"
MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 13 warnings
MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 14 warnings
MDAnalysisTests/analysis/test_persistencelength.py: 1 warning
MDAnalysisTests/coordinates/test_copying.py: 18 warnings
MDAnalysisTests/coordinates/test_timestep_api.py: 3 warnings
MDAnalysisTests/coordinates/test_trz.py: 5 warnings
MDAnalysisTests/core/test_atomgroup.py: 39 warnings
MDAnalysisTests/core/test_atomselections.py: 14 warnings
MDAnalysisTests/core/test_topologyobjects.py: 1 warning
MDAnalysisTests/core/test_universe.py: 3 warnings
MDAnalysisTests/core/test_wrap.py: 13 warnings
MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning
MDAnalysisTests/topology/test_minimal.py: 1 warning
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/TRZ.py:119: DeprecationWarning: The TRZ reader is deprecated and will be removed in MDAnalysis version 3.0.0
warnings.warn(wmsg, DeprecationWarning)
MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 9 warnings
MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 10 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py:377: RuntimeWarning: Desired number of sample points too high, using 6
warnings.warn("Desired number of sample points too high, using {0}"
MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous
/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:62: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
`HydrogenBondAutoCorrel` will be removed in release 3.0.0.
The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
hbond = HBAC(u,
MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous_excl
/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:79: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
`HydrogenBondAutoCorrel` will be removed in release 3.0.0.
The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
hbond = HBAC(u,
MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent
/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:99: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
`HydrogenBondAutoCorrel` will be removed in release 3.0.0.
The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
hbond = HBAC(u,
MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_timecut
/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:117: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
`HydrogenBondAutoCorrel` will be removed in release 3.0.0.
The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
hbond = HBAC(u,
MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_excl
/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:135: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
`HydrogenBondAutoCorrel` will be removed in release 3.0.0.
The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
hbond = HBAC(u,
MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_continuous
/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:156: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
`HydrogenBondAutoCorrel` will be removed in release 3.0.0.
The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
hbond = HBAC(u,
MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_intermittent
/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:181: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
`HydrogenBondAutoCorrel` will be removed in release 3.0.0.
The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
hbond = HBAC(u,
MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_wronglength_DA
/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:210: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
`HydrogenBondAutoCorrel` will be removed in release 3.0.0.
The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
HBAC(u,
MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_exclusions
/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:225: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
`HydrogenBondAutoCorrel` will be removed in release 3.0.0.
The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
HBAC(u,
MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_bond_type_VE
/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:236: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
`HydrogenBondAutoCorrel` will be removed in release 3.0.0.
The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
HBAC(u,
MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_before_run_VE
/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:247: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
`HydrogenBondAutoCorrel` will be removed in release 3.0.0.
The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
hbond = HBAC(u,
MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_unslicable_traj_VE
/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:262: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
`HydrogenBondAutoCorrel` will be removed in release 3.0.0.
The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
HBAC(
MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_repr
/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:272: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
`HydrogenBondAutoCorrel` will be removed in release 3.0.0.
The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
hbond = HBAC(u,
MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_find_donors
/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:300: DeprecationWarning: `find_hydrogen_donors` is deprecated!
`find_hydrogen_donors` will be removed in release 3.0.0.
The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
D = hbonds.find_hydrogen_donors(H)
MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_donors_nobonds
/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:312: DeprecationWarning: `find_hydrogen_donors` is deprecated!
`find_hydrogen_donors` will be removed in release 3.0.0.
The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
hbonds.find_hydrogen_donors(u.atoms)
MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:733: UserWarning: No hydrogen bonds were found given d-a cutoff of 3.0 between Donor, name O, and Acceptor, name O.
warnings.warn(
MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:765: UserWarning: No hydrogen bonds were found given angle of 120.0 between Donor, name O, and Acceptor, name O.
warnings.warn(
MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1
MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1
MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules
MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules
MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules
/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice.
return _methods._mean(a, axis=axis, dtype=dtype,
MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1
MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1
MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules
MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules
MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules
/usr/lib/python3/dist-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide
ret = ret.dtype.type(ret / rcount)
MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type
MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_no_hydrogen_bonds
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:733: UserWarning: No hydrogen bonds were found given d-a cutoff of 3.0 between Donor, type O, and Acceptor, type O.
warnings.warn(
MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:765: UserWarning: No hydrogen bonds were found given angle of 120.0 between Donor, type O, and Acceptor, type O.
warnings.warn(
MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 10 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:733: UserWarning: No hydrogen bonds were found given d-a cutoff of 3.0 between Donor, None, and Acceptor, name OH2.
warnings.warn(
MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 10 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:765: UserWarning: No hydrogen bonds were found given angle of 120.0 between Donor, None, and Acceptor, name OH2.
warnings.warn(
MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:355: UserWarning: donors_sel is an empty selection string - no hydrogen bonds will be found. This may be intended, but please check your selection.
warnings.warn(msg.format(sel))
MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:355: UserWarning: hydrogens_sel is an empty selection string - no hydrogen bonds will be found. This may be intended, but please check your selection.
warnings.warn(msg.format(sel))
MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:355: UserWarning: acceptors_sel is an empty selection string - no hydrogen bonds will be found. This may be intended, but please check your selection.
warnings.warn(msg.format(sel))
MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 23 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/core/groups.py:3218: UserWarning: Empty string to select atoms, empty group returned.
warnings.warn("Empty string to select atoms, empty group returned.",
MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 10 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:733: UserWarning: No hydrogen bonds were found given d-a cutoff of 3.0 between Donor, , and Acceptor, .
warnings.warn(
MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 10 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:765: UserWarning: No hydrogen bonds were found given angle of 150 between Donor, , and Acceptor, .
warnings.warn(
MDAnalysisTests/analysis/test_leaflet.py::TestLeafletFinder::test_write_selection
/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/analysis/test_leaflet.py:175: ResourceWarning: unclosed file <_io.TextIOWrapper name='leaflet.vmd' mode='r' encoding='UTF-8'>
assert self.lines2one(open('leaflet.vmd').readlines()) == expected_output
Enable tracemalloc to get traceback where the object was allocated.
See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info.
MDAnalysisTests/analysis/test_msd.py: 100 warnings
MDAnalysisTests/analysis/test_pca.py: 100 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/topology/PDBParser.py:348: UserWarning: Unknown element X found for some atoms. These have been given an empty element record. If needed they can be guessed using MDAnalysis.topology.guessers.
warnings.warn(wmsg)
MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497]
MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497]
MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721]
MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/nuclinfo.py:302: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
phase_ang = (atan2(D, C) + (pi / 2.)) * 180. / pi
MDAnalysisTests/analysis/test_psa.py::TestPSAnalysis::test_dist_mat_to_vec_i_greater_j
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/psa.py:733: UserWarning: Column index entered (j = 3 is smaller than row index (i = 4). Using symmetric element in upper triangle of distance matrix instead: i --> j, j --> i
warnings.warn("Column index entered (j = {:d} is smaller than row "
MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[residue-8]
MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[segment-0]
MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[chain-8]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/rdf.py:347: DeprecationWarning: The `rdf` attribute was deprecated in MDAnalysis 2.0.0 and will be removed in MDAnalysis 3.0.0. Please use `results.rdf` instead
warnings.warn(wmsg, DeprecationWarning)
MDAnalysisTests/analysis/test_rdf_s.py: 13 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/rdf.py:554: DeprecationWarning: The `u` attribute is superflous and will be removed in MDAnalysis 3.0.0.
warnings.warn("The `u` attribute is superflous and will be removed "
MDAnalysisTests/analysis/test_rdf_s.py::test_density[True-0.021915460340071267]
MDAnalysisTests/analysis/test_rdf_s.py::test_overwrite_norm
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/rdf.py:567: DeprecationWarning: The `density` attribute was deprecated in MDAnalysis 2.3.0 and will be removed in MDAnalysis 3.0.0. Please use `norm=density` instead.
warnings.warn("The `density` attribute was deprecated in "
MDAnalysisTests/analysis/test_wbridge.py::TestWaterBridgeAnalysis::test_nodata
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1782: MissingDataWarning: No data computed, do run() first.
warnings.warn(msg, category=MissingDataWarning)
MDAnalysisTests/auxiliary/test_core.py: 1 warning
MDAnalysisTests/auxiliary/test_xvg.py: 30 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/auxiliary/base.py:175: UserWarning: AuxStep does not support time selection. Reverting to default
warnings.warn("{} does not support time selection. Reverting to "
MDAnalysisTests/auxiliary/test_xvg.py: 50 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/auxiliary/base.py:211: UserWarning: AuxStep does not support data selection. Reverting to default
warnings.warn("{} does not support data selection. Reverting to "
MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderFormats::test_set_all_formats
MDAnalysisTests/coordinates/test_dcd.py::test_other_writer[xtc-2]
/usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xffffac102480>
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1532, in __del__
self.close()
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/chain.py", line 597, in close
self._apply('close')
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/chain.py", line 504, in _apply
return [reader.__getattribute__(method)(**kwargs) for reader in self.readers]
^^^^^^^^^^^^
AttributeError: 'ChainReader' object has no attribute 'readers'
warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderContinuous::test_missing
MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderVacuumBox::test_initial_frame_is_0
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/chain.py:349: UserWarning: Missing frame in continuous chain
warnings.warn("Missing frame in continuous chain", UserWarning)
MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resnames]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/CRD.py:248: UserWarning: Supplied AtomGroup was missing the following attributes: resnames, tempfactors. These will be written with default values.
warnings.warn(
MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resids]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/CRD.py:248: UserWarning: Supplied AtomGroup was missing the following attributes: resids, tempfactors. These will be written with default values.
warnings.warn(
MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[names]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/CRD.py:248: UserWarning: Supplied AtomGroup was missing the following attributes: names, tempfactors. These will be written with default values.
warnings.warn(
MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[tempfactors]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/CRD.py:248: UserWarning: Supplied AtomGroup was missing the following attributes: tempfactors, tempfactors. These will be written with default values.
warnings.warn(
MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1]
MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 2]
MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1 to 3]
MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_empty_asel
MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_atomgroup_asel_mutex
MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices0]
MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices1]
MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices2]
MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_filename_array
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/DCD.py:326: DeprecationWarning: asel argument to timeseries will be renamed to'atomgroup' in 3.0, see #3911
warnings.warn(
MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_empty_dcd
/usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xffffac102480>
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1532, in __del__
self.close()
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/DCD.py", line 181, in close
self._file.close()
^^^^^^^^^^
AttributeError: 'DCDReader' object has no attribute '_file'
warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
MDAnalysisTests/coordinates/test_dcd.py::TestDCDWriter::test_no_container
MDAnalysisTests/coordinates/test_dcd.py::test_write_no_natoms
MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_time_unit
MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_unit
/usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function DCDWriter.__del__ at 0xffffac0b8fe0>
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/DCD.py", line 482, in __del__
self.close()
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/DCD.py", line 479, in close
self._file.close()
^^^^^^^^^^
AttributeError: 'DCDWriter' object has no attribute '_file'
warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
MDAnalysisTests/coordinates/test_dcd.py: 2 warnings
MDAnalysisTests/coordinates/test_netcdf.py: 108 warnings
MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings
MDAnalysisTests/coordinates/test_trj.py: 3 warnings
MDAnalysisTests/coordinates/test_windows.py: 2 warnings
MDAnalysisTests/core/test_atomselections.py: 3 warnings
MDAnalysisTests/topology/test_top.py: 63 warnings
MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/topology/TOPParser.py:299: UserWarning: ATOMIC_NUMBER record not found, elements attribute will not be populated. If needed these can be guessed using MDAnalysis.topology.guessers.
warnings.warn(msg)
MDAnalysisTests/coordinates/test_fhiaims.py::TestFHIAIMSWriter::test_writer_no_atom_names
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[FHIAIMSWriter]
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[FHIAIMSWriter]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/FHIAIMS.py:281: UserWarning: Supplied AtomGroup was missing the following attributes: names, ids. These will be written with default values.
warnings.warn(
MDAnalysisTests/coordinates/test_gro.py: 20 warnings
MDAnalysisTests/coordinates/test_h5md.py: 5 warnings
MDAnalysisTests/coordinates/test_xdr.py: 10 warnings
MDAnalysisTests/coordinates/test_xyz.py: 10 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py:1034: DeprecationWarning: asel argument to timeseries will be renamed to'atomgroup' in 3.0, see #3911
warnings.warn(
MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resnames
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/GRO.py:421: UserWarning: Supplied AtomGroup was missing the following attributes: resnames. These will be written with default values. Alternatively these can be supplied as keyword arguments.
warnings.warn(
MDAnalysisTests/coordinates/test_gro.py: 4 warnings
MDAnalysisTests/coordinates/test_writer_api.py: 2 warnings
MDAnalysisTests/core/test_atomgroup.py: 8 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/GRO.py:479: UserWarning: missing dimension - setting unit cell to zeroed box [0., 0., 0.]
warnings.warn(wmsg)
MDAnalysisTests/coordinates/test_gro.py: 3 warnings
MDAnalysisTests/core/test_atomgroup.py: 8 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/GRO.py:228: UserWarning: Empty box [0., 0., 0.] found - treating as missing unit cell. Dimensions set to `None`.
warnings.warn(wmsg)
MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resids
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/GRO.py:421: UserWarning: Supplied AtomGroup was missing the following attributes: resids. These will be written with default values. Alternatively these can be supplied as keyword arguments.
warnings.warn(
MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_writer_no_atom_names
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/GRO.py:421: UserWarning: Supplied AtomGroup was missing the following attributes: names. These will be written with default values. Alternatively these can be supplied as keyword arguments.
warnings.warn(
MDAnalysisTests/coordinates/test_gro.py: 95 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/GRO.py:216: UserWarning: Not all velocities were present. Unset velocities set to zero.
warnings.warn("Not all velocities were present. "
MDAnalysisTests/coordinates/test_gro.py::test_growriter_resid_truncation
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/GRO.py:421: UserWarning: Supplied AtomGroup was missing the following attributes: names, resnames. These will be written with default values. Alternatively these can be supplied as keyword arguments.
warnings.warn(
MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderWithRealTrajectory::test_wrong_driver
/usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xffffac102480>
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1532, in __del__
self.close()
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/H5MD.py", line 739, in close
self._file.close()
^^^^^^^^^^
AttributeError: 'H5MDReader' object has no attribute '_file'
warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
MDAnalysisTests/coordinates/test_pdb.py: 17 warnings
MDAnalysisTests/coordinates/test_trz.py: 1 warning
MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
MDAnalysisTests/core/test_atomgroup.py: 15 warnings
MDAnalysisTests/transformations/test_nojump.py: 1 warning
MDAnalysisTests/utils/test_modelling.py: 2 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'altLocs' Using default value of ' '
warnings.warn("Found no information for attr: '{}'"
MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
MDAnalysisTests/coordinates/test_pdb.py: 17 warnings
MDAnalysisTests/coordinates/test_trz.py: 1 warning
MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
MDAnalysisTests/core/test_atomgroup.py: 15 warnings
MDAnalysisTests/transformations/test_nojump.py: 1 warning
MDAnalysisTests/utils/test_modelling.py: 2 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'icodes' Using default value of ' '
warnings.warn("Found no information for attr: '{}'"
MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
MDAnalysisTests/coordinates/test_pdb.py: 17 warnings
MDAnalysisTests/coordinates/test_trz.py: 1 warning
MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
MDAnalysisTests/core/test_atomgroup.py: 15 warnings
MDAnalysisTests/transformations/test_nojump.py: 1 warning
MDAnalysisTests/utils/test_modelling.py: 2 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'occupancies' Using default value of '1.0'
warnings.warn("Found no information for attr: '{}'"
MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
MDAnalysisTests/coordinates/test_pdb.py: 17 warnings
MDAnalysisTests/coordinates/test_trz.py: 1 warning
MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
MDAnalysisTests/core/test_atomgroup.py: 15 warnings
MDAnalysisTests/transformations/test_nojump.py: 1 warning
MDAnalysisTests/utils/test_modelling.py: 2 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'tempfactors' Using default value of '0.0'
warnings.warn("Found no information for attr: '{}'"
MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
MDAnalysisTests/coordinates/test_pdb.py: 16 warnings
MDAnalysisTests/coordinates/test_trz.py: 1 warning
MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
MDAnalysisTests/core/test_atomgroup.py: 15 warnings
MDAnalysisTests/transformations/test_nojump.py: 1 warning
MDAnalysisTests/utils/test_modelling.py: 2 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'record_types' Using default value of 'ATOM'
warnings.warn("Found no information for attr: '{}'"
MDAnalysisTests/coordinates/test_h5md.py::TestH5PYNotInstalled::test_reader_no_h5py
/usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xffffac102480>
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1530, in __del__
for aux in self.aux_list:
^^^^^^^^^^^^^
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1170, in aux_list
return self._auxs.keys()
^^^^^^^^^^
AttributeError: 'H5MDReader' object has no attribute '_auxs'
warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
MDAnalysisTests/coordinates/test_lammps.py: 57 warnings
MDAnalysisTests/coordinates/test_windows.py: 20 warnings
MDAnalysisTests/topology/test_lammpsdata.py: 18 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/topology/LAMMPSParser.py:632: UserWarning: Guessed all Masses to 1.0
warnings.warn('Guessed all Masses to 1.0')
MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_time_unit
MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_unit
/usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xffffac102480>
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1530, in __del__
for aux in self.aux_list:
^^^^^^^^^^^^^
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1170, in aux_list
return self._auxs.keys()
^^^^^^^^^^
AttributeError: 'DCDReader' object has no attribute '_auxs'
warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_timeseries_subarray_view
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/memory.py:545: DeprecationWarning: MemoryReader.timeseries inclusive `stop` indexing will be removed in 3.0 in favour of exclusive indexing
warnings.warn("MemoryReader.timeseries inclusive `stop` "
MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times
MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/TRJ.py:554: UserWarning: NCDF trajectory does not contain `time` information; `time` will be set as an increasing index
warnings.warn(wmsg)
MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netCDF4
MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netCDF4
/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:700: RuntimeWarning: Cannot close a netcdf_file opened with mmap=True, when netcdf_variables or arrays referring to its data still exist. All data arrays obtained from such files refer directly to data on disk, and must be copied before the file can be cleanly closed. (See netcdf_file docstring for more information on mmap.)
return self._test_write_trajectory(universe, outfile)
MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf
MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf
MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_factors_default
MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[-2.0--2.0--2.0--2.0--2.0--2.0]
MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[-2.0--2.0--2.0--2.0--2.0--2.0]
MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[1.0-1.0-1.0-1.0-1.0-1.0]
MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[1.0-1.0-1.0-1.0-1.0-1.0]
MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[2.0-4.0-8.0-16.0-32.0-64.0]
MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[2.0-4.0-8.0-16.0-32.0-64.0]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/TRJ.py:969: UserWarning: Could not find netCDF4 module. Falling back to MUCH slower scipy.io.netcdf implementation for writing.
warnings.warn(wmsg)
MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf
MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf
/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:711: RuntimeWarning: Cannot close a netcdf_file opened with mmap=True, when netcdf_variables or arrays referring to its data still exist. All data arrays obtained from such files refer directly to data on disk, and must be copied before the file can be cleanly closed. (See netcdf_file docstring for more information on mmap.)
return self._test_write_trajectory(universe, outfile)
MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
MDAnalysisTests/coordinates/test_pdb.py: 19 warnings
MDAnalysisTests/coordinates/test_trz.py: 1 warning
MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
MDAnalysisTests/core/test_atomgroup.py: 15 warnings
MDAnalysisTests/transformations/test_nojump.py: 1 warning
MDAnalysisTests/utils/test_modelling.py: 2 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'chainIDs' Using default value of ''
warnings.warn("Found no information for attr: '{}'"
MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
MDAnalysisTests/coordinates/test_pdb.py: 56 warnings
MDAnalysisTests/coordinates/test_trz.py: 1 warning
MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
MDAnalysisTests/core/test_atomgroup.py: 15 warnings
MDAnalysisTests/transformations/test_nojump.py: 1 warning
MDAnalysisTests/utils/test_modelling.py: 2 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1200: UserWarning: Found missing chainIDs. Corresponding atoms will use value of 'X'
warnings.warn("Found missing chainIDs."
MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterErrorsWarnings::test_zero_atoms_VE
/usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function WriterBase.__del__ at 0xffffac1027a0>
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1612, in __del__
self.close()
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/TRJ.py", line 1184, in close
if self.trjfile is not None:
^^^^^^^^^^^^
AttributeError: 'NCDFWriter' object has no attribute 'trjfile'
warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resnames
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter]
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter]
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter]
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter]
MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resnames' Using default value of 'UNK'
warnings.warn("Found no information for attr: '{}'"
MDAnalysisTests/coordinates/test_pdb.py: 8 warnings
MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
MDAnalysisTests/transformations/test_nojump.py: 1 warning
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'segids' Using default value of ' '
warnings.warn("Found no information for attr: '{}'"
MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resids
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter]
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter]
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter]
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter]
MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resids' Using default value of '1'
warnings.warn("Found no information for attr: '{}'"
MDAnalysisTests/coordinates/test_pdb.py: 6 warnings
MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
MDAnalysisTests/transformations/test_nojump.py: 1 warning
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'names' Using default value of 'X'
warnings.warn("Found no information for attr: '{}'"
MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[@]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1196: UserWarning: Found chainIDs using unnaccepted character. Corresponding atoms will use value of 'X'
warnings.warn("Found chainIDs using unnaccepted character."
MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[AA]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1192: UserWarning: Found chainIDs with invalid length. Corresponding atoms will use value of 'X'
warnings.warn("Found chainIDs with invalid length."
MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/topology/PDBParser.py:304: UserWarning: Serial numbers went over 100,000. Higher serials have been guessed
warnings.warn("Serial numbers went over 100,000. "
MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/topology/PDBParser.py:423: UserWarning: Invalid atom serials were present, bonds will not be parsed
warnings.warn("Invalid atom serials were present, bonds will not"
MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/topology/PDBParser.py:215: UserWarning: Invalid atom serials were present, bonds will not be parsed
warnings.warn("Invalid atom serials were present, "
MDAnalysisTests/coordinates/test_pdb.py::TestWriterAlignments::test_atomname_alignment
MDAnalysisTests/coordinates/test_pdb.py::TestWriterAlignments::test_atomname_alignment
MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/topology/PDBParser.py:348: UserWarning: Unknown element found for some atoms. These have been given an empty element record. If needed they can be guessed using MDAnalysis.topology.guessers.
warnings.warn(wmsg)
MDAnalysisTests/coordinates/test_pdb.py::test_partially_missing_cryst
/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/coordinates/test_pdb.py:1240: ResourceWarning: unclosed file <_io.TextIOWrapper name='/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/data/incomplete.pdb' mode='r' encoding='UTF-8'>
raw = open(INC_PDB, 'r').readlines()
Enable tracemalloc to get traceback where the object was allocated.
See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info.
MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDBQT.py:296: UserWarning: Supplied AtomGroup was missing the following attributes: altLocs, charges, icodes, occupancies, tempfactors. These will be written with default values.
warnings.warn(
MDAnalysisTests/coordinates/test_tng.py::test_pytng_not_present_raises
/usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xffffac102480>
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1530, in __del__
for aux in self.aux_list:
^^^^^^^^^^^^^
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1170, in aux_list
return self._auxs.keys()
^^^^^^^^^^
AttributeError: 'TNGReader' object has no attribute '_auxs'
warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTriclinicBox::test_trc_n_atoms
MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTruncOctBox::test_universe
MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxOrigin::test_universe
MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxEuler::test_universe
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/TRC.py:265: UserWarning: The trajectory does not contain TIMESTEP blocks!
warnings.warn(
MDAnalysisTests/coordinates/test_trj.py::test_trj_no_natoms
/usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xffffac102480>
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1532, in __del__
self.close()
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/TRJ.py", line 352, in close
if self.trjfile is None:
^^^^^^^^^^^^
AttributeError: 'TRJReader' object has no attribute 'trjfile'
warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer
MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box
MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning
MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other
MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter]
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/TRZ.py:551: UserWarning: Timestep didn't have the following attributes: 'pressure, pressure_tensor, total_energy, potential_energy, kinetic_energy, temperature, step', these will be set to 0 in the output trajectory
warnings.warn("Timestep didn't have the following attributes: '{0}', "
MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer
MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box
MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning
MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other
MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter]
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/TRZ.py:567: UserWarning: Timestep didn't have velocity information, this will be set to zero in output trajectory.
warnings.warn("Timestep didn't have velocity information, "
MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter]
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/TRZ.py:559: UserWarning: Timestep didn't have dimensions information, box will be written as all zero values
warnings.warn("Timestep didn't have dimensions information, "
MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_long_title
/usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function WriterBase.__del__ at 0xffffac1027a0>
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1612, in __del__
self.close()
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/TRZ.py", line 605, in close
if self.trzfile is None:
^^^^^^^^^^^^
AttributeError: 'TRZWriter' object has no attribute 'trzfile'
warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[TRZWriter]
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter]
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/TRZ.py:428: DeprecationWarning: The TRZ writer is deprecated and will be removed in MDAnalysis version 3.0.0
warnings.warn(wmsg, DeprecationWarning)
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[CRDWriter]
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[CRDWriter]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/CRD.py:248: UserWarning: Supplied AtomGroup was missing the following attributes: resnames, resids, names, tempfactors, tempfactors. These will be written with default values.
warnings.warn(
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[GROWriter]
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[GROWriter]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/GRO.py:421: UserWarning: Supplied AtomGroup was missing the following attributes: names, resnames, resids. These will be written with default values. Alternatively these can be supplied as keyword arguments.
warnings.warn(
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBQTWriter]
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBQTWriter]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PDBQT.py:296: UserWarning: Supplied AtomGroup was missing the following attributes: altLocs, charges, icodes, names, occupancies, resids, resnames, tempfactors, types, chainids. These will be written with default values.
warnings.warn(
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PQRWriter]
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PQRWriter]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/PQR.py:301: UserWarning: Supplied AtomGroup was missing the following attributes: names, resnames, resids, charges, radii. These will be written with default values.
warnings.warn(
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[XYZWriter]
MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[XYZWriter]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XYZ.py:193: UserWarning: Input AtomGroup or Universe does not have atom elements or names attributes, writer will default atom names to 'X'
warnings.warn(wmsg)
MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriter_2::test_no_container
/usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function XDRBaseWriter.__del__ at 0xffffa7f25a80>
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py", line 324, in __del__
self.close()
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py", line 321, in close
self._xdr.close()
^^^^^^^^^
AttributeError: 'XTCWriter' object has no attribute '_xdr'
warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriter_2::test_no_container
/usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function XDRBaseWriter.__del__ at 0xffffa7f25a80>
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py", line 324, in __del__
self.close()
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py", line 321, in close
self._xdr.close()
^^^^^^^^^
AttributeError: 'TRRWriter' object has no attribute '_xdr'
warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_io_fails
MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_value_fails
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py:222: UserWarning: Reading offsets from /tmp/pytest-of-debusine-worker/pytest-0/xtc0/.adk_oplsaa.xtc_offsets.npz failed, reading offsets from trajectory instead.
Consider setting 'refresh_offsets=True' when loading your Universe.
warnings.warn(f"Reading offsets from {fname} failed, "
MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_persistent_offsets_readonly
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py:202: UserWarning: Cannot write lock/offset file in same location as /tmp/pytest-of-debusine-worker/pytest-0/test_persistent_offsets_readon0/adk_oplsaa.xtc. Using slow offset calculation.
warnings.warn(f"Cannot write lock/offset file in same location as "
MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_io_fails
MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_value_fails
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py:222: UserWarning: Reading offsets from /tmp/pytest-of-debusine-worker/pytest-0/xtc1/.adk_oplsaa.trr_offsets.npz failed, reading offsets from trajectory instead.
Consider setting 'refresh_offsets=True' when loading your Universe.
warnings.warn(f"Reading offsets from {fname} failed, "
MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_persistent_offsets_readonly
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/coordinates/XDR.py:202: UserWarning: Cannot write lock/offset file in same location as /tmp/pytest-of-debusine-worker/pytest-0/test_persistent_offsets_readon0/adk_oplsaa.trr. Using slow offset calculation.
warnings.warn(f"Cannot write lock/offset file in same location as "
MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[atoms]
MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[atoms]
MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[residues]
MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[residues]
MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[segments]
MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[segments]
/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:88: RuntimeWarning: overflow encountered in reduce
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
MDAnalysisTests/core/test_atomgroup.py: 17 warnings
MDAnalysisTests/core/test_universe.py: 2 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/core/universe.py:833: DeprecationWarning: The bfactor topology attribute is only provided as an alias to the tempfactor attribute. It will be removed in 3.0. Please use the tempfactor attribute instead.
warnings.warn(BFACTOR_WARNING, DeprecationWarning)
MDAnalysisTests/core/test_atomgroup.py: 20 warnings
MDAnalysisTests/core/test_universe.py: 4 warnings
MDAnalysisTests/topology/test_mmtf.py: 3 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/core/topologyattrs.py:295: DeprecationWarning: The bfactor topology attribute is only provided as an alias to the tempfactor attribute. It will be removed in 3.0. Please use the tempfactor attribute instead.
warnings.warn(BFACTOR_WARNING, DeprecationWarning)
MDAnalysisTests/core/test_atomgroup.py: 13840 warnings
MDAnalysisTests/core/test_wrap.py: 3 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/core/groups.py:1074: RuntimeWarning: invalid value encountered in divide
return np.einsum('ij,ij->j',coords,weights[:, None]) / weights.sum()
MDAnalysisTests/core/test_atomgroup.py: 59 warnings
MDAnalysisTests/core/test_wrap.py: 12 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/core/groups.py:1104: RuntimeWarning: invalid value encountered in divide
_centers /= _weights.sum(axis=1)[:, None]
MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/core/selection.py:988: SelectionWarning: Using float equality to select atoms is not recommended because of inherent limitations in representing numbers on computers (see https://docs.python.org/3.8/tutorial/floatingpoint.html for more). Instead, we recommend using a range to select, e.g. 'mass -11.0 to -9.0'. If you still want to compare floats, use the `atol` and `rtol` keywords to modify the tolerance for `np.isclose`.
warnings.warn(msg, category=SelectionWarning)
MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/core/selection.py:988: SelectionWarning: Using float equality to select atoms is not recommended because of inherent limitations in representing numbers on computers (see https://docs.python.org/3.8/tutorial/floatingpoint.html for more). Instead, we recommend using a range to select, e.g. 'mass -4.0 to -2.0'. If you still want to compare floats, use the `atol` and `rtol` keywords to modify the tolerance for `np.isclose`.
warnings.warn(msg, category=SelectionWarning)
MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs12]
MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs13]
MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-5-selkwargs15]
MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-5-selkwargs16]
MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-5-selkwargs16]
MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-10-selkwargs17]
MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-10-selkwargs18]
MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-10-selkwargs19]
MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-10-selkwargs19]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/core/selection.py:988: SelectionWarning: Using float equality to select atoms is not recommended because of inherent limitations in representing numbers on computers (see https://docs.python.org/3.8/tutorial/floatingpoint.html for more). Instead, we recommend using a range to select, e.g. 'mass -0.7 to 1.3'. If you still want to compare floats, use the `atol` and `rtol` keywords to modify the tolerance for `np.isclose`.
warnings.warn(msg, category=SelectionWarning)
MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-fragments]
MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-molecules]
MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-residues]
MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-group]
MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-segments]
MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_cog_pbc
MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_com_pbc
MDAnalysisTests/transformations/test_translate.py::test_center_in_box_coords_all_options
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/core/groups.py:445: DeprecationWarning: The 'pbc' kwarg has been deprecated and will be removed in version 3.0., please use 'wrap' instead
warnings.warn("The 'pbc' kwarg has been deprecated and will be "
MDAnalysisTests/core/test_topologyattrs.py::TestDeprecateBFactor::test_deprecate_bfactor_sel
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/core/selection.py:988: SelectionWarning: Using float equality to select atoms is not recommended because of inherent limitations in representing numbers on computers (see https://docs.python.org/3.8/tutorial/floatingpoint.html for more). Instead, we recommend using a range to select, e.g. 'bfactor 2.0 to 4.0'. If you still want to compare floats, use the `atol` and `rtol` keywords to modify the tolerance for `np.isclose`.
warnings.warn(msg, category=SelectionWarning)
MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[serial]
MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[openmp]
MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[serial]
MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[serial]
MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[openmp]
MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[openmp]
MDAnalysisTests/lib/test_util.py::TestGeometryFunctions::test_vectors[x_axis5-y_axis5-nan]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/lib/mdamath.py:156: RuntimeWarning: invalid value encountered in scalar divide
x = np.dot(a, b) / (norm(a) * norm(b))
MDAnalysisTests/lib/test_util.py: 48 warnings
/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/lib/test_util.py:293: RuntimeWarning: invalid value encountered in sqrt
ref[2, 2] = np.sqrt(z * z - ref[2, 0] ** 2 - ref[2, 1] ** 2)
MDAnalysisTests/lib/test_util.py: 353 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/lib/mdamath.py:392: RuntimeWarning: invalid value encountered in sqrt
box_matrix[2, 2] = np.sqrt(lz * lz - box_matrix[2, 0] ** 2 -
MDAnalysisTests/lib/test_util.py: 339 warnings
/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/lib/test_util.py:324: RuntimeWarning: invalid value encountered in scalar divide
a = np.rad2deg(np.arccos(np.dot(tri_vecs[1], tri_vecs[2]) / (y * z)))
MDAnalysisTests/lib/test_util.py: 363 warnings
/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/lib/test_util.py:325: RuntimeWarning: invalid value encountered in scalar divide
b = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[2]) / (x * z)))
MDAnalysisTests/lib/test_util.py: 756 warnings
/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/lib/test_util.py:326: RuntimeWarning: invalid value encountered in scalar divide
c = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[1]) / (x * y)))
MDAnalysisTests/lib/test_util.py: 43 warnings
/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: invalid value encountered in scalar divide
ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c
MDAnalysisTests/lib/test_util.py: 17 warnings
/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: divide by zero encountered in scalar divide
ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c
MDAnalysisTests/parallelism/test_pickle_transformation.py::test_add_PositionAverager_pickle[u0]
MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_fwd
MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_bwd
MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_reset
MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_specific
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/transformations/positionaveraging.py:193: Warning: Cannot average position for non sequentialiterations. Averager will be reset.
warnings.warn('Cannot average position for non sequential'
MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid
MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid
MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid
MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/topology/PDBParser.py:290: UserWarning: PDB file is missing resid information. Defaulted to '1'
warnings.warn("PDB file is missing resid information. "
MDAnalysisTests/topology/test_top.py: 42 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/topology/TOPParser.py:306: UserWarning: Unknown ATOMIC_NUMBER value found for some atoms, these have been given an empty element record. If needed these can be guessed using MDAnalysis.topology.guessers.
warnings.warn(msg)
MDAnalysisTests/transformations/test_fit.py::test_fit_translation_no_masses
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/align.py:1509: SelectionWarning: Atoms could not be matched since they don't contain masses.
warnings.warn(msg, category=SelectionWarning)
MDAnalysisTests/transformations/test_nojump.py::test_nojump_constantvel_stride_2
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/transformations/nojump.py:139: UserWarning: NoJump detected that the interval between frames is unequal.We are resetting the reference frame to the current timestep.
warnings.warn(
MDAnalysisTests/utils/test_pickleio.py::test_get_right_open_handler_text[f_text0]
MDAnalysisTests/utils/test_pickleio.py::test_get_right_open_handler_text[f_text1]
MDAnalysisTests/utils/test_pickleio.py::test_iopickle_text[f_text0]
MDAnalysisTests/utils/test_pickleio.py::test_iopickle_text[f_text1]
MDAnalysisTests/utils/test_pickleio.py::test_offset_text_to_0[f_text0]
MDAnalysisTests/utils/test_pickleio.py::test_offset_text_to_0[f_text1]
/usr/lib/python3/dist-packages/_pytest/runner.py:142: ResourceWarning: unclosed file <_io.TextIOWrapper name='/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/data/adk_oplsaa.pdb' encoding='UTF-8'>
item.funcargs = None # type: ignore[attr-defined]
Enable tracemalloc to get traceback where the object was allocated.
See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info.
MDAnalysisTests/utils/test_pickleio.py::test_iopickle_text[f_text0]
MDAnalysisTests/utils/test_pickleio.py::test_iopickle_text[f_text1]
MDAnalysisTests/utils/test_pickleio.py::test_offset_text_to_0[f_text0]
MDAnalysisTests/utils/test_pickleio.py::test_offset_text_to_0[f_text1]
MDAnalysisTests/utils/test_pickleio.py::test_context_manager_pickle
/usr/lib/python3/dist-packages/_pytest/python.py:159: ResourceWarning: unclosed file <_io.TextIOWrapper name='/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/data/adk_oplsaa.pdb' encoding='UTF-8'>
result = testfunction(**testargs)
Enable tracemalloc to get traceback where the object was allocated.
See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info.
MDAnalysisTests/utils/test_pickleio.py::test_get_right_open_handler_byte[f_byte0]
MDAnalysisTests/utils/test_pickleio.py::test_iopickle_byte[f_byte0]
MDAnalysisTests/utils/test_pickleio.py::test_offset_byte_to_tell[f_byte0]
/usr/lib/python3/dist-packages/_pytest/runner.py:142: ResourceWarning: unclosed file <BufferIOPicklable name='/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/data/adk_oplsaa.pdb'>
item.funcargs = None # type: ignore[attr-defined]
Enable tracemalloc to get traceback where the object was allocated.
See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info.
MDAnalysisTests/utils/test_pickleio.py::test_iopickle_byte[f_byte0]
MDAnalysisTests/utils/test_pickleio.py::test_offset_byte_to_tell[f_byte0]
MDAnalysisTests/utils/test_pickleio.py::test_fileio_pickle
MDAnalysisTests/utils/test_pickleio.py::test_fileio_pickle
/usr/lib/python3/dist-packages/_pytest/python.py:159: ResourceWarning: unclosed file <_io.FileIO name='/<<PKGBUILDDIR>>/testsuite/MDAnalysisTests/data/adk_oplsaa.pdb' mode='rb' closefd=True>
result = testfunction(**testargs)
Enable tracemalloc to get traceback where the object was allocated.
See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info.
MDAnalysisTests/utils/test_pickleio.py::test_pickle_with_write_mode[unpicklable_f0]
/usr/lib/python3/dist-packages/_pytest/python.py:159: ResourceWarning: unclosed file <_io.FileIO name=local('/tmp/pytest-of-debusine-worker/pytest-0/test_pickle_with_write_mode_un0/pickle/test.pdb') mode='wb' closefd=True>
result = testfunction(**testargs)
Enable tracemalloc to get traceback where the object was allocated.
See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info.
MDAnalysisTests/utils/test_pickleio.py::test_pickle_with_write_mode[unpicklable_f1]
/usr/lib/python3/dist-packages/_pytest/python.py:159: ResourceWarning: unclosed file <_io.FileIO name=local('/tmp/pytest-of-debusine-worker/pytest-0/test_pickle_with_write_mode_un1/pickle/test.pdb') mode='xb' closefd=True>
result = testfunction(**testargs)
Enable tracemalloc to get traceback where the object was allocated.
See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info.
MDAnalysisTests/utils/test_pickleio.py::test_pickle_with_write_mode[unpicklable_f2]
/usr/lib/python3/dist-packages/_pytest/python.py:159: ResourceWarning: unclosed file <_io.FileIO name=local('/tmp/pytest-of-debusine-worker/pytest-0/test_pickle_with_write_mode_un2/pickle/test.pdb') mode='ab' closefd=True>
result = testfunction(**testargs)
Enable tracemalloc to get traceback where the object was allocated.
See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info.
MDAnalysisTests/utils/test_units.py::TestConstants::test_constant[Boltzman_constant-0.008314462159]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/units.py:183: DeprecationWarning: Please use 'Boltzmann_constant' henceforth. The key 'Boltzman_constant' was a typo and will be removed in MDAnalysis 2.8.0.
warnings.warn(wmsg, DeprecationWarning)
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
= 18631 passed, 594 skipped, 7 xfailed, 3 xpassed, 27465 warnings in 657.25s (0:10:57) =
--- Logging error ---
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/duecredit/utils.py", line 209, in wrapped_func
return f(*args, **kwargs)
^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/duecredit/dueswitch.py", line 102, in dump
due_summary.dump()
File "/usr/lib/python3/dist-packages/duecredit/collector.py", line 499, in dump
output.dump()
File "/usr/lib/python3/dist-packages/duecredit/io.py", line 247, in dump
self.fd.write(get_text_rendering(cit.entry, style=self.style))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/duecredit/io.py", line 254, in get_text_rendering
return format_bibtex(get_bibtex_rendering(entry), style=style)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/duecredit/io.py", line 267, in get_bibtex_rendering
return BibTeX(import_doi(entry.doi))
^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/duecredit/io.py", line 50, in import_doi
cached = get_doi_cache_file(doi)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/duecredit/io.py", line 43, in get_doi_cache_file
os.makedirs(CACHE_DIR)
File "<frozen os>", line 215, in makedirs
File "<frozen os>", line 215, in makedirs
File "<frozen os>", line 215, in makedirs
File "<frozen os>", line 225, in makedirs
PermissionError: [Errno 13] Permission denied: '/sbuild-nonexistent'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
ValueError: I/O operation on closed file.
Call stack:
File "/usr/lib/python3/dist-packages/duecredit/utils.py", line 211, in wrapped_func
lgr.warning(
Message: "DueCredit internal failure while running <function DueSwitch.dump at 0xffffabd354e0>: PermissionError(13, 'Permission denied'). Please report to developers at https://github.com/duecredit/duecredit/issues"
Arguments: ()
DueCredit Report:
- Molecular simulation analysis library / MDAnalysis (v 2.7.0) [1, 2]
- Bond-Angle-Torsions Coordinate Transformation / MDAnalysis.analysis.bat.BAT (v 2.7.0) [3]
- Dielectric analysis / MDAnalysis.analysis.dielectric (v 2.7.0) [4]
- ENCORE Ensemble Comparison / MDAnalysis.analysis.encore (v 2.7.0) [5]
- HOLE trajectory analysis with orderparameters, HOLE program / MDAnalysis.analysis.hole2 (v 2.7.0) [6, 7, 8]
- Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.7.0) [9]
- Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel (v 2.7.0) [10]
- LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.7.0) [2]
- Mean Squared Displacements with tidynamics, FCA fast correlation algorithm / MDAnalysis.analysis.msd (v 2.7.0) [11, 12]
- Cumulative overlap / MDAnalysis.analysis.pca (v 2.7.0) [13]
- Path Similarity Analysis algorithm and implementation / MDAnalysis.analysis.psa (v 2.7.0) [14]
- Specifications of the H5MD standard, MDAnalysis trajectory reader/writer of the H5MDformat / MDAnalysis.coordinates.H5MD (v 1.1, 2.7.0) [15, 16]
- MMTF Reader / MDAnalysis.coordinates.MMTF (v 2.7.0) [17]
- The TNG paper / MDAnalysis.coordinates.TNG (v 2.7.0) [18]
- QCProt implementation / MDAnalysis.lib.qcprot (v 2.7.0) [19, 20]
- MMTF Parser / MDAnalysis.topology.MMTFParser (v 2.7.0) [17]
- Works through the orthogonal case for unwrapping, and proposes the non-orthogonal approach. / MDAnalysis.transformations.nojump (v 2.7.0) [21]
- Scientific tools library / numpy (v 1.26.4) [22]
2 packages cited
16 modules cited
0 functions cited
References
----------
[1] make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
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dpkg-deb: building package 'python3-mdanalysis' in '../python3-mdanalysis_2.7.0-5+bd1_arm64.deb'.
dpkg-deb: building package 'python3-mdanalysis-dbgsym' in '../python3-mdanalysis-dbgsym_2.7.0-5+bd1_arm64.deb'.
dpkg-genbuildinfo --build=any -O../mdanalysis_2.7.0-5+bd1_arm64.buildinfo
dpkg-genchanges --build=any -mDebusine Rebuild <debusine@example.net> -O../mdanalysis_2.7.0-5+bd1_arm64.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-source: info: using options from mdanalysis-2.7.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2024-10-24T16:52:02Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
mdanalysis_2.7.0-5+bd1_arm64.changes:
-------------------------------------
Format: 1.8
Date: Thu, 24 Oct 2024 16:35:39 +0000
Source: mdanalysis (2.7.0-5)
Binary: python3-mdanalysis python3-mdanalysis-dbgsym
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Urgency: low
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Changed-By: Debusine Rebuild <debusine@example.net>
Description:
python3-mdanalysis - analyse molecular dynamics files and trajectories
Changes:
mdanalysis (2.7.0-5+bd1) sid; urgency=low, binary-only=yes
.
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.
* Append +bd1 to version number; no source changes
* Binary-only non-maintainer upload for arm64; no source changes.
* Rebuild for python3.13
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87256f99bf774d3a8122e50a77f5297e6246af645e5de8840cc4cf83888855fd 2292112 python3-mdanalysis_2.7.0-5+bd1_arm64.deb
Build-Origin: Debian
Build-Architecture: arm64
Build-Date: Thu, 24 Oct 2024 16:52:02 +0000
Build-Path: /<<PKGBUILDDIR>>
Build-Tainted-By:
merged-usr-via-aliased-dirs
Installed-Build-Depends:
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automake (= 1:1.16.5-1.3),
autopoint (= 0.22.5-2),
autotools-dev (= 20220109.1),
base-files (= 13.5),
base-passwd (= 3.6.5),
bash (= 5.2.32-1+b2),
binutils (= 2.43.1-5),
binutils-aarch64-linux-gnu (= 2.43.1-5),
binutils-common (= 2.43.1-5),
blt (= 2.5.3+dfsg-7),
bsdextrautils (= 2.40.2-9),
bsdutils (= 1:2.40.2-9),
build-essential (= 12.12),
bzip2 (= 1.0.8-6),
ca-certificates (= 20240203),
coreutils (= 9.5-1),
cpp (= 4:14.2.0-1),
cpp-14 (= 14.2.0-7),
cpp-14-aarch64-linux-gnu (= 14.2.0-7),
cpp-aarch64-linux-gnu (= 4:14.2.0-1),
cython3 (= 3.0.11+dfsg-1+debusine1),
dash (= 0.5.12-9),
debconf (= 1.5.87),
debhelper (= 13.20),
debianutils (= 5.20),
dh-autoreconf (= 20),
dh-python (= 6.20240824),
dh-strip-nondeterminism (= 1.14.0-1),
diffutils (= 1:3.10-1),
docutils-common (= 0.21.2+dfsg-2),
dpkg (= 1.22.11),
dpkg-dev (= 1.22.11),
dwz (= 0.15-1+b1),
file (= 1:5.45-3),
findutils (= 4.10.0-3),
fontconfig-config (= 2.15.0-1.1),
fonts-dejavu-core (= 2.37-8),
fonts-dejavu-mono (= 2.37-8),
fonts-font-awesome (= 5.0.10+really4.7.0~dfsg-4.1),
fonts-lato (= 2.015-1),
fonts-lyx (= 2.4.2.1-1),
fonts-urw-base35 (= 20200910-8),
g++ (= 4:14.2.0-1),
g++-14 (= 14.2.0-7),
g++-14-aarch64-linux-gnu (= 14.2.0-7),
g++-aarch64-linux-gnu (= 4:14.2.0-1),
gcc (= 4:14.2.0-1),
gcc-14 (= 14.2.0-7),
gcc-14-aarch64-linux-gnu (= 14.2.0-7),
gcc-14-base (= 14.2.0-7),
gcc-aarch64-linux-gnu (= 4:14.2.0-1),
gettext (= 0.22.5-2),
gettext-base (= 0.22.5-2),
grep (= 3.11-4),
groff-base (= 1.23.0-5),
gzip (= 1.12-1.1),
hostname (= 3.25),
init-system-helpers (= 1.67),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.2-2),
libaec0 (= 1.1.3-1),
libarchive-zip-perl (= 1.68-1),
libasan8 (= 14.2.0-7),
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libattr1 (= 1:2.5.2-2),
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libaudit1 (= 1:4.0.1-1),
libbinutils (= 2.43.1-5),
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libbsd0 (= 0.12.2-2),
libbz2-1.0 (= 1.0.8-6),
libc-bin (= 2.40-3),
libc-dev-bin (= 2.40-3),
libc6 (= 2.40-3),
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libcairo2 (= 1.18.2-2),
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libcap2 (= 1:2.66-5),
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libcrypt-dev (= 1:4.4.36-5),
libcrypt1 (= 1:4.4.36-5),
libctf-nobfd0 (= 2.43.1-5),
libctf0 (= 2.43.1-5),
libcurl3t64-gnutls (= 8.10.1-2),
libcurl4t64 (= 8.10.1-2),
libdb5.3t64 (= 5.3.28+dfsg2-9),
libdebconfclient0 (= 0.272),
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libgcc-s1 (= 14.2.0-7),
libgcrypt20 (= 1.11.0-6),
libgdbm-compat4t64 (= 1.24-2),
libgdbm6t64 (= 1.24-2),
libgfortran5 (= 14.2.0-7),
libglib2.0-0t64 (= 2.82.2-1),
libgmp10 (= 2:6.3.0+dfsg-2+b1),
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libgpg-error0 (= 1.50-4),
libgprofng0 (= 2.43.1-5),
libgraphite2-3 (= 1.3.14-2),
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libharfbuzz0b (= 10.0.1-1),
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libhdf5-hl-100t64 (= 1.10.10+repack-4),
libhogweed6t64 (= 3.10-1),
libhwasan0 (= 14.2.0-7),
libicu72 (= 72.1-5),
libidn2-0 (= 2.3.7-2),
libimagequant0 (= 2.18.0-1+b1),
libisl23 (= 0.27-1),
libitm1 (= 14.2.0-7),
libjansson4 (= 2.14-2+b2),
libjbig0 (= 2.1-6.1+b1),
libjpeg62-turbo (= 1:2.1.5-3),
libjs-jquery (= 3.6.1+dfsg+~3.5.14-1),
libjs-jquery-ui (= 1.13.2+dfsg-1),
libjs-sphinxdoc (= 7.4.7-3),
libjs-underscore (= 1.13.4~dfsg+~1.11.4-3),
libjson-perl (= 4.10000-1),
libk5crypto3 (= 1.21.3-3),
libkeyutils1 (= 1.6.3-4),
libkrb5-3 (= 1.21.3-3),
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liblapack3 (= 3.12.0-3),
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liblz4-1 (= 1.9.4-3),
liblzf1 (= 3.6-4+b1),
liblzma5 (= 5.6.2-2),
libmagic-mgc (= 1:5.45-3),
libmagic1t64 (= 1:5.45-3),
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libmount1 (= 2.40.2-9),
libmpc3 (= 1.3.1-1+b2),
libmpfr6 (= 4.2.1-1+b1),
libncursesw6 (= 6.5-2),
libnetcdf19t64 (= 1:4.9.2-7),
libnettle8t64 (= 3.10-1),
libnghttp2-14 (= 1.63.0-1),
libnghttp3-9 (= 1.4.0-1),
libngtcp2-16 (= 1.6.0-1),
libngtcp2-crypto-gnutls8 (= 1.6.0-1),
libnsl2 (= 1.3.0-3+b2),
libopenjp2-7 (= 2.5.0-2+b3),
libp11-kit0 (= 0.25.5-2),
libpam-modules (= 1.5.3-7),
libpam-modules-bin (= 1.5.3-7),
libpam-runtime (= 1.5.3-7),
libpam0g (= 1.5.3-7),
libpcre2-8-0 (= 10.42-4+b1),
libperl5.40 (= 5.40.0-6),
libpipeline1 (= 1.5.8-1),
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libpng16-16t64 (= 1.6.44-2),
libproc2-0 (= 2:4.0.4-6),
libpsl5t64 (= 0.21.2-1.1),
libpython3-all-dev (= 3.12.6-1+debusine1),
libpython3-dev (= 3.12.6-1+debusine1),
libpython3-stdlib (= 3.12.6-1+debusine1),
libpython3.12-dev (= 3.12.7-1),
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libpython3.12-stdlib (= 3.12.7-1),
libpython3.12t64 (= 3.12.7-1),
libpython3.13 (= 3.13.0-1),
libpython3.13-dev (= 3.13.0-1),
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libpython3.13-stdlib (= 3.13.0-1),
libqhull-r8.0 (= 2020.2-6+b1),
libraqm0 (= 0.10.1-1+b1),
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libsasl2-2 (= 2.1.28+dfsg1-8),
libsasl2-modules-db (= 2.1.28+dfsg1-8),
libseccomp2 (= 2.5.5-1+b1),
libselinux1 (= 3.7-3),
libsframe1 (= 2.43.1-5),
libsharpyuv0 (= 1.4.0-0.1),
libsmartcols1 (= 2.40.2-9),
libsqlite3-0 (= 3.46.1-1),
libssh2-1t64 (= 1.11.1-1),
libssl3t64 (= 3.3.2-1),
libstdc++-14-dev (= 14.2.0-7),
libstdc++6 (= 14.2.0-7),
libsystemd0 (= 256.7-2),
libsz2 (= 1.1.3-1),
libtasn1-6 (= 4.19.0-3+b2),
libtcl8.6 (= 8.6.15+dfsg-2),
libtiff6 (= 4.5.1+git230720-5),
libtinfo6 (= 6.5-2),
libtirpc-common (= 1.3.4+ds-1.3),
libtirpc3t64 (= 1.3.4+ds-1.3),
libtk8.6 (= 8.6.15-1),
libtool (= 2.4.7-7),
libtsan2 (= 14.2.0-7),
libubsan1 (= 14.2.0-7),
libuchardet0 (= 0.0.8-1+b1),
libudev1 (= 256.7-2),
libunistring5 (= 1.2-1),
libuuid1 (= 2.40.2-9),
libwebp7 (= 1.4.0-0.1),
libwebpdemux2 (= 1.4.0-0.1),
libwebpmux3 (= 1.4.0-0.1),
libx11-6 (= 2:1.8.7-1+b1),
libx11-data (= 2:1.8.7-1),
libxau6 (= 1:1.0.9-1+b1),
libxcb-render0 (= 1.17.0-2),
libxcb-shm0 (= 1.17.0-2),
libxcb1 (= 1.17.0-2),
libxdmcp6 (= 1:1.1.2-3+b1),
libxext6 (= 2:1.3.4-1+b2),
libxft2 (= 2.3.6-1+b1),
libxml2 (= 2.12.7+dfsg+really2.9.14-0.1),
libxrender1 (= 1:0.9.10-1.1+b1),
libxslt1.1 (= 1.1.35-1.1),
libxss1 (= 1:1.2.3-1+b1),
libxxhash0 (= 0.8.2-2+b1),
libzstd1 (= 1.5.6+dfsg-1),
linux-libc-dev (= 6.11.4-1),
m4 (= 1.4.19-4),
make (= 4.3-4.1),
man-db (= 2.13.0-1),
mawk (= 1.3.4.20240905-1),
media-types (= 10.1.0),
ncurses-base (= 6.5-2),
ncurses-bin (= 6.5-2),
netbase (= 6.4),
openssl (= 3.3.2-1),
openssl-provider-legacy (= 3.3.2-1),
patch (= 2.7.6-7),
perl (= 5.40.0-6),
perl-base (= 5.40.0-6),
perl-modules-5.40 (= 5.40.0-6),
po-debconf (= 1.0.21+nmu1),
procps (= 2:4.0.4-6),
pybuild-plugin-pyproject (= 6.20240824),
python-babel-localedata (= 2.14.0-1),
python-matplotlib-data (= 3.8.3-3+bootstrap1),
python3 (= 3.12.6-1+debusine1),
python3-alabaster (= 0.7.16-0.1),
python3-all (= 3.12.6-1+debusine1),
python3-all-dev (= 3.12.6-1+debusine1),
python3-appdirs (= 1.4.4-4),
python3-attr (= 24.2.0-1),
python3-autocommand (= 2.2.2-3),
python3-babel (= 2.14.0-1),
python3-biopython (= 1.84+dfsg-3+bd1),
python3-brotli (= 1.1.0-2+b4),
python3-build (= 1.2.2-1),
python3-cairo (= 1.26.1-2),
python3-certifi (= 2024.8.30+dfsg-1),
python3-cftime (= 1.6.4-1+b1),
python3-chardet (= 5.2.0+dfsg-1),
python3-charset-normalizer (= 3.4.0-1),
python3-citeproc (= 0.6.0-3),
python3-contourpy (= 1.3.0-2),
python3-cycler (= 0.12.1-1),
python3-dateutil (= 2.9.0-3),
python3-decorator (= 5.1.1-5),
python3-defusedxml (= 0.7.1-2),
python3-dev (= 3.12.6-1+debusine1),
python3-docutils (= 0.21.2+dfsg-2),
python3-duecredit (= 0.10.2-2),
python3-fasteners (= 0.18-2),
python3-fonttools (= 4.54.1-4),
python3-freetype (= 2.5.1-1),
python3-fs (= 2.4.16-4),
python3-griddataformats (= 1.0.2-2),
python3-gsd (= 3.3.0-1+bd1),
python3-h5py (= 3.11.0-7),
python3-h5py-serial (= 3.11.0-7+bd1),
python3-hypothesis (= 6.115.3-1),
python3-idna (= 3.8-2),
python3-imagesize (= 1.4.1-1),
python3-inflect (= 7.3.1-2),
python3-iniconfig (= 1.1.1-2),
python3-installer (= 0.7.0+dfsg1-3),
python3-jaraco.context (= 6.0.0-1),
python3-jaraco.functools (= 4.1.0-1),
python3-jaraco.text (= 4.0.0-1),
python3-jinja2 (= 3.1.3-1),
python3-joblib (= 1.3.2-4),
python3-kiwisolver (= 1.4.7-2),
python3-looseversion (= 1.3.0-3),
python3-lxml (= 5.3.0-1),
python3-lz4 (= 4.0.2+dfsg-1+b4),
python3-markupsafe (= 2.1.5-1+b1),
python3-matplotlib (= 3.8.3-3+bootstrap1),
python3-mda-xdrlib (= 0.2.0-3),
python3-minimal (= 3.12.6-1+debusine1),
python3-mmtf (= 1.1.3-1),
python3-monotonic (= 1.6-2),
python3-more-itertools (= 10.5.0-1),
python3-mpmath (= 1.3.0-1),
python3-mrcfile (= 1.5.3-3),
python3-msgpack (= 1.0.3-3+b2),
python3-netcdf4 (= 1.7.2-1+bd1),
python3-networkx (= 3.2.1-4),
python3-numpy (= 1:1.26.4+ds-11+bootstrap1),
python3-packaging (= 24.1-1),
python3-pandas (= 2.2.3+dfsg-4),
python3-pandas-lib (= 2.2.3+dfsg-4),
python3-pil (= 10.4.0-1),
python3-pil.imagetk (= 10.4.0-1),
python3-pkg-resources (= 75.2.0-1),
python3-pluggy (= 1.5.0-1),
python3-pygments (= 2.18.0+dfsg-1),
python3-pyparsing (= 3.1.2-1),
python3-pyproject-hooks (= 1.1.0-2),
python3-pytest (= 8.3.3-1),
python3-reportlab (= 4.2.5-1),
python3-requests (= 2.32.3+dfsg-1),
python3-rlpycairo (= 0.3.0-3),
python3-roman (= 4.2-1),
python3-scipy (= 1.13.1-5+nocheck1),
python3-seaborn (= 0.13.2-4),
python3-setuptools (= 75.2.0-1),
python3-six (= 1.16.0-7),
python3-sklearn (= 1.4.2+dfsg-6),
python3-sklearn-lib (= 1.4.2+dfsg-6+debusine1),
python3-snowballstemmer (= 2.2.0-4),
python3-sortedcontainers (= 2.4.0-2),
python3-sphinx (= 7.4.7-3),
python3-sympy (= 1.13.3-1),
python3-threadpoolctl (= 3.1.0-1),
python3-tk (= 3.12.6-1),
python3-toml (= 0.10.2-1),
python3-tqdm (= 4.66.5-1),
python3-typeguard (= 4.3.0-1),
python3-typing-extensions (= 4.12.2-2),
python3-tz (= 2024.1-2),
python3-ufolib2 (= 0.16.0+dfsg1-1),
python3-urllib3 (= 2.0.7-2),
python3-wheel (= 0.44.0-2),
python3-zipp (= 3.20.2-1),
python3.12 (= 3.12.7-1),
python3.12-dev (= 3.12.7-1),
python3.12-minimal (= 3.12.7-1),
python3.12-tk (= 3.12.7-1),
python3.13 (= 3.13.0-1),
python3.13-dev (= 3.13.0-1),
python3.13-minimal (= 3.13.0-1),
python3.13-tk (= 3.13.0-1),
readline-common (= 8.2-5),
rpcsvc-proto (= 1.4.3-1),
sed (= 4.9-2),
sensible-utils (= 0.0.24),
sgml-base (= 1.31),
sphinx-common (= 7.4.7-3),
sphinx-rtd-theme-common (= 3.0.1+dfsg-1),
sysvinit-utils (= 3.11-1),
tar (= 1.35+dfsg-3),
tk8.6-blt2.5 (= 2.5.3+dfsg-7),
tzdata (= 2024b-3),
unicode-data (= 15.1.0-1),
util-linux (= 2.40.2-9),
w3c-sgml-lib (= 1.3-3),
x11-common (= 1:7.7+23.1),
xfonts-encodings (= 1:1.0.4-2.2),
xfonts-utils (= 1:7.7+7),
xml-core (= 0.19),
xz-utils (= 5.6.2-2),
zlib1g (= 1:1.3.dfsg+really1.3.1-1),
zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1)
Environment:
DEB_BUILD_OPTIONS="parallel=8"
LANG="C.UTF-8"
LC_COLLATE="C.UTF-8"
LC_CTYPE="C.UTF-8"
SOURCE_DATE_EPOCH="1729787739"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
python3-mdanalysis-dbgsym_2.7.0-5+bd1_arm64.deb
-----------------------------------------------
new Debian package, version 2.0.
size 11119056 bytes: control archive=1876 bytes.
1515 bytes, 12 lines control
3064 bytes, 29 lines md5sums
Package: python3-mdanalysis-dbgsym
Source: mdanalysis (2.7.0-5)
Version: 2.7.0-5+bd1
Auto-Built-Package: debug-symbols
Architecture: arm64
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Installed-Size: 11800
Depends: python3-mdanalysis (= 2.7.0-5+bd1)
Section: debug
Priority: optional
Description: debug symbols for python3-mdanalysis
Build-Ids: 058207cc0f6b222e535f00ceb099748303f668c5 0ae00e416d3926f8edb16d0be487249c83f74a8f 0d978de07af5d95130a88b4ac2648a1cd9d267c4 10e90384ababbdc08d94203e7cb9d8d36349f59e 15b942189a9954aa754dda868037b33eb35b4af4 187a5f2539821e20cd9608cf552cf8be622b74ad 1bd482b031655f769ef934e9fbb20eec2dc50f39 29adce07bb174da9be584b0f5077129a35715e61 31d9ee14a44ebff944fe3f5c0ce9f20226ab9229 3266d7526f5e474a55eaf9ab6545a4ce4ab00b3b 366ddfe594d2c0d55a57f51e93c74a696f808bbc 4cbb88b2f1200ef3166ccf75a471b9d30ae8648a 5bc386ef4adad6c89476609056876b79e76e75d7 6c6f1bd28a810fb095c67815fdb70ded16cd3876 708adf549bded59667236c6e02158b289145b241 79d8dfca16f9d21a57413cf2f7db50ec9827d708 89a7fd2dc420431e587ae0b3fda3a8d6f618cdfb 9bee656a6a14603db785c9ca9f35fdd0183aad65 acf0e3f69c8f2dfeb57ce1aa5c1e6e1e5ca59980 b3559ddc4930714ee82e6cfe9230991bda3659c1 bedd071decf142d1e37c7d9b9d2462418983e25a da16f04d86157096abb498ea394529d80246a860 dadef79c893be961acea708796cb827449dda268 dd6481f6c325cc99dd9a67929263147ec6a4e390 e32a57db13bcf38d458d7fd86fd1324d71bd8814 f9d7624966ab2b341fef563261628f91c44fd9c5 fd05035e780aad61ac6b9072b41e9f858d89b8b6 ff5efa414761d1f6aca74e329e420377cc7f8c72
drwxr-xr-x root/root 0 2024-10-24 16:35 ./
drwxr-xr-x root/root 0 2024-10-24 16:35 ./usr/
drwxr-xr-x root/root 0 2024-10-24 16:35 ./usr/lib/
drwxr-xr-x root/root 0 2024-10-24 16:35 ./usr/lib/debug/
drwxr-xr-x root/root 0 2024-10-24 16:35 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2024-10-24 16:35 ./usr/lib/debug/.build-id/05/
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drwxr-xr-x root/root 0 2024-10-24 16:35 ./usr/lib/debug/.build-id/0a/
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drwxr-xr-x root/root 0 2024-10-24 16:35 ./usr/lib/debug/.build-id/0d/
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Package: python3-mdanalysis
Source: mdanalysis (2.7.0-5)
Version: 2.7.0-5+bd1
Architecture: arm64
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Installed-Size: 25424
Depends: python3-duecredit, python3 (<< 3.14), python3 (>= 3.12~), python3-fasteners, python3-griddataformats, python3-joblib, python3-matplotlib, python3-mda-xdrlib, python3-mmtf, python3-numpy (>= 1:1.25.0), python3-numpy-abi9, python3-packaging, python3-scipy, python3-threadpoolctl, python3-tqdm, python3:any, libc6 (>= 2.17), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libstdc++6 (>= 11)
Recommends: python3-sklearn
Suggests: python-mdanalysis-doc
Section: python
Priority: optional
Homepage: https://www.mdanalysis.org/
Description: analyse molecular dynamics files and trajectories
MDAnalysis is a Python library for the analysis of computer
simulations of many-body systems at the molecular scale, spanning use
cases from interactions of drugs with proteins to novel materials. It
is widely used in the scientific community and is written by
scientists for scientists.
.
MDAnalysis allows one to read particle-based trajectories (including
individual coordinate frames such as biomolecules in the PDB format)
and access the atomic coordinates through NumPy arrays. This provides
a flexible and relatively fast framework for complex analysis tasks.
In addition, powerful atom selection commands are implemented.
Trajectories can also be manipulated (for instance, fit to a
reference structure) and written out.
.
It works with a wide range of popular simulation packages including
Gromacs, Amber, NAMD, CHARMM, DL_Poly, HooMD, LAMMPS and many others
— see the lists of supported trajectory formats and topology formats.
MDAnalysis also includes widely used analysis algorithms in the
MDAnalysis.analysis module.
.
The MDAnalysis project uses an open governance model and is fiscally
sponsored by NumFOCUS.
.
This package installs the library for Python 3.
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