Artifact prody_2.4.1+dfsg-2+bd1_arm64-2024-11-01T16:09:31Z

sbuild (Debian sbuild) 0.85.11~bpo12+1 (31 August 2024) on debusine-worker-arm64-demeter-02.freexian.com

+==============================================================================+
| prody 2.4.1+dfsg-2+bd1 (arm64)               Fri, 01 Nov 2024 16:09:31 +0000 |
+==============================================================================+

Package: prody
Version: 2.4.1+dfsg-2+bd1
Source Version: 2.4.1+dfsg-2
Distribution: sid
Machine Architecture: arm64
Host Architecture: arm64
Build Architecture: arm64
Build Type: any

I: No tarballs found in /var/lib/debusine/worker/.cache/sbuild
Unpacking /var/lib/debusine/worker/system-images/894003/system.tar.xz to /tmp/tmp.sbuild.K1YcMyObiQ...
I: NOTICE: Log filtering will replace 'sbuild-unshare-dummy-location' with '<<CHROOT>>'

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| Chroot Setup Commands                                                        |
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rm -f /etc/resolv.conf
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I: Finished running 'rm -f /etc/resolv.conf'.

Finished processing commands.
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Copying /tmp/debusine-fetch-exec-upload-ov32oqs_/libpython3-all-dbg_3.12.6-1+debusine1_arm64.deb to /<<CHROOT>>...
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Copying /tmp/debusine-fetch-exec-upload-ov32oqs_/libpython3-dbg_3.12.6-1+debusine1_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-ov32oqs_/libpython3-dev_3.12.6-1+debusine1_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-ov32oqs_/libpython3-stdlib_3.12.6-1+debusine1_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-ov32oqs_/python3-all-dbg_3.12.6-1+debusine1_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-ov32oqs_/python3-all-dev_3.12.6-1+debusine1_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-ov32oqs_/python3-all-venv_3.12.6-1+debusine1_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-ov32oqs_/python3-all_3.12.6-1+debusine1_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-ov32oqs_/python3-dbg_3.12.6-1+debusine1_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-ov32oqs_/python3-dev_3.12.6-1+debusine1_arm64.deb to /<<CHROOT>>...
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Copying /tmp/debusine-fetch-exec-upload-ov32oqs_/python3_3.12.6-1+debusine1_arm64.deb to /<<CHROOT>>...
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Copying /tmp/debusine-fetch-exec-upload-ov32oqs_/idle_3.12.6-1+debusine1_all.deb to /<<CHROOT>>...
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Copying /tmp/debusine-fetch-exec-upload-ov32oqs_/python3-examples_3.12.6-1+debusine1_all.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-ov32oqs_/python3-scipy-dbgsym_1.13.1-5+nocheck1_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-ov32oqs_/python3-scipy_1.13.1-5+nocheck1_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-ov32oqs_/python-scipy-doc_1.13.1-5+nocheck1_all.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-ov32oqs_/python3-biopython-dbgsym_1.84+dfsg-4+bd1_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-ov32oqs_/python3-biopython_1.84+dfsg-4+bd1_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-ov32oqs_/python3-numpy-dbgsym_1.26.4+ds-11+bd1_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-ov32oqs_/python3-numpy_1.26.4+ds-11+bd1_arm64.deb to /<<CHROOT>>...
I: NOTICE: Log filtering will replace 'build/prody-SE87CF/resolver-Y83xia' with '<<RESOLVERDIR>>'

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| Update chroot                                                                |
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Get:1 file:/build/prody-SE87CF/resolver-WcAFkN/apt_archive ./ InRelease
Ign:1 file:/build/prody-SE87CF/resolver-WcAFkN/apt_archive ./ InRelease
Get:2 file:/build/prody-SE87CF/resolver-WcAFkN/apt_archive ./ Release [609 B]
Get:2 file:/build/prody-SE87CF/resolver-WcAFkN/apt_archive ./ Release [609 B]
Get:3 http://deb.debian.org/debian sid InRelease [202 kB]
Get:4 file:/build/prody-SE87CF/resolver-WcAFkN/apt_archive ./ Release.gpg
Ign:4 file:/build/prody-SE87CF/resolver-WcAFkN/apt_archive ./ Release.gpg
Get:5 file:/build/prody-SE87CF/resolver-WcAFkN/apt_archive ./ Packages [40.0 kB]
Get:6 http://deb.debian.org/debian sid/main arm64 Packages [9936 kB]
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Reading package lists...
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Calculating upgrade...
The following packages will be upgraded:
  coreutils dash debianutils diffutils e2fsprogs gpgv grep gzip libacl1
  libaudit-common libaudit1 libcap2 libcom-err2 libdebconfclient0
  libext2fs2t64 libgmp10 libgnutls30t64 libidn2-0 liblz4-1 libmd0 libseccomp2
  libss2 libtasn1-6 logsave
24 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 7340 kB of archives.
After this operation, 157 kB of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main arm64 coreutils arm64 9.5-1+b1 [2858 kB]
Get:2 http://deb.debian.org/debian sid/main arm64 debianutils arm64 5.20+b1 [89.8 kB]
Get:3 http://deb.debian.org/debian sid/main arm64 dash arm64 0.5.12-9+b1 [91.4 kB]
Get:4 http://deb.debian.org/debian sid/main arm64 diffutils arm64 1:3.10-1+b1 [373 kB]
Get:5 http://deb.debian.org/debian sid/main arm64 grep arm64 3.11-4+b1 [426 kB]
Get:6 http://deb.debian.org/debian sid/main arm64 gzip arm64 1.12-1.1+b1 [131 kB]
Get:7 http://deb.debian.org/debian sid/main arm64 logsave arm64 1.47.1-1+b1 [22.9 kB]
Get:8 http://deb.debian.org/debian sid/main arm64 libext2fs2t64 arm64 1.47.1-1+b1 [203 kB]
Get:9 http://deb.debian.org/debian sid/main arm64 e2fsprogs arm64 1.47.1-1+b1 [560 kB]
Get:10 http://deb.debian.org/debian sid/main arm64 gpgv arm64 2.2.45-2 [199 kB]
Get:11 http://deb.debian.org/debian sid/main arm64 libacl1 arm64 2.3.2-2+b1 [32.2 kB]
Get:12 http://deb.debian.org/debian sid/main arm64 libaudit-common all 1:4.0.1-2 [12.3 kB]
Get:13 http://deb.debian.org/debian sid/main arm64 libaudit1 arm64 1:4.0.1-2 [53.8 kB]
Get:14 http://deb.debian.org/debian sid/main arm64 libcap2 arm64 1:2.66-5+b1 [27.2 kB]
Get:15 http://deb.debian.org/debian sid/main arm64 libdebconfclient0 arm64 0.272+b1 [10.5 kB]
Get:16 http://deb.debian.org/debian sid/main arm64 libgmp10 arm64 2:6.3.0+dfsg-2+b2 [535 kB]
Get:17 http://deb.debian.org/debian sid/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB]
Get:18 http://deb.debian.org/debian sid/main arm64 libtasn1-6 arm64 4.19.0-3+b3 [46.9 kB]
Get:19 http://deb.debian.org/debian sid/main arm64 libgnutls30t64 arm64 3.8.6-2+b1 [1355 kB]
Get:20 http://deb.debian.org/debian sid/main arm64 liblz4-1 arm64 1.9.4-3+b1 [55.8 kB]
Get:21 http://deb.debian.org/debian sid/main arm64 libmd0 arm64 1.1.0-2+b1 [33.7 kB]
Get:22 http://deb.debian.org/debian sid/main arm64 libseccomp2 arm64 2.5.5-1+b2 [46.8 kB]
Get:23 http://deb.debian.org/debian sid/main arm64 libcom-err2 arm64 1.47.1-1+b1 [23.1 kB]
Get:24 http://deb.debian.org/debian sid/main arm64 libss2 arm64 1.47.1-1+b1 [27.5 kB]
debconf: delaying package configuration, since apt-utils is not installed
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+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Local sources
-------------

/tmp/debusine-fetch-exec-upload-ov32oqs_/prody_2.4.1+dfsg-2.dsc exists in /tmp/debusine-fetch-exec-upload-ov32oqs_; copying to chroot
I: NOTICE: Log filtering will replace 'build/prody-SE87CF/prody-2.4.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/prody-SE87CF' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-biopython, python3-numpy, python3-pyparsing, python3-scipy, python3-setuptools, python3-zombie-imp, build-essential, fakeroot, dumb-init
Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-biopython, python3-numpy, python3-pyparsing, python3-scipy, python3-setuptools, python3-zombie-imp, build-essential, fakeroot, dumb-init
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
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Install main build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev binutils
  binutils-aarch64-linux-gnu binutils-common bsdextrautils build-essential
  bzip2 cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper
  dh-autoreconf dh-python dh-strip-nondeterminism dpkg-dev dumb-init dwz
  fakeroot file fontconfig-config fonts-dejavu-core fonts-dejavu-mono
  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 gettext
  gettext-base groff-base intltool-debian libarchive-zip-perl libasan8
  libatomic1 libbinutils libblas3 libbrotli1 libc-dev-bin libc6-dev libcairo2
  libcc1-0 libcrypt-dev libctf-nobfd0 libctf0 libdebhelper-perl libdeflate0
  libdpkg-perl libelf1t64 libexpat1 libexpat1-dev libfakeroot
  libfile-stripnondeterminism-perl libfontconfig1 libfontenc1 libfreetype6
  libfribidi0 libgcc-14-dev libgdbm-compat4t64 libgdbm6t64 libgfortran5
  libglib2.0-0t64 libgomp1 libgprofng0 libgraphite2-3 libgssapi-krb5-2
  libharfbuzz0b libhwasan0 libicu72 libimagequant0 libisl23 libitm1
  libjansson4 libjbig0 libjpeg62-turbo libjs-jquery libjs-sphinxdoc
  libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
  liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblsan0 libmagic-mgc libmagic1t64
  libmpc3 libmpfr6 libncursesw6 libnsl2 libopenjp2-7 libperl5.40 libpipeline1
  libpixman-1-0 libpng16-16t64 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 libraqm0 libreadline8t64
  libsframe1 libsharpyuv0 libsqlite3-0 libstdc++-14-dev libtiff6
  libtirpc-common libtirpc3t64 libtool libtsan2 libubsan1 libuchardet0
  libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6
  libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxrender1
  linux-libc-dev m4 make man-db media-types netbase patch perl
  perl-modules-5.40 po-debconf python3 python3-all python3-all-dev
  python3-autocommand python3-biopython python3-cairo python3-chardet
  python3-decorator python3-dev python3-freetype python3-inflect
  python3-jaraco.context python3-jaraco.functools python3-jaraco.text
  python3-minimal python3-more-itertools python3-numpy python3-pil
  python3-pkg-resources python3-pyparsing python3-reportlab python3-rlpycairo
  python3-scipy python3-setuptools python3-typeguard python3-typing-extensions
  python3-zipp python3-zombie-imp python3.12 python3.12-dev python3.12-minimal
  python3.13 python3.13-dev python3.13-minimal readline-common rpcsvc-proto
  sensible-utils sgml-base w3c-sgml-lib x11-common xfonts-encodings
  xfonts-utils xml-core xz-utils zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc binutils-doc gprofng-gui
  bzip2-doc cpp-doc gcc-14-locales cpp-14-doc dh-make flit python3-build
  python3-installer python3-wheel debian-keyring fonts-freefont-otf
  | fonts-freefont-ttf fonts-texgyre gcc-14-doc gcc-multilib manpages-dev flex
  bison gdb gcc-doc gdb-aarch64-linux-gnu gettext-doc libasprintf-dev
  libgettextpo-dev groff libc-devtools glibc-doc gnupg | sq | sqop
  | pgpainless-cli | sequoia-chameleon-gnupg git bzr gdbm-l10n
  low-memory-monitor krb5-doc krb5-user liblcms2-utils libstdc++-14-doc
  libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc make-doc apparmor
  less www-browser ed diffutils-doc perl-doc libterm-readline-gnu-perl
  | libterm-readline-perl-perl libtap-harness-archive-perl libmail-box-perl
  python3-doc python3-tk python3-venv bwa clustalo clustalw dialign dssp
  emboss fasttree mafft muscle3 phylip phyml prank probcons python3-mysqldb
  python3-matplotlib python3-mmtf python3-rdflib python3-psycopg2 raxml
  samtools t-coffee wise gfortran python-numpy-doc python3-pytest
  python-pil-doc python-pyparsing-doc pdf-viewer python3-egenix-mxtexttools
  python-reportlab-doc rl-accel rl-renderpm python-scipy-doc
  python-setuptools-doc python3.12-venv python3.12-doc binfmt-support
  python3.13-venv python3.13-doc readline-doc sgml-base-doc
Recommended packages:
  gnupg | sq | sqop | pgpainless-cli | sequoia-chameleon-gnupg
  libalgorithm-merge-perl curl | wget | lynx manpages manpages-dev
  libfile-fcntllock-perl liblocale-gettext-perl libarchive-cpio-perl
  libglib2.0-data shared-mime-info xdg-user-dirs javascript-common
  krb5-locales libgpm2 libltdl-dev libmail-sendmail-perl python-biopython-doc
  ncbi-blast+ python3-olefile fonts-dejavu-extra ca-certificates
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev binutils
  binutils-aarch64-linux-gnu binutils-common bsdextrautils build-essential
  bzip2 cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper
  dh-autoreconf dh-python dh-strip-nondeterminism dpkg-dev dumb-init dwz
  fakeroot file fontconfig-config fonts-dejavu-core fonts-dejavu-mono
  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 gettext
  gettext-base groff-base intltool-debian libarchive-zip-perl libasan8
  libatomic1 libbinutils libblas3 libbrotli1 libc-dev-bin libc6-dev libcairo2
  libcc1-0 libcrypt-dev libctf-nobfd0 libctf0 libdebhelper-perl libdeflate0
  libdpkg-perl libelf1t64 libexpat1 libexpat1-dev libfakeroot
  libfile-stripnondeterminism-perl libfontconfig1 libfontenc1 libfreetype6
  libfribidi0 libgcc-14-dev libgdbm-compat4t64 libgdbm6t64 libgfortran5
  libglib2.0-0t64 libgomp1 libgprofng0 libgraphite2-3 libgssapi-krb5-2
  libharfbuzz0b libhwasan0 libicu72 libimagequant0 libisl23 libitm1
  libjansson4 libjbig0 libjpeg62-turbo libjs-jquery libjs-sphinxdoc
  libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
  liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblsan0 libmagic-mgc libmagic1t64
  libmpc3 libmpfr6 libncursesw6 libnsl2 libopenjp2-7 libperl5.40 libpipeline1
  libpixman-1-0 libpng16-16t64 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 libraqm0 libreadline8t64
  libsframe1 libsharpyuv0 libsqlite3-0 libstdc++-14-dev libtiff6
  libtirpc-common libtirpc3t64 libtool libtsan2 libubsan1 libuchardet0
  libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6
  libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxrender1
  linux-libc-dev m4 make man-db media-types netbase patch perl
  perl-modules-5.40 po-debconf python3 python3-all python3-all-dev
  python3-autocommand python3-biopython python3-cairo python3-chardet
  python3-decorator python3-dev python3-freetype python3-inflect
  python3-jaraco.context python3-jaraco.functools python3-jaraco.text
  python3-minimal python3-more-itertools python3-numpy python3-pil
  python3-pkg-resources python3-pyparsing python3-reportlab python3-rlpycairo
  python3-scipy python3-setuptools python3-typeguard python3-typing-extensions
  python3-zipp python3-zombie-imp python3.12 python3.12-dev python3.12-minimal
  python3.13 python3.13-dev python3.13-minimal readline-common rpcsvc-proto
  sbuild-build-depends-main-dummy sensible-utils sgml-base w3c-sgml-lib
  x11-common xfonts-encodings xfonts-utils xml-core xz-utils zlib1g-dev
0 upgraded, 198 newly installed, 0 to remove and 0 not upgraded.
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Get:2 file:/<<BUILDDIR>>/resolver-WcAFkN/apt_archive ./ python3-minimal 3.12.6-1+debusine1 [26.8 kB]
Get:3 file:/<<BUILDDIR>>/resolver-WcAFkN/apt_archive ./ libpython3-stdlib 3.12.6-1+debusine1 [9732 B]
Get:4 file:/<<BUILDDIR>>/resolver-WcAFkN/apt_archive ./ python3 3.12.6-1+debusine1 [27.8 kB]
Get:5 file:/<<BUILDDIR>>/resolver-WcAFkN/apt_archive ./ libpython3-dev 3.12.6-1+debusine1 [9992 B]
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Get:7 file:/<<BUILDDIR>>/resolver-WcAFkN/apt_archive ./ python3-all 3.12.6-1+debusine1 [1056 B]
Get:8 file:/<<BUILDDIR>>/resolver-WcAFkN/apt_archive ./ python3-dev 3.12.6-1+debusine1 [26.1 kB]
Get:9 file:/<<BUILDDIR>>/resolver-WcAFkN/apt_archive ./ python3-all-dev 3.12.6-1+debusine1 [1084 B]
Get:10 http://deb.debian.org/debian sid/main arm64 perl-modules-5.40 all 5.40.0-6 [3022 kB]
Get:11 file:/<<BUILDDIR>>/resolver-WcAFkN/apt_archive ./ python3-numpy 1:1.26.4+ds-11+bd1 [3816 kB]
Get:12 file:/<<BUILDDIR>>/resolver-WcAFkN/apt_archive ./ python3-biopython 1.84+dfsg-4+bd1 [1644 kB]
Get:13 http://deb.debian.org/debian sid/main arm64 libgdbm6t64 arm64 1.24-2 [74.0 kB]
Get:14 http://deb.debian.org/debian sid/main arm64 libgdbm-compat4t64 arm64 1.24-2 [50.3 kB]
Get:15 http://deb.debian.org/debian sid/main arm64 libperl5.40 arm64 5.40.0-6 [4149 kB]
Get:16 http://deb.debian.org/debian sid/main arm64 perl arm64 5.40.0-6 [267 kB]
Get:17 http://deb.debian.org/debian sid/main arm64 libpython3.12-minimal arm64 3.12.7-1 [807 kB]
Get:18 http://deb.debian.org/debian sid/main arm64 libexpat1 arm64 2.6.3-2 [90.1 kB]
Get:19 http://deb.debian.org/debian sid/main arm64 python3.12-minimal arm64 3.12.7-1 [1941 kB]
Get:20 file:/<<BUILDDIR>>/resolver-WcAFkN/apt_archive ./ python3-scipy 1.13.1-5+nocheck1 [18.1 MB]
Get:21 http://deb.debian.org/debian sid/main arm64 media-types all 10.1.0 [26.9 kB]
Get:22 http://deb.debian.org/debian sid/main arm64 netbase all 6.4 [12.8 kB]
Get:23 http://deb.debian.org/debian sid/main arm64 libncursesw6 arm64 6.5-2 [124 kB]
Get:24 http://deb.debian.org/debian sid/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB]
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Get:29 http://deb.debian.org/debian sid/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
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Get:32 http://deb.debian.org/debian sid/main arm64 readline-common all 8.2-5 [69.3 kB]
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Get:34 http://deb.debian.org/debian sid/main arm64 libsqlite3-0 arm64 3.46.1-1 [852 kB]
Get:35 http://deb.debian.org/debian sid/main arm64 libpython3.12-stdlib arm64 3.12.7-1 [1901 kB]
Get:36 http://deb.debian.org/debian sid/main arm64 python3.12 arm64 3.12.7-1 [671 kB]
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Get:38 http://deb.debian.org/debian sid/main arm64 python3.13-minimal arm64 3.13.0-1 [1835 kB]
Get:39 http://deb.debian.org/debian sid/main arm64 sgml-base all 1.31 [15.4 kB]
Get:40 http://deb.debian.org/debian sid/main arm64 sensible-utils all 0.0.24 [24.8 kB]
Get:41 http://deb.debian.org/debian sid/main arm64 bzip2 arm64 1.0.8-6 [39.5 kB]
Get:42 http://deb.debian.org/debian sid/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB]
Get:43 http://deb.debian.org/debian sid/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB]
Get:44 http://deb.debian.org/debian sid/main arm64 file arm64 1:5.45-3+b1 [43.4 kB]
Get:45 http://deb.debian.org/debian sid/main arm64 gettext-base arm64 0.22.5-2 [198 kB]
Get:46 http://deb.debian.org/debian sid/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB]
Get:47 http://deb.debian.org/debian sid/main arm64 groff-base arm64 1.23.0-5 [1129 kB]
Get:48 http://deb.debian.org/debian sid/main arm64 bsdextrautils arm64 2.40.2-9 [96.6 kB]
Get:49 http://deb.debian.org/debian sid/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB]
Get:50 http://deb.debian.org/debian sid/main arm64 man-db arm64 2.13.0-1 [1404 kB]
Get:51 http://deb.debian.org/debian sid/main arm64 xz-utils arm64 5.6.3-1 [540 kB]
Get:52 http://deb.debian.org/debian sid/main arm64 m4 arm64 1.4.19-4 [277 kB]
Get:53 http://deb.debian.org/debian sid/main arm64 autoconf all 2.72-3 [493 kB]
Get:54 http://deb.debian.org/debian sid/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get:55 http://deb.debian.org/debian sid/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get:56 http://deb.debian.org/debian sid/main arm64 autopoint all 0.22.5-2 [723 kB]
Get:57 http://deb.debian.org/debian sid/main arm64 binutils-common arm64 2.43.1-5 [2631 kB]
Get:58 http://deb.debian.org/debian sid/main arm64 libsframe1 arm64 2.43.1-5 [76.5 kB]
Get:59 http://deb.debian.org/debian sid/main arm64 libbinutils arm64 2.43.1-5 [657 kB]
Get:60 http://deb.debian.org/debian sid/main arm64 libctf-nobfd0 arm64 2.43.1-5 [151 kB]
Get:61 http://deb.debian.org/debian sid/main arm64 libctf0 arm64 2.43.1-5 [84.0 kB]
Get:62 http://deb.debian.org/debian sid/main arm64 libgprofng0 arm64 2.43.1-5 [690 kB]
Get:63 http://deb.debian.org/debian sid/main arm64 libjansson4 arm64 2.14-2+b3 [39.2 kB]
Get:64 http://deb.debian.org/debian sid/main arm64 binutils-aarch64-linux-gnu arm64 2.43.1-5 [2800 kB]
Get:65 http://deb.debian.org/debian sid/main arm64 binutils arm64 2.43.1-5 [67.8 kB]
Get:66 http://deb.debian.org/debian sid/main arm64 libc-dev-bin arm64 2.40-3 [50.9 kB]
Get:67 http://deb.debian.org/debian sid/main arm64 linux-libc-dev all 6.11.5-1 [2443 kB]
Get:68 http://deb.debian.org/debian sid/main arm64 libcrypt-dev arm64 1:4.4.36-5 [122 kB]
Get:69 http://deb.debian.org/debian sid/main arm64 rpcsvc-proto arm64 1.4.3-1+b1 [60.5 kB]
Get:70 http://deb.debian.org/debian sid/main arm64 libc6-dev arm64 2.40-3 [1591 kB]
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Get:73 http://deb.debian.org/debian sid/main arm64 libmpc3 arm64 1.3.1-1+b2 [50.2 kB]
Get:74 http://deb.debian.org/debian sid/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-7 [9164 kB]
Get:75 http://deb.debian.org/debian sid/main arm64 cpp-14 arm64 14.2.0-7 [1280 B]
Get:76 http://deb.debian.org/debian sid/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1 [4832 B]
Get:77 http://deb.debian.org/debian sid/main arm64 cpp arm64 4:14.2.0-1 [1568 B]
Get:78 http://deb.debian.org/debian sid/main arm64 libcc1-0 arm64 14.2.0-7 [42.2 kB]
Get:79 http://deb.debian.org/debian sid/main arm64 libgomp1 arm64 14.2.0-7 [124 kB]
Get:80 http://deb.debian.org/debian sid/main arm64 libitm1 arm64 14.2.0-7 [24.2 kB]
Get:81 http://deb.debian.org/debian sid/main arm64 libatomic1 arm64 14.2.0-7 [10.1 kB]
Get:82 http://deb.debian.org/debian sid/main arm64 libasan8 arm64 14.2.0-7 [2578 kB]
Get:83 http://deb.debian.org/debian sid/main arm64 liblsan0 arm64 14.2.0-7 [1162 kB]
Get:84 http://deb.debian.org/debian sid/main arm64 libtsan2 arm64 14.2.0-7 [2386 kB]
Get:85 http://deb.debian.org/debian sid/main arm64 libubsan1 arm64 14.2.0-7 [1040 kB]
Get:86 http://deb.debian.org/debian sid/main arm64 libhwasan0 arm64 14.2.0-7 [1442 kB]
Get:87 http://deb.debian.org/debian sid/main arm64 libgcc-14-dev arm64 14.2.0-7 [2365 kB]
Get:88 http://deb.debian.org/debian sid/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-7 [17.7 MB]
Get:89 http://deb.debian.org/debian sid/main arm64 gcc-14 arm64 14.2.0-7 [517 kB]
Get:90 http://deb.debian.org/debian sid/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1 [1440 B]
Get:91 http://deb.debian.org/debian sid/main arm64 gcc arm64 4:14.2.0-1 [5136 B]
Get:92 http://deb.debian.org/debian sid/main arm64 libstdc++-14-dev arm64 14.2.0-7 [2265 kB]
Get:93 http://deb.debian.org/debian sid/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-7 [10.1 MB]
Get:94 http://deb.debian.org/debian sid/main arm64 g++-14 arm64 14.2.0-7 [20.0 kB]
Get:95 http://deb.debian.org/debian sid/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1 [1200 B]
Get:96 http://deb.debian.org/debian sid/main arm64 g++ arm64 4:14.2.0-1 [1332 B]
Get:97 http://deb.debian.org/debian sid/main arm64 make arm64 4.3-4.1+b1 [372 kB]
Get:98 http://deb.debian.org/debian sid/main arm64 libdpkg-perl all 1.22.11 [644 kB]
Get:99 http://deb.debian.org/debian sid/main arm64 patch arm64 2.7.6-7+b1 [118 kB]
Get:100 http://deb.debian.org/debian sid/main arm64 dpkg-dev all 1.22.11 [1332 kB]
Get:101 http://deb.debian.org/debian sid/main arm64 build-essential arm64 12.12 [4624 B]
Get:102 http://deb.debian.org/debian sid/main arm64 libdebhelper-perl all 13.20 [89.7 kB]
Get:103 http://deb.debian.org/debian sid/main arm64 libtool all 2.4.7-7 [517 kB]
Get:104 http://deb.debian.org/debian sid/main arm64 dh-autoreconf all 20 [17.1 kB]
Get:105 http://deb.debian.org/debian sid/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get:106 http://deb.debian.org/debian sid/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get:107 http://deb.debian.org/debian sid/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get:108 http://deb.debian.org/debian sid/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get:109 http://deb.debian.org/debian sid/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get:110 http://deb.debian.org/debian sid/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB]
Get:111 http://deb.debian.org/debian sid/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.1 [630 kB]
Get:112 http://deb.debian.org/debian sid/main arm64 gettext arm64 0.22.5-2 [1532 kB]
Get:113 http://deb.debian.org/debian sid/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:114 http://deb.debian.org/debian sid/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:115 http://deb.debian.org/debian sid/main arm64 debhelper all 13.20 [915 kB]
Get:116 http://deb.debian.org/debian sid/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get:117 http://deb.debian.org/debian sid/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB]
Get:118 http://deb.debian.org/debian sid/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get:119 http://deb.debian.org/debian sid/main arm64 python3-typeguard all 4.4.0-1 [36.9 kB]
Get:120 http://deb.debian.org/debian sid/main arm64 python3-inflect all 7.3.1-2 [32.4 kB]
Get:121 http://deb.debian.org/debian sid/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B]
Get:122 http://deb.debian.org/debian sid/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get:123 http://deb.debian.org/debian sid/main arm64 python3-pkg-resources all 75.2.0-1 [213 kB]
Get:124 http://deb.debian.org/debian sid/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get:125 http://deb.debian.org/debian sid/main arm64 python3-zipp all 3.20.2-1 [10.3 kB]
Get:126 http://deb.debian.org/debian sid/main arm64 python3-setuptools all 75.2.0-1 [731 kB]
Get:127 http://deb.debian.org/debian sid/main arm64 dh-python all 6.20241024 [109 kB]
Get:128 http://deb.debian.org/debian sid/main arm64 dumb-init arm64 1.2.5-3 [13.4 kB]
Get:129 http://deb.debian.org/debian sid/main arm64 libfakeroot arm64 1.36-1 [29.1 kB]
Get:130 http://deb.debian.org/debian sid/main arm64 fakeroot arm64 1.36-1 [74.4 kB]
Get:131 http://deb.debian.org/debian sid/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get:132 http://deb.debian.org/debian sid/main arm64 fonts-dejavu-core all 2.37-8 [840 kB]
Get:133 http://deb.debian.org/debian sid/main arm64 libfontenc1 arm64 1:1.1.8-1+b1 [22.5 kB]
Get:134 http://deb.debian.org/debian sid/main arm64 libbrotli1 arm64 1.1.0-2+b5 [296 kB]
Get:135 http://deb.debian.org/debian sid/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB]
Get:136 http://deb.debian.org/debian sid/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB]
Get:137 http://deb.debian.org/debian sid/main arm64 x11-common all 1:7.7+23.1 [216 kB]
Get:138 http://deb.debian.org/debian sid/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB]
Get:139 http://deb.debian.org/debian sid/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB]
Get:140 http://deb.debian.org/debian sid/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB]
Get:141 http://deb.debian.org/debian sid/main arm64 fontconfig-config arm64 2.15.0-1.1+b1 [318 kB]
Get:142 http://deb.debian.org/debian sid/main arm64 libblas3 arm64 3.12.0-3+b1 [98.9 kB]
Get:143 http://deb.debian.org/debian sid/main arm64 libfontconfig1 arm64 2.15.0-1.1+b1 [387 kB]
Get:144 http://deb.debian.org/debian sid/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB]
Get:145 http://deb.debian.org/debian sid/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB]
Get:146 http://deb.debian.org/debian sid/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB]
Get:147 http://deb.debian.org/debian sid/main arm64 libxcb1 arm64 1.17.0-2 [143 kB]
Get:148 http://deb.debian.org/debian sid/main arm64 libx11-data all 2:1.8.7-1 [328 kB]
Get:149 http://deb.debian.org/debian sid/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB]
Get:150 http://deb.debian.org/debian sid/main arm64 libxcb-render0 arm64 1.17.0-2 [115 kB]
Get:151 http://deb.debian.org/debian sid/main arm64 libxcb-shm0 arm64 1.17.0-2 [105 kB]
Get:152 http://deb.debian.org/debian sid/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB]
Get:153 http://deb.debian.org/debian sid/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB]
Get:154 http://deb.debian.org/debian sid/main arm64 libcairo2 arm64 1.18.2-2 [483 kB]
Get:155 http://deb.debian.org/debian sid/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB]
Get:156 http://deb.debian.org/debian sid/main arm64 libexpat1-dev arm64 2.6.3-2 [142 kB]
Get:157 http://deb.debian.org/debian sid/main arm64 libfribidi0 arm64 1.0.15-1 [71.8 kB]
Get:158 http://deb.debian.org/debian sid/main arm64 libgfortran5 arm64 14.2.0-7 [361 kB]
Get:159 http://deb.debian.org/debian sid/main arm64 libglib2.0-0t64 arm64 2.82.2-2 [1409 kB]
Get:160 http://deb.debian.org/debian sid/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB]
Get:161 http://deb.debian.org/debian sid/main arm64 libharfbuzz0b arm64 10.0.1-1 [441 kB]
Get:162 http://deb.debian.org/debian sid/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB]
Get:163 http://deb.debian.org/debian sid/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB]
Get:164 http://deb.debian.org/debian sid/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB]
Get:165 http://deb.debian.org/debian sid/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:166 http://deb.debian.org/debian sid/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get:167 http://deb.debian.org/debian sid/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB]
Get:168 http://deb.debian.org/debian sid/main arm64 liblapack3 arm64 3.12.0-3+b1 [1812 kB]
Get:169 http://deb.debian.org/debian sid/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b2 [25.6 kB]
Get:170 http://deb.debian.org/debian sid/main arm64 liblcms2-2 arm64 2.16-2 [151 kB]
Get:171 http://deb.debian.org/debian sid/main arm64 liblerc4 arm64 4.0.0+ds-4+b2 [154 kB]
Get:172 http://deb.debian.org/debian sid/main arm64 libopenjp2-7 arm64 2.5.0-2+b3 [177 kB]
Get:173 http://deb.debian.org/debian sid/main arm64 libpython3.12t64 arm64 3.12.7-1 [1982 kB]
Get:174 http://deb.debian.org/debian sid/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB]
Get:175 http://deb.debian.org/debian sid/main arm64 libpython3.12-dev arm64 3.12.7-1 [4793 kB]
Get:176 http://deb.debian.org/debian sid/main arm64 libpython3.13-stdlib arm64 3.13.0-1 [1920 kB]
Get:177 http://deb.debian.org/debian sid/main arm64 libpython3.13 arm64 3.13.0-1 [1960 kB]
Get:178 http://deb.debian.org/debian sid/main arm64 libpython3.13-dev arm64 3.13.0-1 [4668 kB]
Get:179 http://deb.debian.org/debian sid/main arm64 libraqm0 arm64 0.10.1-1+b1 [13.7 kB]
Get:180 http://deb.debian.org/debian sid/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [111 kB]
Get:181 http://deb.debian.org/debian sid/main arm64 libwebp7 arm64 1.4.0-0.1 [267 kB]
Get:182 http://deb.debian.org/debian sid/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB]
Get:183 http://deb.debian.org/debian sid/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [110 kB]
Get:184 http://deb.debian.org/debian sid/main arm64 libwebpmux3 arm64 1.4.0-0.1 [122 kB]
Get:185 http://deb.debian.org/debian sid/main arm64 python3.13 arm64 3.13.0-1 [730 kB]
Get:186 http://deb.debian.org/debian sid/main arm64 python3.12-dev arm64 3.12.7-1 [505 kB]
Get:187 http://deb.debian.org/debian sid/main arm64 python3.13-dev arm64 3.13.0-1 [504 kB]
Get:188 http://deb.debian.org/debian sid/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 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 xml-core all 0.19 [20.1 kB]
Get:195 http://deb.debian.org/debian sid/main arm64 w3c-sgml-lib all 1.3-3 [273 kB]
Get:196 http://deb.debian.org/debian sid/main arm64 python3-decorator all 5.1.1-5 [15.1 kB]
Get:197 http://deb.debian.org/debian sid/main arm64 python3-pyparsing all 3.1.2-1 [146 kB]
Get:198 http://deb.debian.org/debian sid/main arm64 python3-zombie-imp all 0.0.2-2 [11.7 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libexpat1:arm64 (2.6.3-2) ...
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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Unpacking libkrb5support0:arm64 (1.21.3-3) ...
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Unpacking libk5crypto3:arm64 (1.21.3-3) ...
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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'
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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
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Setting up python3-minimal (3.12.6-1+debusine1) ...
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Processing triggers for libc-bin (2.40-3) ...
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+------------------------------------------------------------------------------+
| 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_6.11.5-1
Package versions: 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 bsdextrautils_2.40.2-9 bsdutils_1:2.40.2-9 build-essential_12.12 bzip2_1.0.8-6 coreutils_9.5-1+b1 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 dash_0.5.12-9+b1 debconf_1.5.87 debhelper_13.20 debian-archive-keyring_2023.4 debianutils_5.20+b1 dh-autoreconf_20 dh-python_6.20241024 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1+b1 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+b1 fakeroot_1.36-1 file_1:5.45-3+b1 findutils_4.10.0-3 fontconfig-config_2.15.0-1.1+b1 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 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 gpgv_2.2.45-2 grep_3.11-4+b1 groff-base_1.23.0-5 gzip_1.12-1.1+b1 hostname_3.25 init-system-helpers_1.67 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libapt-pkg6.0t64_2.9.10 libarchive-zip-perl_1.68-1 libasan8_14.2.0-7 libatomic1_14.2.0-7 libattr1_1:2.5.2-2 libaudit-common_1:4.0.1-2 libaudit1_1:4.0.1-2 libbinutils_2.43.1-5 libblas3_3.12.0-3+b1 libblkid1_2.40.2-9 libbrotli1_1.1.0-2+b5 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 libc6-dev_2.40-3 libcairo2_1.18.2-2 libcap-ng0_0.8.5-3 libcap2_1:2.66-5+b1 libcc1-0_14.2.0-7 libcom-err2_1.47.1-1+b1 libcrypt-dev_1:4.4.36-5 libcrypt1_1:4.4.36-5 libctf-nobfd0_2.43.1-5 libctf0_2.43.1-5 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.272+b1 libdebhelper-perl_13.20 libdeflate0_1.22-1 libdpkg-perl_1.22.11 libelf1t64_0.192-4 libexpat1_2.6.3-2 libexpat1-dev_2.6.3-2 libext2fs2t64_1.47.1-1+b1 libfakeroot_1.36-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libfontconfig1_2.15.0-1.1+b1 libfontenc1_1:1.1.8-1+b1 libfreetype6_2.13.3+dfsg-1 libfribidi0_1.0.15-1 libgcc-14-dev_14.2.0-7 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_2.82.2-2 libgmp10_2:6.3.0+dfsg-2+b2 libgnutls30t64_3.8.6-2+b1 libgomp1_14.2.0-7 libgpg-error0_1.50-4 libgprofng0_2.43.1-5 libgraphite2-3_1.3.14-2+b1 libgssapi-krb5-2_1.21.3-3 libharfbuzz0b_10.0.1-1 libhogweed6t64_3.10-1 libhwasan0_14.2.0-7 libicu72_72.1-5+b1 libidn2-0_2.3.7-2+b1 libimagequant0_2.18.0-1+b2 libisl23_0.27-1 libitm1_14.2.0-7 libjansson4_2.14-2+b3 libjbig0_2.1-6.1+b2 libjpeg62-turbo_1:2.1.5-3+b1 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-sphinxdoc_7.4.7-4 libjs-underscore_1.13.4~dfsg+~1.11.4-3 libk5crypto3_1.21.3-3 libkeyutils1_1.6.3-4 libkrb5-3_1.21.3-3 libkrb5support0_1.21.3-3 liblapack3_3.12.0-3+b1 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libsemanage-common_3.7-2 libsemanage2_3.7-2 libsepol2_3.7-1 libsframe1_2.43.1-5 libsharpyuv0_1.4.0-0.1 libsmartcols1_2.40.2-9 libsqlite3-0_3.46.1-1 libss2_1.47.1-1+b1 libssl3t64_3.3.2-2 libstdc++-14-dev_14.2.0-7 libstdc++6_14.2.0-7 libsystemd0_256.7-2 libtasn1-6_4.19.0-3+b3 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+b1 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 libxml2_2.12.7+dfsg+really2.9.14-0.1 libxrender1_1:0.9.10-1.1+b1 libxxhash0_0.8.2-2+b1 libzstd1_1.5.6+dfsg-1 linux-libc-dev_6.11.5-1 login_1:4.16.0-2+really2.40.2-9 login.defs_1:4.16.0-4 logsave_1.47.1-1+b1 m4_1.4.19-4 make_4.3-4.1+b1 man-db_2.13.0-1 mawk_1.3.4.20240905-1 media-types_10.1.0 mount_2.40.2-9 ncurses-base_6.5-2 ncurses-bin_6.5-2 netbase_6.4 openssl-provider-legacy_3.3.2-2 passwd_1:4.16.0-4 patch_2.7.6-7+b1 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 python3_3.12.6-1+debusine1 python3-all_3.12.6-1+debusine1 python3-all-dev_3.12.6-1+debusine1 python3-autocommand_2.2.2-3 python3-biopython_1.84+dfsg-4+bd1 python3-cairo_1.26.1-2 python3-chardet_5.2.0+dfsg-1 python3-decorator_5.1.1-5 python3-dev_3.12.6-1+debusine1 python3-freetype_2.5.1-1 python3-inflect_7.3.1-2 python3-jaraco.context_6.0.0-1 python3-jaraco.functools_4.1.0-1 python3-jaraco.text_4.0.0-1 python3-minimal_3.12.6-1+debusine1 python3-more-itertools_10.5.0-1 python3-numpy_1:1.26.4+ds-11+bd1 python3-pil_10.4.0-1 python3-pkg-resources_75.2.0-1 python3-pyparsing_3.1.2-1 python3-reportlab_4.2.5-1 python3-rlpycairo_0.3.0-3 python3-scipy_1.13.1-5+nocheck1 python3-setuptools_75.2.0-1 python3-typeguard_4.4.0-1 python3-typing-extensions_4.12.2-2 python3-zipp_3.20.2-1 python3-zombie-imp_0.0.2-2 python3.12_3.12.7-1 python3.12-dev_3.12.7-1 python3.12-minimal_3.12.7-1 python3.13_3.13.0-1 python3.13-dev_3.13.0-1 python3.13-minimal_3.13.0-1 readline-common_8.2-5 rpcsvc-proto_1.4.3-1+b1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 sgml-base_1.31 sysvinit-utils_3.11-1 tar_1.35+dfsg-3 tzdata_2024b-3 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_5.6.3-1 zlib1g_1:1.3.dfsg+really1.3.1-1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 3.0 (quilt)
Source: prody
Binary: python3-prody, python3-prody-tests
Architecture: any all
Version: 2.4.1+dfsg-2
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Uploaders:  Andrius Merkys <merkys@debian.org>,
Homepage: https://github.com/prody/ProDy
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/debichem-team/prody
Vcs-Git: https://salsa.debian.org/debichem-team/prody.git
Testsuite: autopkgtest-pkg-pybuild
Build-Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-biopython <!nocheck>, python3-numpy, python3-pyparsing <!nocheck>, python3-scipy <!nocheck>, python3-setuptools, python3-zombie-imp <!nocheck>
Package-List:
 python3-prody deb science optional arch=any
 python3-prody-tests deb science optional arch=all
Checksums-Sha1:
 9d0ead7d3fce8424a0c35a2396639566d5ebea77 16085288 prody_2.4.1+dfsg.orig.tar.xz
 8197a08210bb98599434307c0619ecfaa172cb91 9728 prody_2.4.1+dfsg-2.debian.tar.xz
Checksums-Sha256:
 f66b7affa47693dd3d8cf0f0ac833c4d313135420b1e6ece0767259099f5ad87 16085288 prody_2.4.1+dfsg.orig.tar.xz
 0579e775804f9943152c3885561b5fcac4ed2c27557f32e6f20866a4d7c465e4 9728 prody_2.4.1+dfsg-2.debian.tar.xz
Files:
 295e44486fd6cb8cbe38f64aad51439e 16085288 prody_2.4.1+dfsg.orig.tar.xz
 b0b64099072b904019ec3863f8cf0801 9728 prody_2.4.1+dfsg-2.debian.tar.xz

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gpgv: Signature made Tue Feb 13 07:18:28 2024 UTC
gpgv:                using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287
gpgv:                issuer "merkys@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./prody_2.4.1+dfsg-2.dsc: no acceptable signature found
dpkg-source: info: extracting prody in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking prody_2.4.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking prody_2.4.1+dfsg-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying no-network-access.patch
dpkg-source: info: applying add-missing-test-files.patch
dpkg-source: info: applying numpy-1.24.patch
dpkg-source: info: applying 1816.patch
dpkg-source: info: applying skip-equals-on-vector.patch

Check disk space
----------------

Sufficient free space for build

Hack binNMU version
-------------------

Created changelog entry for binNMU version 2.4.1+dfsg-2+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 prody
dpkg-buildpackage: info: source version 2.4.1+dfsg-2+bd1
dpkg-buildpackage: info: source distribution sid
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
 debian/rules clean
dh clean --buildsystem pybuild --with numpy3,python3
   dh_auto_clean -O--buildsystem=pybuild
I: pybuild base:311: python3.13 setup.py clean 
running clean
removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build' (and everything under it)
'build/bdist.linux-aarch64' does not exist -- can't clean it
'build/scripts-3.13' does not exist -- can't clean it
I: pybuild base:311: python3.12 setup.py clean 
running clean
removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build' (and everything under it)
'build/bdist.linux-aarch64' does not exist -- can't clean it
'build/scripts-3.12' does not exist -- can't clean it
   debian/rules execute_after_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -rf ProDy.egg-info
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
 debian/rules binary-arch
dh binary-arch --buildsystem pybuild --with numpy3,python3
   dh_update_autotools_config -a -O--buildsystem=pybuild
   dh_autoreconf -a -O--buildsystem=pybuild
   dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:311: python3.13 setup.py config 
running config
I: pybuild base:311: python3.12 setup.py config 
running config
   dh_auto_build -a -O--buildsystem=pybuild
I: pybuild base:311: /usr/bin/python3.13 setup.py build 
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody
copying prody/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
copying prody/atomic/fields.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
copying prody/atomic/acceptor.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
copying prody/atomic/improper.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
copying prody/atomic/flags.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
copying prody/atomic/crossterm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
copying prody/atomic/pointer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
copying prody/atomic/chain.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
copying prody/atomic/select.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
copying prody/atomic/segment.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
copying prody/atomic/atomgroup.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
copying prody/atomic/atomic.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
copying prody/atomic/nbexclusion.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
copying prody/atomic/dihedral.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
copying prody/atomic/subset.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
copying prody/atomic/functions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
copying prody/atomic/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
copying prody/atomic/angle.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
copying prody/atomic/hierview.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
copying prody/atomic/selection.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
copying prody/atomic/atom.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
copying prody/atomic/donor.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
copying prody/atomic/residue.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
copying prody/atomic/bond.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
copying prody/atomic/atommap.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/database
copying prody/database/uniprot.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/database
copying prody/database/cath.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/database
copying prody/database/pfam.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/database
copying prody/database/quartataweb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/database
copying prody/database/dali.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/database
copying prody/database/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/database
copying prody/database/goa.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/database
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/imanm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/rtb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/vmdfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
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copying prody/tests/measure/test_contacts.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/measure
copying prody/tests/measure/test_measure.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/measure
copying prody/tests/measure/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/measure
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/proteins
copying prody/tests/proteins/test_dssp.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/proteins
copying prody/tests/proteins/test_header.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/proteins
copying prody/tests/proteins/test_ciffile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/proteins
copying prody/tests/proteins/test_pdbfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/proteins
copying prody/tests/proteins/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/proteins
copying prody/tests/proteins/test_wwpdb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/proteins
copying prody/tests/proteins/test_localpdb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/proteins
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/sequence
copying prody/tests/sequence/test_analysis.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/sequence
copying prody/tests/sequence/test_msafile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/sequence
copying prody/tests/sequence/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/sequence
copying prody/tests/sequence/test_msa.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/sequence
copying prody/tests/sequence/test_sequence.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/sequence
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/trajectory
copying prody/tests/trajectory/test_dcdfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/trajectory
copying prody/tests/trajectory/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/trajectory
copying prody/tests/trajectory/test_frame.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/trajectory
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/utilities
copying prody/tests/utilities/test_misctools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/utilities
copying prody/tests/utilities/test_pathtools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/utilities
copying prody/tests/utilities/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/utilities
copying prody/tests/utilities/test_checkers.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/utilities
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/utilities/datafiles
copying prody/utilities/datafiles/saxs_water.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/utilities/datafiles
copying prody/utilities/datafiles/mod_res_map.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/utilities/datafiles
copying prody/tests/datafiles/pdb2nwl-opm.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdb3o21.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdb1ubi_ca.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdb3hsy.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdbRTER.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdb2k39_truncated.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdb1tw7_step3_charmm2namd_doubled_hex.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdb2k39_ca.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdb1ejg.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdb4v8r_hex.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdb3mht.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdb1tw7_step3_charmm2namd_doubled_h36.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdb1r19_dssp.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdb2gb1_truncated.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdb6fpj_Bb_fixed_solv_ions.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdb4v8r_h36.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdb1tw7_step3_charmm2namd.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdb1ubi.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdb1ejg_oneatom.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdb3p3w.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/exanm2nwl_vectors.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/gnm1ubi_evalues.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/hit1ubi.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/msa_Cys_knot_di.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/anm1ubi_vectors.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/anm1ubi_evalues.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/gnm1ubi_vectors.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/commute1ubi.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/msa_Cys_knot_sca.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pca2k39_evalues.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pca2k39_vectors.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/exanm2nwl_evalues.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/mmcif_6zu5.cif -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/mmcif_6yfy.cif -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pca2k39_cov.coo -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/rtb2gb1_project.coo -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/gnm1ubi_kirchhoff.coo -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/rtb2gb1_hessian.coo -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/anm1ubi_hessian.coo -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/exanm2nwl_hessian.coo -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/dcd2k39_truncated.dcd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/xmlSTI.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/msa_Cys_knot.slx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/msa_3hsyA_3o21A_new.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/msa_Cys_knot.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/msa_Cys_knot.sth -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/msa_3hsyA_3o21A.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
running build_ext
building 'prody.dynamics.rtbtools' extension
creating build/temp.linux-aarch64-cpython-313/prody/dynamics
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 prody/dynamics/rtbtools.c -o build/temp.linux-aarch64-cpython-313/prody/dynamics/rtbtools.o
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/prody/dynamics/rtbtools.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics/rtbtools.cpython-313-aarch64-linux-gnu.so
building 'prody.dynamics.smtools' 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 prody/dynamics/smtools.c -o build/temp.linux-aarch64-cpython-313/prody/dynamics/smtools.o
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/prody/dynamics/smtools.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics/smtools.cpython-313-aarch64-linux-gnu.so
building 'prody.sequence.msatools' extension
creating build/temp.linux-aarch64-cpython-313/prody/sequence
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 prody/sequence/msatools.c -o build/temp.linux-aarch64-cpython-313/prody/sequence/msatools.o
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/prody/sequence/msatools.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/sequence/msatools.cpython-313-aarch64-linux-gnu.so
building 'prody.sequence.msaio' 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 prody/sequence/msaio.c -o build/temp.linux-aarch64-cpython-313/prody/sequence/msaio.o
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/prody/sequence/msaio.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/sequence/msaio.cpython-313-aarch64-linux-gnu.so
building 'prody.sequence.seqtools' 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 prody/sequence/seqtools.c -o build/temp.linux-aarch64-cpython-313/prody/sequence/seqtools.o
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/prody/sequence/seqtools.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/sequence/seqtools.cpython-313-aarch64-linux-gnu.so
building 'prody.kdtree._CKDTree' extension
creating build/temp.linux-aarch64-cpython-313/prody/kdtree
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 prody/kdtree/KDTree.c -o build/temp.linux-aarch64-cpython-313/prody/kdtree/KDTree.o
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 prody/kdtree/KDTreemodule.c -o build/temp.linux-aarch64-cpython-313/prody/kdtree/KDTreemodule.o
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/prody/kdtree/KDTree.o build/temp.linux-aarch64-cpython-313/prody/kdtree/KDTreemodule.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/kdtree/_CKDTree.cpython-313-aarch64-linux-gnu.so
building 'prody.proteins.ccealign' extension
creating build/temp.linux-aarch64-cpython-313/prody/proteins/ccealign
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 -Iprody/utilities/tnt -I/usr/include/python3.13 -c prody/proteins/ccealign/ccealignmodule.cpp -o build/temp.linux-aarch64-cpython-313/prody/proteins/ccealign/ccealignmodule.o
In file included from prody/utilities/tnt/tnt.h:41,
                 from prody/proteins/ccealign/ccealignmodule.h:43,
                 from prody/proteins/ccealign/ccealignmodule.cpp:38:
In member function ‘void TNT::Array1D<T>::set_(T*, T*, const T&) [with T = double]’,
    inlined from ‘TNT::Array1D<T>::Array1D(int, const T&) [with T = double]’ at prody/utilities/tnt/tnt_array1d.h:118:6,
    inlined from ‘PyObject* findBest(pcePoint, pcePoint, pathCache, int, int, int)’ at prody/proteins/ccealign/ccealignmodule.cpp:630:26:
prody/utilities/tnt/tnt_array1d.h:260:20: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ specified bound between 18446744056529682432 and 18446744073709551608 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
  260 |                 *p = a;
      |                 ~~~^~~
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/prody/proteins/ccealign/ccealignmodule.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/proteins/ccealign.cpython-313-aarch64-linux-gnu.so
I: pybuild base:311: /usr/bin/python3 setup.py build 
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody
copying prody/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic
copying prody/atomic/fields.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic
copying prody/atomic/acceptor.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic
copying prody/atomic/improper.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic
copying prody/atomic/flags.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic
copying prody/atomic/crossterm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic
copying prody/atomic/pointer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic
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copying prody/tests/atomic/test_select.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/atomic
copying prody/tests/atomic/test_hierview.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/atomic
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creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles
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copying prody/tests/dynamics/test_enms.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/dynamics
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creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/ensemble
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copying prody/tests/ensemble/test_ensemble.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/ensemble
copying prody/tests/ensemble/test_conformation.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/ensemble
copying prody/tests/ensemble/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/ensemble
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/kdtree
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copying prody/tests/kdtree/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/kdtree
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/measure
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copying prody/tests/measure/test_measure.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/measure
copying prody/tests/measure/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/measure
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins
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copying prody/tests/proteins/test_pdbfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins
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copying prody/tests/proteins/test_wwpdb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins
copying prody/tests/proteins/test_localpdb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/sequence
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copying prody/tests/sequence/test_msafile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/sequence
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copying prody/tests/sequence/test_msa.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/sequence
copying prody/tests/sequence/test_sequence.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/sequence
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/trajectory
copying prody/tests/trajectory/test_dcdfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/trajectory
copying prody/tests/trajectory/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/trajectory
copying prody/tests/trajectory/test_frame.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/trajectory
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/utilities
copying prody/tests/utilities/test_misctools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/utilities
copying prody/tests/utilities/test_pathtools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/utilities
copying prody/tests/utilities/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/utilities
copying prody/tests/utilities/test_checkers.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/utilities
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/utilities/datafiles
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copying prody/utilities/datafiles/mod_res_map.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/utilities/datafiles
copying prody/tests/datafiles/pdb2nwl-opm.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles
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copying prody/tests/datafiles/pdb3hsy.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdbRTER.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdb2k39_truncated.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles
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copying prody/tests/datafiles/pdb1r19_dssp.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdb2gb1_truncated.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdb6fpj_Bb_fixed_solv_ions.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/pdb4v8r_h36.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles
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copying prody/tests/datafiles/pdb1ejg_oneatom.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles
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copying prody/tests/datafiles/rtb2gb1_project.coo -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles
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copying prody/tests/datafiles/rtb2gb1_hessian.coo -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles
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copying prody/tests/datafiles/msa_3hsyA_3o21A_new.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/msa_Cys_knot.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/msa_Cys_knot.sth -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles
copying prody/tests/datafiles/msa_3hsyA_3o21A.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles
running build_ext
building 'prody.dynamics.rtbtools' extension
creating build/temp.linux-aarch64-cpython-312/prody/dynamics
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 prody/dynamics/rtbtools.c -o build/temp.linux-aarch64-cpython-312/prody/dynamics/rtbtools.o
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/prody/dynamics/rtbtools.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics/rtbtools.cpython-312-aarch64-linux-gnu.so
building 'prody.dynamics.smtools' 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 prody/dynamics/smtools.c -o build/temp.linux-aarch64-cpython-312/prody/dynamics/smtools.o
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/prody/dynamics/smtools.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics/smtools.cpython-312-aarch64-linux-gnu.so
building 'prody.sequence.msatools' extension
creating build/temp.linux-aarch64-cpython-312/prody/sequence
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 prody/sequence/msatools.c -o build/temp.linux-aarch64-cpython-312/prody/sequence/msatools.o
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/prody/sequence/msatools.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/sequence/msatools.cpython-312-aarch64-linux-gnu.so
building 'prody.sequence.msaio' 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 prody/sequence/msaio.c -o build/temp.linux-aarch64-cpython-312/prody/sequence/msaio.o
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/prody/sequence/msaio.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/sequence/msaio.cpython-312-aarch64-linux-gnu.so
building 'prody.sequence.seqtools' 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 prody/sequence/seqtools.c -o build/temp.linux-aarch64-cpython-312/prody/sequence/seqtools.o
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/prody/sequence/seqtools.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/sequence/seqtools.cpython-312-aarch64-linux-gnu.so
building 'prody.kdtree._CKDTree' extension
creating build/temp.linux-aarch64-cpython-312/prody/kdtree
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 prody/kdtree/KDTree.c -o build/temp.linux-aarch64-cpython-312/prody/kdtree/KDTree.o
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 prody/kdtree/KDTreemodule.c -o build/temp.linux-aarch64-cpython-312/prody/kdtree/KDTreemodule.o
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/prody/kdtree/KDTree.o build/temp.linux-aarch64-cpython-312/prody/kdtree/KDTreemodule.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/kdtree/_CKDTree.cpython-312-aarch64-linux-gnu.so
building 'prody.proteins.ccealign' extension
creating build/temp.linux-aarch64-cpython-312/prody/proteins/ccealign
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 -Iprody/utilities/tnt -I/usr/include/python3.12 -c prody/proteins/ccealign/ccealignmodule.cpp -o build/temp.linux-aarch64-cpython-312/prody/proteins/ccealign/ccealignmodule.o
In file included from prody/utilities/tnt/tnt.h:41,
                 from prody/proteins/ccealign/ccealignmodule.h:43,
                 from prody/proteins/ccealign/ccealignmodule.cpp:38:
In member function ‘void TNT::Array1D<T>::set_(T*, T*, const T&) [with T = double]’,
    inlined from ‘TNT::Array1D<T>::Array1D(int, const T&) [with T = double]’ at prody/utilities/tnt/tnt_array1d.h:118:6,
    inlined from ‘PyObject* findBest(pcePoint, pcePoint, pathCache, int, int, int)’ at prody/proteins/ccealign/ccealignmodule.cpp:630:26:
prody/utilities/tnt/tnt_array1d.h:260:20: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ specified bound between 18446744056529682432 and 18446744073709551608 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
  260 |                 *p = a;
      |                 ~~~^~~
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/prody/proteins/ccealign/ccealignmodule.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/proteins/ccealign.cpython-312-aarch64-linux-gnu.so
   dh_auto_test -a -O--buildsystem=pybuild
I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build; python3.13 -m unittest discover -v 
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/utilities/doctools.py:48: SyntaxWarning: invalid escape sequence '\i'
  """Returns wrapped lines from :func:`textwrap.wrap` after *join*\ing them.
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic/flags.py:463: SyntaxWarning: invalid escape sequence '\ '
  __doc__ += """
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic/select.py:2: SyntaxWarning: invalid escape sequence '\|'
  """This module defines a class for selecting subsets of atoms.  You can read
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic/select.py:719: SyntaxWarning: invalid escape sequence '\w'
  RE_SCHARS = re_compile('`[\w\W]*?`')
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic/select.py:738: SyntaxWarning: invalid escape sequence '\w'
  RE_REGEXP = re_compile('"[\w\W]*"')
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic/select.py:757: SyntaxWarning: invalid escape sequence '\d'
  _ = '[-+]?\d+(\.\d*)?([eE]\d+)?'
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic/select.py:758: SyntaxWarning: invalid escape sequence '\ '
  RE_NRANGE = re_compile(_ + '\ *(to|:)\ *' + _)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic/select.py:761: SyntaxWarning: invalid escape sequence '\ '
  pp.Optional(pp.Regex('(\ *:\ *' + _ + ')')))
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/sequence/analysis.py:169: SyntaxWarning: invalid escape sequence '\{'
  """Apply one of the normalizations discussed in [MLC05]_ to *mutinfo*
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/proteins/localpdb.py:438: SyntaxWarning: invalid escape sequence '\.'
  pdbext = compile('\.(pdb|ent)(\.gz)?$', IGNORECASE)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/proteins/localpdb.py:440: SyntaxWarning: invalid escape sequence '\.'
  pdbext = compile('\.(pdb|ent)\.gz$', IGNORECASE)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/proteins/localpdb.py:442: SyntaxWarning: invalid escape sequence '\.'
  pdbext = compile('\.(pdb|ent)$', IGNORECASE)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/proteins/dssp.py:78: SyntaxWarning: invalid escape sequence '\*'
  """Parse DSSP data from file *dssp* into :class:`.AtomGroup` instance
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics/pca.py:59: SyntaxWarning: invalid escape sequence '\_'
  """Build a covariance matrix for *coordsets* using mean coordinates
prody.tests.apps.test_prody_anm (unittest.loader._FailedTest.prody.tests.apps.test_prody_anm) ... ERROR
prody.tests.apps.test_prody_catdcd (unittest.loader._FailedTest.prody.tests.apps.test_prody_catdcd) ... ERROR
prody.tests.apps.test_prody_examples (unittest.loader._FailedTest.prody.tests.apps.test_prody_examples) ... ERROR
prody.tests.apps.test_prody_gnm (unittest.loader._FailedTest.prody.tests.apps.test_prody_gnm) ... ERROR
prody.tests.apps.test_prody_pca (unittest.loader._FailedTest.prody.tests.apps.test_prody_pca) ... ERROR
testAtomGroup (prody.tests.atomic.test_atomic.TestAtomIterations.testAtomGroup) ... ok
testAtomMap (prody.tests.atomic.test_atomic.TestAtomIterations.testAtomMap) ... ok
testChain (prody.tests.atomic.test_atomic.TestAtomIterations.testChain) ... ok
testResidue (prody.tests.atomic.test_atomic.TestAtomIterations.testResidue) ... ok
testSelection (prody.tests.atomic.test_atomic.TestAtomIterations.testSelection) ... ok
testAtom (prody.tests.atomic.test_atomic.TestPickling.testAtom) ... ok
testAtomGroup (prody.tests.atomic.test_atomic.TestPickling.testAtomGroup) ... ok
testSelection (prody.tests.atomic.test_atomic.TestPickling.testSelection) ... ok
testSaveLoad (prody.tests.atomic.test_atomic.TestSaveLoad.testSaveLoad) ... ok
testInstantiation (prody.tests.atomic.test_atommap.TestInstantiation.testInstantiation) ... ok
testAllSelection (prody.tests.atomic.test_atommap.TestSelection.testAllSelection) ... ok
testChainSelection (prody.tests.atomic.test_atommap.TestSelection.testChainSelection) ... ok
testGetBoolArray (prody.tests.atomic.test_atommap.TestSelection.testGetBoolArray) ... ok
testNameSelection (prody.tests.atomic.test_atommap.TestSelection.testNameSelection) ... ok
testSplit (prody.tests.atomic.test_fragment.TestFragment.testSplit) ... ok
testSplitCopy (prody.tests.atomic.test_fragment.TestFragment.testSplitCopy) ... ok
testSplitNoh (prody.tests.atomic.test_fragment.TestFragment.testSplitNoh) ... ok
testSplitNohCopy (prody.tests.atomic.test_fragment.TestFragment.testSplitNohCopy) ... ok
testWhole (prody.tests.atomic.test_fragment.TestFragment.testWhole) ... ok
testWhole2 (prody.tests.atomic.test_fragment.TestFragment.testWhole2) ... ok
testWholeAll (prody.tests.atomic.test_fragment.TestFragment.testWholeAll) ... ok
testWholeCopy (prody.tests.atomic.test_fragment.TestFragment.testWholeCopy) ... ok
testWholeNoh (prody.tests.atomic.test_fragment.TestFragment.testWholeNoh) ... ok
testWholeNohCopy (prody.tests.atomic.test_fragment.TestFragment.testWholeNohCopy) ... ok
testCA (prody.tests.atomic.test_hierview.TestShuffled.testCA) ... ok
testProtein (prody.tests.atomic.test_hierview.TestShuffled.testProtein) ... ok
testNumResidues (prody.tests.atomic.test_hierview.TestTerRecord.testNumResidues) ... ok
testResidueIndexing (prody.tests.atomic.test_hierview.TestTerRecord.testResidueIndexing) ... ok
testSelectionResidueIndexing (prody.tests.atomic.test_hierview.TestTerRecord.testSelectionResidueIndexing) ... ok
testSelectionResidueIndexing2 (prody.tests.atomic.test_hierview.TestTerRecord.testSelectionResidueIndexing2) ... ok
prody.tests.atomic.test_select (unittest.loader._FailedTest.prody.tests.atomic.test_select) ... ERROR
testSetData (prody.tests.atomic.test_subset.TestUserData.testSetData) ... ok
testDatafile_1ejg (prody.tests.datafiles.TestDatafiles.testDatafile_1ejg)
Test presence of "pdb1ejg.pdb" ... ok
testDatafile_1ubi (prody.tests.datafiles.TestDatafiles.testDatafile_1ubi)
Test presence of "pdb1ubi.pdb" ... ok
testDatafile_1ubi_ca (prody.tests.datafiles.TestDatafiles.testDatafile_1ubi_ca)
Test presence of "pdb1ubi_ca.pdb" ... ok
testDatafile_2gb1_truncated (prody.tests.datafiles.TestDatafiles.testDatafile_2gb1_truncated)
Test presence of "pdb2gb1_truncated.pdb" ... ok
testDatafile_2k39_ca (prody.tests.datafiles.TestDatafiles.testDatafile_2k39_ca)
Test presence of "pdb2k39_ca.pdb" ... ok
testDatafile_2nwl (prody.tests.datafiles.TestDatafiles.testDatafile_2nwl)
Test presence of "pdb2nwl-opm.pdb" ... ok
testDatafile_3hsy (prody.tests.datafiles.TestDatafiles.testDatafile_3hsy)
Test presence of "pdb3hsy.pdb" ... ok
testDatafile_3mht (prody.tests.datafiles.TestDatafiles.testDatafile_3mht)
Test presence of "pdb3mht.pdb" ... ok
testDatafile_3o21 (prody.tests.datafiles.TestDatafiles.testDatafile_3o21)
Test presence of "pdb3o21.pdb" ... ok
testDatafile_3p3w (prody.tests.datafiles.TestDatafiles.testDatafile_3p3w)
Test presence of "pdb3p3w.pdb" ... ok
testDatafile_DI (prody.tests.datafiles.TestDatafiles.testDatafile_DI)
Test presence of "msa_Cys_knot_di.dat" ... ok
testDatafile_Fasta (prody.tests.datafiles.TestDatafiles.testDatafile_Fasta)
Test presence of "msa_Cys_knot.fasta" ... ok
testDatafile_MSA (prody.tests.datafiles.TestDatafiles.testDatafile_MSA)
Test presence of "msa_3hsyA_3o21A.fasta" ... ok
testDatafile_MSA_MEW (prody.tests.datafiles.TestDatafiles.testDatafile_MSA_MEW)
Test presence of "msa_3hsyA_3o21A_new.fasta" ... ok
testDatafile_RTER (prody.tests.datafiles.TestDatafiles.testDatafile_RTER)
Test presence of "pdbRTER.pdb" ... ok
testDatafile_SCA (prody.tests.datafiles.TestDatafiles.testDatafile_SCA)
Test presence of "msa_Cys_knot_sca.dat" ... ok
testDatafile_Selex (prody.tests.datafiles.TestDatafiles.testDatafile_Selex)
Test presence of "msa_Cys_knot.slx" ... ok
testDatafile_Stockholm (prody.tests.datafiles.TestDatafiles.testDatafile_Stockholm)
Test presence of "msa_Cys_knot.sth" ... ok
testDatafile_anm1ubi_evalues (prody.tests.datafiles.TestDatafiles.testDatafile_anm1ubi_evalues)
Test presence of "anm1ubi_evalues.dat" ... ok
testDatafile_anm1ubi_hessian (prody.tests.datafiles.TestDatafiles.testDatafile_anm1ubi_hessian)
Test presence of "anm1ubi_hessian.coo" ... ok
testDatafile_anm1ubi_vectors (prody.tests.datafiles.TestDatafiles.testDatafile_anm1ubi_vectors)
Test presence of "anm1ubi_vectors.dat" ... ok
testDatafile_commute1ubi (prody.tests.datafiles.TestDatafiles.testDatafile_commute1ubi)
Test presence of "commute1ubi.dat" ... ok
testDatafile_dcd (prody.tests.datafiles.TestDatafiles.testDatafile_dcd)
Test presence of "dcd2k39_truncated.dcd" ... ok
testDatafile_dssp (prody.tests.datafiles.TestDatafiles.testDatafile_dssp)
Test presence of "pdb1r19_dssp.pdb" ... ok
testDatafile_five_digits (prody.tests.datafiles.TestDatafiles.testDatafile_five_digits)
Test presence of "pdb1tw7_step3_charmm2namd.pdb" ... ok
testDatafile_gnm1ubi_evalues (prody.tests.datafiles.TestDatafiles.testDatafile_gnm1ubi_evalues)
Test presence of "gnm1ubi_evalues.dat" ... ok
testDatafile_gnm1ubi_kirchhoff (prody.tests.datafiles.TestDatafiles.testDatafile_gnm1ubi_kirchhoff)
Test presence of "gnm1ubi_kirchhoff.coo" ... ok
testDatafile_gnm1ubi_vectors (prody.tests.datafiles.TestDatafiles.testDatafile_gnm1ubi_vectors)
Test presence of "gnm1ubi_vectors.dat" ... ok
testDatafile_gromacs (prody.tests.datafiles.TestDatafiles.testDatafile_gromacs)
Test presence of "pdb6fpj_Bb_fixed_solv_ions.pdb" ... ok
testDatafile_h36 (prody.tests.datafiles.TestDatafiles.testDatafile_h36)
Test presence of "pdb1tw7_step3_charmm2namd_doubled_h36.pdb" ... ok
testDatafile_h36_ter (prody.tests.datafiles.TestDatafiles.testDatafile_h36_ter)
Test presence of "pdb4v8r_h36.pdb" ... ok
testDatafile_hex (prody.tests.datafiles.TestDatafiles.testDatafile_hex)
Test presence of "pdb1tw7_step3_charmm2namd_doubled_hex.pdb" ... ok
testDatafile_hex_ter (prody.tests.datafiles.TestDatafiles.testDatafile_hex_ter)
Test presence of "pdb4v8r_hex.pdb" ... ok
testDatafile_hit1ubi (prody.tests.datafiles.TestDatafiles.testDatafile_hit1ubi)
Test presence of "hit1ubi.dat" ... ok
testDatafile_long_chid_cif (prody.tests.datafiles.TestDatafiles.testDatafile_long_chid_cif)
Test presence of "mmcif_6zu5.cif" ... ok
testDatafile_multi_model_cif (prody.tests.datafiles.TestDatafiles.testDatafile_multi_model_cif)
Test presence of "mmcif_6yfy.cif" ... ok
testDatafile_multi_model_truncated (prody.tests.datafiles.TestDatafiles.testDatafile_multi_model_truncated)
Test presence of "pdb2k39_truncated.pdb" ... ok
testDatafile_oneatom (prody.tests.datafiles.TestDatafiles.testDatafile_oneatom)
Test presence of "pdb1ejg_oneatom.pdb" ... ok
testDatafile_pca2k39_cov (prody.tests.datafiles.TestDatafiles.testDatafile_pca2k39_cov)
Test presence of "pca2k39_cov.coo" ... ok
testDatafile_pca2k39_evalues (prody.tests.datafiles.TestDatafiles.testDatafile_pca2k39_evalues)
Test presence of "pca2k39_evalues.dat" ... ok
testDatafile_pca2k39_vectors (prody.tests.datafiles.TestDatafiles.testDatafile_pca2k39_vectors)
Test presence of "pca2k39_vectors.dat" ... ok
testDatafile_rtb2gb1_hessian (prody.tests.datafiles.TestDatafiles.testDatafile_rtb2gb1_hessian)
Test presence of "rtb2gb1_hessian.coo" ... ok
testDatafile_rtb2gb1_project (prody.tests.datafiles.TestDatafiles.testDatafile_rtb2gb1_project)
Test presence of "rtb2gb1_project.coo" ... ok
testDatafile_sti (prody.tests.datafiles.TestDatafiles.testDatafile_sti)
Test presence of "xmlSTI.xml" ... ok
testMode1d (prody.tests.dynamics.test_editing.TestExtending.testMode1d) ... ok
testMode3d (prody.tests.dynamics.test_editing.TestExtending.testMode3d) ... ok
testModel1d (prody.tests.dynamics.test_editing.TestExtending.testModel1d) ... ok
testModel3d (prody.tests.dynamics.test_editing.TestExtending.testModel3d) ... ok
testVector1d (prody.tests.dynamics.test_editing.TestExtending.testVector1d) ... ok
testVector3d (prody.tests.dynamics.test_editing.TestExtending.testVector3d) ... ok
testModel3d (prody.tests.dynamics.test_editing.TestInterpolating.testModel3d) ... ok
testMode1d (prody.tests.dynamics.test_editing.TestSlicing.testMode1d) ... ok
testMode3d (prody.tests.dynamics.test_editing.TestSlicing.testMode3d) ... ok
testModel1d (prody.tests.dynamics.test_editing.TestSlicing.testModel1d) ... ok
testModel3d (prody.tests.dynamics.test_editing.TestSlicing.testModel3d) ... ok
testVector1d (prody.tests.dynamics.test_editing.TestSlicing.testVector1d) ... ok
testVector3d (prody.tests.dynamics.test_editing.TestSlicing.testVector3d) ... ok
prody.tests.dynamics.test_enms (unittest.loader._FailedTest.prody.tests.dynamics.test_enms) ... ERROR
prody.tests.dynamics.test_pca (unittest.loader._FailedTest.prody.tests.dynamics.test_pca) ... ERROR
testSlicing (prody.tests.dynamics.test_signature.TestSDArray.testSlicing) ... ok
testCoordinates (prody.tests.ensemble.test_conformation.TestConformation.testCoordinates) ... ok
testCoordinatesForAll (prody.tests.ensemble.test_conformation.TestConformation.testCoordinatesForAll) ... ok
testGetIndex (prody.tests.ensemble.test_conformation.TestConformation.testGetIndex)
Test get index function. ... ok
testGetNumAtoms (prody.tests.ensemble.test_conformation.TestConformation.testGetNumAtoms)
Test get index function. ... ok
testWeights (prody.tests.ensemble.test_conformation.TestConformation.testWeights) ... ok
testCoordinates (prody.tests.ensemble.test_conformation.TestPDBConformation.testCoordinates) ... ok
testCoordinatesForAll (prody.tests.ensemble.test_conformation.TestPDBConformation.testCoordinatesForAll) ... ok
testGetIndex (prody.tests.ensemble.test_conformation.TestPDBConformation.testGetIndex) ... ok
testGetNumAtoms (prody.tests.ensemble.test_conformation.TestPDBConformation.testGetNumAtoms) ... ok
testWeights (prody.tests.ensemble.test_conformation.TestPDBConformation.testWeights) ... ok
testWeightsForAll (prody.tests.ensemble.test_conformation.TestPDBConformation.testWeightsForAll) ... ok
testConcatenation (prody.tests.ensemble.test_ensemble.TestEnsemble.testConcatenation)
Test concatenation of ensembles without weights. ... ok
testConcatenationNoweightsWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testConcatenationNoweightsWeights)
Test concatenation of ensembles without and with weights. ... ok
testConcatenationWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testConcatenationWeights)
Test concatenation of ensembles with weights. ... ok
testConcatenationWeightsNoweights (prody.tests.ensemble.test_ensemble.TestEnsemble.testConcatenationWeightsNoweights)
Test concatenation of ensembles with and without weights. ... ok
testDelCoordsetAll (prody.tests.ensemble.test_ensemble.TestEnsemble.testDelCoordsetAll) ... ok
testDelCoordsetMiddle (prody.tests.ensemble.test_ensemble.TestEnsemble.testDelCoordsetMiddle) ... ok
testGetCoordinates (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetCoordinates)
Test correctness of reference coordinates. ... ok
testGetCoordsets (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetCoordsets)
Test correctness of all coordinates. ... ok
testGetNumAtoms (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetNumAtoms) ... ok
testGetNumCsets (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetNumCsets) ... ok
testGetRMSDs (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetRMSDs) ... ok
testGetRMSDsWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetRMSDsWeights) ... ok
testGetWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetWeights)
Test correctness of all weights. ... ok
testIterCoordsets (prody.tests.ensemble.test_ensemble.TestEnsemble.testIterCoordsets)
Test coordinate iteration. ... ok
testSelection (prody.tests.ensemble.test_ensemble.TestEnsemble.testSelection)
Test atom selection of ensemble. ... ERROR
testSlicing (prody.tests.ensemble.test_ensemble.TestEnsemble.testSlicing)
Test slicing operation. ... ok
testSlicingCopy (prody.tests.ensemble.test_ensemble.TestEnsemble.testSlicingCopy)
Test making a copy by slicing operation. ... ok
testSlicingList (prody.tests.ensemble.test_ensemble.TestEnsemble.testSlicingList)
Test slicing with a list. ... ok
testSlicingWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testSlicingWeights)
Test slicing operation with weights. ... ok
testSuperpose (prody.tests.ensemble.test_ensemble.TestEnsemble.testSuperpose) ... ok
testSuperposeWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testSuperposeWeights) ... ok
testResults (prody.tests.ensemble.test_functions.TestBuildPDBEnsemble.testResults) ... ok
testInvalidType (prody.tests.ensemble.test_functions.TestCalcOccupancies.testInvalidType) ... ok
testResults (prody.tests.ensemble.test_functions.TestCalcOccupancies.testResults) ... ok
testWeightsNone (prody.tests.ensemble.test_functions.TestCalcOccupancies.testWeightsNone) ... ok
testResults (prody.tests.ensemble.test_functions.TestTrimPDBEnsemble.testResults) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/sequence/sequence.py:52: DeprecationWarning: tostring() is deprecated. Use tobytes() instead.
  return self._array.tostring().decode()
ok
testAddCoordsets (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testAddCoordsets) ... ok
testConcatenation (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testConcatenation)
Test concatenation of PDB ensembles. ... ok
testDelCoordsetAll (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testDelCoordsetAll)
Test consequences of deleting all coordinate sets. ... ok
testDelCoordsetMiddle (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testDelCoordsetMiddle) ... ok
testDelCoordsetMiddleTrans (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testDelCoordsetMiddleTrans) ... ok
testGetCoordinates (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testGetCoordinates) ... ok
testGetCoordsets (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testGetCoordsets) ... ok
testGetNumAtoms (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testGetNumAtoms) ... ok
testGetNumCsets (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testGetNumCsets) ... ok
testGetWeights (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testGetWeights) ... ok
testIterCoordsets (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testIterCoordsets) ... ok
testSlicing (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testSlicing) ... ok
testSlicingCopy (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testSlicingCopy) ... ok
testSlicingList (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testSlicingList) ... ok
testSlicingWeights (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testSlicingWeights) ... ok
testAllSearch (prody.tests.kdtree.test_kdtree.TestKDTree.testAllSearch) ... ok
testSearch (prody.tests.kdtree.test_kdtree.TestKDTree.testSearch) ... ok
testPairNoPBC (prody.tests.kdtree.test_kdtree.TestKDTreePBC.testPairNoPBC) ... ok
testPairPBC (prody.tests.kdtree.test_kdtree.TestKDTreePBC.testPairPBC) ... ok
testPointNoPBC (prody.tests.kdtree.test_kdtree.TestKDTreePBC.testPointNoPBC) ... ok
testPointPBC (prody.tests.kdtree.test_kdtree.TestKDTreePBC.testPointPBC) ... ok
testMINvsMAX (prody.tests.measure.test_contacts.TestContacts.testMINvsMAX) ... ok
testPBCvsNONE (prody.tests.measure.test_contacts.TestContacts.testPBCvsNONE) ... ok
testAtomicArgumentSwitching (prody.tests.measure.test_contacts.TestNeighbors.testAtomicArgumentSwitching) ... ok
testCoordArgumentSwitching (prody.tests.measure.test_contacts.TestNeighbors.testCoordArgumentSwitching) ... ok
testNoPBC (prody.tests.measure.test_contacts.TestNeighbors.testNoPBC) ... ok
testPBC (prody.tests.measure.test_contacts.TestNeighbors.testPBC) ... ok
testPBCAtomicArgumentSwitching (prody.tests.measure.test_contacts.TestNeighbors.testPBCAtomicArgumentSwitching) ... ok
testPBCCoordArgumentSwitching (prody.tests.measure.test_contacts.TestNeighbors.testPBCCoordArgumentSwitching) ... ok
testCenter (prody.tests.measure.test_measure.TestCenter.testCenter) ... ok
testCenterWithWeights (prody.tests.measure.test_measure.TestCenter.testCenterWithWeights) ... ok
testMultiCoordsets (prody.tests.measure.test_measure.TestCenter.testMultiCoordsets) ... ok
testMultiCoordsetsWithWeights (prody.tests.measure.test_measure.TestCenter.testMultiCoordsetsWithWeights) ... ok
testCTerPhi (prody.tests.measure.test_measure.TestDihedrals.testCTerPhi) ... ok
testCTerPsi (prody.tests.measure.test_measure.TestDihedrals.testCTerPsi) ... ok
testCalcPhi (prody.tests.measure.test_measure.TestDihedrals.testCalcPhi) ... ok
testCalcPsi (prody.tests.measure.test_measure.TestDihedrals.testCalcPsi) ... ok
testNTerPhi (prody.tests.measure.test_measure.TestDihedrals.testNTerPhi) ... ok
testNTerPsi (prody.tests.measure.test_measure.TestDihedrals.testNTerPsi) ... ok
testPBC (prody.tests.measure.test_measure.TestDistances.testPBC) ... ok
testPBCSymmetry (prody.tests.measure.test_measure.TestDistances.testPBCSymmetry) ... ok
testMSF (prody.tests.measure.test_measure.TestMSF.testMSF) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/trajectory/dcdfile.py:273: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
  xyz = fromstring(self._file.read(self._itemsize * n_floats),
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/trajectory/dcdfile.py:320: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
  data = fromstring(data, self._dtype)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/trajectory/dcdfile.py:294: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
  unitcell = fromstring(self._file.read(48), dtype=np.float64)
ok
testMSFfloat (prody.tests.measure.test_measure.TestMSF.testMSFfloat) ... ok
testByArgument (prody.tests.measure.test_transform.TestMoveAtoms.testByArgument) ... ok
testToArgument (prody.tests.measure.test_transform.TestMoveAtoms.testToArgument) ... ok
testTransformation (prody.tests.measure.test_transform.TestMoveAtoms.testTransformation) ... ok
testWrap (prody.tests.measure.test_transform.TestWrapAtoms.testWrap) ... ok
prody.tests.proteins.test_ciffile (unittest.loader._FailedTest.prody.tests.proteins.test_ciffile) ... ERROR
prody.tests.proteins.test_dssp (unittest.loader._FailedTest.prody.tests.proteins.test_dssp) ... ERROR
testHeaderContent (prody.tests.proteins.test_header.TestParsePDBHeaderOnly.testHeaderContent) ... ok
testHeaderType (prody.tests.proteins.test_header.TestParsePDBHeaderOnly.testHeaderType) ... ok
prody.tests.proteins.test_localpdb (unittest.loader._FailedTest.prody.tests.proteins.test_localpdb) ... ERROR
prody.tests.proteins.test_pdbfile (unittest.loader._FailedTest.prody.tests.proteins.test_pdbfile) ... ERROR
prody.tests.proteins.test_wwpdb (unittest.loader._FailedTest.prody.tests.proteins.test_wwpdb) ... ERROR
testBuildMSAlocal (prody.tests.sequence.test_analysis.TestBuildMSA.testBuildMSAlocal) ... ok
testResidueCount (prody.tests.sequence.test_analysis.TestCalcMSAOccupancy.testResidueCount) ... ok
testResidueOccupancy (prody.tests.sequence.test_analysis.TestCalcMSAOccupancy.testResidueOccupancy) ... ok
testSequenceCount (prody.tests.sequence.test_analysis.TestCalcMSAOccupancy.testSequenceCount) ... ok
testSequenceOccupancy (prody.tests.sequence.test_analysis.TestCalcMSAOccupancy.testSequenceOccupancy) ... ok
testMATLAB (prody.tests.sequence.test_analysis.TestCalcMeff.testMATLAB) ... ok
testTwenty (prody.tests.sequence.test_analysis.TestCalcMeff.testTwenty) ... ok
testTwentyReversed (prody.tests.sequence.test_analysis.TestCalcMeff.testTwentyReversed) ... ok
testZero1 (prody.tests.sequence.test_analysis.TestCalcMeff.testZero1) ... ok
testZero2 (prody.tests.sequence.test_analysis.TestCalcMeff.testZero2) ... ok
testAmbiguity (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity) ... ok
testAmbiguity2 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity2) ... ok
testAmbiguity3 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity3) ... ok
testAmbiguity4 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity4) ... ok
testAmbiguity5 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity5) ... ok
testAmbiguity6 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity6) ... ok
testAmbiguity7 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity7) ... ok
testInf (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testInf) ... ok
testNoAmbiguity (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testNoAmbiguity) ... ok
testNorm (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testNorm) ... ok
testNorm2 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testNorm2) ... ok
testSixSequences (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testSixSequences) ... ok
testTwenty (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testTwenty) ... ok
testTwentyReversed (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testTwentyReversed) ... ok
testAmbiguity (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity) ... ok
testAmbiguity2 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity2) ... ok
testAmbiguity3 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity3) ... ok
testAmbiguity4 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity4) ... ok
testAmbiguity5 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity5) ... ok
testAmbiguity6 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity6) ... ok
testAmbiguity7 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity7) ... ok
testFourSequences (prody.tests.sequence.test_analysis.TestCalcOMES.testFourSequences) ... ok
testInf (prody.tests.sequence.test_analysis.TestCalcOMES.testInf) ... ok
testNoAmbiguity (prody.tests.sequence.test_analysis.TestCalcOMES.testNoAmbiguity) ... ok
testTwenty (prody.tests.sequence.test_analysis.TestCalcOMES.testTwenty) ... ok
testTwentyReversed (prody.tests.sequence.test_analysis.TestCalcOMES.testTwentyReversed) ... ok
testZero (prody.tests.sequence.test_analysis.TestCalcOMES.testZero) ... ok
testMATLAB (prody.tests.sequence.test_analysis.TestCalcSCA.testMATLAB) ... ok
testZero (prody.tests.sequence.test_analysis.TestCalcSCA.testZero) ... ok
testAmbiguous (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testAmbiguous) ... ok
testGapDividend (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testGapDividend) ... ok
testSixSequences (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testSixSequences) ... ok
testSmallProbability (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testSmallProbability) ... ok
testTwenty (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testTwenty) ... ok
testMATLAB10 (prody.tests.sequence.test_analysis.TestDirectInfo.testMATLAB10) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/sequence/analysis.py:592: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
  c = matrix.dot(matrix(zeros((length*q, 1), float)),
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/sequence/analysis.py:593: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
  matrix(zeros((1, length*q), float)))
/usr/lib/python3/dist-packages/numpy/matrixlib/defmatrix.py:70: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
  return matrix(data, dtype=dtype, copy=False)
ok
testMATLAB8 (prody.tests.sequence.test_analysis.TestDirectInfo.testMATLAB8) ... ok
testTwenty (prody.tests.sequence.test_analysis.TestDirectInfo.testTwenty) ... ok
testTwentyReversed (prody.tests.sequence.test_analysis.TestDirectInfo.testTwentyReversed) ... ok
testZero (prody.tests.sequence.test_analysis.TestDirectInfo.testZero) ... ok
testZero1 (prody.tests.sequence.test_analysis.TestDirectInfo.testZero1) ... ok
testZero2 (prody.tests.sequence.test_analysis.TestDirectInfo.testZero2) ... ok
testZero3 (prody.tests.sequence.test_analysis.TestDirectInfo.testZero3) ... ok
testZero4 (prody.tests.sequence.test_analysis.TestDirectInfo.testZero4) ... ok
testIdentityMatrix (prody.tests.sequence.test_analysis.TestIdentity.testIdentityMatrix) ... ok
testIdentityMatrixNonTurbo (prody.tests.sequence.test_analysis.TestIdentity.testIdentityMatrixNonTurbo) ... ok
testUnique (prody.tests.sequence.test_analysis.TestUnique.testUnique) ... ok
testUnique2 (prody.tests.sequence.test_analysis.TestUnique.testUnique2) ... ok
testMerge (prody.tests.sequence.test_msa.TestMerging.testMerge) ... ok
testAddition (prody.tests.sequence.test_msa.TestRefinement.testAddition) ... ok
testAll (prody.tests.sequence.test_msa.TestRefinement.testAll) ... ok
testColocc (prody.tests.sequence.test_msa.TestRefinement.testColocc) ... ok
testExtension (prody.tests.sequence.test_msa.TestRefinement.testExtension) ... ok
testLabel (prody.tests.sequence.test_msa.TestRefinement.testLabel) ... ok
testRowCol (prody.tests.sequence.test_msa.TestRefinement.testRowCol) ... ok
testRowocc (prody.tests.sequence.test_msa.TestRefinement.testRowocc) ... ok
testSeqid (prody.tests.sequence.test_msa.TestRefinement.testSeqid) ... ok
testSeqidLabel (prody.tests.sequence.test_msa.TestRefinement.testSeqidLabel) ... ok
prody.tests.sequence.test_msafile (unittest.loader._FailedTest.prody.tests.sequence.test_msafile) ... ERROR
testStringConversion (prody.tests.sequence.test_sequence.TestSequence.testStringConversion) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/sequence/sequence.py:36: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
  self._seq = fromstring(args[0], '|S1')
ok
testParseDCD (prody.tests.trajectory.test_dcdfile.TestDCDFile.testParseDCD) ... ok
testWrite (prody.tests.trajectory.test_dcdfile.TestDCDFile.testWrite) ... ok
testWriteDCD (prody.tests.trajectory.test_dcdfile.TestDCDFile.testWriteDCD) ... ok
testWriteModeAppend (prody.tests.trajectory.test_dcdfile.TestDCDFile.testWriteModeAppend) ... ok
testAll (prody.tests.trajectory.test_frame.TestSuperpose.testAll) ... ok
testCarbon (prody.tests.trajectory.test_frame.TestSuperpose.testCarbon) ... ok
testCoords (prody.tests.utilities.test_checkers.TestCheckCoords.testCoords) ... ok
testCoordset (prody.tests.utilities.test_checkers.TestCheckCoords.testCoordset) ... ok
testCoordsetNatoms (prody.tests.utilities.test_checkers.TestCheckCoords.testCoordsetNatoms) ... ok
testInvalidCoords (prody.tests.utilities.test_checkers.TestCheckCoords.testInvalidCoords) ... ok
testCorrectMonotypeOneArg (prody.tests.utilities.test_checkers.testCheckTypes.testCorrectMonotypeOneArg) ... ok
testCorrectMonotypeTwoArgs (prody.tests.utilities.test_checkers.testCheckTypes.testCorrectMonotypeTwoArgs) ... ok
testCorrectMultitypeOneArg (prody.tests.utilities.test_checkers.testCheckTypes.testCorrectMultitypeOneArg) ... ok
testWrongMonotypeOneArg (prody.tests.utilities.test_checkers.testCheckTypes.testWrongMonotypeOneArg) ... ok
testWrongMonotypeTwoArgs (prody.tests.utilities.test_checkers.testCheckTypes.testWrongMonotypeTwoArgs) ... ok
testWrongMultitypeOneArg (prody.tests.utilities.test_checkers.testCheckTypes.testWrongMultitypeOneArg) ... ok
testContinuous (prody.tests.utilities.test_misctools.TestRangeString.testContinuous) ... ok
testGapped (prody.tests.utilities.test_misctools.TestRangeString.testGapped) ... ok
testNegative (prody.tests.utilities.test_misctools.TestRangeString.testNegative) ... ok
testRepeated (prody.tests.utilities.test_misctools.TestRangeString.testRepeated) ... ok
testBuffer (prody.tests.utilities.test_pathtools.TestGunzip.testBuffer) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/utilities/test_pathtools.py:34: ResourceWarning: unclosed file <_io.BufferedReader name='/tmp/compressed.txt.gz'>
  buff = open(self.gzfn, 'rb').read()
ResourceWarning: Enable tracemalloc to get the object allocation traceback
ok
testFile (prody.tests.utilities.test_pathtools.TestGunzip.testFile) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/utilities/test_pathtools.py:29: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/compressed.txt' mode='r' encoding='UTF-8'>
  text = open(fn).read()
ResourceWarning: Enable tracemalloc to get the object allocation traceback
ok

======================================================================
ERROR: prody.tests.apps.test_prody_anm (unittest.loader._FailedTest.prody.tests.apps.test_prody_anm)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.apps.test_prody_anm
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/apps/test_prody_anm.py", line 9, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
  File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
    ~~~~~~~~~~^^^^^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/apps/test_prody_anm.py", line 11, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: prody.tests.apps.test_prody_catdcd (unittest.loader._FailedTest.prody.tests.apps.test_prody_catdcd)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.apps.test_prody_catdcd
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/apps/test_prody_catdcd.py", line 8, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
  File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
    ~~~~~~~~~~^^^^^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/apps/test_prody_catdcd.py", line 10, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: prody.tests.apps.test_prody_examples (unittest.loader._FailedTest.prody.tests.apps.test_prody_examples)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.apps.test_prody_examples
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/apps/test_prody_examples.py", line 10, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
  File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
    ~~~~~~~~~~^^^^^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/apps/test_prody_examples.py", line 12, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: prody.tests.apps.test_prody_gnm (unittest.loader._FailedTest.prody.tests.apps.test_prody_gnm)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.apps.test_prody_gnm
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/apps/test_prody_gnm.py", line 8, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
  File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
    ~~~~~~~~~~^^^^^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/apps/test_prody_gnm.py", line 10, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: prody.tests.apps.test_prody_pca (unittest.loader._FailedTest.prody.tests.apps.test_prody_pca)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.apps.test_prody_pca
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/apps/test_prody_pca.py", line 8, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
  File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
    ~~~~~~~~~~^^^^^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/apps/test_prody_pca.py", line 10, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: prody.tests.atomic.test_select (unittest.loader._FailedTest.prody.tests.atomic.test_select)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.atomic.test_select
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/atomic/test_select.py", line 9, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
  File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
    ~~~~~~~~~~^^^^^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/atomic/test_select.py", line 11, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: prody.tests.dynamics.test_enms (unittest.loader._FailedTest.prody.tests.dynamics.test_enms)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.dynamics.test_enms
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/dynamics/test_enms.py", line 7, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
  File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
    ~~~~~~~~~~^^^^^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/dynamics/test_enms.py", line 9, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: prody.tests.dynamics.test_pca (unittest.loader._FailedTest.prody.tests.dynamics.test_pca)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.dynamics.test_pca
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/dynamics/test_pca.py", line 7, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
  File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
    ~~~~~~~~~~^^^^^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/dynamics/test_pca.py", line 9, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: testSelection (prody.tests.ensemble.test_ensemble.TestEnsemble.testSelection)
Test atom selection of ensemble.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/ensemble/test_ensemble.py", line 191, in testSelection
    sel = ATOMS.select('resnum 1 to 3')
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic/atomic.py", line 232, in select
    return SELECT.select(self, selstr, **kwargs)
           ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic/select.py", line 895, in select
    indices = self.getIndices(atoms, selstr, **kwargs)
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic/select.py", line 953, in getIndices
    torf = self.getBoolArray(atoms, selstr, **kwargs)
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic/select.py", line 1004, in getBoolArray
    parser = self._getParser(selstr)
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic/select.py", line 1103, in _getParser
    parser.enablePackrat()
    ~~~~~~~~~~~~~~~~~~~~^^
  File "/usr/lib/python3/dist-packages/pyparsing/util.py", line 265, in _inner
    return fn(*args, **kwargs)
  File "/usr/lib/python3/dist-packages/pyparsing/core.py", line 1132, in enable_packrat
    ParserElement.packrat_cache = _FifoCache(cache_size_limit)  # type: ignore[assignment]
                                  ~~~~~~~~~~^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3/dist-packages/pyparsing/util.py", line 105, in __init__
    keyring = [object()] * size
              ~~~~~~~~~~~^~~~~~
TypeError: can't multiply sequence by non-int of type 'Forward'

======================================================================
ERROR: prody.tests.proteins.test_ciffile (unittest.loader._FailedTest.prody.tests.proteins.test_ciffile)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.proteins.test_ciffile
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/proteins/test_ciffile.py", line 8, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
  File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
    ~~~~~~~~~~^^^^^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/proteins/test_ciffile.py", line 10, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: prody.tests.proteins.test_dssp (unittest.loader._FailedTest.prody.tests.proteins.test_dssp)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.proteins.test_dssp
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/proteins/test_dssp.py", line 5, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
  File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
    ~~~~~~~~~~^^^^^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/proteins/test_dssp.py", line 7, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: prody.tests.proteins.test_localpdb (unittest.loader._FailedTest.prody.tests.proteins.test_localpdb)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.proteins.test_localpdb
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/proteins/test_localpdb.py", line 8, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
  File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
    ~~~~~~~~~~^^^^^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/proteins/test_localpdb.py", line 10, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: prody.tests.proteins.test_pdbfile (unittest.loader._FailedTest.prody.tests.proteins.test_pdbfile)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.proteins.test_pdbfile
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/proteins/test_pdbfile.py", line 8, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
  File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
    ~~~~~~~~~~^^^^^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/proteins/test_pdbfile.py", line 10, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: prody.tests.proteins.test_wwpdb (unittest.loader._FailedTest.prody.tests.proteins.test_wwpdb)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.proteins.test_wwpdb
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/proteins/test_wwpdb.py", line 7, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
  File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
    ~~~~~~~~~~^^^^^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/proteins/test_wwpdb.py", line 9, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: prody.tests.sequence.test_msafile (unittest.loader._FailedTest.prody.tests.sequence.test_msafile)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.sequence.test_msafile
Traceback (most recent call last):
  File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
  File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
    ~~~~~~~~~~^^^^^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/sequence/test_msafile.py", line 8, in <module>
    from numpy.testing import assert_array_equal, dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


----------------------------------------------------------------------
Ran 279 tests in 10.716s

FAILED (errors=15)
E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build; python3.13 -m unittest discover -v 
I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build; python3.12 -m unittest discover -v 
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/utilities/doctools.py:48: SyntaxWarning: invalid escape sequence '\i'
  """Returns wrapped lines from :func:`textwrap.wrap` after *join*\ing them.
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic/flags.py:463: SyntaxWarning: invalid escape sequence '\ '
  __doc__ += """
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic/select.py:2: SyntaxWarning: invalid escape sequence '\|'
  """This module defines a class for selecting subsets of atoms.  You can read
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic/select.py:719: SyntaxWarning: invalid escape sequence '\w'
  RE_SCHARS = re_compile('`[\w\W]*?`')
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic/select.py:738: SyntaxWarning: invalid escape sequence '\w'
  RE_REGEXP = re_compile('"[\w\W]*"')
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic/select.py:757: SyntaxWarning: invalid escape sequence '\d'
  _ = '[-+]?\d+(\.\d*)?([eE]\d+)?'
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic/select.py:758: SyntaxWarning: invalid escape sequence '\ '
  RE_NRANGE = re_compile(_ + '\ *(to|:)\ *' + _)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic/select.py:761: SyntaxWarning: invalid escape sequence '\ '
  pp.Optional(pp.Regex('(\ *:\ *' + _ + ')')))
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/sequence/analysis.py:169: SyntaxWarning: invalid escape sequence '\{'
  """Apply one of the normalizations discussed in [MLC05]_ to *mutinfo*
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/proteins/localpdb.py:438: SyntaxWarning: invalid escape sequence '\.'
  pdbext = compile('\.(pdb|ent)(\.gz)?$', IGNORECASE)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/proteins/localpdb.py:440: SyntaxWarning: invalid escape sequence '\.'
  pdbext = compile('\.(pdb|ent)\.gz$', IGNORECASE)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/proteins/localpdb.py:442: SyntaxWarning: invalid escape sequence '\.'
  pdbext = compile('\.(pdb|ent)$', IGNORECASE)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/proteins/dssp.py:78: SyntaxWarning: invalid escape sequence '\*'
  """Parse DSSP data from file *dssp* into :class:`.AtomGroup` instance
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics/pca.py:59: SyntaxWarning: invalid escape sequence '\_'
  """Build a covariance matrix for *coordsets* using mean coordinates
prody.tests.apps.test_prody_anm (unittest.loader._FailedTest.prody.tests.apps.test_prody_anm) ... ERROR
prody.tests.apps.test_prody_catdcd (unittest.loader._FailedTest.prody.tests.apps.test_prody_catdcd) ... ERROR
prody.tests.apps.test_prody_examples (unittest.loader._FailedTest.prody.tests.apps.test_prody_examples) ... ERROR
prody.tests.apps.test_prody_gnm (unittest.loader._FailedTest.prody.tests.apps.test_prody_gnm) ... ERROR
prody.tests.apps.test_prody_pca (unittest.loader._FailedTest.prody.tests.apps.test_prody_pca) ... ERROR
testAtomGroup (prody.tests.atomic.test_atomic.TestAtomIterations.testAtomGroup) ... ok
testAtomMap (prody.tests.atomic.test_atomic.TestAtomIterations.testAtomMap) ... ok
testChain (prody.tests.atomic.test_atomic.TestAtomIterations.testChain) ... ok
testResidue (prody.tests.atomic.test_atomic.TestAtomIterations.testResidue) ... ok
testSelection (prody.tests.atomic.test_atomic.TestAtomIterations.testSelection) ... ok
testAtom (prody.tests.atomic.test_atomic.TestPickling.testAtom) ... ok
testAtomGroup (prody.tests.atomic.test_atomic.TestPickling.testAtomGroup) ... ok
testSelection (prody.tests.atomic.test_atomic.TestPickling.testSelection) ... ok
testSaveLoad (prody.tests.atomic.test_atomic.TestSaveLoad.testSaveLoad) ... ok
testInstantiation (prody.tests.atomic.test_atommap.TestInstantiation.testInstantiation) ... ok
testAllSelection (prody.tests.atomic.test_atommap.TestSelection.testAllSelection) ... ok
testChainSelection (prody.tests.atomic.test_atommap.TestSelection.testChainSelection) ... ok
testGetBoolArray (prody.tests.atomic.test_atommap.TestSelection.testGetBoolArray) ... ok
testNameSelection (prody.tests.atomic.test_atommap.TestSelection.testNameSelection) ... ok
testSplit (prody.tests.atomic.test_fragment.TestFragment.testSplit) ... ok
testSplitCopy (prody.tests.atomic.test_fragment.TestFragment.testSplitCopy) ... ok
testSplitNoh (prody.tests.atomic.test_fragment.TestFragment.testSplitNoh) ... ok
testSplitNohCopy (prody.tests.atomic.test_fragment.TestFragment.testSplitNohCopy) ... ok
testWhole (prody.tests.atomic.test_fragment.TestFragment.testWhole) ... ok
testWhole2 (prody.tests.atomic.test_fragment.TestFragment.testWhole2) ... ok
testWholeAll (prody.tests.atomic.test_fragment.TestFragment.testWholeAll) ... ok
testWholeCopy (prody.tests.atomic.test_fragment.TestFragment.testWholeCopy) ... ok
testWholeNoh (prody.tests.atomic.test_fragment.TestFragment.testWholeNoh) ... ok
testWholeNohCopy (prody.tests.atomic.test_fragment.TestFragment.testWholeNohCopy) ... ok
testCA (prody.tests.atomic.test_hierview.TestShuffled.testCA) ... ok
testProtein (prody.tests.atomic.test_hierview.TestShuffled.testProtein) ... ok
testNumResidues (prody.tests.atomic.test_hierview.TestTerRecord.testNumResidues) ... ok
testResidueIndexing (prody.tests.atomic.test_hierview.TestTerRecord.testResidueIndexing) ... ok
testSelectionResidueIndexing (prody.tests.atomic.test_hierview.TestTerRecord.testSelectionResidueIndexing) ... ok
testSelectionResidueIndexing2 (prody.tests.atomic.test_hierview.TestTerRecord.testSelectionResidueIndexing2) ... ok
prody.tests.atomic.test_select (unittest.loader._FailedTest.prody.tests.atomic.test_select) ... ERROR
testSetData (prody.tests.atomic.test_subset.TestUserData.testSetData) ... ok
testDatafile_1ejg (prody.tests.datafiles.TestDatafiles.testDatafile_1ejg)
Test presence of "pdb1ejg.pdb" ... ok
testDatafile_1ubi (prody.tests.datafiles.TestDatafiles.testDatafile_1ubi)
Test presence of "pdb1ubi.pdb" ... ok
testDatafile_1ubi_ca (prody.tests.datafiles.TestDatafiles.testDatafile_1ubi_ca)
Test presence of "pdb1ubi_ca.pdb" ... ok
testDatafile_2gb1_truncated (prody.tests.datafiles.TestDatafiles.testDatafile_2gb1_truncated)
Test presence of "pdb2gb1_truncated.pdb" ... ok
testDatafile_2k39_ca (prody.tests.datafiles.TestDatafiles.testDatafile_2k39_ca)
Test presence of "pdb2k39_ca.pdb" ... ok
testDatafile_2nwl (prody.tests.datafiles.TestDatafiles.testDatafile_2nwl)
Test presence of "pdb2nwl-opm.pdb" ... ok
testDatafile_3hsy (prody.tests.datafiles.TestDatafiles.testDatafile_3hsy)
Test presence of "pdb3hsy.pdb" ... ok
testDatafile_3mht (prody.tests.datafiles.TestDatafiles.testDatafile_3mht)
Test presence of "pdb3mht.pdb" ... ok
testDatafile_3o21 (prody.tests.datafiles.TestDatafiles.testDatafile_3o21)
Test presence of "pdb3o21.pdb" ... ok
testDatafile_3p3w (prody.tests.datafiles.TestDatafiles.testDatafile_3p3w)
Test presence of "pdb3p3w.pdb" ... ok
testDatafile_DI (prody.tests.datafiles.TestDatafiles.testDatafile_DI)
Test presence of "msa_Cys_knot_di.dat" ... ok
testDatafile_Fasta (prody.tests.datafiles.TestDatafiles.testDatafile_Fasta)
Test presence of "msa_Cys_knot.fasta" ... ok
testDatafile_MSA (prody.tests.datafiles.TestDatafiles.testDatafile_MSA)
Test presence of "msa_3hsyA_3o21A.fasta" ... ok
testDatafile_MSA_MEW (prody.tests.datafiles.TestDatafiles.testDatafile_MSA_MEW)
Test presence of "msa_3hsyA_3o21A_new.fasta" ... ok
testDatafile_RTER (prody.tests.datafiles.TestDatafiles.testDatafile_RTER)
Test presence of "pdbRTER.pdb" ... ok
testDatafile_SCA (prody.tests.datafiles.TestDatafiles.testDatafile_SCA)
Test presence of "msa_Cys_knot_sca.dat" ... ok
testDatafile_Selex (prody.tests.datafiles.TestDatafiles.testDatafile_Selex)
Test presence of "msa_Cys_knot.slx" ... ok
testDatafile_Stockholm (prody.tests.datafiles.TestDatafiles.testDatafile_Stockholm)
Test presence of "msa_Cys_knot.sth" ... ok
testDatafile_anm1ubi_evalues (prody.tests.datafiles.TestDatafiles.testDatafile_anm1ubi_evalues)
Test presence of "anm1ubi_evalues.dat" ... ok
testDatafile_anm1ubi_hessian (prody.tests.datafiles.TestDatafiles.testDatafile_anm1ubi_hessian)
Test presence of "anm1ubi_hessian.coo" ... ok
testDatafile_anm1ubi_vectors (prody.tests.datafiles.TestDatafiles.testDatafile_anm1ubi_vectors)
Test presence of "anm1ubi_vectors.dat" ... ok
testDatafile_commute1ubi (prody.tests.datafiles.TestDatafiles.testDatafile_commute1ubi)
Test presence of "commute1ubi.dat" ... ok
testDatafile_dcd (prody.tests.datafiles.TestDatafiles.testDatafile_dcd)
Test presence of "dcd2k39_truncated.dcd" ... ok
testDatafile_dssp (prody.tests.datafiles.TestDatafiles.testDatafile_dssp)
Test presence of "pdb1r19_dssp.pdb" ... ok
testDatafile_five_digits (prody.tests.datafiles.TestDatafiles.testDatafile_five_digits)
Test presence of "pdb1tw7_step3_charmm2namd.pdb" ... ok
testDatafile_gnm1ubi_evalues (prody.tests.datafiles.TestDatafiles.testDatafile_gnm1ubi_evalues)
Test presence of "gnm1ubi_evalues.dat" ... ok
testDatafile_gnm1ubi_kirchhoff (prody.tests.datafiles.TestDatafiles.testDatafile_gnm1ubi_kirchhoff)
Test presence of "gnm1ubi_kirchhoff.coo" ... ok
testDatafile_gnm1ubi_vectors (prody.tests.datafiles.TestDatafiles.testDatafile_gnm1ubi_vectors)
Test presence of "gnm1ubi_vectors.dat" ... ok
testDatafile_gromacs (prody.tests.datafiles.TestDatafiles.testDatafile_gromacs)
Test presence of "pdb6fpj_Bb_fixed_solv_ions.pdb" ... ok
testDatafile_h36 (prody.tests.datafiles.TestDatafiles.testDatafile_h36)
Test presence of "pdb1tw7_step3_charmm2namd_doubled_h36.pdb" ... ok
testDatafile_h36_ter (prody.tests.datafiles.TestDatafiles.testDatafile_h36_ter)
Test presence of "pdb4v8r_h36.pdb" ... ok
testDatafile_hex (prody.tests.datafiles.TestDatafiles.testDatafile_hex)
Test presence of "pdb1tw7_step3_charmm2namd_doubled_hex.pdb" ... ok
testDatafile_hex_ter (prody.tests.datafiles.TestDatafiles.testDatafile_hex_ter)
Test presence of "pdb4v8r_hex.pdb" ... ok
testDatafile_hit1ubi (prody.tests.datafiles.TestDatafiles.testDatafile_hit1ubi)
Test presence of "hit1ubi.dat" ... ok
testDatafile_long_chid_cif (prody.tests.datafiles.TestDatafiles.testDatafile_long_chid_cif)
Test presence of "mmcif_6zu5.cif" ... ok
testDatafile_multi_model_cif (prody.tests.datafiles.TestDatafiles.testDatafile_multi_model_cif)
Test presence of "mmcif_6yfy.cif" ... ok
testDatafile_multi_model_truncated (prody.tests.datafiles.TestDatafiles.testDatafile_multi_model_truncated)
Test presence of "pdb2k39_truncated.pdb" ... ok
testDatafile_oneatom (prody.tests.datafiles.TestDatafiles.testDatafile_oneatom)
Test presence of "pdb1ejg_oneatom.pdb" ... ok
testDatafile_pca2k39_cov (prody.tests.datafiles.TestDatafiles.testDatafile_pca2k39_cov)
Test presence of "pca2k39_cov.coo" ... ok
testDatafile_pca2k39_evalues (prody.tests.datafiles.TestDatafiles.testDatafile_pca2k39_evalues)
Test presence of "pca2k39_evalues.dat" ... ok
testDatafile_pca2k39_vectors (prody.tests.datafiles.TestDatafiles.testDatafile_pca2k39_vectors)
Test presence of "pca2k39_vectors.dat" ... ok
testDatafile_rtb2gb1_hessian (prody.tests.datafiles.TestDatafiles.testDatafile_rtb2gb1_hessian)
Test presence of "rtb2gb1_hessian.coo" ... ok
testDatafile_rtb2gb1_project (prody.tests.datafiles.TestDatafiles.testDatafile_rtb2gb1_project)
Test presence of "rtb2gb1_project.coo" ... ok
testDatafile_sti (prody.tests.datafiles.TestDatafiles.testDatafile_sti)
Test presence of "xmlSTI.xml" ... ok
testMode1d (prody.tests.dynamics.test_editing.TestExtending.testMode1d) ... ok
testMode3d (prody.tests.dynamics.test_editing.TestExtending.testMode3d) ... ok
testModel1d (prody.tests.dynamics.test_editing.TestExtending.testModel1d) ... ok
testModel3d (prody.tests.dynamics.test_editing.TestExtending.testModel3d) ... ok
testVector1d (prody.tests.dynamics.test_editing.TestExtending.testVector1d) ... ok
testVector3d (prody.tests.dynamics.test_editing.TestExtending.testVector3d) ... ok
testModel3d (prody.tests.dynamics.test_editing.TestInterpolating.testModel3d) ... ok
testMode1d (prody.tests.dynamics.test_editing.TestSlicing.testMode1d) ... ok
testMode3d (prody.tests.dynamics.test_editing.TestSlicing.testMode3d) ... ok
testModel1d (prody.tests.dynamics.test_editing.TestSlicing.testModel1d) ... ok
testModel3d (prody.tests.dynamics.test_editing.TestSlicing.testModel3d) ... ok
testVector1d (prody.tests.dynamics.test_editing.TestSlicing.testVector1d) ... ok
testVector3d (prody.tests.dynamics.test_editing.TestSlicing.testVector3d) ... ok
prody.tests.dynamics.test_enms (unittest.loader._FailedTest.prody.tests.dynamics.test_enms) ... ERROR
prody.tests.dynamics.test_pca (unittest.loader._FailedTest.prody.tests.dynamics.test_pca) ... ERROR
testSlicing (prody.tests.dynamics.test_signature.TestSDArray.testSlicing) ... ok
testCoordinates (prody.tests.ensemble.test_conformation.TestConformation.testCoordinates) ... ok
testCoordinatesForAll (prody.tests.ensemble.test_conformation.TestConformation.testCoordinatesForAll) ... ok
testGetIndex (prody.tests.ensemble.test_conformation.TestConformation.testGetIndex)
Test get index function. ... ok
testGetNumAtoms (prody.tests.ensemble.test_conformation.TestConformation.testGetNumAtoms)
Test get index function. ... ok
testWeights (prody.tests.ensemble.test_conformation.TestConformation.testWeights) ... ok
testCoordinates (prody.tests.ensemble.test_conformation.TestPDBConformation.testCoordinates) ... ok
testCoordinatesForAll (prody.tests.ensemble.test_conformation.TestPDBConformation.testCoordinatesForAll) ... ok
testGetIndex (prody.tests.ensemble.test_conformation.TestPDBConformation.testGetIndex) ... ok
testGetNumAtoms (prody.tests.ensemble.test_conformation.TestPDBConformation.testGetNumAtoms) ... ok
testWeights (prody.tests.ensemble.test_conformation.TestPDBConformation.testWeights) ... ok
testWeightsForAll (prody.tests.ensemble.test_conformation.TestPDBConformation.testWeightsForAll) ... ok
testConcatenation (prody.tests.ensemble.test_ensemble.TestEnsemble.testConcatenation)
Test concatenation of ensembles without weights. ... ok
testConcatenationNoweightsWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testConcatenationNoweightsWeights)
Test concatenation of ensembles without and with weights. ... ok
testConcatenationWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testConcatenationWeights)
Test concatenation of ensembles with weights. ... ok
testConcatenationWeightsNoweights (prody.tests.ensemble.test_ensemble.TestEnsemble.testConcatenationWeightsNoweights)
Test concatenation of ensembles with and without weights. ... ok
testDelCoordsetAll (prody.tests.ensemble.test_ensemble.TestEnsemble.testDelCoordsetAll) ... ok
testDelCoordsetMiddle (prody.tests.ensemble.test_ensemble.TestEnsemble.testDelCoordsetMiddle) ... ok
testGetCoordinates (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetCoordinates)
Test correctness of reference coordinates. ... ok
testGetCoordsets (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetCoordsets)
Test correctness of all coordinates. ... ok
testGetNumAtoms (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetNumAtoms) ... ok
testGetNumCsets (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetNumCsets) ... ok
testGetRMSDs (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetRMSDs) ... ok
testGetRMSDsWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetRMSDsWeights) ... ok
testGetWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetWeights)
Test correctness of all weights. ... ok
testIterCoordsets (prody.tests.ensemble.test_ensemble.TestEnsemble.testIterCoordsets)
Test coordinate iteration. ... ok
testSelection (prody.tests.ensemble.test_ensemble.TestEnsemble.testSelection)
Test atom selection of ensemble. ... ERROR
testSlicing (prody.tests.ensemble.test_ensemble.TestEnsemble.testSlicing)
Test slicing operation. ... ok
testSlicingCopy (prody.tests.ensemble.test_ensemble.TestEnsemble.testSlicingCopy)
Test making a copy by slicing operation. ... ok
testSlicingList (prody.tests.ensemble.test_ensemble.TestEnsemble.testSlicingList)
Test slicing with a list. ... ok
testSlicingWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testSlicingWeights)
Test slicing operation with weights. ... ok
testSuperpose (prody.tests.ensemble.test_ensemble.TestEnsemble.testSuperpose) ... ok
testSuperposeWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testSuperposeWeights) ... ok
testResults (prody.tests.ensemble.test_functions.TestBuildPDBEnsemble.testResults) ... ok
testInvalidType (prody.tests.ensemble.test_functions.TestCalcOccupancies.testInvalidType) ... ok
testResults (prody.tests.ensemble.test_functions.TestCalcOccupancies.testResults) ... ok
testWeightsNone (prody.tests.ensemble.test_functions.TestCalcOccupancies.testWeightsNone) ... ok
testResults (prody.tests.ensemble.test_functions.TestTrimPDBEnsemble.testResults) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/sequence/sequence.py:52: DeprecationWarning: tostring() is deprecated. Use tobytes() instead.
  return self._array.tostring().decode()
ok
testAddCoordsets (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testAddCoordsets) ... ok
testConcatenation (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testConcatenation)
Test concatenation of PDB ensembles. ... ok
testDelCoordsetAll (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testDelCoordsetAll)
Test consequences of deleting all coordinate sets. ... ok
testDelCoordsetMiddle (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testDelCoordsetMiddle) ... ok
testDelCoordsetMiddleTrans (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testDelCoordsetMiddleTrans) ... ok
testGetCoordinates (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testGetCoordinates) ... ok
testGetCoordsets (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testGetCoordsets) ... ok
testGetNumAtoms (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testGetNumAtoms) ... ok
testGetNumCsets (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testGetNumCsets) ... ok
testGetWeights (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testGetWeights) ... ok
testIterCoordsets (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testIterCoordsets) ... ok
testSlicing (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testSlicing) ... ok
testSlicingCopy (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testSlicingCopy) ... ok
testSlicingList (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testSlicingList) ... ok
testSlicingWeights (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testSlicingWeights) ... ok
testAllSearch (prody.tests.kdtree.test_kdtree.TestKDTree.testAllSearch) ... ok
testSearch (prody.tests.kdtree.test_kdtree.TestKDTree.testSearch) ... ok
testPairNoPBC (prody.tests.kdtree.test_kdtree.TestKDTreePBC.testPairNoPBC) ... ok
testPairPBC (prody.tests.kdtree.test_kdtree.TestKDTreePBC.testPairPBC) ... ok
testPointNoPBC (prody.tests.kdtree.test_kdtree.TestKDTreePBC.testPointNoPBC) ... ok
testPointPBC (prody.tests.kdtree.test_kdtree.TestKDTreePBC.testPointPBC) ... ok
testMINvsMAX (prody.tests.measure.test_contacts.TestContacts.testMINvsMAX) ... ok
testPBCvsNONE (prody.tests.measure.test_contacts.TestContacts.testPBCvsNONE) ... ok
testAtomicArgumentSwitching (prody.tests.measure.test_contacts.TestNeighbors.testAtomicArgumentSwitching) ... ok
testCoordArgumentSwitching (prody.tests.measure.test_contacts.TestNeighbors.testCoordArgumentSwitching) ... ok
testNoPBC (prody.tests.measure.test_contacts.TestNeighbors.testNoPBC) ... ok
testPBC (prody.tests.measure.test_contacts.TestNeighbors.testPBC) ... ok
testPBCAtomicArgumentSwitching (prody.tests.measure.test_contacts.TestNeighbors.testPBCAtomicArgumentSwitching) ... ok
testPBCCoordArgumentSwitching (prody.tests.measure.test_contacts.TestNeighbors.testPBCCoordArgumentSwitching) ... ok
testCenter (prody.tests.measure.test_measure.TestCenter.testCenter) ... ok
testCenterWithWeights (prody.tests.measure.test_measure.TestCenter.testCenterWithWeights) ... ok
testMultiCoordsets (prody.tests.measure.test_measure.TestCenter.testMultiCoordsets) ... ok
testMultiCoordsetsWithWeights (prody.tests.measure.test_measure.TestCenter.testMultiCoordsetsWithWeights) ... ok
testCTerPhi (prody.tests.measure.test_measure.TestDihedrals.testCTerPhi) ... ok
testCTerPsi (prody.tests.measure.test_measure.TestDihedrals.testCTerPsi) ... ok
testCalcPhi (prody.tests.measure.test_measure.TestDihedrals.testCalcPhi) ... ok
testCalcPsi (prody.tests.measure.test_measure.TestDihedrals.testCalcPsi) ... ok
testNTerPhi (prody.tests.measure.test_measure.TestDihedrals.testNTerPhi) ... ok
testNTerPsi (prody.tests.measure.test_measure.TestDihedrals.testNTerPsi) ... ok
testPBC (prody.tests.measure.test_measure.TestDistances.testPBC) ... ok
testPBCSymmetry (prody.tests.measure.test_measure.TestDistances.testPBCSymmetry) ... ok
testMSF (prody.tests.measure.test_measure.TestMSF.testMSF) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/trajectory/dcdfile.py:273: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
  xyz = fromstring(self._file.read(self._itemsize * n_floats),
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/trajectory/dcdfile.py:320: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
  data = fromstring(data, self._dtype)
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/trajectory/dcdfile.py:294: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
  unitcell = fromstring(self._file.read(48), dtype=np.float64)
ok
testMSFfloat (prody.tests.measure.test_measure.TestMSF.testMSFfloat) ... ok
testByArgument (prody.tests.measure.test_transform.TestMoveAtoms.testByArgument) ... ok
testToArgument (prody.tests.measure.test_transform.TestMoveAtoms.testToArgument) ... ok
testTransformation (prody.tests.measure.test_transform.TestMoveAtoms.testTransformation) ... ok
testWrap (prody.tests.measure.test_transform.TestWrapAtoms.testWrap) ... ok
prody.tests.proteins.test_ciffile (unittest.loader._FailedTest.prody.tests.proteins.test_ciffile) ... ERROR
prody.tests.proteins.test_dssp (unittest.loader._FailedTest.prody.tests.proteins.test_dssp) ... ERROR
testHeaderContent (prody.tests.proteins.test_header.TestParsePDBHeaderOnly.testHeaderContent) ... ok
testHeaderType (prody.tests.proteins.test_header.TestParsePDBHeaderOnly.testHeaderType) ... ok
prody.tests.proteins.test_localpdb (unittest.loader._FailedTest.prody.tests.proteins.test_localpdb) ... ERROR
prody.tests.proteins.test_pdbfile (unittest.loader._FailedTest.prody.tests.proteins.test_pdbfile) ... ERROR
prody.tests.proteins.test_wwpdb (unittest.loader._FailedTest.prody.tests.proteins.test_wwpdb) ... ERROR
testBuildMSAlocal (prody.tests.sequence.test_analysis.TestBuildMSA.testBuildMSAlocal) ... ok
testResidueCount (prody.tests.sequence.test_analysis.TestCalcMSAOccupancy.testResidueCount) ... ok
testResidueOccupancy (prody.tests.sequence.test_analysis.TestCalcMSAOccupancy.testResidueOccupancy) ... ok
testSequenceCount (prody.tests.sequence.test_analysis.TestCalcMSAOccupancy.testSequenceCount) ... ok
testSequenceOccupancy (prody.tests.sequence.test_analysis.TestCalcMSAOccupancy.testSequenceOccupancy) ... ok
testMATLAB (prody.tests.sequence.test_analysis.TestCalcMeff.testMATLAB) ... ok
testTwenty (prody.tests.sequence.test_analysis.TestCalcMeff.testTwenty) ... ok
testTwentyReversed (prody.tests.sequence.test_analysis.TestCalcMeff.testTwentyReversed) ... ok
testZero1 (prody.tests.sequence.test_analysis.TestCalcMeff.testZero1) ... ok
testZero2 (prody.tests.sequence.test_analysis.TestCalcMeff.testZero2) ... ok
testAmbiguity (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity) ... ok
testAmbiguity2 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity2) ... ok
testAmbiguity3 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity3) ... ok
testAmbiguity4 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity4) ... ok
testAmbiguity5 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity5) ... ok
testAmbiguity6 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity6) ... ok
testAmbiguity7 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity7) ... ok
testInf (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testInf) ... ok
testNoAmbiguity (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testNoAmbiguity) ... ok
testNorm (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testNorm) ... ok
testNorm2 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testNorm2) ... ok
testSixSequences (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testSixSequences) ... ok
testTwenty (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testTwenty) ... ok
testTwentyReversed (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testTwentyReversed) ... ok
testAmbiguity (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity) ... ok
testAmbiguity2 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity2) ... ok
testAmbiguity3 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity3) ... ok
testAmbiguity4 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity4) ... ok
testAmbiguity5 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity5) ... ok
testAmbiguity6 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity6) ... ok
testAmbiguity7 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity7) ... ok
testFourSequences (prody.tests.sequence.test_analysis.TestCalcOMES.testFourSequences) ... ok
testInf (prody.tests.sequence.test_analysis.TestCalcOMES.testInf) ... ok
testNoAmbiguity (prody.tests.sequence.test_analysis.TestCalcOMES.testNoAmbiguity) ... ok
testTwenty (prody.tests.sequence.test_analysis.TestCalcOMES.testTwenty) ... ok
testTwentyReversed (prody.tests.sequence.test_analysis.TestCalcOMES.testTwentyReversed) ... ok
testZero (prody.tests.sequence.test_analysis.TestCalcOMES.testZero) ... ok
testMATLAB (prody.tests.sequence.test_analysis.TestCalcSCA.testMATLAB) ... ok
testZero (prody.tests.sequence.test_analysis.TestCalcSCA.testZero) ... ok
testAmbiguous (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testAmbiguous) ... ok
testGapDividend (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testGapDividend) ... ok
testSixSequences (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testSixSequences) ... ok
testSmallProbability (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testSmallProbability) ... ok
testTwenty (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testTwenty) ... ok
testMATLAB10 (prody.tests.sequence.test_analysis.TestDirectInfo.testMATLAB10) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/sequence/analysis.py:592: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
  c = matrix.dot(matrix(zeros((length*q, 1), float)),
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/sequence/analysis.py:593: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
  matrix(zeros((1, length*q), float)))
/usr/lib/python3/dist-packages/numpy/matrixlib/defmatrix.py:70: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
  return matrix(data, dtype=dtype, copy=False)
ok
testMATLAB8 (prody.tests.sequence.test_analysis.TestDirectInfo.testMATLAB8) ... ok
testTwenty (prody.tests.sequence.test_analysis.TestDirectInfo.testTwenty) ... ok
testTwentyReversed (prody.tests.sequence.test_analysis.TestDirectInfo.testTwentyReversed) ... ok
testZero (prody.tests.sequence.test_analysis.TestDirectInfo.testZero) ... ok
testZero1 (prody.tests.sequence.test_analysis.TestDirectInfo.testZero1) ... ok
testZero2 (prody.tests.sequence.test_analysis.TestDirectInfo.testZero2) ... ok
testZero3 (prody.tests.sequence.test_analysis.TestDirectInfo.testZero3) ... ok
testZero4 (prody.tests.sequence.test_analysis.TestDirectInfo.testZero4) ... ok
testIdentityMatrix (prody.tests.sequence.test_analysis.TestIdentity.testIdentityMatrix) ... ok
testIdentityMatrixNonTurbo (prody.tests.sequence.test_analysis.TestIdentity.testIdentityMatrixNonTurbo) ... ok
testUnique (prody.tests.sequence.test_analysis.TestUnique.testUnique) ... ok
testUnique2 (prody.tests.sequence.test_analysis.TestUnique.testUnique2) ... ok
testMerge (prody.tests.sequence.test_msa.TestMerging.testMerge) ... ok
testAddition (prody.tests.sequence.test_msa.TestRefinement.testAddition) ... ok
testAll (prody.tests.sequence.test_msa.TestRefinement.testAll) ... ok
testColocc (prody.tests.sequence.test_msa.TestRefinement.testColocc) ... ok
testExtension (prody.tests.sequence.test_msa.TestRefinement.testExtension) ... ok
testLabel (prody.tests.sequence.test_msa.TestRefinement.testLabel) ... ok
testRowCol (prody.tests.sequence.test_msa.TestRefinement.testRowCol) ... ok
testRowocc (prody.tests.sequence.test_msa.TestRefinement.testRowocc) ... ok
testSeqid (prody.tests.sequence.test_msa.TestRefinement.testSeqid) ... ok
testSeqidLabel (prody.tests.sequence.test_msa.TestRefinement.testSeqidLabel) ... ok
prody.tests.sequence.test_msafile (unittest.loader._FailedTest.prody.tests.sequence.test_msafile) ... ERROR
testStringConversion (prody.tests.sequence.test_sequence.TestSequence.testStringConversion) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/sequence/sequence.py:36: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
  self._seq = fromstring(args[0], '|S1')
ok
testParseDCD (prody.tests.trajectory.test_dcdfile.TestDCDFile.testParseDCD) ... ok
testWrite (prody.tests.trajectory.test_dcdfile.TestDCDFile.testWrite) ... ok
testWriteDCD (prody.tests.trajectory.test_dcdfile.TestDCDFile.testWriteDCD) ... ok
testWriteModeAppend (prody.tests.trajectory.test_dcdfile.TestDCDFile.testWriteModeAppend) ... ok
testAll (prody.tests.trajectory.test_frame.TestSuperpose.testAll) ... ok
testCarbon (prody.tests.trajectory.test_frame.TestSuperpose.testCarbon) ... ok
testCoords (prody.tests.utilities.test_checkers.TestCheckCoords.testCoords) ... ok
testCoordset (prody.tests.utilities.test_checkers.TestCheckCoords.testCoordset) ... ok
testCoordsetNatoms (prody.tests.utilities.test_checkers.TestCheckCoords.testCoordsetNatoms) ... ok
testInvalidCoords (prody.tests.utilities.test_checkers.TestCheckCoords.testInvalidCoords) ... ok
testCorrectMonotypeOneArg (prody.tests.utilities.test_checkers.testCheckTypes.testCorrectMonotypeOneArg) ... ok
testCorrectMonotypeTwoArgs (prody.tests.utilities.test_checkers.testCheckTypes.testCorrectMonotypeTwoArgs) ... ok
testCorrectMultitypeOneArg (prody.tests.utilities.test_checkers.testCheckTypes.testCorrectMultitypeOneArg) ... ok
testWrongMonotypeOneArg (prody.tests.utilities.test_checkers.testCheckTypes.testWrongMonotypeOneArg) ... ok
testWrongMonotypeTwoArgs (prody.tests.utilities.test_checkers.testCheckTypes.testWrongMonotypeTwoArgs) ... ok
testWrongMultitypeOneArg (prody.tests.utilities.test_checkers.testCheckTypes.testWrongMultitypeOneArg) ... ok
testContinuous (prody.tests.utilities.test_misctools.TestRangeString.testContinuous) ... ok
testGapped (prody.tests.utilities.test_misctools.TestRangeString.testGapped) ... ok
testNegative (prody.tests.utilities.test_misctools.TestRangeString.testNegative) ... ok
testRepeated (prody.tests.utilities.test_misctools.TestRangeString.testRepeated) ... ok
testBuffer (prody.tests.utilities.test_pathtools.TestGunzip.testBuffer) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/utilities/test_pathtools.py:34: ResourceWarning: unclosed file <_io.BufferedReader name='/tmp/compressed.txt.gz'>
  buff = open(self.gzfn, 'rb').read()
ResourceWarning: Enable tracemalloc to get the object allocation traceback
ok
testFile (prody.tests.utilities.test_pathtools.TestGunzip.testFile) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/utilities/test_pathtools.py:29: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/compressed.txt' mode='r' encoding='UTF-8'>
  text = open(fn).read()
ResourceWarning: Enable tracemalloc to get the object allocation traceback
ok

======================================================================
ERROR: prody.tests.apps.test_prody_anm (unittest.loader._FailedTest.prody.tests.apps.test_prody_anm)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.apps.test_prody_anm
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/apps/test_prody_anm.py", line 9, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.12/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/apps/test_prody_anm.py", line 11, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: prody.tests.apps.test_prody_catdcd (unittest.loader._FailedTest.prody.tests.apps.test_prody_catdcd)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.apps.test_prody_catdcd
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/apps/test_prody_catdcd.py", line 8, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.12/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/apps/test_prody_catdcd.py", line 10, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: prody.tests.apps.test_prody_examples (unittest.loader._FailedTest.prody.tests.apps.test_prody_examples)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.apps.test_prody_examples
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/apps/test_prody_examples.py", line 10, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.12/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/apps/test_prody_examples.py", line 12, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: prody.tests.apps.test_prody_gnm (unittest.loader._FailedTest.prody.tests.apps.test_prody_gnm)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.apps.test_prody_gnm
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/apps/test_prody_gnm.py", line 8, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.12/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/apps/test_prody_gnm.py", line 10, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: prody.tests.apps.test_prody_pca (unittest.loader._FailedTest.prody.tests.apps.test_prody_pca)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.apps.test_prody_pca
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/apps/test_prody_pca.py", line 8, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.12/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/apps/test_prody_pca.py", line 10, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: prody.tests.atomic.test_select (unittest.loader._FailedTest.prody.tests.atomic.test_select)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.atomic.test_select
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/atomic/test_select.py", line 9, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.12/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/atomic/test_select.py", line 11, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: prody.tests.dynamics.test_enms (unittest.loader._FailedTest.prody.tests.dynamics.test_enms)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.dynamics.test_enms
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/dynamics/test_enms.py", line 7, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.12/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/dynamics/test_enms.py", line 9, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: prody.tests.dynamics.test_pca (unittest.loader._FailedTest.prody.tests.dynamics.test_pca)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.dynamics.test_pca
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/dynamics/test_pca.py", line 7, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.12/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/dynamics/test_pca.py", line 9, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: testSelection (prody.tests.ensemble.test_ensemble.TestEnsemble.testSelection)
Test atom selection of ensemble.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/ensemble/test_ensemble.py", line 191, in testSelection
    sel = ATOMS.select('resnum 1 to 3')
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic/atomic.py", line 232, in select
    return SELECT.select(self, selstr, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic/select.py", line 895, in select
    indices = self.getIndices(atoms, selstr, **kwargs)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic/select.py", line 953, in getIndices
    torf = self.getBoolArray(atoms, selstr, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic/select.py", line 1004, in getBoolArray
    parser = self._getParser(selstr)
             ^^^^^^^^^^^^^^^^^^^^^^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic/select.py", line 1103, in _getParser
    parser.enablePackrat()
  File "/usr/lib/python3/dist-packages/pyparsing/util.py", line 265, in _inner
    return fn(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3/dist-packages/pyparsing/core.py", line 1132, in enable_packrat
    ParserElement.packrat_cache = _FifoCache(cache_size_limit)  # type: ignore[assignment]
                                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3/dist-packages/pyparsing/util.py", line 105, in __init__
    keyring = [object()] * size
              ~~~~~~~~~~~^~~~~~
TypeError: can't multiply sequence by non-int of type 'Forward'

======================================================================
ERROR: prody.tests.proteins.test_ciffile (unittest.loader._FailedTest.prody.tests.proteins.test_ciffile)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.proteins.test_ciffile
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins/test_ciffile.py", line 8, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.12/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins/test_ciffile.py", line 10, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: prody.tests.proteins.test_dssp (unittest.loader._FailedTest.prody.tests.proteins.test_dssp)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.proteins.test_dssp
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins/test_dssp.py", line 5, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.12/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins/test_dssp.py", line 7, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: prody.tests.proteins.test_localpdb (unittest.loader._FailedTest.prody.tests.proteins.test_localpdb)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.proteins.test_localpdb
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins/test_localpdb.py", line 8, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.12/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins/test_localpdb.py", line 10, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: prody.tests.proteins.test_pdbfile (unittest.loader._FailedTest.prody.tests.proteins.test_pdbfile)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.proteins.test_pdbfile
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins/test_pdbfile.py", line 8, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.12/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins/test_pdbfile.py", line 10, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: prody.tests.proteins.test_wwpdb (unittest.loader._FailedTest.prody.tests.proteins.test_wwpdb)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.proteins.test_wwpdb
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins/test_wwpdb.py", line 7, in <module>
    import numpy.testing.decorators as dec
ModuleNotFoundError: No module named 'numpy.testing.decorators'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3.12/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins/test_wwpdb.py", line 9, in <module>
    from numpy.testing import dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


======================================================================
ERROR: prody.tests.sequence.test_msafile (unittest.loader._FailedTest.prody.tests.sequence.test_msafile)
----------------------------------------------------------------------
ImportError: Failed to import test module: prody.tests.sequence.test_msafile
Traceback (most recent call last):
  File "/usr/lib/python3.12/unittest/loader.py", line 396, in _find_test_path
    module = self._get_module_from_name(name)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/unittest/loader.py", line 339, in _get_module_from_name
    __import__(name)
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/sequence/test_msafile.py", line 8, in <module>
    from numpy.testing import assert_array_equal, dec
ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py). Did you mean: 'rec'?


----------------------------------------------------------------------
Ran 279 tests in 10.841s

FAILED (errors=15)
E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build; python3.12 -m unittest discover -v 
dh_auto_test: error: pybuild --test -i python{version} -p "3.13 3.12" returned exit code 13
make: *** [debian/rules:6: binary-arch] Error 25
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2024-11-01T16:13:06Z

Finished
--------


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: arm64
Build Type: any
Build-Space: 316012
Build-Time: 50
Distribution: sid
Fail-Stage: build
Host Architecture: arm64
Install-Time: 128
Job: /tmp/debusine-fetch-exec-upload-ov32oqs_/prody_2.4.1+dfsg-2.dsc
Machine Architecture: arm64
Package: prody
Package-Time: 215
Source-Version: 2.4.1+dfsg-2
Space: 316012
Status: attempted
Version: 2.4.1+dfsg-2+bd1
--------------------------------------------------------------------------------
Finished at 2024-11-01T16:13:06Z
Build needed 00:03:35, 316012k disk space