sbuild (Debian sbuild) 0.85.11~bpo12+1 (31 August 2024) on debusine-worker-arm64-demeter-07.freexian.com
+==============================================================================+
| prody 2.4.1+dfsg-2+bd1 (arm64) Fri, 18 Oct 2024 19:03:27 +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
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Get:1 file:/build/prody-ypg3vE/resolver-sccnGJ/apt_archive ./ InRelease
Ign:1 file:/build/prody-ypg3vE/resolver-sccnGJ/apt_archive ./ InRelease
Get:2 file:/build/prody-ypg3vE/resolver-sccnGJ/apt_archive ./ Release [609 B]
Get:3 http://deb.debian.org/debian sid InRelease [202 kB]
Get:2 file:/build/prody-ypg3vE/resolver-sccnGJ/apt_archive ./ Release [609 B]
Get:4 file:/build/prody-ypg3vE/resolver-sccnGJ/apt_archive ./ Release.gpg
Ign:4 file:/build/prody-ypg3vE/resolver-sccnGJ/apt_archive ./ Release.gpg
Get:5 file:/build/prody-ypg3vE/resolver-sccnGJ/apt_archive ./ Packages [40.0 kB]
Get:6 http://deb.debian.org/debian sid/main arm64 Packages [9921 kB]
Get:7 http://deb.debian.org/debian sid/main arm64 Components [4904 kB]
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Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages were automatically installed and are no longer required:
libperl5.38t64 perl-modules-5.38
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
libperl5.40 perl-modules-5.40
The following packages will be upgraded:
apt libapt-pkg-perl libapt-pkg6.0t64 libb-hooks-op-check-perl
libberkeleydb-perl libclass-xsaccessor-perl libclone-perl
libcpanel-json-xs-perl libdata-messagepack-perl libdb5.3t64
libdevel-callchecker-perl libdevel-size-perl libemail-address-xs-perl
libhtml-parser-perl libldap-2.5-0 libmouse-perl libnet-ssleay-perl
libnetaddr-ip-perl libparams-classify-perl libparams-util-perl
libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl
libsereal-decoder-perl libsereal-encoder-perl libsub-identify-perl
libsub-name-perl libsyntax-keyword-try-perl libterm-readkey-perl
libtext-levenshteinxs-perl libtext-markdown-discount-perl
libtext-xslate-perl libtime-moment-perl libunicode-utf8-perl
libvariable-magic-perl libxml-libxml-perl libxmlb2 libxs-parse-keyword-perl
libyaml-libyaml-perl perl perl-base sysvinit-utils
42 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
Need to get 14.4 MB of archives.
After this operation, 52.5 MB of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main arm64 libyaml-libyaml-perl arm64 0.902.0+ds-2+b1 [33.9 kB]
Get:2 http://deb.debian.org/debian sid/main arm64 libxs-parse-keyword-perl arm64 0.46-1+b1 [63.6 kB]
Get:3 http://deb.debian.org/debian sid/main arm64 libxml-libxml-perl arm64 2.0207+dfsg+really+2.0134-5+b1 [300 kB]
Get:4 http://deb.debian.org/debian sid/main arm64 libvariable-magic-perl arm64 0.64-1+b1 [43.9 kB]
Get:5 http://deb.debian.org/debian sid/main arm64 libunicode-utf8-perl arm64 0.62-2+b3 [20.1 kB]
Get:6 http://deb.debian.org/debian sid/main arm64 libtime-moment-perl arm64 0.44-2+b4 [72.0 kB]
Get:7 http://deb.debian.org/debian sid/main arm64 libtext-xslate-perl arm64 3.5.9-2+b1 [172 kB]
Get:8 http://deb.debian.org/debian sid/main arm64 libtext-markdown-discount-perl arm64 0.16-1+b3 [13.1 kB]
Get:9 http://deb.debian.org/debian sid/main arm64 libtext-levenshteinxs-perl arm64 0.03-5+b4 [8772 B]
Get:10 http://deb.debian.org/debian sid/main arm64 libterm-readkey-perl arm64 2.38-2+b4 [24.5 kB]
Get:11 http://deb.debian.org/debian sid/main arm64 libsyntax-keyword-try-perl arm64 0.30-1+b1 [27.1 kB]
Get:12 http://deb.debian.org/debian sid/main arm64 libsub-name-perl arm64 0.27-1+b3 [12.4 kB]
Get:13 http://deb.debian.org/debian sid/main arm64 libsub-identify-perl arm64 0.14-3+b3 [11.2 kB]
Get:14 http://deb.debian.org/debian sid/main arm64 libsereal-decoder-perl arm64 5.004+ds-1+b3 [96.7 kB]
Get:15 http://deb.debian.org/debian sid/main arm64 libsereal-encoder-perl arm64 5.004+ds-1+b3 [99.0 kB]
Get:16 http://deb.debian.org/debian sid/main arm64 libproc-processtable-perl arm64 0.636-1+b3 [41.7 kB]
Get:17 http://deb.debian.org/debian sid/main arm64 libperlio-utf8-strict-perl arm64 0.010-1+b3 [11.4 kB]
Get:18 http://deb.debian.org/debian sid/main arm64 libperlio-gzip-perl arm64 0.20-1+b4 [17.4 kB]
Get:19 http://deb.debian.org/debian sid/main arm64 libparams-util-perl arm64 1.102-3+b1 [23.7 kB]
Get:20 http://deb.debian.org/debian sid/main arm64 libparams-classify-perl arm64 0.015-2+b4 [22.3 kB]
Get:21 http://deb.debian.org/debian sid/main arm64 libnetaddr-ip-perl arm64 4.079+dfsg-2+b4 [97.7 kB]
Get:22 http://deb.debian.org/debian sid/main arm64 libnet-ssleay-perl arm64 1.94-1+b2 [323 kB]
Get:23 http://deb.debian.org/debian sid/main arm64 libmouse-perl arm64 2.5.11-1+b1 [141 kB]
Get:24 http://deb.debian.org/debian sid/main arm64 libhtml-parser-perl arm64 3.83-1+b1 [97.5 kB]
Get:25 http://deb.debian.org/debian sid/main arm64 libemail-address-xs-perl arm64 1.05-1+b4 [28.2 kB]
Get:26 http://deb.debian.org/debian sid/main arm64 libdevel-size-perl arm64 0.84-1+b1 [24.1 kB]
Get:27 http://deb.debian.org/debian sid/main arm64 libdevel-callchecker-perl arm64 0.009-1+b1 [16.3 kB]
Get:28 http://deb.debian.org/debian sid/main arm64 libdata-messagepack-perl arm64 1.02-1+b4 [31.2 kB]
Get:29 http://deb.debian.org/debian sid/main arm64 libcpanel-json-xs-perl arm64 4.38-1+b1 [127 kB]
Get:30 http://deb.debian.org/debian sid/main arm64 libclone-perl arm64 0.47-1+b1 [13.7 kB]
Get:31 http://deb.debian.org/debian sid/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b4 [34.9 kB]
Get:32 http://deb.debian.org/debian sid/main arm64 libberkeleydb-perl arm64 0.64-2+b4 [116 kB]
Get:33 http://deb.debian.org/debian sid/main arm64 libb-hooks-op-check-perl arm64 0.22-3+b2 [10.6 kB]
Get:34 http://deb.debian.org/debian sid/main arm64 libapt-pkg-perl arm64 0.1.40+b6 [63.8 kB]
Get:35 http://deb.debian.org/debian sid/main arm64 perl-modules-5.40 all 5.40.0-6 [3022 kB]
Get:36 http://deb.debian.org/debian sid/main arm64 libperl5.40 arm64 5.40.0-6 [4149 kB]
Get:37 http://deb.debian.org/debian sid/main arm64 perl arm64 5.40.0-6 [267 kB]
Get:38 http://deb.debian.org/debian sid/main arm64 perl-base arm64 5.40.0-6 [1534 kB]
Get:39 http://deb.debian.org/debian sid/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-9 [629 kB]
Get:40 http://deb.debian.org/debian sid/main arm64 libapt-pkg6.0t64 arm64 2.9.9 [922 kB]
Get:41 http://deb.debian.org/debian sid/main arm64 apt arm64 2.9.9 [1331 kB]
Get:42 http://deb.debian.org/debian sid/main arm64 sysvinit-utils arm64 3.10-3 [32.9 kB]
Get:43 http://deb.debian.org/debian sid/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3+b1 [175 kB]
Get:44 http://deb.debian.org/debian sid/main arm64 libxmlb2 arm64 0.3.21-1 [59.1 kB]
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update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
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+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Local sources
-------------
/tmp/debusine-fetch-exec-upload-68tm2ves/prody_2.4.1+dfsg-2.dsc exists in /tmp/debusine-fetch-exec-upload-68tm2ves; copying to chroot
I: NOTICE: Log filtering will replace 'build/prody-ypg3vE/prody-2.4.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/prody-ypg3vE' 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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Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libperl5.38t64 perl-modules-5.38
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev build-essential cpp cpp-14
cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper dh-autoreconf
dh-python dh-strip-nondeterminism dumb-init dwz fakeroot 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 libasan8 libblas3
libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libdebhelper-perl
libdeflate0 libelf1t64 libexpat1 libexpat1-dev libfakeroot
libfile-stripnondeterminism-perl libfontconfig1 libfontenc1 libfreetype6
libfribidi0 libgcc-14-dev libgfortran5 libgraphite2-3 libharfbuzz0b
libhwasan0 libimagequant0 libisl23 libitm1 libjbig0 libjpeg62-turbo
libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0
liblcms2-2 liblerc4 liblsan0 libmpc3 libmpfr6 libncursesw6 libnsl2
libopenjp2-7 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 libsharpyuv0
libstdc++-14-dev libtiff6 libtirpc-common libtirpc3t64 libtool libtsan2
libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6
libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxrender1
linux-libc-dev m4 media-types 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-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 rpcsvc-proto sgml-base w3c-sgml-lib
x11-common xfonts-encodings xfonts-utils xml-core zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cpp-doc gcc-14-locales
cpp-14-doc dh-make flit python3-build python3-installer python3-wheel
fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gcc-14-doc
gcc-multilib manpages-dev flex bison gdb gcc-doc gdb-aarch64-linux-gnu
libc-devtools glibc-doc liblcms2-utils libstdc++-14-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc 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 sgml-base-doc
Recommended packages:
manpages manpages-dev libarchive-cpio-perl javascript-common libgpm2
libltdl-dev libmail-sendmail-perl python-biopython-doc ncbi-blast+
python3-olefile fonts-dejavu-extra
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev build-essential cpp cpp-14
cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper dh-autoreconf
dh-python dh-strip-nondeterminism dumb-init dwz fakeroot 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 libasan8 libblas3
libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libdebhelper-perl
libdeflate0 libelf1t64 libexpat1 libexpat1-dev libfakeroot
libfile-stripnondeterminism-perl libfontconfig1 libfontenc1 libfreetype6
libfribidi0 libgcc-14-dev libgfortran5 libgraphite2-3 libharfbuzz0b
libhwasan0 libimagequant0 libisl23 libitm1 libjbig0 libjpeg62-turbo
libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0
liblcms2-2 liblerc4 liblsan0 libmpc3 libmpfr6 libncursesw6 libnsl2
libopenjp2-7 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 libsharpyuv0
libstdc++-14-dev libtiff6 libtirpc-common libtirpc3t64 libtool libtsan2
libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6
libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxrender1
linux-libc-dev m4 media-types 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-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 rpcsvc-proto
sbuild-build-depends-main-dummy sgml-base w3c-sgml-lib x11-common
xfonts-encodings xfonts-utils xml-core zlib1g-dev
0 upgraded, 149 newly installed, 0 to remove and 0 not upgraded.
Need to get 113 MB/137 MB of archives.
After this operation, 577 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [948 B]
Get:2 file:/<<BUILDDIR>>/resolver-sccnGJ/apt_archive ./ python3-minimal 3.12.6-1+debusine1 [26.8 kB]
Get:3 file:/<<BUILDDIR>>/resolver-sccnGJ/apt_archive ./ libpython3-stdlib 3.12.6-1+debusine1 [9732 B]
Get:4 file:/<<BUILDDIR>>/resolver-sccnGJ/apt_archive ./ python3 3.12.6-1+debusine1 [27.8 kB]
Get:5 file:/<<BUILDDIR>>/resolver-sccnGJ/apt_archive ./ libpython3-dev 3.12.6-1+debusine1 [9992 B]
Get:6 file:/<<BUILDDIR>>/resolver-sccnGJ/apt_archive ./ libpython3-all-dev 3.12.6-1+debusine1 [1084 B]
Get:7 file:/<<BUILDDIR>>/resolver-sccnGJ/apt_archive ./ python3-all 3.12.6-1+debusine1 [1056 B]
Get:8 file:/<<BUILDDIR>>/resolver-sccnGJ/apt_archive ./ python3-dev 3.12.6-1+debusine1 [26.1 kB]
Get:9 file:/<<BUILDDIR>>/resolver-sccnGJ/apt_archive ./ python3-all-dev 3.12.6-1+debusine1 [1084 B]
Get:10 http://deb.debian.org/debian sid/main arm64 libpython3.12-minimal arm64 3.12.7-1 [807 kB]
Get:11 file:/<<BUILDDIR>>/resolver-sccnGJ/apt_archive ./ python3-numpy 1:1.26.4+ds-11+bootstrap1 [3815 kB]
Get:12 http://deb.debian.org/debian sid/main arm64 libexpat1 arm64 2.6.3-1 [90.2 kB]
Get:13 http://deb.debian.org/debian sid/main arm64 python3.12-minimal arm64 3.12.7-1 [1941 kB]
Get:14 file:/<<BUILDDIR>>/resolver-sccnGJ/apt_archive ./ python3-biopython 1.84+dfsg-3+bd1 [1643 kB]
Get:15 http://deb.debian.org/debian sid/main arm64 media-types all 10.1.0 [26.9 kB]
Get:16 http://deb.debian.org/debian sid/main arm64 libncursesw6 arm64 6.5-2 [124 kB]
Get:17 http://deb.debian.org/debian sid/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get:18 http://deb.debian.org/debian sid/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3 [78.4 kB]
Get:19 http://deb.debian.org/debian sid/main arm64 libnsl2 arm64 1.3.0-3+b2 [37.7 kB]
Get:20 http://deb.debian.org/debian sid/main arm64 libpython3.12-stdlib arm64 3.12.7-1 [1901 kB]
Get:21 http://deb.debian.org/debian sid/main arm64 python3.12 arm64 3.12.7-1 [671 kB]
Get:22 http://deb.debian.org/debian sid/main arm64 libpython3.13-minimal arm64 3.13.0-1 [849 kB]
Get:23 http://deb.debian.org/debian sid/main arm64 python3.13-minimal arm64 3.13.0-1 [1835 kB]
Get:24 http://deb.debian.org/debian sid/main arm64 sgml-base all 1.31 [15.4 kB]
Get:25 http://deb.debian.org/debian sid/main arm64 m4 arm64 1.4.19-4 [277 kB]
Get:26 http://deb.debian.org/debian sid/main arm64 autoconf all 2.72-3 [493 kB]
Get:27 http://deb.debian.org/debian sid/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get:28 http://deb.debian.org/debian sid/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get:29 http://deb.debian.org/debian sid/main arm64 autopoint all 0.22.5-2 [723 kB]
Get:30 http://deb.debian.org/debian sid/main arm64 libc-dev-bin arm64 2.40-3 [50.9 kB]
Get:31 http://deb.debian.org/debian sid/main arm64 linux-libc-dev all 6.11.2-1 [2424 kB]
Get:32 file:/<<BUILDDIR>>/resolver-sccnGJ/apt_archive ./ python3-scipy 1.13.1-5+nocheck1 [18.1 MB]
Get:33 http://deb.debian.org/debian sid/main arm64 libcrypt-dev arm64 1:4.4.36-5 [122 kB]
Get:34 http://deb.debian.org/debian sid/main arm64 rpcsvc-proto arm64 1.4.3-1 [59.7 kB]
Get:35 http://deb.debian.org/debian sid/main arm64 libc6-dev arm64 2.40-3 [1591 kB]
Get:36 http://deb.debian.org/debian sid/main arm64 libisl23 arm64 0.27-1 [601 kB]
Get:37 http://deb.debian.org/debian sid/main arm64 libmpfr6 arm64 4.2.1-1+b1 [674 kB]
Get:38 http://deb.debian.org/debian sid/main arm64 libmpc3 arm64 1.3.1-1+b2 [50.2 kB]
Get:39 http://deb.debian.org/debian sid/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-6 [9165 kB]
Get:40 http://deb.debian.org/debian sid/main arm64 cpp-14 arm64 14.2.0-6 [1280 B]
Get:41 http://deb.debian.org/debian sid/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1 [4832 B]
Get:42 http://deb.debian.org/debian sid/main arm64 cpp arm64 4:14.2.0-1 [1568 B]
Get:43 http://deb.debian.org/debian sid/main arm64 libcc1-0 arm64 14.2.0-6 [42.3 kB]
Get:44 http://deb.debian.org/debian sid/main arm64 libitm1 arm64 14.2.0-6 [24.1 kB]
Get:45 http://deb.debian.org/debian sid/main arm64 libasan8 arm64 14.2.0-6 [2578 kB]
Get:46 http://deb.debian.org/debian sid/main arm64 liblsan0 arm64 14.2.0-6 [1162 kB]
Get:47 http://deb.debian.org/debian sid/main arm64 libtsan2 arm64 14.2.0-6 [2386 kB]
Get:48 http://deb.debian.org/debian sid/main arm64 libubsan1 arm64 14.2.0-6 [1039 kB]
Get:49 http://deb.debian.org/debian sid/main arm64 libhwasan0 arm64 14.2.0-6 [1442 kB]
Get:50 http://deb.debian.org/debian sid/main arm64 libgcc-14-dev arm64 14.2.0-6 [2364 kB]
Get:51 http://deb.debian.org/debian sid/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-6 [17.7 MB]
Get:52 http://deb.debian.org/debian sid/main arm64 gcc-14 arm64 14.2.0-6 [515 kB]
Get:53 http://deb.debian.org/debian sid/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1 [1440 B]
Get:54 http://deb.debian.org/debian sid/main arm64 gcc arm64 4:14.2.0-1 [5136 B]
Get:55 http://deb.debian.org/debian sid/main arm64 libstdc++-14-dev arm64 14.2.0-6 [2265 kB]
Get:56 http://deb.debian.org/debian sid/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-6 [10.1 MB]
Get:57 http://deb.debian.org/debian sid/main arm64 g++-14 arm64 14.2.0-6 [19.9 kB]
Get:58 http://deb.debian.org/debian sid/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1 [1200 B]
Get:59 http://deb.debian.org/debian sid/main arm64 g++ arm64 4:14.2.0-1 [1332 B]
Get:60 http://deb.debian.org/debian sid/main arm64 build-essential arm64 12.12 [4624 B]
Get:61 http://deb.debian.org/debian sid/main arm64 libdebhelper-perl all 13.20 [89.7 kB]
Get:62 http://deb.debian.org/debian sid/main arm64 libtool all 2.4.7-7 [517 kB]
Get:63 http://deb.debian.org/debian sid/main arm64 dh-autoreconf all 20 [17.1 kB]
Get:64 http://deb.debian.org/debian sid/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get:65 http://deb.debian.org/debian sid/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get:66 http://deb.debian.org/debian sid/main arm64 libelf1t64 arm64 0.191-2 [188 kB]
Get:67 http://deb.debian.org/debian sid/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get:68 http://deb.debian.org/debian sid/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:69 http://deb.debian.org/debian sid/main arm64 debhelper all 13.20 [915 kB]
Get:70 http://deb.debian.org/debian sid/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get:71 http://deb.debian.org/debian sid/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB]
Get:72 http://deb.debian.org/debian sid/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get:73 http://deb.debian.org/debian sid/main arm64 python3-typeguard all 4.3.0-1 [36.5 kB]
Get:74 http://deb.debian.org/debian sid/main arm64 python3-inflect all 7.3.1-2 [32.4 kB]
Get:75 http://deb.debian.org/debian sid/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B]
Get:76 http://deb.debian.org/debian sid/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get:77 http://deb.debian.org/debian sid/main arm64 python3-pkg-resources all 74.1.2-2 [213 kB]
Get:78 http://deb.debian.org/debian sid/main arm64 python3-zipp all 3.20.2-1 [10.3 kB]
Get:79 http://deb.debian.org/debian sid/main arm64 python3-setuptools all 74.1.2-2 [736 kB]
Get:80 http://deb.debian.org/debian sid/main arm64 dh-python all 6.20240824 [109 kB]
Get:81 http://deb.debian.org/debian sid/main arm64 dumb-init arm64 1.2.5-3 [13.4 kB]
Get:82 http://deb.debian.org/debian sid/main arm64 libfakeroot arm64 1.36-1 [29.1 kB]
Get:83 http://deb.debian.org/debian sid/main arm64 fakeroot arm64 1.36-1 [74.4 kB]
Get:84 http://deb.debian.org/debian sid/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get:85 http://deb.debian.org/debian sid/main arm64 fonts-dejavu-core all 2.37-8 [840 kB]
Get:86 http://deb.debian.org/debian sid/main arm64 libfontenc1 arm64 1:1.1.8-1 [22.2 kB]
Get:87 http://deb.debian.org/debian sid/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB]
Get:88 http://deb.debian.org/debian sid/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB]
Get:89 http://deb.debian.org/debian sid/main arm64 x11-common all 1:7.7+23.1 [216 kB]
Get:90 http://deb.debian.org/debian sid/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB]
Get:91 http://deb.debian.org/debian sid/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB]
Get:92 http://deb.debian.org/debian sid/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB]
Get:93 http://deb.debian.org/debian sid/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB]
Get:94 http://deb.debian.org/debian sid/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB]
Get:95 http://deb.debian.org/debian sid/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB]
Get:96 http://deb.debian.org/debian sid/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB]
Get:97 http://deb.debian.org/debian sid/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB]
Get:98 http://deb.debian.org/debian sid/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB]
Get:99 http://deb.debian.org/debian sid/main arm64 libxcb1 arm64 1.17.0-2 [143 kB]
Get:100 http://deb.debian.org/debian sid/main arm64 libx11-data all 2:1.8.7-1 [328 kB]
Get:101 http://deb.debian.org/debian sid/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB]
Get:102 http://deb.debian.org/debian sid/main arm64 libxcb-render0 arm64 1.17.0-2 [115 kB]
Get:103 http://deb.debian.org/debian sid/main arm64 libxcb-shm0 arm64 1.17.0-2 [105 kB]
Get:104 http://deb.debian.org/debian sid/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB]
Get:105 http://deb.debian.org/debian sid/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB]
Get:106 http://deb.debian.org/debian sid/main arm64 libcairo2 arm64 1.18.2-2 [483 kB]
Get:107 http://deb.debian.org/debian sid/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB]
Get:108 http://deb.debian.org/debian sid/main arm64 libexpat1-dev arm64 2.6.3-1 [142 kB]
Get:109 http://deb.debian.org/debian sid/main arm64 libfribidi0 arm64 1.0.15-1 [71.8 kB]
Get:110 http://deb.debian.org/debian sid/main arm64 libgfortran5 arm64 14.2.0-6 [361 kB]
Get:111 http://deb.debian.org/debian sid/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB]
Get:112 http://deb.debian.org/debian sid/main arm64 libharfbuzz0b arm64 10.0.1-1 [441 kB]
Get:113 http://deb.debian.org/debian sid/main arm64 libimagequant0 arm64 2.18.0-1+b1 [34.6 kB]
Get:114 http://deb.debian.org/debian sid/main arm64 libjbig0 arm64 2.1-6.1+b1 [30.4 kB]
Get:115 http://deb.debian.org/debian sid/main arm64 libjpeg62-turbo arm64 1:2.1.5-3 [172 kB]
Get:116 http://deb.debian.org/debian sid/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:117 http://deb.debian.org/debian sid/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get:118 http://deb.debian.org/debian sid/main arm64 libjs-sphinxdoc all 7.4.7-3 [158 kB]
Get:119 http://deb.debian.org/debian sid/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB]
Get:120 http://deb.debian.org/debian sid/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b1 [25.0 kB]
Get:121 http://deb.debian.org/debian sid/main arm64 liblcms2-2 arm64 2.16-2 [151 kB]
Get:122 http://deb.debian.org/debian sid/main arm64 liblerc4 arm64 4.0.0+ds-4+b1 [142 kB]
Get:123 http://deb.debian.org/debian sid/main arm64 libopenjp2-7 arm64 2.5.0-2+b3 [177 kB]
Get:124 http://deb.debian.org/debian sid/main arm64 libpython3.12t64 arm64 3.12.7-1 [1982 kB]
Get:125 http://deb.debian.org/debian sid/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB]
Get:126 http://deb.debian.org/debian sid/main arm64 libpython3.12-dev arm64 3.12.7-1 [4793 kB]
Get:127 http://deb.debian.org/debian sid/main arm64 libpython3.13-stdlib arm64 3.13.0-1 [1920 kB]
Get:128 http://deb.debian.org/debian sid/main arm64 libpython3.13 arm64 3.13.0-1 [1960 kB]
Get:129 http://deb.debian.org/debian sid/main arm64 libpython3.13-dev arm64 3.13.0-1 [4668 kB]
Get:130 http://deb.debian.org/debian sid/main arm64 libraqm0 arm64 0.10.1-1+b1 [13.7 kB]
Get:131 http://deb.debian.org/debian sid/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [111 kB]
Get:132 http://deb.debian.org/debian sid/main arm64 libwebp7 arm64 1.4.0-0.1 [267 kB]
Get:133 http://deb.debian.org/debian sid/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB]
Get:134 http://deb.debian.org/debian sid/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [110 kB]
Get:135 http://deb.debian.org/debian sid/main arm64 libwebpmux3 arm64 1.4.0-0.1 [122 kB]
Get:136 http://deb.debian.org/debian sid/main arm64 python3.13 arm64 3.13.0-1 [730 kB]
Get:137 http://deb.debian.org/debian sid/main arm64 python3.12-dev arm64 3.12.7-1 [505 kB]
Get:138 http://deb.debian.org/debian sid/main arm64 python3.13-dev arm64 3.13.0-1 [504 kB]
Get:139 http://deb.debian.org/debian sid/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB]
Get:140 http://deb.debian.org/debian sid/main arm64 python3-pil arm64 10.4.0-1 [480 kB]
Get:141 http://deb.debian.org/debian sid/main arm64 python3-cairo arm64 1.26.1-2 [113 kB]
Get:142 http://deb.debian.org/debian sid/main arm64 python3-freetype all 2.5.1-1 [89.3 kB]
Get:143 http://deb.debian.org/debian sid/main arm64 python3-rlpycairo all 0.3.0-3 [9904 B]
Get:144 http://deb.debian.org/debian sid/main arm64 python3-reportlab all 4.2.5-1 [1117 kB]
Get:145 http://deb.debian.org/debian sid/main arm64 xml-core all 0.19 [20.1 kB]
Get:146 http://deb.debian.org/debian sid/main arm64 w3c-sgml-lib all 1.3-3 [273 kB]
Get:147 http://deb.debian.org/debian sid/main arm64 python3-decorator all 5.1.1-5 [15.1 kB]
Get:148 http://deb.debian.org/debian sid/main arm64 python3-pyparsing all 3.1.2-1 [146 kB]
Get:149 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 libpython3.12-minimal:arm64 (3.12.7-1) ...
Setting up libexpat1:arm64 (2.6.3-1) ...
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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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Setting up python3-minimal (3.12.6-1+debusine1) ...
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Setting up python3-rlpycairo (0.3.0-3) ...
Setting up libpython3-all-dev:arm64 (3.12.6-1+debusine1) ...
Setting up python3-dev (3.12.6-1+debusine1) ...
Setting up g++ (4:14.2.0-1) ...
update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
Setting up build-essential (12.12) ...
Setting up python3-pkg-resources (74.1.2-2) ...
Setting up python3-all-dev (3.12.6-1+debusine1) ...
Setting up python3-setuptools (74.1.2-2) ...
Setting up debhelper (13.20) ...
Setting up python3-chardet (5.2.0+dfsg-1) ...
Setting up python3-numpy (1:1.26.4+ds-11+bootstrap1) ...
Setting up python3-reportlab (4.2.5-1) ...
Setting up dh-python (6.20240824) ...
Setting up python3-scipy (1.13.1-5+nocheck1) ...
Processing triggers for libc-bin (2.40-3) ...
Processing triggers for man-db (2.13.0-1) ...
Processing triggers for sgml-base (1.31) ...
Setting up w3c-sgml-lib (1.3-3) ...
Setting up python3-biopython (1.84+dfsg-3+bd1) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (arm64 included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 6.1.0-26-cloud-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) arm64 (aarch64)
Toolchain package versions: binutils_2.43.1-5 dpkg-dev_1.22.11 g++-14_14.2.0-6 gcc-14_14.2.0-6 libc6-dev_2.40-3 libstdc++-14-dev_14.2.0-6 libstdc++6_14.2.0-6 linux-libc-dev_6.11.2-1
Package versions: appstream_1.0.3-1 apt_2.9.9 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_3.6.4 bash_5.2.32-1+b1 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 ca-certificates_20240203 coreutils_9.4-3.1 cpp_4:14.2.0-1 cpp-14_14.2.0-6 cpp-14-aarch64-linux-gnu_14.2.0-6 cpp-aarch64-linux-gnu_4:14.2.0-1 dash_0.5.12-9 debconf_1.5.87 debhelper_13.20 debian-archive-keyring_2023.4 debianutils_5.20 dh-autoreconf_20 dh-python_6.20240824 dh-strip-nondeterminism_1.14.0-1 diffstat_1.66-1 diffutils_1:3.10-1 dpkg_1.22.11 dpkg-dev_1.22.11 dumb-init_1.2.5-3 dwz_0.15-1+b1 e2fsprogs_1.47.1-1 fakeroot_1.36-1 file_1:5.45-3 findutils_4.10.0-3 fontconfig-config_2.15.0-1.1 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 fonts-urw-base35_20200910-8 g++_4:14.2.0-1 g++-14_14.2.0-6 g++-14-aarch64-linux-gnu_14.2.0-6 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+------------------------------------------------------------------------------+
| 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:
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8197a08210bb98599434307c0619ecfaa172cb91 9728 prody_2.4.1+dfsg-2.debian.tar.xz
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Files:
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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/acceptor.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/__init__.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/selection.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/fields.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/hierview.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/atommap.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/chain.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/flags.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/residue.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/bond.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/functions.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/atomgroup.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/atomic
copying prody/atomic/nbexclusion.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/__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
copying prody/database/quartataweb.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/dali.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/database
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/entropy.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/nma.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/exgnm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/signature.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/sampling.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/mechstiff.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/bbenm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/adaptive.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/__init__.py -> /<<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/modeset.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/gnm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/bildfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/compare.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/anm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/essa.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/mode.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/heatmapper.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/gamma.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/vmdfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/exanm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/analysis.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/perturb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/nmdfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/functions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/pca.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/clustenm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/plotting.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
copying prody/dynamics/editing.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/dynamics
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/ensemble
copying prody/ensemble/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/ensemble
copying prody/ensemble/pdbensemble.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/ensemble
copying prody/ensemble/ensemble.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/ensemble
copying prody/ensemble/functions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/ensemble
copying prody/ensemble/conformation.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/ensemble
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/kdtree
copying prody/kdtree/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/kdtree
copying prody/kdtree/kdtree.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/kdtree
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/measure
copying prody/measure/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/measure
copying prody/measure/measure.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/measure
copying prody/measure/contacts.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/measure
copying prody/measure/transform.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/measure
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/proteins
copying prody/proteins/ciffile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/proteins
copying prody/proteins/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/proteins
copying prody/proteins/starfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/proteins
copying prody/proteins/waterbridges.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/proteins
copying prody/proteins/wwpdb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/proteins
copying prody/proteins/cifheader.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/proteins
copying prody/proteins/compare.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/proteins
copying prody/proteins/localpdb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/proteins
copying prody/proteins/fixer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/proteins
copying prody/proteins/header.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/proteins
copying prody/proteins/emdfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/proteins
copying prody/proteins/dssp.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/proteins
copying prody/proteins/blastpdb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/proteins
copying prody/proteins/pdbclusters.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/proteins
copying prody/proteins/functions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/proteins
copying prody/proteins/stride.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/proteins
copying prody/proteins/pdbfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/proteins
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/sequence
copying prody/sequence/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/sequence
copying prody/sequence/msa.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/sequence
copying prody/sequence/analysis.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/sequence
copying prody/sequence/sequence.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/sequence
copying prody/sequence/msafile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/sequence
copying prody/sequence/plotting.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/sequence
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/trajectory
copying prody/trajectory/psffile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/trajectory
copying prody/trajectory/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/trajectory
copying prody/trajectory/trajfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/trajectory
copying prody/trajectory/trajectory.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/trajectory
copying prody/trajectory/dcdfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/trajectory
copying prody/trajectory/frame.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/trajectory
copying prody/trajectory/trajbase.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/trajectory
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/chromatin
copying prody/chromatin/hic.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/chromatin
copying prody/chromatin/cluster.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/chromatin
copying prody/chromatin/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/chromatin
copying prody/chromatin/norm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/chromatin
copying prody/chromatin/straw.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/chromatin
copying prody/chromatin/functions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/chromatin
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/compounds
copying prody/compounds/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/compounds
copying prody/compounds/pdbligands.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/compounds
copying prody/compounds/functions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/compounds
copying prody/compounds/ccd.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/compounds
copying prody/compounds/bird.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/compounds
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/domain_decomposition
copying prody/domain_decomposition/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/domain_decomposition
copying prody/domain_decomposition/spectrus.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/domain_decomposition
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/utilities
copying prody/utilities/checkers.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/utilities
copying prody/utilities/seqtools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/utilities
copying prody/utilities/catchall.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/utilities
copying prody/utilities/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/utilities
copying prody/utilities/eigtools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/utilities
copying prody/utilities/TreeConstruction.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/utilities
copying prody/utilities/logger.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/utilities
copying prody/utilities/pathtools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/utilities
copying prody/utilities/drawtools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/utilities
copying prody/utilities/misctools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/utilities
copying prody/utilities/legacy.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/utilities
copying prody/utilities/settings.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/utilities
copying prody/utilities/doctools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/utilities
copying prody/utilities/laptools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/utilities
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps
copying prody/apps/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps
copying prody/apps/apptools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/prody_apps
copying prody/apps/prody_apps/prody_blast.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/prody_apps
copying prody/apps/prody_apps/prody_clustenm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/prody_apps
copying prody/apps/prody_apps/prody_biomol.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/prody_apps
copying prody/apps/prody_apps/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/prody_apps
copying prody/apps/prody_apps/prody_contacts.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/prody_apps
copying prody/apps/prody_apps/prody_energy.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/prody_apps
copying prody/apps/prody_apps/prody_catdcd.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/prody_apps
copying prody/apps/prody_apps/prody_eda.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/prody_apps
copying prody/apps/prody_apps/nmaoptions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/prody_apps
copying prody/apps/prody_apps/prody_select.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/prody_apps
copying prody/apps/prody_apps/prody_align.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/prody_apps
copying prody/apps/prody_apps/prody_pca.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/prody_apps
copying prody/apps/prody_apps/prody_fetch.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/prody_apps
copying prody/apps/prody_apps/prody_anm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/prody_apps
copying prody/apps/prody_apps/prody_gnm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/prody_apps
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/evol_apps
copying prody/apps/evol_apps/evol_filter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/evol_apps
copying prody/apps/evol_apps/evol_conserv.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/evol_apps
copying prody/apps/evol_apps/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/evol_apps
copying prody/apps/evol_apps/evol_rankorder.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/evol_apps
copying prody/apps/evol_apps/evol_merge.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/evol_apps
copying prody/apps/evol_apps/evol_occupancy.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/evol_apps
copying prody/apps/evol_apps/evol_search.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/evol_apps
copying prody/apps/evol_apps/evol_fetch.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/evol_apps
copying prody/apps/evol_apps/evol_coevol.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/evol_apps
copying prody/apps/evol_apps/evol_refine.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/apps/evol_apps
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests
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creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/apps
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copying prody/tests/apps/test_prody_pca.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/apps
copying prody/tests/apps/test_prody_examples.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/apps
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copying prody/tests/apps/test_prody_catdcd.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/apps
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copying prody/tests/atomic/test_atommap.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/atomic
copying prody/tests/atomic/test_hierview.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/atomic
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creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
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copying prody/tests/ensemble/test_conformation.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/ensemble
copying prody/tests/ensemble/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/ensemble
copying prody/tests/ensemble/test_functions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/ensemble
copying prody/tests/ensemble/test_pdbensemble.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/ensemble
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/kdtree
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creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/measure
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copying prody/tests/measure/__init__.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/test_contacts.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/measure
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/proteins
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copying prody/tests/proteins/test_localpdb.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_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_pdbfile.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
creating /<<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_analysis.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
copying prody/tests/sequence/test_msa.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
creating /<<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
copying prody/tests/trajectory/test_dcdfile.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/__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
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
creating /<<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/utilities/datafiles/saxs_water.dat -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/utilities/datafiles
copying prody/tests/datafiles/pdb1ejg_oneatom.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
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copying prody/tests/datafiles/pdb2k39_ca.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/pdb4v8r_h36.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
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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
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copying prody/tests/datafiles/pdb3mht.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/pdb3o21.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
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copying prody/tests/datafiles/pdb2nwl-opm.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/pdb6fpj_Bb_fixed_solv_ions.pdb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
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copying prody/tests/datafiles/exanm2nwl_vectors.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/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
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copying prody/tests/datafiles/gnm1ubi_evalues.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
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copying prody/tests/datafiles/mmcif_6zu5.cif -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_prody/build/prody/tests/datafiles
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copying prody/tests/datafiles/rtb2gb1_hessian.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
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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.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
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.slx -> /<<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
running build_ext
building 'prody.dynamics.rtbtools' extension
creating build
creating build/temp.linux-aarch64-cpython-313
creating build/temp.linux-aarch64-cpython-313/prody
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
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/acceptor.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic
copying prody/atomic/angle.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic
copying prody/atomic/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic
copying prody/atomic/atomic.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic
copying prody/atomic/selection.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic
copying prody/atomic/select.py -> /<<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/subset.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic
copying prody/atomic/hierview.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic
copying prody/atomic/atom.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic
copying prody/atomic/atommap.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/chain.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic
copying prody/atomic/donor.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/dihedral.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic
copying prody/atomic/residue.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic
copying prody/atomic/segment.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic
copying prody/atomic/bond.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/functions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic
copying prody/atomic/pointer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic
copying prody/atomic/atomgroup.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic
copying prody/atomic/nbexclusion.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/atomic
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/database
copying prody/database/uniprot.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/database
copying prody/database/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/database
copying prody/database/goa.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/database
copying prody/database/quartataweb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/database
copying prody/database/cath.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/database
copying prody/database/pfam.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/database
copying prody/database/dali.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/database
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/entropy.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/nma.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/exgnm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/signature.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/sampling.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/mechstiff.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/bbenm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/adaptive.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/imanm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/modeset.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/gnm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/bildfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/compare.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/anm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/essa.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/mode.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/heatmapper.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/gamma.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/vmdfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/exanm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/analysis.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/perturb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/nmdfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/functions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/pca.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/rtb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/clustenm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/plotting.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
copying prody/dynamics/editing.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/dynamics
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/ensemble
copying prody/ensemble/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/ensemble
copying prody/ensemble/pdbensemble.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/ensemble
copying prody/ensemble/ensemble.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/ensemble
copying prody/ensemble/functions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/ensemble
copying prody/ensemble/conformation.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/ensemble
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/kdtree
copying prody/kdtree/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/kdtree
copying prody/kdtree/kdtree.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/kdtree
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/measure
copying prody/measure/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/measure
copying prody/measure/measure.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/measure
copying prody/measure/contacts.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/measure
copying prody/measure/transform.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/measure
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/proteins
copying prody/proteins/ciffile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/proteins
copying prody/proteins/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/proteins
copying prody/proteins/starfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/proteins
copying prody/proteins/waterbridges.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/proteins
copying prody/proteins/wwpdb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/proteins
copying prody/proteins/cifheader.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/proteins
copying prody/proteins/compare.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/proteins
copying prody/proteins/localpdb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/proteins
copying prody/proteins/fixer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/proteins
copying prody/proteins/header.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/proteins
copying prody/proteins/emdfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/proteins
copying prody/proteins/dssp.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/proteins
copying prody/proteins/blastpdb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/proteins
copying prody/proteins/pdbclusters.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/proteins
copying prody/proteins/functions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/proteins
copying prody/proteins/stride.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/proteins
copying prody/proteins/pdbfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/proteins
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/sequence
copying prody/sequence/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/sequence
copying prody/sequence/msa.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/sequence
copying prody/sequence/analysis.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/sequence
copying prody/sequence/sequence.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/sequence
copying prody/sequence/msafile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/sequence
copying prody/sequence/plotting.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/sequence
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/trajectory
copying prody/trajectory/psffile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/trajectory
copying prody/trajectory/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/trajectory
copying prody/trajectory/trajfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/trajectory
copying prody/trajectory/trajectory.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/trajectory
copying prody/trajectory/dcdfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/trajectory
copying prody/trajectory/frame.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/trajectory
copying prody/trajectory/trajbase.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/trajectory
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/chromatin
copying prody/chromatin/hic.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/chromatin
copying prody/chromatin/cluster.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/chromatin
copying prody/chromatin/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/chromatin
copying prody/chromatin/norm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/chromatin
copying prody/chromatin/straw.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/chromatin
copying prody/chromatin/functions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/chromatin
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/compounds
copying prody/compounds/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/compounds
copying prody/compounds/pdbligands.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/compounds
copying prody/compounds/functions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/compounds
copying prody/compounds/ccd.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/compounds
copying prody/compounds/bird.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/compounds
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/domain_decomposition
copying prody/domain_decomposition/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/domain_decomposition
copying prody/domain_decomposition/spectrus.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/domain_decomposition
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/utilities
copying prody/utilities/checkers.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/utilities
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copying prody/tests/datafiles/msa_3hsyA_3o21A.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles
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running build_ext
building 'prody.dynamics.rtbtools' extension
creating build/temp.linux-aarch64-cpython-312
creating build/temp.linux-aarch64-cpython-312/prody
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
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 10.817s
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 10.774s
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 2024-10-18T19:07:01Z
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: 49
Distribution: sid
Fail-Stage: build
Host Architecture: arm64
Install-Time: 118
Job: /tmp/debusine-fetch-exec-upload-68tm2ves/prody_2.4.1+dfsg-2.dsc
Machine Architecture: arm64
Package: prody
Package-Time: 214
Source-Version: 2.4.1+dfsg-2
Space: 316012
Status: attempted
Version: 2.4.1+dfsg-2+bd1
--------------------------------------------------------------------------------
Finished at 2024-10-18T19:07:01Z
Build needed 00:03:34, 316012k disk space