Tue May 14 14:32:41 UTC 2024 I: starting to build prody/unstable/arm64 on jenkins on '2024-05-14 14:32' Tue May 14 14:32:41 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_3/35641/console.log Tue May 14 14:32:41 UTC 2024 I: Downloading source for unstable/prody=2.4.1+dfsg-2 --2024-05-14 14:32:42-- http://deb.debian.org/debian/pool/main/p/prody/prody_2.4.1%2bdfsg-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2243 (2.2K) [text/prs.lines.tag] Saving to: ‘prody_2.4.1+dfsg-2.dsc’ 0K .. 100% 348M=0s 2024-05-14 14:32:42 (348 MB/s) - ‘prody_2.4.1+dfsg-2.dsc’ saved [2243/2243] Tue May 14 14:32:42 UTC 2024 I: prody_2.4.1+dfsg-2.dsc -----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 Uploaders: Andrius Merkys , 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 , python3-numpy, python3-pyparsing , python3-scipy , python3-setuptools, python3-zombie-imp Package-List: python3-prody deb science optional arch=any python3-prody-tests deb science optional arch=all Checksums-Sha1: 9d0ead7d3fce8424a0c35a2396639566d5ebea77 16085288 prody_2.4.1+dfsg.orig.tar.xz 8197a08210bb98599434307c0619ecfaa172cb91 9728 prody_2.4.1+dfsg-2.debian.tar.xz Checksums-Sha256: f66b7affa47693dd3d8cf0f0ac833c4d313135420b1e6ece0767259099f5ad87 16085288 prody_2.4.1+dfsg.orig.tar.xz 0579e775804f9943152c3885561b5fcac4ed2c27557f32e6f20866a4d7c465e4 9728 prody_2.4.1+dfsg-2.debian.tar.xz Files: 295e44486fd6cb8cbe38f64aad51439e 16085288 prody_2.4.1+dfsg.orig.tar.xz b0b64099072b904019ec3863f8cf0801 9728 prody_2.4.1+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEdyKS9veshfrgQdQe5fQ/nCc08ocFAmXLF8QSHG1lcmt5c0Bk ZWJpYW4ub3JnAAoJEOX0P5wnNPKHJOYP/26FvLav1XZ1RkFUEwcX3U3CbXGw4asp U2QemYIXOfBoCAS7wuiWBDy/tzvjsp3he5V6jfM8x9DmHniyU7YSfeszZ6ogQR2m gsjCa+saWm93F5/I28ZQgY7soUCITQp3kdvMPJZO1fDr4CstwY42iBUxVO/X3k3R EqtERe8UkGwo5NLB9tu82KviG3IOni5IOeRpNUeZoSmdRMdssqmS8de+g+wBkvC5 L/A9bz2FPSLxG7UHGZlUuL5gKWEnCEsXmGVrzHZRr1/eqgnqRplr2M96tWolnoEy GytOsGn4pOA5XvPO2E/ZcCyKGQa3N8qVZl9/Az+JHxdgAEIHjWjEyRMBlXMQDwnA t8CHNsbXYmTjbvREQrPok3AbUQ7Wx7Q0M0HWsZDYDKqtD1FmNqu5avKhPgu7PSst wG9BCPfeM/+PBoRXjQcUhJ7PkkdGNwJ8XQLyli3qFaexeFAHFdKKXqFlc0V17zVU YNYyMcprmT/Nx+b1phYxFxQi3RKSai8FsWQlZJvTjfA5/VeGxOnPNS5gByWMQDrD 6asxG4WlZEt+DPTPx0jhj+jXfNhmH+sdqZTYhLsTEgI+2NrUqI6Dv/6WCghtj+g9 bRT0Mi3LjCqMSaS/cJ8sGkoHn7SlIvNPRtB2jTnzkSmGCPiAPFCRGx4hXqJma0Xp Yj+AfNx5Kb8D =NqP7 -----END PGP SIGNATURE----- Tue May 14 14:32:42 UTC 2024 I: Checking whether the package is not for us Tue May 14 14:32:42 UTC 2024 I: Starting 1st build on remote node codethink01-arm64.debian.net. Tue May 14 14:32:42 UTC 2024 I: Preparing to do remote build '1' on codethink01-arm64.debian.net. Tue May 14 14:36:40 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jun 16 08:55:45 -12 2025 I: pbuilder-time-stamp: 1750107345 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [prody_2.4.1+dfsg-2.dsc] I: copying [./prody_2.4.1+dfsg.orig.tar.xz] I: copying [./prody_2.4.1+dfsg-2.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Feb 13 07:18:28 2024 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 prody-2.4.1+dfsg 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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/765434/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='3f31c4a78a5641d2b1fff26d8a73376d' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='765434' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.H9ccXi6q/pbuilderrc_EInx --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.H9ccXi6q/b1 --logfile b1/build.log prody_2.4.1+dfsg-2.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink01-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 15 14:05 /bin -> usr/bin I: user script /srv/workspace/pbuilder/765434/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-biopython, python3-numpy, python3-pyparsing, python3-scipy, python3-setuptools, python3-zombie-imp dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19744 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pyparsing; however: Package python3-pyparsing is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-zombie-imp; however: Package python3-zombie-imp is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libcairo2{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libharfbuzz0b{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.11t64{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libraqm0{a} libreadline8t64{a} libsharpyuv0{a} libsub-override-perl{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxrender1{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-biopython{a} python3-cairo{a} python3-chardet{a} python3-decorator{a} python3-dev{a} python3-distutils{a} python3-freetype{a} python3-lib2to3{a} python3-minimal{a} python3-numpy{a} python3-pil{a} python3-pkg-resources{a} python3-pyparsing{a} python3-reportlab{a} python3-rlpycairo{a} python3-scipy{a} python3-setuptools{a} python3-zombie-imp{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tzdata{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-extra javascript-common libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx ncbi-blast+ python-biopython-doc python3-olefile shared-mime-info wget xdg-user-dirs 0 packages upgraded, 128 newly installed, 0 to remove and 0 not upgraded. Need to get 97.2 MB of archives. After unpacking 414 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.11-minimal arm64 3.11.9-1 [813 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.11-minimal arm64 3.11.9-1 [1767 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libpython3.11-stdlib arm64 3.11.9-1 [1775 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 python3.11 arm64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3.12-minimal arm64 3.12.3-1 [802 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 python3.12-minimal arm64 3.12.3-1 [1931 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.71-3 [332 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.21-14 [496 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 39 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.15.3 [901 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 python3-distutils all 3.12.3-1 [131 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 68.1.2-2 [468 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20240422 [107 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libfontenc1 arm64 1:1.1.8-1 [22.2 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.43-5 [272 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.2+dfsg-1+b4 [408 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+23 [252 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 xfonts-utils arm64 1:7.7+6 [85.6 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 62 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libbsd0 arm64 0.12.2-1 [129 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-1 [143 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-1 [114 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-1 [105 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.0-3+b1 [478 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.6.2-1 [278 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.13-3+b1 [71.3 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14-20240429-1 [361 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.80.2-1 [1393 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 8.3.0-2+b1 [2178 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libimagequant0 arm64 2.18.0-1+b1 [34.6 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b1 [30.4 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3 [172 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 7.2.6-7 [150 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b1 [25.0 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.14-2+b1 [144 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-4+b1 [142 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libopenjp2-7 arm64 2.5.0-2+b3 [177 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libpython3.11t64 arm64 3.11.9-1 [1814 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libpython3.11-dev arm64 3.11.9-1 [4358 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.11.8-1 [9564 B] Get: 99 http://deb.debian.org/debian unstable/main arm64 libpython3.12-stdlib arm64 3.12.3-1 [1889 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libpython3.12t64 arm64 3.12.3-1 [1948 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libpython3.12-dev arm64 3.12.3-1 [4745 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libpython3-all-dev arm64 3.11.8-1 [1072 B] Get: 103 http://deb.debian.org/debian unstable/main arm64 libraqm0 arm64 0.10.1-1+b1 [13.7 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [111 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.4.0-0.1 [267 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-4 [307 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [110 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libwebpmux3 arm64 1.4.0-0.1 [122 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.3-1 [659 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 python3-all arm64 3.11.8-1 [1056 B] Get: 111 http://deb.debian.org/debian unstable/main arm64 python3.11-dev arm64 3.11.9-1 [501 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.11.8-1 [26.1 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 python3.12-dev arm64 3.12.3-1 [499 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 python3-all-dev arm64 3.11.8-1 [1072 B] Get: 115 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:1.26.4+ds-8 [4219 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 python3-pil arm64 10.3.0-2 [552 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 python3-cairo arm64 1.26.0-1 [139 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 python3-freetype all 2.4.0-1 [80.3 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 121 http://deb.debian.org/debian unstable/main arm64 python3-reportlab all 4.2.0-2 [1149 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 python3-biopython arm64 1.83+dfsg1-2 [1620 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 python3-scipy arm64 1.11.4-8 [17.5 MB] Get: 128 http://deb.debian.org/debian unstable/main arm64 python3-zombie-imp all 0.0.2-2 [11.7 kB] Fetched 97.2 MB in 1s (119 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19744 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.9-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.2-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_arm64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:arm64 (3.11.9-1) ... Setting up libexpat1:arm64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20060 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_arm64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../5-libreadline8t64_8.2-4_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_arm64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21052 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_arm64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libpython3.12-minimal:arm64. Preparing to unpack .../001-libpython3.12-minimal_3.12.3-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../002-python3.12-minimal_3.12.3-1_arm64.deb ... Unpacking python3.12-minimal (3.12.3-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../003-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../006-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../009-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../010-groff-base_1.23.0-4_arm64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.40-8_arm64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../012-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../013-man-db_2.12.1-1_arm64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../014-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../015-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../016-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../017-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../018-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../019-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../020-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../021-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../022-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../023-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../024-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../025-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../026-libelf1t64_0.191-1+b1_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../027-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../028-libicu72_72.1-4+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-4+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../029-libxml2_2.9.14+dfsg-1.3+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../030-gettext_0.21-14+b1_arm64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../031-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../032-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../033-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../034-python3-pkg-resources_68.1.2-2_all.deb ... Unpacking python3-pkg-resources (68.1.2-2) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../035-python3-lib2to3_3.12.3-1_all.deb ... Unpacking python3-lib2to3 (3.12.3-1) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../036-python3-distutils_3.12.3-1_all.deb ... Unpacking python3-distutils (3.12.3-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../037-python3-setuptools_68.1.2-2_all.deb ... Unpacking python3-setuptools (68.1.2-2) ... Selecting previously unselected package dh-python. Preparing to unpack .../038-dh-python_6.20240422_all.deb ... Unpacking dh-python (6.20240422) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../039-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../040-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package libfontenc1:arm64. Preparing to unpack .../041-libfontenc1_1%3a1.1.8-1_arm64.deb ... Unpacking libfontenc1:arm64 (1:1.1.8-1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../042-libbrotli1_1.1.0-2+b3_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b3) ... Selecting previously unselected package libpng16-16t64:arm64. Preparing to unpack .../043-libpng16-16t64_1.6.43-5_arm64.deb ... Unpacking libpng16-16t64:arm64 (1.6.43-5) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../044-libfreetype6_2.13.2+dfsg-1+b4_arm64.deb ... Unpacking libfreetype6:arm64 (2.13.2+dfsg-1+b4) ... Selecting previously unselected package x11-common. Preparing to unpack .../045-x11-common_1%3a7.7+23_all.deb ... Unpacking x11-common (1:7.7+23) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../046-xfonts-encodings_1%3a1.0.4-2.2_all.deb ... Unpacking xfonts-encodings (1:1.0.4-2.2) ... Selecting previously unselected package xfonts-utils. Preparing to unpack .../047-xfonts-utils_1%3a7.7+6_arm64.deb ... Unpacking xfonts-utils (1:7.7+6) ... Selecting previously unselected package fonts-urw-base35. Preparing to unpack .../048-fonts-urw-base35_20200910-8_all.deb ... Unpacking fonts-urw-base35 (20200910-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../049-fontconfig-config_2.15.0-1.1_arm64.deb ... Unpacking fontconfig-config (2.15.0-1.1) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../050-libblas3_3.12.0-3_arm64.deb ... Unpacking libblas3:arm64 (3.12.0-3) ... Selecting previously unselected package libbsd0:arm64. Preparing to unpack .../051-libbsd0_0.12.2-1_arm64.deb ... Unpacking libbsd0:arm64 (0.12.2-1) ... Selecting previously unselected package libfontconfig1:arm64. Preparing to unpack .../052-libfontconfig1_2.15.0-1.1_arm64.deb ... Unpacking libfontconfig1:arm64 (2.15.0-1.1) ... Selecting previously unselected package libpixman-1-0:arm64. Preparing to unpack .../053-libpixman-1-0_0.42.2-1+b1_arm64.deb ... Unpacking libpixman-1-0:arm64 (0.42.2-1+b1) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../054-libxau6_1%3a1.0.9-1+b1_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.9-1+b1) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../055-libxdmcp6_1%3a1.1.2-3+b1_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.2-3+b1) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../056-libxcb1_1.17.0-1_arm64.deb ... Unpacking libxcb1:arm64 (1.17.0-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../057-libx11-data_2%3a1.8.7-1_all.deb ... Unpacking libx11-data (2:1.8.7-1) ... Selecting previously unselected package libx11-6:arm64. Preparing to unpack .../058-libx11-6_2%3a1.8.7-1+b1_arm64.deb ... Unpacking libx11-6:arm64 (2:1.8.7-1+b1) ... Selecting previously unselected package libxcb-render0:arm64. Preparing to unpack .../059-libxcb-render0_1.17.0-1_arm64.deb ... Unpacking libxcb-render0:arm64 (1.17.0-1) ... Selecting previously unselected package libxcb-shm0:arm64. Preparing to unpack .../060-libxcb-shm0_1.17.0-1_arm64.deb ... Unpacking libxcb-shm0:arm64 (1.17.0-1) ... Selecting previously unselected package libxext6:arm64. Preparing to unpack .../061-libxext6_2%3a1.3.4-1+b1_arm64.deb ... Unpacking libxext6:arm64 (2:1.3.4-1+b1) ... Selecting previously unselected package libxrender1:arm64. Preparing to unpack .../062-libxrender1_1%3a0.9.10-1.1+b1_arm64.deb ... Unpacking libxrender1:arm64 (1:0.9.10-1.1+b1) ... Selecting previously unselected package libcairo2:arm64. Preparing to unpack .../063-libcairo2_1.18.0-3+b1_arm64.deb ... Unpacking libcairo2:arm64 (1.18.0-3+b1) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../064-libdeflate0_1.20-1_arm64.deb ... Unpacking libdeflate0:arm64 (1.20-1) ... Selecting previously unselected package libexpat1-dev:arm64. Preparing to unpack .../065-libexpat1-dev_2.6.2-1_arm64.deb ... Unpacking libexpat1-dev:arm64 (2.6.2-1) ... Selecting previously unselected package libfribidi0:arm64. Preparing to unpack .../066-libfribidi0_1.0.13-3+b1_arm64.deb ... Unpacking libfribidi0:arm64 (1.0.13-3+b1) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../067-libgfortran5_14-20240429-1_arm64.deb ... Unpacking libgfortran5:arm64 (14-20240429-1) ... Selecting previously unselected package libglib2.0-0t64:arm64. Preparing to unpack .../068-libglib2.0-0t64_2.80.2-1_arm64.deb ... Unpacking libglib2.0-0t64:arm64 (2.80.2-1) ... Selecting previously unselected package libgraphite2-3:arm64. Preparing to unpack .../069-libgraphite2-3_1.3.14-2_arm64.deb ... Unpacking libgraphite2-3:arm64 (1.3.14-2) ... Selecting previously unselected package libharfbuzz0b:arm64. Preparing to unpack .../070-libharfbuzz0b_8.3.0-2+b1_arm64.deb ... Unpacking libharfbuzz0b:arm64 (8.3.0-2+b1) ... Selecting previously unselected package libimagequant0:arm64. Preparing to unpack .../071-libimagequant0_2.18.0-1+b1_arm64.deb ... Unpacking libimagequant0:arm64 (2.18.0-1+b1) ... Selecting previously unselected package libjbig0:arm64. Preparing to unpack .../072-libjbig0_2.1-6.1+b1_arm64.deb ... Unpacking libjbig0:arm64 (2.1-6.1+b1) ... Selecting previously unselected package libjpeg62-turbo:arm64. Preparing to unpack .../073-libjpeg62-turbo_1%3a2.1.5-3_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:2.1.5-3) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../074-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../075-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../076-libjs-sphinxdoc_7.2.6-7_all.deb ... Unpacking libjs-sphinxdoc (7.2.6-7) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../077-liblapack3_3.12.0-3_arm64.deb ... Unpacking liblapack3:arm64 (3.12.0-3) ... Selecting previously unselected package liblbfgsb0:arm64. Preparing to unpack .../078-liblbfgsb0_3.0+dfsg.4-1+b1_arm64.deb ... Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1+b1) ... Selecting previously unselected package liblcms2-2:arm64. Preparing to unpack .../079-liblcms2-2_2.14-2+b1_arm64.deb ... Unpacking liblcms2-2:arm64 (2.14-2+b1) ... Selecting previously unselected package liblerc4:arm64. Preparing to unpack .../080-liblerc4_4.0.0+ds-4+b1_arm64.deb ... Unpacking liblerc4:arm64 (4.0.0+ds-4+b1) ... Selecting previously unselected package libopenjp2-7:arm64. Preparing to unpack .../081-libopenjp2-7_2.5.0-2+b3_arm64.deb ... Unpacking libopenjp2-7:arm64 (2.5.0-2+b3) ... Selecting previously unselected package libpython3.11t64:arm64. Preparing to unpack .../082-libpython3.11t64_3.11.9-1_arm64.deb ... Unpacking libpython3.11t64:arm64 (3.11.9-1) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../083-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1) ... Selecting previously unselected package libpython3.11-dev:arm64. Preparing to unpack .../084-libpython3.11-dev_3.11.9-1_arm64.deb ... Unpacking libpython3.11-dev:arm64 (3.11.9-1) ... Selecting previously unselected package libpython3-dev:arm64. Preparing to unpack .../085-libpython3-dev_3.11.8-1_arm64.deb ... Unpacking libpython3-dev:arm64 (3.11.8-1) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../086-libpython3.12-stdlib_3.12.3-1_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.3-1) ... Selecting previously unselected package libpython3.12t64:arm64. Preparing to unpack .../087-libpython3.12t64_3.12.3-1_arm64.deb ... Unpacking libpython3.12t64:arm64 (3.12.3-1) ... Selecting previously unselected package libpython3.12-dev:arm64. Preparing to unpack .../088-libpython3.12-dev_3.12.3-1_arm64.deb ... Unpacking libpython3.12-dev:arm64 (3.12.3-1) ... Selecting previously unselected package libpython3-all-dev:arm64. Preparing to unpack .../089-libpython3-all-dev_3.11.8-1_arm64.deb ... Unpacking libpython3-all-dev:arm64 (3.11.8-1) ... Selecting previously unselected package libraqm0:arm64. Preparing to unpack .../090-libraqm0_0.10.1-1+b1_arm64.deb ... Unpacking libraqm0:arm64 (0.10.1-1+b1) ... Selecting previously unselected package libsharpyuv0:arm64. Preparing to unpack .../091-libsharpyuv0_1.4.0-0.1_arm64.deb ... Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ... Selecting previously unselected package libwebp7:arm64. Preparing to unpack .../092-libwebp7_1.4.0-0.1_arm64.deb ... Unpacking libwebp7:arm64 (1.4.0-0.1) ... Selecting previously unselected package libtiff6:arm64. Preparing to unpack .../093-libtiff6_4.5.1+git230720-4_arm64.deb ... Unpacking libtiff6:arm64 (4.5.1+git230720-4) ... Selecting previously unselected package libwebpdemux2:arm64. Preparing to unpack .../094-libwebpdemux2_1.4.0-0.1_arm64.deb ... Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... Selecting previously unselected package libwebpmux3:arm64. Preparing to unpack .../095-libwebpmux3_1.4.0-0.1_arm64.deb ... Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... Selecting previously unselected package python3.12. Preparing to unpack .../096-python3.12_3.12.3-1_arm64.deb ... Unpacking python3.12 (3.12.3-1) ... Selecting previously unselected package python3-all. Preparing to unpack .../097-python3-all_3.11.8-1_arm64.deb ... Unpacking python3-all (3.11.8-1) ... Selecting previously unselected package python3.11-dev. Preparing to unpack .../098-python3.11-dev_3.11.9-1_arm64.deb ... Unpacking python3.11-dev (3.11.9-1) ... Selecting previously unselected package python3-dev. Preparing to unpack .../099-python3-dev_3.11.8-1_arm64.deb ... Unpacking python3-dev (3.11.8-1) ... Selecting previously unselected package python3.12-dev. Preparing to unpack .../100-python3.12-dev_3.12.3-1_arm64.deb ... Unpacking python3.12-dev (3.12.3-1) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../101-python3-all-dev_3.11.8-1_arm64.deb ... Unpacking python3-all-dev (3.11.8-1) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../102-python3-numpy_1%3a1.26.4+ds-8_arm64.deb ... Unpacking python3-numpy (1:1.26.4+ds-8) ... Selecting previously unselected package python3-chardet. Preparing to unpack .../103-python3-chardet_5.2.0+dfsg-1_all.deb ... Unpacking python3-chardet (5.2.0+dfsg-1) ... Selecting previously unselected package python3-pil:arm64. Preparing to unpack .../104-python3-pil_10.3.0-2_arm64.deb ... Unpacking python3-pil:arm64 (10.3.0-2) ... Selecting previously unselected package python3-cairo. Preparing to unpack .../105-python3-cairo_1.26.0-1_arm64.deb ... Unpacking python3-cairo (1.26.0-1) ... Selecting previously unselected package python3-freetype. Preparing to unpack .../106-python3-freetype_2.4.0-1_all.deb ... Unpacking python3-freetype (2.4.0-1) ... Selecting previously unselected package python3-rlpycairo. Preparing to unpack .../107-python3-rlpycairo_0.3.0-3_all.deb ... Unpacking python3-rlpycairo (0.3.0-3) ... Selecting previously unselected package python3-reportlab. Preparing to unpack .../108-python3-reportlab_4.2.0-2_all.deb ... Unpacking python3-reportlab (4.2.0-2) ... Selecting previously unselected package xml-core. Preparing to unpack .../109-xml-core_0.19_all.deb ... Unpacking xml-core (0.19) ... Selecting previously unselected package w3c-sgml-lib. Preparing to unpack .../110-w3c-sgml-lib_1.3-3_all.deb ... Unpacking w3c-sgml-lib (1.3-3) ... Selecting previously unselected package python3-biopython. Preparing to unpack .../111-python3-biopython_1.83+dfsg1-2_arm64.deb ... Unpacking python3-biopython (1.83+dfsg1-2) ... Selecting previously unselected package python3-decorator. Preparing to unpack .../112-python3-decorator_5.1.1-5_all.deb ... Unpacking python3-decorator (5.1.1-5) ... Selecting previously unselected package python3-pyparsing. Preparing to unpack .../113-python3-pyparsing_3.1.2-1_all.deb ... Unpacking python3-pyparsing (3.1.2-1) ... Selecting previously unselected package python3-scipy. Preparing to unpack .../114-python3-scipy_1.11.4-8_arm64.deb ... Unpacking python3-scipy (1.11.4-8) ... Selecting previously unselected package python3-zombie-imp. Preparing to unpack .../115-python3-zombie-imp_0.0.2-2_all.deb ... Unpacking python3-zombie-imp (0.0.2-2) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.7-2) ... Setting up libgraphite2-3:arm64 (1.3.14-2) ... Setting up liblcms2-2:arm64 (2.14-2+b1) ... Setting up libpixman-1-0:arm64 (0.42.2-1+b1) ... Setting up libsharpyuv0:arm64 (1.4.0-0.1) ... Setting up libxau6:arm64 (1:1.0.9-1+b1) ... Setting up libicu72:arm64 (72.1-4+b1) ... Setting up liblerc4:arm64 (4.0.0+ds-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:arm64 (1.1.0-2+b3) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up libpython3.12-minimal:arm64 (3.12.3-1) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libdeflate0:arm64 (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libjbig0:arm64 (2.1-6.1+b1) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Jun 16 20:56:37 UTC 2025. Universal Time is now: Mon Jun 16 20:56:37 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:arm64 (1:1.1.8-1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:arm64 (2.80.2-1) ... No schema files found: doing nothing. Setting up libblas3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libexpat1-dev:arm64 (2.6.2-1) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:arm64 (1.0.13-3+b1) ... Setting up libimagequant0:arm64 (2.18.0-1+b1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.43-5) ... Setting up autopoint (0.21-14) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libgfortran5:arm64 (14-20240429-1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:arm64 (1.4.0-0.1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libtiff6:arm64 (4.5.1+git230720-4) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libopenjp2-7:arm64 (2.5.0-2+b3) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libwebpmux3:arm64 (1.4.0-0.1) ... Setting up libbsd0:arm64 (0.12.2-1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.12-minimal (3.12.3-1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3+b1) ... Setting up liblapack3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (1.17.0-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:arm64 (1.17.0-1) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libwebpdemux2:arm64 (1.4.0-0.1) ... Setting up libxcb-shm0:arm64 (1.17.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libfreetype6:arm64 (2.13.2+dfsg-1+b4) ... Setting up libjs-sphinxdoc (7.2.6-7) ... Setting up libreadline8t64:arm64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up xml-core (0.19) ... Setting up libx11-6:arm64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:arm64 (8.3.0-2+b1) ... Setting up libfontconfig1:arm64 (2.15.0-1.1) ... Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1+b1) ... Setting up libpython3.12-stdlib:arm64 (3.12.3-1) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.9-1) ... Setting up python3.12 (3.12.3-1) ... Setting up libpython3.11t64:arm64 (3.11.9-1) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.0-3+b1) ... Setting up libpython3.12t64:arm64 (3.12.3-1) ... Setting up libpython3.11-dev:arm64 (3.11.9-1) ... Setting up libraqm0:arm64 (0.10.1-1+b1) ... Setting up libpython3-stdlib:arm64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up libpython3-dev:arm64 (3.11.8-1) ... Setting up python3.11-dev (3.11.9-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up libpython3.12-dev:arm64 (3.12.3-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-freetype (2.4.0-1) ... Setting up python3-pil:arm64 (10.3.0-2) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up libpython3-all-dev:arm64 (3.11.8-1) ... Setting up python3.12-dev (3.12.3-1) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... python3.12: can't get files for byte-compilation Setting up python3-zombie-imp (0.0.2-2) ... Setting up python3-cairo (1.26.0-1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-all (3.11.8-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-dev (3.11.8-1) ... Setting up python3-numpy (1:1.26.4+ds-8) ... Setting up python3-reportlab (4.2.0-2) ... Setting up dh-python (6.20240422) ... Setting up python3-all-dev (3.11.8-1) ... Setting up python3-scipy (1.11.4-8) ... Processing triggers for libc-bin (2.38-11) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.83+dfsg1-2) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/prody-2.4.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../prody_2.4.1+dfsg-2_source.changes dpkg-buildpackage: info: source package prody dpkg-buildpackage: info: source version 2.4.1+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys 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: python3.12 setup.py clean running clean removing '/build/reproducible-path/prody-2.4.1+dfsg/.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 I: pybuild base:311: python3.11 setup.py clean running clean removing '/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/prody-2.4.1+dfsg' rm -rf ProDy.egg-info make[1]: Leaving directory '/build/reproducible-path/prody-2.4.1+dfsg' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem pybuild --with numpy3,python3 dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py config running config I: pybuild base:311: python3.11 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.12 setup.py build running build running build_py creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody copying prody/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/pointer.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/atom.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/subset.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/selection.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/select.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/segment.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/residue.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/nbexclusion.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/improper.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/hierview.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/flags.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/fields.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/donor.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/dihedral.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/crossterm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/chain.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/bond.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/atommap.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/atomic.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/atomgroup.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/angle.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/acceptor.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/database copying prody/database/uniprot.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/database copying prody/database/quartataweb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/database copying prody/database/pfam.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/database copying prody/database/goa.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/database copying prody/database/dali.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/database copying prody/database/cath.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/database copying prody/database/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/database creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/vmdfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/signature.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/sampling.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/rtb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/plotting.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/perturb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/pca.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/nmdfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/nma.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/modeset.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/mode.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/mechstiff.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/imanm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/heatmapper.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/gnm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/gamma.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/exgnm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/exanm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/essa.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/entropy.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/editing.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/compare.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/clustenm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/bildfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/bbenm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/anm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/analysis.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/adaptive.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/ensemble copying prody/ensemble/pdbensemble.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/ensemble copying prody/ensemble/functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/ensemble copying prody/ensemble/ensemble.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/ensemble copying prody/ensemble/conformation.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/ensemble copying prody/ensemble/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/ensemble creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/kdtree copying prody/kdtree/kdtree.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/kdtree copying prody/kdtree/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/kdtree creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/measure copying prody/measure/transform.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/measure copying prody/measure/measure.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/measure copying prody/measure/contacts.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/measure copying prody/measure/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/measure creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/ciffile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/pdbfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/wwpdb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/waterbridges.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/stride.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/starfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/pdbclusters.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/localpdb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/header.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/fixer.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/emdfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/dssp.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/compare.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/cifheader.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/blastpdb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/sequence copying prody/sequence/msa.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/sequence copying prody/sequence/sequence.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/sequence copying prody/sequence/plotting.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/sequence copying prody/sequence/msafile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/sequence copying prody/sequence/analysis.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/sequence copying prody/sequence/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/sequence creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/trajectory copying prody/trajectory/trajfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/trajectory copying prody/trajectory/trajectory.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/trajectory copying prody/trajectory/trajbase.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/trajectory copying prody/trajectory/psffile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/trajectory copying prody/trajectory/frame.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/trajectory copying prody/trajectory/dcdfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/trajectory copying prody/trajectory/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/trajectory creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/chromatin copying prody/chromatin/straw.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/chromatin copying prody/chromatin/norm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/chromatin copying prody/chromatin/hic.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/chromatin copying prody/chromatin/functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/chromatin copying prody/chromatin/cluster.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/chromatin copying prody/chromatin/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/chromatin creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/compounds copying prody/compounds/pdbligands.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/compounds copying prody/compounds/functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/compounds copying prody/compounds/ccd.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/compounds copying prody/compounds/bird.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/compounds copying prody/compounds/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/compounds creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/domain_decomposition copying prody/domain_decomposition/spectrus.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/domain_decomposition copying prody/domain_decomposition/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/domain_decomposition creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/catchall.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/seqtools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/settings.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/pathtools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/misctools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/logger.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/legacy.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/laptools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/eigtools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/drawtools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/doctools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/checkers.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/TreeConstruction.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps copying prody/apps/apptools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps copying prody/apps/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_select.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_pca.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_gnm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_fetch.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_energy.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_eda.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_contacts.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_clustenm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_catdcd.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_blast.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_biomol.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_anm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_align.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/nmaoptions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_search.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_refine.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_rankorder.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_occupancy.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_merge.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_filter.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_fetch.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_conserv.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_coevol.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/evol_apps creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests copying prody/tests/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/apps copying prody/tests/apps/test_prody_pca.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/apps copying prody/tests/apps/test_prody_gnm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/apps copying prody/tests/apps/test_prody_examples.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/apps copying prody/tests/apps/test_prody_catdcd.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/apps copying prody/tests/apps/test_prody_anm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/apps copying prody/tests/apps/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/apps creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/atomic copying prody/tests/atomic/test_select.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/atomic copying prody/tests/atomic/test_subset.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/atomic copying prody/tests/atomic/test_hierview.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/atomic copying prody/tests/atomic/test_fragment.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/atomic copying prody/tests/atomic/test_atommap.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/atomic copying prody/tests/atomic/test_atomic.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/atomic copying prody/tests/atomic/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/atomic creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/dynamics copying prody/tests/dynamics/test_signature.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/dynamics copying prody/tests/dynamics/test_pca.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/dynamics copying prody/tests/dynamics/test_enms.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/dynamics copying prody/tests/dynamics/test_editing.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/dynamics copying prody/tests/dynamics/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/dynamics creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/ensemble copying prody/tests/ensemble/test_pdbensemble.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/ensemble copying prody/tests/ensemble/test_functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/ensemble copying prody/tests/ensemble/test_ensemble.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/ensemble copying prody/tests/ensemble/test_conformation.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/ensemble copying prody/tests/ensemble/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/ensemble creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/kdtree copying prody/tests/kdtree/test_kdtree.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/kdtree copying prody/tests/kdtree/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/kdtree creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/measure copying prody/tests/measure/test_transform.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/measure copying prody/tests/measure/test_measure.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/measure copying prody/tests/measure/test_contacts.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/measure copying prody/tests/measure/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/measure creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins copying prody/tests/proteins/test_wwpdb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins copying prody/tests/proteins/test_localpdb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins copying prody/tests/proteins/test_pdbfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins copying prody/tests/proteins/test_header.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins copying prody/tests/proteins/test_dssp.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins copying prody/tests/proteins/test_ciffile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins copying prody/tests/proteins/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/sequence copying prody/tests/sequence/test_analysis.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/sequence copying prody/tests/sequence/test_sequence.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/sequence copying prody/tests/sequence/test_msafile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/sequence copying prody/tests/sequence/test_msa.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/sequence copying prody/tests/sequence/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/sequence creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/trajectory copying prody/tests/trajectory/test_frame.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/trajectory copying prody/tests/trajectory/test_dcdfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/trajectory copying prody/tests/trajectory/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/trajectory creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/utilities copying prody/tests/utilities/test_pathtools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/utilities copying prody/tests/utilities/test_misctools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/utilities copying prody/tests/utilities/test_checkers.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/utilities copying prody/tests/utilities/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/utilities creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities/datafiles copying prody/utilities/datafiles/saxs_water.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities/datafiles copying prody/utilities/datafiles/mod_res_map.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities/datafiles copying prody/tests/datafiles/pdbRTER.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb6fpj_Bb_fixed_solv_ions.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb4v8r_hex.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb4v8r_h36.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb3p3w.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb3o21.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb3mht.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb3hsy.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb2nwl-opm.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb2k39_truncated.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb2k39_ca.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb2gb1_truncated.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1ubi_ca.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1ubi.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1tw7_step3_charmm2namd_doubled_hex.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1tw7_step3_charmm2namd_doubled_h36.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1tw7_step3_charmm2namd.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1r19_dssp.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1ejg_oneatom.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1ejg.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pca2k39_vectors.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pca2k39_evalues.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_Cys_knot_sca.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_Cys_knot_di.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/hit1ubi.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/gnm1ubi_vectors.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/gnm1ubi_evalues.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/exanm2nwl_vectors.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/exanm2nwl_evalues.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/commute1ubi.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/anm1ubi_vectors.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/anm1ubi_evalues.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/mmcif_6zu5.cif -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/mmcif_6yfy.cif -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/rtb2gb1_project.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/rtb2gb1_hessian.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pca2k39_cov.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/gnm1ubi_kirchhoff.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/exanm2nwl_hessian.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/anm1ubi_hessian.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/dcd2k39_truncated.dcd -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/xmlSTI.xml -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_3hsyA_3o21A_new.fasta -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_Cys_knot.sth -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_Cys_knot.slx -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_Cys_knot.fasta -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_3hsyA_3o21A.fasta -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles running build_ext building 'prody.dynamics.rtbtools' extension creating build 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=/build/reproducible-path/prody-2.4.1+dfsg=. -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=/build/reproducible-path/prody-2.4.1+dfsg=. -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 /build/reproducible-path/prody-2.4.1+dfsg/.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=/build/reproducible-path/prody-2.4.1+dfsg=. -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=/build/reproducible-path/prody-2.4.1+dfsg=. -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 /build/reproducible-path/prody-2.4.1+dfsg/.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=/build/reproducible-path/prody-2.4.1+dfsg=. -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=/build/reproducible-path/prody-2.4.1+dfsg=. -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 /build/reproducible-path/prody-2.4.1+dfsg/.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=/build/reproducible-path/prody-2.4.1+dfsg=. -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=/build/reproducible-path/prody-2.4.1+dfsg=. -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 /build/reproducible-path/prody-2.4.1+dfsg/.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=/build/reproducible-path/prody-2.4.1+dfsg=. -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=/build/reproducible-path/prody-2.4.1+dfsg=. -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 /build/reproducible-path/prody-2.4.1+dfsg/.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=/build/reproducible-path/prody-2.4.1+dfsg=. -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=/build/reproducible-path/prody-2.4.1+dfsg=. -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=/build/reproducible-path/prody-2.4.1+dfsg=. -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 /build/reproducible-path/prody-2.4.1+dfsg/.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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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::set_(T*, T*, const T&) [with T = double]', inlined from 'TNT::Array1D::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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -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 /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins/ccealign.cpython-312-aarch64-linux-gnu.so I: pybuild base:311: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody copying prody/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/pointer.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/atom.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/subset.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/selection.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/select.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/segment.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/residue.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/nbexclusion.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/improper.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/hierview.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/flags.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/fields.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/donor.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/dihedral.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/crossterm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/chain.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/bond.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/atommap.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/atomic.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/atomgroup.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/angle.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/acceptor.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/database copying prody/database/uniprot.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/database copying prody/database/quartataweb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/database copying prody/database/pfam.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/database copying prody/database/goa.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/database copying prody/database/dali.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/database copying prody/database/cath.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/database copying prody/database/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/database creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/vmdfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/signature.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/sampling.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/rtb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/plotting.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/perturb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/pca.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/nmdfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/nma.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/modeset.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/mode.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/mechstiff.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/imanm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/heatmapper.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/gnm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/gamma.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/exgnm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/exanm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/essa.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/entropy.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/editing.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/compare.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/clustenm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/bildfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/bbenm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/anm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/analysis.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/adaptive.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/ensemble copying prody/ensemble/pdbensemble.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/ensemble copying prody/ensemble/functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/ensemble copying prody/ensemble/ensemble.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/ensemble copying prody/ensemble/conformation.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/ensemble copying prody/ensemble/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/ensemble creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/kdtree copying prody/kdtree/kdtree.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/kdtree copying prody/kdtree/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/kdtree creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/measure copying prody/measure/transform.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/measure copying prody/measure/measure.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/measure copying prody/measure/contacts.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/measure copying prody/measure/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/measure creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/ciffile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/pdbfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/wwpdb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/waterbridges.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/stride.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/starfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/pdbclusters.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/localpdb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/header.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/fixer.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/emdfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/dssp.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/compare.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/cifheader.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/blastpdb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence copying prody/sequence/msa.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence copying prody/sequence/sequence.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence copying prody/sequence/plotting.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence copying prody/sequence/msafile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence copying prody/sequence/analysis.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence copying prody/sequence/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/trajectory copying prody/trajectory/trajfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/trajectory copying prody/trajectory/trajectory.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/trajectory copying prody/trajectory/trajbase.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/trajectory copying prody/trajectory/psffile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/trajectory copying prody/trajectory/frame.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/trajectory copying prody/trajectory/dcdfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/trajectory copying prody/trajectory/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/trajectory creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/chromatin copying prody/chromatin/straw.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/chromatin copying prody/chromatin/norm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/chromatin copying prody/chromatin/hic.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/chromatin copying prody/chromatin/functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/chromatin copying prody/chromatin/cluster.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/chromatin copying prody/chromatin/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/chromatin creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/compounds copying prody/compounds/pdbligands.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/compounds copying prody/compounds/functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/compounds copying prody/compounds/ccd.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/compounds copying prody/compounds/bird.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/compounds copying prody/compounds/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/compounds creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/domain_decomposition copying prody/domain_decomposition/spectrus.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/domain_decomposition copying prody/domain_decomposition/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/domain_decomposition creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/catchall.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/seqtools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/settings.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/pathtools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/misctools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/logger.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/legacy.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/laptools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/eigtools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/drawtools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/doctools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/checkers.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/TreeConstruction.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps copying prody/apps/apptools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps copying prody/apps/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_select.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_pca.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_gnm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_fetch.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_energy.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_eda.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_contacts.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_clustenm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_catdcd.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_blast.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_biomol.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_anm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_align.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/nmaoptions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_search.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_refine.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_rankorder.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_occupancy.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_merge.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_filter.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_fetch.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_conserv.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_coevol.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests copying prody/tests/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/apps copying prody/tests/apps/test_prody_pca.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/apps copying prody/tests/apps/test_prody_gnm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/apps copying prody/tests/apps/test_prody_examples.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/apps copying prody/tests/apps/test_prody_catdcd.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/apps copying prody/tests/apps/test_prody_anm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/apps copying prody/tests/apps/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/apps creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic copying prody/tests/atomic/test_select.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic copying prody/tests/atomic/test_subset.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic copying prody/tests/atomic/test_hierview.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic copying prody/tests/atomic/test_fragment.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic copying prody/tests/atomic/test_atommap.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic copying prody/tests/atomic/test_atomic.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic copying prody/tests/atomic/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics copying prody/tests/dynamics/test_signature.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics copying prody/tests/dynamics/test_pca.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics copying prody/tests/dynamics/test_enms.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics copying prody/tests/dynamics/test_editing.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics copying prody/tests/dynamics/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/ensemble copying prody/tests/ensemble/test_pdbensemble.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/ensemble copying prody/tests/ensemble/test_functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/ensemble copying prody/tests/ensemble/test_ensemble.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/ensemble copying prody/tests/ensemble/test_conformation.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/ensemble copying prody/tests/ensemble/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/ensemble creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/kdtree copying prody/tests/kdtree/test_kdtree.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/kdtree copying prody/tests/kdtree/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/kdtree creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/measure copying prody/tests/measure/test_transform.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/measure copying prody/tests/measure/test_measure.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/measure copying prody/tests/measure/test_contacts.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/measure copying prody/tests/measure/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/measure creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins copying prody/tests/proteins/test_wwpdb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins copying prody/tests/proteins/test_localpdb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins copying prody/tests/proteins/test_pdbfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins copying prody/tests/proteins/test_header.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins copying prody/tests/proteins/test_dssp.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins copying prody/tests/proteins/test_ciffile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins copying prody/tests/proteins/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/sequence copying prody/tests/sequence/test_analysis.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/sequence copying prody/tests/sequence/test_sequence.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/sequence copying prody/tests/sequence/test_msafile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/sequence copying prody/tests/sequence/test_msa.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/sequence copying prody/tests/sequence/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/sequence creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/trajectory copying prody/tests/trajectory/test_frame.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/trajectory copying prody/tests/trajectory/test_dcdfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/trajectory copying prody/tests/trajectory/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/trajectory creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/utilities copying prody/tests/utilities/test_pathtools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/utilities copying prody/tests/utilities/test_misctools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/utilities copying prody/tests/utilities/test_checkers.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/utilities copying prody/tests/utilities/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/utilities creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities/datafiles copying prody/utilities/datafiles/saxs_water.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities/datafiles copying prody/utilities/datafiles/mod_res_map.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities/datafiles copying prody/tests/datafiles/pdbRTER.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb6fpj_Bb_fixed_solv_ions.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb4v8r_hex.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb4v8r_h36.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb3p3w.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb3o21.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb3mht.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb3hsy.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb2nwl-opm.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb2k39_truncated.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb2k39_ca.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb2gb1_truncated.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1ubi_ca.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1ubi.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1tw7_step3_charmm2namd_doubled_hex.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1tw7_step3_charmm2namd_doubled_h36.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1tw7_step3_charmm2namd.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1r19_dssp.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1ejg_oneatom.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1ejg.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pca2k39_vectors.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pca2k39_evalues.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_Cys_knot_sca.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_Cys_knot_di.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/hit1ubi.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/gnm1ubi_vectors.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/gnm1ubi_evalues.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/exanm2nwl_vectors.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/exanm2nwl_evalues.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/commute1ubi.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/anm1ubi_vectors.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/anm1ubi_evalues.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/mmcif_6zu5.cif -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/mmcif_6yfy.cif -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/rtb2gb1_project.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/rtb2gb1_hessian.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pca2k39_cov.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/gnm1ubi_kirchhoff.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/exanm2nwl_hessian.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/anm1ubi_hessian.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/dcd2k39_truncated.dcd -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/xmlSTI.xml -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_3hsyA_3o21A_new.fasta -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_Cys_knot.sth -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_Cys_knot.slx -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_Cys_knot.fasta -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_3hsyA_3o21A.fasta -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles running build_ext building 'prody.dynamics.rtbtools' extension creating build/temp.linux-aarch64-cpython-311 creating build/temp.linux-aarch64-cpython-311/prody creating build/temp.linux-aarch64-cpython-311/prody/dynamics aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -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/python3.11 -c prody/dynamics/rtbtools.c -o build/temp.linux-aarch64-cpython-311/prody/dynamics/rtbtools.o aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/prody/dynamics/rtbtools.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics/rtbtools.cpython-311-aarch64-linux-gnu.so building 'prody.dynamics.smtools' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -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/python3.11 -c prody/dynamics/smtools.c -o build/temp.linux-aarch64-cpython-311/prody/dynamics/smtools.o aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/prody/dynamics/smtools.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics/smtools.cpython-311-aarch64-linux-gnu.so building 'prody.sequence.msatools' extension creating build/temp.linux-aarch64-cpython-311/prody/sequence aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -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/python3.11 -c prody/sequence/msatools.c -o build/temp.linux-aarch64-cpython-311/prody/sequence/msatools.o aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/prody/sequence/msatools.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence/msatools.cpython-311-aarch64-linux-gnu.so building 'prody.sequence.msaio' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -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/python3.11 -c prody/sequence/msaio.c -o build/temp.linux-aarch64-cpython-311/prody/sequence/msaio.o aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/prody/sequence/msaio.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence/msaio.cpython-311-aarch64-linux-gnu.so building 'prody.sequence.seqtools' extension aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -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/python3.11 -c prody/sequence/seqtools.c -o build/temp.linux-aarch64-cpython-311/prody/sequence/seqtools.o aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/prody/sequence/seqtools.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence/seqtools.cpython-311-aarch64-linux-gnu.so building 'prody.kdtree._CKDTree' extension creating build/temp.linux-aarch64-cpython-311/prody/kdtree aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -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/python3.11 -c prody/kdtree/KDTree.c -o build/temp.linux-aarch64-cpython-311/prody/kdtree/KDTree.o aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -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/python3.11 -c prody/kdtree/KDTreemodule.c -o build/temp.linux-aarch64-cpython-311/prody/kdtree/KDTreemodule.o aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/prody/kdtree/KDTree.o build/temp.linux-aarch64-cpython-311/prody/kdtree/KDTreemodule.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/kdtree/_CKDTree.cpython-311-aarch64-linux-gnu.so building 'prody.proteins.ccealign' extension creating build/temp.linux-aarch64-cpython-311/prody/proteins creating build/temp.linux-aarch64-cpython-311/prody/proteins/ccealign aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -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/python3.11 -c prody/proteins/ccealign/ccealignmodule.cpp -o build/temp.linux-aarch64-cpython-311/prody/proteins/ccealign/ccealignmodule.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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::set_(T*, T*, const T&) [with T = double]', inlined from 'TNT::Array1D::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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/prody/proteins/ccealign/ccealignmodule.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins/ccealign.cpython-311-aarch64-linux-gnu.so dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build; python3.12 -m unittest discover -v /build/reproducible-path/prody-2.4.1+dfsg/.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. /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic/flags.py:463: SyntaxWarning: invalid escape sequence '\ ' __doc__ += """ /build/reproducible-path/prody-2.4.1+dfsg/.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 /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic/select.py:719: SyntaxWarning: invalid escape sequence '\w' RE_SCHARS = re_compile('`[\w\W]*?`') /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic/select.py:738: SyntaxWarning: invalid escape sequence '\w' RE_REGEXP = re_compile('"[\w\W]*"') /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic/select.py:757: SyntaxWarning: invalid escape sequence '\d' _ = '[-+]?\d+(\.\d*)?([eE]\d+)?' /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic/select.py:758: SyntaxWarning: invalid escape sequence '\ ' RE_NRANGE = re_compile(_ + '\ *(to|:)\ *' + _) /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic/select.py:761: SyntaxWarning: invalid escape sequence '\ ' pp.Optional(pp.Regex('(\ *:\ *' + _ + ')'))) /build/reproducible-path/prody-2.4.1+dfsg/.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* /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins/localpdb.py:438: SyntaxWarning: invalid escape sequence '\.' pdbext = compile('\.(pdb|ent)(\.gz)?$', IGNORECASE) /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins/localpdb.py:440: SyntaxWarning: invalid escape sequence '\.' pdbext = compile('\.(pdb|ent)\.gz$', IGNORECASE) /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins/localpdb.py:442: SyntaxWarning: invalid escape sequence '\.' pdbext = compile('\.(pdb|ent)$', IGNORECASE) /build/reproducible-path/prody-2.4.1+dfsg/.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 /build/reproducible-path/prody-2.4.1+dfsg/.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) ... /build/reproducible-path/prody-2.4.1+dfsg/.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) ... /build/reproducible-path/prody-2.4.1+dfsg/.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), /build/reproducible-path/prody-2.4.1+dfsg/.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) /build/reproducible-path/prody-2.4.1+dfsg/.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) ... /build/reproducible-path/prody-2.4.1+dfsg/.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)), /build/reproducible-path/prody-2.4.1+dfsg/.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) ... /build/reproducible-path/prody-2.4.1+dfsg/.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) ... /build/reproducible-path/prody-2.4.1+dfsg/.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) ... /build/reproducible-path/prody-2.4.1+dfsg/.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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/apps/test_prody_anm.py", line 9, in 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 394, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/unittest/loader.py", line 337, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/apps/test_prody_anm.py", line 11, in 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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/apps/test_prody_catdcd.py", line 8, in 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 394, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/unittest/loader.py", line 337, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/apps/test_prody_catdcd.py", line 10, in 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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/apps/test_prody_examples.py", line 10, in 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 394, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/unittest/loader.py", line 337, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/apps/test_prody_examples.py", line 12, in 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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/apps/test_prody_gnm.py", line 8, in 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 394, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/unittest/loader.py", line 337, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/apps/test_prody_gnm.py", line 10, in 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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/apps/test_prody_pca.py", line 8, in 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 394, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/unittest/loader.py", line 337, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/apps/test_prody_pca.py", line 10, in 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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/atomic/test_select.py", line 9, in 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 394, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/unittest/loader.py", line 337, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/atomic/test_select.py", line 11, in 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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/dynamics/test_enms.py", line 7, in 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 394, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/unittest/loader.py", line 337, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/dynamics/test_enms.py", line 9, in 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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/dynamics/test_pca.py", line 7, in 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 394, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/unittest/loader.py", line 337, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/dynamics/test_pca.py", line 9, in 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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/ensemble/test_ensemble.py", line 191, in testSelection sel = ATOMS.select('resnum 1 to 3') ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic/atomic.py", line 232, in select return SELECT.select(self, selstr, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic/select.py", line 895, in select indices = self.getIndices(atoms, selstr, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic/select.py", line 953, in getIndices torf = self.getBoolArray(atoms, selstr, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic/select.py", line 1004, in getBoolArray parser = self._getParser(selstr) ^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/prody-2.4.1+dfsg/.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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins/test_ciffile.py", line 8, in 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 394, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/unittest/loader.py", line 337, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins/test_ciffile.py", line 10, in 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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins/test_dssp.py", line 5, in 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 394, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/unittest/loader.py", line 337, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins/test_dssp.py", line 7, in 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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins/test_localpdb.py", line 8, in 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 394, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/unittest/loader.py", line 337, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins/test_localpdb.py", line 10, in 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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins/test_pdbfile.py", line 8, in 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 394, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/unittest/loader.py", line 337, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins/test_pdbfile.py", line 10, in 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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins/test_wwpdb.py", line 7, in 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 394, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/unittest/loader.py", line 337, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins/test_wwpdb.py", line 9, in 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 394, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/unittest/loader.py", line 337, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/sequence/test_msafile.py", line 8, in 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 16.077s FAILED (errors=15) E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build; python3.12 -m unittest discover -v I: pybuild base:311: cd /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build; python3.11 -m unittest discover -v 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) ... /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_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) ... /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_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), /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_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) /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_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) ... /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_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)), /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_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) ... /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_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) ... /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_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) ... /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/apps/test_prody_anm.py", line 9, in 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/python3.11/unittest/loader.py", line 419, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/apps/test_prody_anm.py", line 11, in from numpy.testing import dec ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py) ====================================================================== 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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/apps/test_prody_catdcd.py", line 8, in 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/python3.11/unittest/loader.py", line 419, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/apps/test_prody_catdcd.py", line 10, in from numpy.testing import dec ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py) ====================================================================== 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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/apps/test_prody_examples.py", line 10, in 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/python3.11/unittest/loader.py", line 419, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/apps/test_prody_examples.py", line 12, in from numpy.testing import dec ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py) ====================================================================== 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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/apps/test_prody_gnm.py", line 8, in 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/python3.11/unittest/loader.py", line 419, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/apps/test_prody_gnm.py", line 10, in from numpy.testing import dec ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py) ====================================================================== 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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/apps/test_prody_pca.py", line 8, in 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/python3.11/unittest/loader.py", line 419, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/apps/test_prody_pca.py", line 10, in from numpy.testing import dec ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py) ====================================================================== 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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic/test_select.py", line 9, in 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/python3.11/unittest/loader.py", line 419, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic/test_select.py", line 11, in from numpy.testing import dec ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py) ====================================================================== 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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics/test_enms.py", line 7, in 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/python3.11/unittest/loader.py", line 419, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics/test_enms.py", line 9, in from numpy.testing import dec ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py) ====================================================================== 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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics/test_pca.py", line 7, in 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/python3.11/unittest/loader.py", line 419, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics/test_pca.py", line 9, in from numpy.testing import dec ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py) ====================================================================== ERROR: testSelection (prody.tests.ensemble.test_ensemble.TestEnsemble.testSelection) Test atom selection of ensemble. ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/ensemble/test_ensemble.py", line 191, in testSelection sel = ATOMS.select('resnum 1 to 3') ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic/atomic.py", line 232, in select return SELECT.select(self, selstr, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic/select.py", line 895, in select indices = self.getIndices(atoms, selstr, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic/select.py", line 953, in getIndices torf = self.getBoolArray(atoms, selstr, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic/select.py", line 1004, in getBoolArray parser = self._getParser(selstr) ^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins/test_ciffile.py", line 8, in 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/python3.11/unittest/loader.py", line 419, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins/test_ciffile.py", line 10, in from numpy.testing import dec ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py) ====================================================================== 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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins/test_dssp.py", line 5, in 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/python3.11/unittest/loader.py", line 419, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins/test_dssp.py", line 7, in from numpy.testing import dec ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py) ====================================================================== 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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins/test_localpdb.py", line 8, in 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/python3.11/unittest/loader.py", line 419, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins/test_localpdb.py", line 10, in from numpy.testing import dec ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py) ====================================================================== 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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins/test_pdbfile.py", line 8, in 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/python3.11/unittest/loader.py", line 419, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins/test_pdbfile.py", line 10, in from numpy.testing import dec ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py) ====================================================================== 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 "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins/test_wwpdb.py", line 7, in 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/python3.11/unittest/loader.py", line 419, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins/test_wwpdb.py", line 9, in from numpy.testing import dec ImportError: cannot import name 'dec' from 'numpy.testing' (/usr/lib/python3/dist-packages/numpy/testing/__init__.py) ====================================================================== 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/python3.11/unittest/loader.py", line 419, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name __import__(name) File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/sequence/test_msafile.py", line 8, in 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) ---------------------------------------------------------------------- Ran 279 tests in 15.825s FAILED (errors=15) E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build; python3.11 -m unittest discover -v dh_auto_test: error: pybuild --test -i python{version} -p "3.12 3.11" returned exit code 13 make: *** [debian/rules:6: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/765434 and its subdirectories Tue May 14 14:36:42 UTC 2024 W: No second build log, what happened?