Mon May 6 14:41:06 UTC 2024 I: starting to build python-pymbar/trixie/arm64 on jenkins on '2024-05-06 14:40' Mon May 6 14:41:06 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_24/33613/console.log Mon May 6 14:41:06 UTC 2024 I: Downloading source for trixie/python-pymbar=3.1.0-4 --2024-05-06 14:41:06-- http://deb.debian.org/debian/pool/main/p/python-pymbar/python-pymbar_3.1.0-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2363 (2.3K) [text/prs.lines.tag] Saving to: ‘python-pymbar_3.1.0-4.dsc’ 0K .. 100% 291M=0s 2024-05-06 14:41:06 (291 MB/s) - ‘python-pymbar_3.1.0-4.dsc’ saved [2363/2363] Mon May 6 14:41:06 UTC 2024 I: python-pymbar_3.1.0-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: python-pymbar Binary: python3-pymbar Architecture: all Version: 3.1.0-4 Maintainer: Debian Science Maintainers Uploaders: Andrius Merkys , Homepage: https://simtk.org/home/pymbar Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/science-team/python-pymbar Vcs-Git: https://salsa.debian.org/science-team/python-pymbar.git Testsuite: autopkgtest, autopkgtest-pkg-python Testsuite-Triggers: python3-pytest Build-Depends: debhelper-compat (= 13), dh-python, dh-sequence-python3, python3-all, python3-numpy, python3-pytest , python3-scipy , python3-setuptools, python3-six Package-List: python3-pymbar deb science optional arch=all Checksums-Sha1: 0e59d4595d3d6f340975a71af14cd19b026a65ac 17140372 python-pymbar_3.1.0.orig.tar.gz bf17acf1c361e84b93321b61eaeaf27e8e5a545e 3916 python-pymbar_3.1.0-4.debian.tar.xz Checksums-Sha256: 41cd65cbd89e1ae2f5cf08434ab91533512343185f48b4edb2e704616e0896cf 17140372 python-pymbar_3.1.0.orig.tar.gz 48e8c600c6255eea09141fbc854682a3ed2a317e103f5ff0318253937568a4a7 3916 python-pymbar_3.1.0-4.debian.tar.xz Files: 18fd3c7aa97fc4490937ef6dd432a4c7 17140372 python-pymbar_3.1.0.orig.tar.gz b8aa16ff3c8c93808d92ecb163f00a76 3916 python-pymbar_3.1.0-4.debian.tar.xz Dgit: cc500449956b5f5586265155be33bad8cbf1e156 debian archive/debian/3.1.0-4 https://git.dgit.debian.org/python-pymbar -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmPa0zUUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdowLg/6A6dy20fi4BQY4p1ScWKEoesRREjR vI7QjhN8E3DQKCkwdM5lU8Z+7mzJl3bscDngcPhijJgg0yO7AftDuGLOtFa9T8qL 2RQDygGLLttt6ndyNwJ687+DY/ePpkeFNRFqBIPphIdRLcIwucriXH9vDkbkw1Kg ufNu8we9X9ijECR9IRHINo3HEuR11aPkHfkCiE/LWAnKNQvS9jSe7D9qpKluU1pT PJKcgWSNFfBnrbht/GuaMvG9u254xDY1AT+GZfkHHoKjJxpoJFUKYJpY65xS4VGQ ztupnmOpBCsgMA96Fd+7Y9ANO8nOKEPaUkbP922Tct0fl8MYKGNB+Qri0RS94vis Z4o+do7EexRQ8Z2jEx73c6SzctrwTJeRwerN+j2qs/U14kce36VFQao0DHxWdzWg D9570h5lxdSN0XEuP9d39aJdO3RCOXQjH4+IjwXJNA7wgrBrGmFZ16xICklIlbhQ nGsZXe2puo89QkATK7QHSCzb1fYoSTzRhVFuvHrHHSxDIEAKDk2ILjz0d7gdny4I QBOQ5iA1qOWNsM9g8Nb3Oi6NcKw4HkIKIusYuc/uuTbjkflwnei16d4xOLlrnQj+ FG9/YkLdpjd1lV/7/Qbr6pngLeil22yc+gq0J3FQ/prFsU9/OrSlcbXt6IvXAWDW yRktoj051XKH4Xg= =i4s/ -----END PGP SIGNATURE----- Mon May 6 14:41:06 UTC 2024 I: Checking whether the package is not for us Mon May 6 14:41:06 UTC 2024 I: Starting 1st build on remote node codethink04-arm64.debian.net. Mon May 6 14:41:06 UTC 2024 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Mon May 6 14:47:35 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon May 6 02:41:09 -12 2024 I: pbuilder-time-stamp: 1715006469 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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 [python-pymbar_3.1.0-4.dsc] I: copying [./python-pymbar_3.1.0.orig.tar.gz] I: copying [./python-pymbar_3.1.0-4.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Feb 1 21:01:41 2023 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./python-pymbar_3.1.0-4.dsc: no acceptable signature found dpkg-source: info: extracting python-pymbar in python-pymbar-3.1.0 dpkg-source: info: unpacking python-pymbar_3.1.0.orig.tar.gz dpkg-source: info: unpacking python-pymbar_3.1.0-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying numpy-1.24.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1538591/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='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='928b0e420d9348c8b3d5c85589bc1d5d' 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='1538591' 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.dVlYlJaw/pbuilderrc_onv0 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dVlYlJaw/b1 --logfile b1/build.log python-pymbar_3.1.0-4.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 codethink04-arm64 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 5 11:23 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1538591/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, dh-sequence-python3, python3-all, python3-numpy, python3-pytest, python3-scipy, python3-setuptools, python3-six dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19743 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 dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest 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-six; however: Package python3-six 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} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libicu72{a} liblapack3{a} liblbfgsb0{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-decorator{a} python3-distutils{a} python3-iniconfig{a} python3-lib2to3{a} python3-minimal{a} python3-numpy{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-pytest{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3.11{a} python3.11-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx python3-pil python3-pygments wget 0 packages upgraded, 65 newly installed, 0 to remove and 0 not upgraded. Need to get 54.9 MB of archives. After unpacking 269 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libpython3.11-minimal arm64 3.11.9-1 [813 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 python3.11-minimal arm64 3.11.9-1 [1767 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024a-3 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libpython3.11-stdlib arm64 3.11.9-1 [1775 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 python3.11 arm64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libpython3.12-minimal arm64 3.12.3-1 [802 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 python3.12-minimal arm64 3.12.3-1 [1931 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 38 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 python3-distutils all 3.12.3-1 [131 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 68.1.2-2 [468 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20240422 [107 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14-20240330-1 [361 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b1 [25.0 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libpython3.12-stdlib arm64 3.12.3-1 [1889 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.3-1 [659 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 python3-all arm64 3.11.8-1 [1056 B] Get: 58 http://deb.debian.org/debian trixie/main arm64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 60 http://deb.debian.org/debian trixie/main arm64 python3-numpy arm64 1:1.26.4+ds-8 [4219 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.0-1 [45.5 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 python3-pytest all 7.4.4-3 [239 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 python3-scipy arm64 1.11.4-6 [17.5 MB] Get: 65 http://deb.debian.org/debian trixie/main arm64 python3-six all 1.16.0-6 [16.3 kB] Fetched 54.9 MB in 0s (135 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 ... 19743 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 ... 20059 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-3_all.deb ... Unpacking tzdata (2024a-3) ... 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) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/python-pymbar-3.1.0/ && 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 > ../python-pymbar_3.1.0-4_source.changes dpkg-buildpackage: info: source package python-pymbar dpkg-buildpackage: info: source version 3.1.0-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 dpkg-source: info: using options from python-pymbar-3.1.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --buildsystem pybuild --with python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/python-pymbar-3.1.0' dh_auto_clean I: pybuild base:311: python3.12 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:744: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) author Levi N. Naden and Michael R. Shirts and John D. Chodera author_emaillevi.naden@choderalab.org, michael.shirts@virginia.edu, john.chodera@choderalab.org data_files [('pymbar', ['pymbar/_pymbar.c'])] descriptionPython implementation of the multistate Bennett acceptance ratio (MBAR) method. download_url http://github.com/choderalab/pymbar ext_modules [] license MIT long_description Pymbar (https://simtk.org/home/pymbar) is a library that provides tools for optimally combining simulations from multiple thermodynamic states using maximum likelihood methods to compute free energies (normalization constants) and expectation values from all of the samples simultaneously. name pymbar package_dir {'pymbar': 'pymbar', 'pymbar.tests': 'pymbar/tests'} packages ['pymbar', 'pymbar.testsystems', 'pymbar.tests'] platforms ['Linux', 'Mac OS X', 'Windows'] requires ['numpy', 'scipy', 'pytest', 'numexpr'] url http://github.com/choderalab/pymbar version 3.0.5 zip_safe False running clean removing '/build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/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 /usr/lib/python3/dist-packages/setuptools/dist.py:744: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) author Levi N. Naden and Michael R. Shirts and John D. Chodera author_emaillevi.naden@choderalab.org, michael.shirts@virginia.edu, john.chodera@choderalab.org data_files [('pymbar', ['pymbar/_pymbar.c'])] descriptionPython implementation of the multistate Bennett acceptance ratio (MBAR) method. download_url http://github.com/choderalab/pymbar ext_modules [] license MIT long_description Pymbar (https://simtk.org/home/pymbar) is a library that provides tools for optimally combining simulations from multiple thermodynamic states using maximum likelihood methods to compute free energies (normalization constants) and expectation values from all of the samples simultaneously. name pymbar package_dir {'pymbar': 'pymbar', 'pymbar.tests': 'pymbar/tests'} packages ['pymbar', 'pymbar.testsystems', 'pymbar.tests'] platforms ['Linux', 'Mac OS X', 'Windows'] requires ['numpy', 'scipy', 'pytest', 'numexpr'] url http://github.com/choderalab/pymbar version 3.0.5 zip_safe False running clean removing '/build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/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 rm -rf pymbar.egg-info make[1]: Leaving directory '/build/reproducible-path/python-pymbar-3.1.0' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem pybuild --with 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 /usr/lib/python3/dist-packages/setuptools/dist.py:744: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) author Levi N. Naden and Michael R. Shirts and John D. Chodera author_emaillevi.naden@choderalab.org, michael.shirts@virginia.edu, john.chodera@choderalab.org data_files [('pymbar', ['pymbar/_pymbar.c'])] descriptionPython implementation of the multistate Bennett acceptance ratio (MBAR) method. download_url http://github.com/choderalab/pymbar ext_modules [] license MIT long_description Pymbar (https://simtk.org/home/pymbar) is a library that provides tools for optimally combining simulations from multiple thermodynamic states using maximum likelihood methods to compute free energies (normalization constants) and expectation values from all of the samples simultaneously. name pymbar package_dir {'pymbar': 'pymbar', 'pymbar.tests': 'pymbar/tests'} packages ['pymbar', 'pymbar.testsystems', 'pymbar.tests'] platforms ['Linux', 'Mac OS X', 'Windows'] requires ['numpy', 'scipy', 'pytest', 'numexpr'] url http://github.com/choderalab/pymbar version 3.0.5 zip_safe False running config I: pybuild base:311: python3.11 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:744: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) author Levi N. Naden and Michael R. Shirts and John D. Chodera author_emaillevi.naden@choderalab.org, michael.shirts@virginia.edu, john.chodera@choderalab.org data_files [('pymbar', ['pymbar/_pymbar.c'])] descriptionPython implementation of the multistate Bennett acceptance ratio (MBAR) method. download_url http://github.com/choderalab/pymbar ext_modules [] license MIT long_description Pymbar (https://simtk.org/home/pymbar) is a library that provides tools for optimally combining simulations from multiple thermodynamic states using maximum likelihood methods to compute free energies (normalization constants) and expectation values from all of the samples simultaneously. name pymbar package_dir {'pymbar': 'pymbar', 'pymbar.tests': 'pymbar/tests'} packages ['pymbar', 'pymbar.testsystems', 'pymbar.tests'] platforms ['Linux', 'Mac OS X', 'Windows'] requires ['numpy', 'scipy', 'pytest', 'numexpr'] url http://github.com/choderalab/pymbar version 3.0.5 zip_safe False running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.12 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:744: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) author Levi N. Naden and Michael R. Shirts and John D. Chodera author_emaillevi.naden@choderalab.org, michael.shirts@virginia.edu, john.chodera@choderalab.org data_files [('pymbar', ['pymbar/_pymbar.c'])] descriptionPython implementation of the multistate Bennett acceptance ratio (MBAR) method. download_url http://github.com/choderalab/pymbar ext_modules [] license MIT long_description Pymbar (https://simtk.org/home/pymbar) is a library that provides tools for optimally combining simulations from multiple thermodynamic states using maximum likelihood methods to compute free energies (normalization constants) and expectation values from all of the samples simultaneously. name pymbar package_dir {'pymbar': 'pymbar', 'pymbar.tests': 'pymbar/tests'} packages ['pymbar', 'pymbar.testsystems', 'pymbar.tests'] platforms ['Linux', 'Mac OS X', 'Windows'] requires ['numpy', 'scipy', 'pytest', 'numexpr'] url http://github.com/choderalab/pymbar version 3.0.5 zip_safe False running build running build_py creating /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar copying pymbar/version.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar copying pymbar/utils_for_testing.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar copying pymbar/utils.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar copying pymbar/timeseries.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar copying pymbar/old_mbar.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar copying pymbar/mbar_solvers.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar copying pymbar/mbar.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar copying pymbar/exp.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar copying pymbar/confidenceintervals.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar copying pymbar/bar.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar copying pymbar/__init__.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar creating /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems copying pymbar/testsystems/harmonic_oscillators.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems copying pymbar/testsystems/exponential_distributions.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems copying pymbar/testsystems/timeseries.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems copying pymbar/testsystems/gaussian_work.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems copying pymbar/testsystems/__init__.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems creating /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests copying pymbar/tests/test_mbar.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests copying pymbar/tests/test_utils.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests copying pymbar/tests/test_timeseries.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests copying pymbar/tests/test_mbar_solvers.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests copying pymbar/tests/test_covariance.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests copying pymbar/tests/test_bar.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests copying pymbar/tests/__init__.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:744: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) author Levi N. Naden and Michael R. Shirts and John D. Chodera author_emaillevi.naden@choderalab.org, michael.shirts@virginia.edu, john.chodera@choderalab.org data_files [('pymbar', ['pymbar/_pymbar.c'])] descriptionPython implementation of the multistate Bennett acceptance ratio (MBAR) method. download_url http://github.com/choderalab/pymbar ext_modules [] license MIT long_description Pymbar (https://simtk.org/home/pymbar) is a library that provides tools for optimally combining simulations from multiple thermodynamic states using maximum likelihood methods to compute free energies (normalization constants) and expectation values from all of the samples simultaneously. name pymbar package_dir {'pymbar': 'pymbar', 'pymbar.tests': 'pymbar/tests'} packages ['pymbar', 'pymbar.testsystems', 'pymbar.tests'] platforms ['Linux', 'Mac OS X', 'Windows'] requires ['numpy', 'scipy', 'pytest', 'numexpr'] url http://github.com/choderalab/pymbar version 3.0.5 zip_safe False running build running build_py creating /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar copying pymbar/version.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar copying pymbar/utils_for_testing.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar copying pymbar/utils.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar copying pymbar/timeseries.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar copying pymbar/old_mbar.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar copying pymbar/mbar_solvers.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar copying pymbar/mbar.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar copying pymbar/exp.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar copying pymbar/confidenceintervals.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar copying pymbar/bar.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar copying pymbar/__init__.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar creating /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems copying pymbar/testsystems/harmonic_oscillators.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems copying pymbar/testsystems/exponential_distributions.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems copying pymbar/testsystems/timeseries.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems copying pymbar/testsystems/gaussian_work.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems copying pymbar/testsystems/__init__.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems creating /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests copying pymbar/tests/test_mbar.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests copying pymbar/tests/test_utils.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests copying pymbar/tests/test_timeseries.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests copying pymbar/tests/test_mbar_solvers.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests copying pymbar/tests/test_covariance.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests copying pymbar/tests/test_bar.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests copying pymbar/tests/__init__.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/python-pymbar-3.1.0' dh_auto_test -- --test-pytest I: pybuild base:311: cd /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build; python3.12 -m pytest ============================= test session starts ============================== platform linux -- Python 3.12.3, pytest-7.4.4, pluggy-1.5.0 rootdir: /build/reproducible-path/python-pymbar-3.1.0 collected 37 items pymbar/tests/test_bar.py .. [ 5%] pymbar/tests/test_covariance.py ... [ 13%] pymbar/tests/test_mbar.py ................ [ 56%] pymbar/tests/test_mbar_solvers.py .... [ 67%] pymbar/tests/test_timeseries.py ..ss.ss.. [ 91%] pymbar/tests/test_utils.py ... [100%] =============================== warnings summary =============================== pymbar/utils.py:230 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/utils.py:230: SyntaxWarning: invalid escape sequence '\l' """Compute the log of a sum of exponentiated terms exp(a_n) in a numerically-stable manner. pymbar/utils.py:359 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/utils.py:359: SyntaxWarning: invalid escape sequence '\s' 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % pymbar/utils.py:368 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/utils.py:368: SyntaxWarning: invalid escape sequence '\s' 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % pymbar/testsystems/gaussian_work.py:5 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems/gaussian_work.py:5: SyntaxWarning: invalid escape sequence '\e' """Generate samples from forward and reverse Gaussian work distributions. pymbar/mbar.py:381 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:381: SyntaxWarning: invalid escape sequence '\s' """ pymbar/mbar.py:442 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:442: SyntaxWarning: invalid escape sequence '\i' """ pymbar/mbar.py:865 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:865: SyntaxWarning: invalid escape sequence '\s' """ pymbar/mbar.py:1436 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:1436: SyntaxWarning: invalid escape sequence '\s' """ pymbar/mbar.py:1866 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:1866: SyntaxWarning: invalid escape sequence '\l' """ pymbar/bar.py:56 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/bar.py:56: SyntaxWarning: invalid escape sequence '\s' """A function that when zeroed is equivalent to the solution of pymbar/old_mbar.py:957 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/old_mbar.py:957: SyntaxWarning: invalid escape sequence '\i' """Compute estimate of overlap matrix between the states. pymbar/old_mbar.py:1376 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/old_mbar.py:1376: SyntaxWarning: invalid escape sequence '\s' """Compute the free energy of occupying a number of bins. pymbar/old_mbar.py:1864 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/old_mbar.py:1864: SyntaxWarning: invalid escape sequence '\s' 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % pymbar/old_mbar.py:1873 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/old_mbar.py:1873: SyntaxWarning: invalid escape sequence '\s' 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % pymbar/old_mbar.py:2078 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/old_mbar.py:2078: SyntaxWarning: invalid escape sequence '\l' """ pymbar/utils_for_testing.py:29 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/utils_for_testing.py:29: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html from pkg_resources import resource_filename .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_bar.py: 4 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py: 9 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py: 8 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar_solvers.py: 11 warnings /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:561: 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. f_i = np.matrix(self.f_k) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_bar.py: 4 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py: 3 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py: 29 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar_solvers.py: 11 warnings /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:1772: 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. Ndiag = np.matrix(np.diag(N_k), dtype=np.float64) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_bar.py: 4 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py: 3 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py: 29 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar_solvers.py: 11 warnings /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:1773: 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. W = np.matrix(W, dtype=np.float64) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_bar.py: 40 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py: 78 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py: 287 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar_solvers.py: 99 warnings /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) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_bar.py: 4 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py: 3 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py: 29 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar_solvers.py: 11 warnings /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:1783: 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. Sigma = np.matrix(np.diag(np.sqrt(S2))) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_bar.py: 4 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py: 3 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py: 29 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar_solvers.py: 11 warnings /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:1784: 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. V = np.matrix(V) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_bar.py: 4 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py: 9 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py: 23 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar_solvers.py: 11 warnings /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:1636: 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. diag = np.matrix(cov.diagonal()) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_bar.py::test_bar_computeOverlap .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_bar.py::test_bar_computeOverlap /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/bar.py:527: FutureWarning: Warning: This API is experimental and subject to change in future releases warnings.warn("Warning: This API is experimental and subject to change in future releases", FutureWarning) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_bar.py::test_bar_computeOverlap .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_bar.py::test_bar_computeOverlap .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_bar.py::test_bar_computeOverlap .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_bar.py::test_bar_computeOverlap .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeOverlap .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeOverlap .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeOverlap .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeOverlap /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:485: 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. W = np.matrix(self.getWeights(), np.float64) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:1753: 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. Ndiag = np.matrix(np.diag(N_k), dtype=np.float64) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:1754: 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. W = np.matrix(W, dtype=np.float64) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:1759: 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. Sigma = np.matrix(np.diag(S)) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:1760: 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. V = np.matrix(Vt).T .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/old_mbar.py:385: 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. f_i = np.matrix(self.f_k) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/old_mbar.py:1925: 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. Ndiag = np.matrix(np.diag(N_k), dtype=np.float64) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/old_mbar.py:1926: 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. W = np.matrix(W, dtype=np.float64) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/old_mbar.py:1931: 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. Sigma = np.matrix(np.diag(S)) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/old_mbar.py:1932: 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. V = np.matrix(Vt).T .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/old_mbar.py:1784: 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. Ainv = np.matrix(np.zeros([M, M], dtype=np.float64)) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py: 560 warnings /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:579: 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. diffm[:,:,b] = np.matrix(self.f_k_boots[b,:]) - np.matrix(self.f_k_boots[b,:]).transpose() .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeExpectations_position_differences .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeExpectations_position_differences /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:1088: 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. A_im = np.matrix(inner_results['observables']) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py: 16 warnings /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py:23: 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. xa_ij = np.array(np.matrix(xa) - np.matrix(xa).transpose()) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:1377: 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. Adiag = np.matrix(np.zeros([3*K,3*K],dtype=np.float64)) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:1382: 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. f_k = np.matrix(inner_results['f']) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:1389: 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. u_k = np.matrix(inner_results['observables']) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py:253: 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. fa_ij = np.array(np.matrix(fa) - np.matrix(fa).transpose()) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py:254: 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. ua_ij = np.array(np.matrix(ua) - np.matrix(ua).transpose()) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py:255: 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. sa_ij = np.array(np.matrix(sa) - np.matrix(sa).transpose()) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeOverlap /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py:301: 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. reference_matrix = np.matrix((1.0/d)*np.ones([d,d])) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:1280: 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. f_k = np.matrix(inner_results['f']) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========== 33 passed, 4 skipped, 1446 warnings in 164.93s (0:02:44) =========== I: pybuild base:311: cd /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build; python3.11 -m pytest ============================= test session starts ============================== platform linux -- Python 3.11.9, pytest-7.4.4, pluggy-1.5.0 rootdir: /build/reproducible-path/python-pymbar-3.1.0 collected 37 items pymbar/tests/test_bar.py .. [ 5%] pymbar/tests/test_covariance.py ... [ 13%] pymbar/tests/test_mbar.py ................ [ 56%] pymbar/tests/test_mbar_solvers.py .... [ 67%] pymbar/tests/test_timeseries.py ..ss.ss.. [ 91%] pymbar/tests/test_utils.py ... [100%] =============================== warnings summary =============================== pymbar/utils.py:230 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/utils.py:230: DeprecationWarning: invalid escape sequence '\l' """Compute the log of a sum of exponentiated terms exp(a_n) in a numerically-stable manner. pymbar/utils.py:359 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/utils.py:359: DeprecationWarning: invalid escape sequence '\s' 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % pymbar/utils.py:368 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/utils.py:368: DeprecationWarning: invalid escape sequence '\s' 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % pymbar/testsystems/gaussian_work.py:5 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems/gaussian_work.py:5: DeprecationWarning: invalid escape sequence '\e' """Generate samples from forward and reverse Gaussian work distributions. pymbar/mbar.py:381 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:381: DeprecationWarning: invalid escape sequence '\s' """ pymbar/mbar.py:442 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:442: DeprecationWarning: invalid escape sequence '\i' """ pymbar/mbar.py:865 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:865: DeprecationWarning: invalid escape sequence '\s' """ pymbar/mbar.py:1436 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:1436: DeprecationWarning: invalid escape sequence '\s' """ pymbar/mbar.py:1866 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:1866: DeprecationWarning: invalid escape sequence '\l' """ pymbar/bar.py:56 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/bar.py:56: DeprecationWarning: invalid escape sequence '\s' """A function that when zeroed is equivalent to the solution of pymbar/old_mbar.py:957 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/old_mbar.py:957: DeprecationWarning: invalid escape sequence '\i' """Compute estimate of overlap matrix between the states. pymbar/old_mbar.py:1376 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/old_mbar.py:1376: DeprecationWarning: invalid escape sequence '\s' """Compute the free energy of occupying a number of bins. pymbar/old_mbar.py:1864 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/old_mbar.py:1864: DeprecationWarning: invalid escape sequence '\s' 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % pymbar/old_mbar.py:1873 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/old_mbar.py:1873: DeprecationWarning: invalid escape sequence '\s' 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % pymbar/old_mbar.py:2078 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/old_mbar.py:2078: DeprecationWarning: invalid escape sequence '\l' """ pymbar/utils_for_testing.py:29 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/utils_for_testing.py:29: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html from pkg_resources import resource_filename .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_bar.py: 4 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py: 9 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py: 8 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar_solvers.py: 11 warnings /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:561: 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. f_i = np.matrix(self.f_k) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_bar.py: 4 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py: 3 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py: 29 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar_solvers.py: 11 warnings /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:1772: 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. Ndiag = np.matrix(np.diag(N_k), dtype=np.float64) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_bar.py: 4 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py: 3 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py: 29 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar_solvers.py: 11 warnings /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:1773: 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. W = np.matrix(W, dtype=np.float64) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_bar.py: 40 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py: 78 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py: 287 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar_solvers.py: 99 warnings /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) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_bar.py: 4 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py: 3 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py: 29 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar_solvers.py: 11 warnings /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:1783: 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. Sigma = np.matrix(np.diag(np.sqrt(S2))) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_bar.py: 4 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py: 3 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py: 29 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar_solvers.py: 11 warnings /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:1784: 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. V = np.matrix(V) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_bar.py: 4 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py: 9 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py: 23 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar_solvers.py: 11 warnings /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:1636: 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. diag = np.matrix(cov.diagonal()) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_bar.py::test_bar_computeOverlap .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_bar.py::test_bar_computeOverlap /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/bar.py:527: FutureWarning: Warning: This API is experimental and subject to change in future releases warnings.warn("Warning: This API is experimental and subject to change in future releases", FutureWarning) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_bar.py::test_bar_computeOverlap .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_bar.py::test_bar_computeOverlap .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_bar.py::test_bar_computeOverlap .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_bar.py::test_bar_computeOverlap .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeOverlap .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeOverlap .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeOverlap .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeOverlap /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:485: 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. W = np.matrix(self.getWeights(), np.float64) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:1753: 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. Ndiag = np.matrix(np.diag(N_k), dtype=np.float64) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:1754: 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. W = np.matrix(W, dtype=np.float64) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:1759: 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. Sigma = np.matrix(np.diag(S)) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:1760: 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. V = np.matrix(Vt).T .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/old_mbar.py:385: 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. f_i = np.matrix(self.f_k) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/old_mbar.py:1925: 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. Ndiag = np.matrix(np.diag(N_k), dtype=np.float64) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/old_mbar.py:1926: 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. W = np.matrix(W, dtype=np.float64) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/old_mbar.py:1931: 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. Sigma = np.matrix(np.diag(S)) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/old_mbar.py:1932: 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. V = np.matrix(Vt).T .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_100x100_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_oscillators .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py::test_200x50_exponentials /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/old_mbar.py:1784: 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. Ainv = np.matrix(np.zeros([M, M], dtype=np.float64)) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py: 560 warnings /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:579: 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. diffm[:,:,b] = np.matrix(self.f_k_boots[b,:]) - np.matrix(self.f_k_boots[b,:]).transpose() .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeExpectations_position_differences .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeExpectations_position_differences /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:1088: 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. A_im = np.matrix(inner_results['observables']) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py: 16 warnings /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py:23: 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. xa_ij = np.array(np.matrix(xa) - np.matrix(xa).transpose()) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:1377: 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. Adiag = np.matrix(np.zeros([3*K,3*K],dtype=np.float64)) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:1382: 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. f_k = np.matrix(inner_results['f']) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:1389: 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. u_k = np.matrix(inner_results['observables']) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py:253: 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. fa_ij = np.array(np.matrix(fa) - np.matrix(fa).transpose()) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py:254: 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. ua_ij = np.array(np.matrix(ua) - np.matrix(ua).transpose()) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py:255: 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. sa_ij = np.array(np.matrix(sa) - np.matrix(sa).transpose()) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computeOverlap /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py:301: 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. reference_matrix = np.matrix((1.0/d)*np.ones([d,d])) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:1280: 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. f_k = np.matrix(inner_results['f']) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========== 33 passed, 4 skipped, 1446 warnings in 170.33s (0:02:50) =========== make[1]: Leaving directory '/build/reproducible-path/python-pymbar-3.1.0' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/python-pymbar-3.1.0' dh_auto_install I: pybuild base:311: /usr/bin/python3.12 setup.py install --root /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar /usr/lib/python3/dist-packages/setuptools/dist.py:744: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) author Levi N. Naden and Michael R. Shirts and John D. Chodera author_emaillevi.naden@choderalab.org, michael.shirts@virginia.edu, john.chodera@choderalab.org data_files [('pymbar', ['pymbar/_pymbar.c'])] descriptionPython implementation of the multistate Bennett acceptance ratio (MBAR) method. download_url http://github.com/choderalab/pymbar ext_modules [] license MIT long_description Pymbar (https://simtk.org/home/pymbar) is a library that provides tools for optimally combining simulations from multiple thermodynamic states using maximum likelihood methods to compute free energies (normalization constants) and expectation values from all of the samples simultaneously. name pymbar package_dir {'pymbar': 'pymbar', 'pymbar.tests': 'pymbar/tests'} packages ['pymbar', 'pymbar.testsystems', 'pymbar.tests'] platforms ['Linux', 'Mac OS X', 'Windows'] requires ['numpy', 'scipy', 'pytest', 'numexpr'] url http://github.com/choderalab/pymbar version 3.0.5 zip_safe False running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py copying pymbar/version.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar running install_lib creating /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr creating /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib creating /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12 creating /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages creating /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/version.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar creating /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/__pycache__/utils_for_testing.cpython-312.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/__pycache__/old_mbar.cpython-312.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/__pycache__/exp.cpython-312.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/__pycache__/bar.cpython-312.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/__pycache__/mbar_solvers.cpython-312.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/__pycache__/mbar.cpython-312.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/__pycache__/version.cpython-312.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/__pycache__/confidenceintervals.cpython-312.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/__pycache__/utils.cpython-312.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/__pycache__/timeseries.cpython-312.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/__pycache__ creating /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests creating /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests/__pycache__/test_utils.cpython-312-pytest-7.4.4.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests/__pycache__/test_timeseries.cpython-312-pytest-7.4.4.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests/__pycache__/test_mbar_solvers.cpython-312-pytest-7.4.4.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests/__pycache__/test_mbar.cpython-312-pytest-7.4.4.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests/__pycache__/test_covariance.cpython-312-pytest-7.4.4.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests/__pycache__/test_bar.cpython-312-pytest-7.4.4.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests/__init__.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_bar.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar_solvers.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_timeseries.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_utils.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests creating /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems creating /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems/__pycache__/gaussian_work.cpython-312.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems/__pycache__/timeseries.cpython-312.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems/__pycache__/exponential_distributions.cpython-312.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems/__pycache__/harmonic_oscillators.cpython-312.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems/__init__.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems/gaussian_work.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems/timeseries.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems/exponential_distributions.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems/harmonic_oscillators.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/__init__.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/bar.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/confidenceintervals.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/exp.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar_solvers.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/old_mbar.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/timeseries.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/utils.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/utils_for_testing.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/version.py to version.cpython-312.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests/test_bar.py to test_bar.cpython-312.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests/test_covariance.py to test_covariance.cpython-312.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests/test_mbar_solvers.py to test_mbar_solvers.cpython-312.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests/test_timeseries.py to test_timeseries.cpython-312.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests/test_utils.py to test_utils.cpython-312.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests/test_mbar.py to test_mbar.cpython-312.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems/gaussian_work.py to gaussian_work.cpython-312.pyc /usr/lib/python3.12/dist-packages/pymbar/testsystems/gaussian_work.py:5: SyntaxWarning: invalid escape sequence '\e' byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems/timeseries.py to timeseries.cpython-312.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems/exponential_distributions.py to exponential_distributions.cpython-312.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems/harmonic_oscillators.py to harmonic_oscillators.cpython-312.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/bar.py to bar.cpython-312.pyc /usr/lib/python3.12/dist-packages/pymbar/bar.py:56: SyntaxWarning: invalid escape sequence '\s' byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/confidenceintervals.py to confidenceintervals.cpython-312.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/exp.py to exp.cpython-312.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/mbar.py to mbar.cpython-312.pyc /usr/lib/python3.12/dist-packages/pymbar/mbar.py:381: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.12/dist-packages/pymbar/mbar.py:442: SyntaxWarning: invalid escape sequence '\i' /usr/lib/python3.12/dist-packages/pymbar/mbar.py:865: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.12/dist-packages/pymbar/mbar.py:1436: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.12/dist-packages/pymbar/mbar.py:1866: SyntaxWarning: invalid escape sequence '\l' byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/mbar_solvers.py to mbar_solvers.cpython-312.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/old_mbar.py to old_mbar.cpython-312.pyc /usr/lib/python3.12/dist-packages/pymbar/old_mbar.py:957: SyntaxWarning: invalid escape sequence '\i' /usr/lib/python3.12/dist-packages/pymbar/old_mbar.py:1376: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.12/dist-packages/pymbar/old_mbar.py:1864: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.12/dist-packages/pymbar/old_mbar.py:1873: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.12/dist-packages/pymbar/old_mbar.py:2078: SyntaxWarning: invalid escape sequence '\l' byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/timeseries.py to timeseries.cpython-312.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/utils.py to utils.cpython-312.pyc /usr/lib/python3.12/dist-packages/pymbar/utils.py:230: SyntaxWarning: invalid escape sequence '\l' /usr/lib/python3.12/dist-packages/pymbar/utils.py:359: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.12/dist-packages/pymbar/utils.py:368: SyntaxWarning: invalid escape sequence '\s' byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/utils_for_testing.py to utils_for_testing.cpython-312.pyc running install_data creating /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/pymbar copying pymbar/_pymbar.c -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/pymbar running install_egg_info running egg_info creating pymbar.egg-info writing pymbar.egg-info/PKG-INFO writing dependency_links to pymbar.egg-info/dependency_links.txt writing top-level names to pymbar.egg-info/top_level.txt writing manifest file 'pymbar.egg-info/SOURCES.txt' reading manifest file 'pymbar.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'pymbar.egg-info/SOURCES.txt' Copying pymbar.egg-info to /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar-3.0.5.egg-info Skipping SOURCES.txt running install_scripts I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar /usr/lib/python3/dist-packages/setuptools/dist.py:744: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) author Levi N. Naden and Michael R. Shirts and John D. Chodera author_emaillevi.naden@choderalab.org, michael.shirts@virginia.edu, john.chodera@choderalab.org data_files [('pymbar', ['pymbar/_pymbar.c'])] descriptionPython implementation of the multistate Bennett acceptance ratio (MBAR) method. download_url http://github.com/choderalab/pymbar ext_modules [] license MIT long_description Pymbar (https://simtk.org/home/pymbar) is a library that provides tools for optimally combining simulations from multiple thermodynamic states using maximum likelihood methods to compute free energies (normalization constants) and expectation values from all of the samples simultaneously. name pymbar package_dir {'pymbar': 'pymbar', 'pymbar.tests': 'pymbar/tests'} packages ['pymbar', 'pymbar.testsystems', 'pymbar.tests'] platforms ['Linux', 'Mac OS X', 'Windows'] requires ['numpy', 'scipy', 'pytest', 'numexpr'] url http://github.com/choderalab/pymbar version 3.0.5 zip_safe False running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py copying pymbar/version.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar running install_lib creating /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11 creating /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages creating /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/version.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar creating /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/utils_for_testing.cpython-311.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/old_mbar.cpython-311.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/exp.cpython-311.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/bar.cpython-311.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/mbar_solvers.cpython-311.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/mbar.cpython-311.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/version.cpython-311.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/confidenceintervals.cpython-311.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/utils.cpython-311.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/timeseries.cpython-311.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ creating /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests creating /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/__pycache__/test_utils.cpython-311-pytest-7.4.4.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/__pycache__/test_timeseries.cpython-311-pytest-7.4.4.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/__pycache__/test_mbar_solvers.cpython-311-pytest-7.4.4.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/__pycache__/test_mbar.cpython-311-pytest-7.4.4.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/__pycache__/test_covariance.cpython-311-pytest-7.4.4.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/__pycache__/test_bar.cpython-311-pytest-7.4.4.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/__init__.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_bar.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar_solvers.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_timeseries.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_utils.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests creating /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems creating /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems/__pycache__/gaussian_work.cpython-311.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems/__pycache__/timeseries.cpython-311.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems/__pycache__/exponential_distributions.cpython-311.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems/__pycache__/harmonic_oscillators.cpython-311.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems/__init__.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems/gaussian_work.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems/timeseries.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems/exponential_distributions.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems/harmonic_oscillators.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__init__.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/bar.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/confidenceintervals.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/exp.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar_solvers.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/old_mbar.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/timeseries.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/utils.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/utils_for_testing.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/version.py to version.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/test_bar.py to test_bar.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/test_covariance.py to test_covariance.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/test_mbar_solvers.py to test_mbar_solvers.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/test_timeseries.py to test_timeseries.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/test_utils.py to test_utils.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/test_mbar.py to test_mbar.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems/gaussian_work.py to gaussian_work.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems/timeseries.py to timeseries.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems/exponential_distributions.py to exponential_distributions.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems/harmonic_oscillators.py to harmonic_oscillators.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/bar.py to bar.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/confidenceintervals.py to confidenceintervals.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/exp.py to exp.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/mbar.py to mbar.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/mbar_solvers.py to mbar_solvers.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/old_mbar.py to old_mbar.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/timeseries.py to timeseries.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/utils.py to utils.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/utils_for_testing.py to utils_for_testing.cpython-311.pyc running install_data copying pymbar/_pymbar.c -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/pymbar running install_egg_info running egg_info writing pymbar.egg-info/PKG-INFO writing dependency_links to pymbar.egg-info/dependency_links.txt writing top-level names to pymbar.egg-info/top_level.txt reading manifest file 'pymbar.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'pymbar.egg-info/SOURCES.txt' Copying pymbar.egg-info to /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar-3.0.5.egg-info Skipping SOURCES.txt running install_scripts rm -r debian/python3-pymbar/usr/pymbar make[1]: Leaving directory '/build/reproducible-path/python-pymbar-3.1.0' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-pymbar' in '../python3-pymbar_3.1.0-4_all.deb'. dpkg-genbuildinfo --build=binary -O../python-pymbar_3.1.0-4_arm64.buildinfo dpkg-genchanges --build=binary -O../python-pymbar_3.1.0-4_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from python-pymbar-3.1.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration 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/1538591 and its subdirectories I: Current time: Mon May 6 02:47:34 -12 2024 I: pbuilder-time-stamp: 1715006854 Mon May 6 14:47:36 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Mon May 6 14:47:36 UTC 2024 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Mon May 6 14:54:35 UTC 2024 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Mon May 6 14:54:36 UTC 2024 I: python-pymbar_3.1.0-4_arm64.changes: Format: 1.8 Date: Wed, 01 Feb 2023 21:30:52 +0100 Source: python-pymbar Binary: python3-pymbar Architecture: all Version: 3.1.0-4 Distribution: unstable Urgency: medium Maintainer: Debian Science Maintainers Changed-By: Étienne Mollier Description: python3-pymbar - Python implementation of the multistate Bennett acceptance ratio Closes: 1027217 Changes: python-pymbar (3.1.0-4) unstable; urgency=medium . * Team upload. . [ Bas Couwenberg ] * Add gbp.conf to use pristine-tar & --source-only-changes by default. * Add patch to fix test failure with Numpy 1.24. (closes: #1027217) . [ Étienne Mollier ] * Update standards version to 4.6.2, no changes needed. Checksums-Sha1: 4c857815ad363efa4909998a6a80b08d5c913f31 5960 python-pymbar_3.1.0-4_arm64.buildinfo 03c4eafef9306ac4b893e7b51a50bfc3ed3847fd 66816 python3-pymbar_3.1.0-4_all.deb Checksums-Sha256: a5f566c051af0682b359efc5b52f2f4447f121577ce8b6a8e84f097ed4452304 5960 python-pymbar_3.1.0-4_arm64.buildinfo bdfd4d0d1a33667a72c15bf1b0376988eb4176b90eb8fd217664a6b7fd69856a 66816 python3-pymbar_3.1.0-4_all.deb Files: 79080ffe989be7fbec5526873a64b5e8 5960 science optional python-pymbar_3.1.0-4_arm64.buildinfo 6cc43edee9830a30122d13c35aa4a1a7 66816 science optional python3-pymbar_3.1.0-4_all.deb Mon May 6 14:54:37 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_24-33613.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.dVlYlJaw/python-pymbar_3.1.0-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.dVlYlJaw/python-pymbar_3.1.0-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.dVlYlJaw/python-pymbar_3.1.0-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.dVlYlJaw/b1/python-pymbar_3.1.0-4_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.dVlYlJaw/b2/python-pymbar_3.1.0-4_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.383s) 0.383s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.017s) 0.017s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 767ms CPU time consumed: 767ms Mon May 6 14:54:38 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Mon May 6 14:54:38 UTC 2024 I: python-pymbar from trixie built successfully and reproducibly on arm64. Mon May 6 14:54:40 UTC 2024 I: Submitting .buildinfo files to external archives: Mon May 6 14:54:40 UTC 2024 I: Submitting 8.0K b1/python-pymbar_3.1.0-4_arm64.buildinfo.asc Mon May 6 14:54:41 UTC 2024 I: Submitting 8.0K b2/python-pymbar_3.1.0-4_arm64.buildinfo.asc Mon May 6 14:54:41 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon May 6 14:54:41 UTC 2024 I: Done submitting .buildinfo files. Mon May 6 14:54:41 UTC 2024 I: Removing signed python-pymbar_3.1.0-4_arm64.buildinfo.asc files: removed './b1/python-pymbar_3.1.0-4_arm64.buildinfo.asc' removed './b2/python-pymbar_3.1.0-4_arm64.buildinfo.asc'