Fri Apr 5 13:22:42 UTC 2024 I: starting to build python-pymbar/trixie/i386 on jenkins on '2024-04-05 13:22' Fri Apr 5 13:22:42 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_5/14664/console.log Fri Apr 5 13:22:42 UTC 2024 I: Downloading source for trixie/python-pymbar=3.1.0-4 --2024-04-05 13:22:43-- http://deb.debian.org/debian/pool/main/p/python-pymbar/python-pymbar_3.1.0-4.dsc Connecting to 78.137.99.97:3128... 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% 315M=0s 2024-04-05 13:22:43 (315 MB/s) - ‘python-pymbar_3.1.0-4.dsc’ saved [2363/2363] Fri Apr 5 13:22:43 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----- Fri Apr 5 13:22:43 UTC 2024 I: Checking whether the package is not for us Fri Apr 5 13:22:43 UTC 2024 I: Starting 1st build on remote node ionos12-i386.debian.net. Fri Apr 5 13:22:43 UTC 2024 I: Preparing to do remote build '1' on ionos12-i386.debian.net. Fri Apr 5 14:04:25 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Apr 5 01:22:45 -12 2024 I: pbuilder-time-stamp: 1712323365 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: using eatmydata during job 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/30148/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='ac7ac6aae8d24c5daa9b5a9413a40144' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='30148' 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.RepOT3Zc/pbuilderrc_t1bm --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.RepOT3Zc/b1 --logfile b1/build.log python-pymbar_3.1.0-4.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos12-i386 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 4 11:26 /bin -> usr/bin I: user script /srv/workspace/pbuilder/30148/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: i386 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 ... 19876 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} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libicu72{a} liblapack3{a} liblbfgsb0{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8{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 59.2 MB of archives. After unpacking 272 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 libpython3.11-minimal i386 3.11.8-1 [817 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.5.0-2+b2 [104 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 python3.11-minimal i386 3.11.8-1 [2087 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.11.6-1 [26.2 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 tzdata all 2024a-1 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-3 [69.1 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 libreadline8 i386 8.2-3+b1 [171 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 libpython3.11-stdlib i386 3.11.8-1 [1821 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 python3.11 i386 3.11.8-1 [597 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.11.6-1 [9224 B] Get: 13 http://deb.debian.org/debian trixie/main i386 python3 i386 3.11.6-1 [26.2 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 libpython3.12-minimal i386 3.12.2-1 [807 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 python3.12-minimal i386 3.12.2-1 [2244 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-2+b1 [314 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 libmagic1 i386 1:5.45-2+b1 [114 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-2+b1 [43.0 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-3 [1195 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.39.3-6 [93.3 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.7-1+b2 [39.6 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 man-db i386 2.12.0-3 [1413 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 autoconf all 2.71-3 [332 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 autopoint all 0.21-14 [496 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 38 http://deb.debian.org/debian trixie/main i386 libelf1 i386 0.190-1+b1 [182 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1 [118 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.9.14+dfsg-1.3+b2 [727 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 debhelper all 13.15.3 [901 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 python3-lib2to3 all 3.11.5-1 [77.5 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 python3-distutils all 3.11.5-1 [131 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 python3-setuptools all 68.1.2-2 [468 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 dh-python all 6.20240401 [107 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 libblas3 i386 3.12.0-3 [140 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14-20240201-3 [733 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 liblapack3 i386 3.12.0-3 [2167 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 liblbfgsb0 i386 3.0+dfsg.4-1+b1 [29.1 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 libpython3.12-stdlib i386 3.12.2-1 [1927 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 python3.12 i386 3.12.2-1 [653 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 python3-all i386 3.11.6-1 [1060 B] Get: 58 http://deb.debian.org/debian trixie/main i386 python3-decorator all 5.1.1-5 [15.1 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 python3-iniconfig all 1.1.1-2 [6396 B] Get: 60 http://deb.debian.org/debian trixie/main i386 python3-numpy i386 1:1.24.2-2 [4879 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 python3-packaging all 23.2-1 [44.8 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 python3-pluggy all 1.4.0-1 [26.2 kB] Get: 63 http://deb.debian.org/debian trixie/main i386 python3-pytest all 7.4.4-3 [239 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 python3-scipy i386 1.11.4-6 [19.0 MB] Get: 65 http://deb.debian.org/debian trixie/main i386 python3-six all 1.16.0-6 [16.3 kB] Fetched 59.2 MB in 1s (59.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:i386. (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 ... 19876 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.8-1_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.8-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.5.0-2+b2_i386.deb ... Unpacking libexpat1:i386 (2.5.0-2+b2) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.8-1_i386.deb ... Unpacking python3.11-minimal (3.11.8-1) ... Setting up libpython3.11-minimal:i386 (3.11.8-1) ... Setting up libexpat1:i386 (2.5.0-2+b2) ... Setting up python3.11-minimal (3.11.8-1) ... 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 ... 20193 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.6-1_i386.deb ... Unpacking python3-minimal (3.11.6-1) ... 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-1_all.deb ... Unpacking tzdata (2024a-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-3_all.deb ... Unpacking readline-common (8.2-3) ... Selecting previously unselected package libreadline8:i386. Preparing to unpack .../5-libreadline8_8.2-3+b1_i386.deb ... Unpacking libreadline8:i386 (8.2-3+b1) ... Selecting previously unselected package libpython3.11-stdlib:i386. Preparing to unpack .../6-libpython3.11-stdlib_3.11.8-1_i386.deb ... Unpacking libpython3.11-stdlib:i386 (3.11.8-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.8-1_i386.deb ... Unpacking python3.11 (3.11.8-1) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../8-libpython3-stdlib_3.11.6-1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.11.6-1) ... Setting up python3-minimal (3.11.6-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21181 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.6-1_i386.deb ... Unpacking python3 (3.11.6-1) ... Selecting previously unselected package libpython3.12-minimal:i386. Preparing to unpack .../01-libpython3.12-minimal_3.12.2-1_i386.deb ... Unpacking libpython3.12-minimal:i386 (3.12.2-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../02-python3.12-minimal_3.12.2-1_i386.deb ... Unpacking python3.12-minimal (3.12.2-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.45-2+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../05-libmagic1_1%3a5.45-2+b1_i386.deb ... Unpacking libmagic1:i386 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.45-2+b1_i386.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.21-14+b1_i386.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../08-libuchardet0_0.0.8-1+b1_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.23.0-3_i386.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.39.3-6_i386.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../11-libpipeline1_1.5.7-1+b2_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-1+b2) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.12.0-3_i386.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../18-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../19-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../20-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../21-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../22-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../23-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../24-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../25-libelf1_0.190-1+b1_i386.deb ... Unpacking libelf1:i386 (0.190-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../26-dwz_0.15-1_i386.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../27-libicu72_72.1-4+b1_i386.deb ... Unpacking libicu72:i386 (72.1-4+b1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../28-libxml2_2.9.14+dfsg-1.3+b2_i386.deb ... Unpacking libxml2:i386 (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../29-gettext_0.21-14+b1_i386.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../30-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../31-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../32-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../33-python3-pkg-resources_68.1.2-2_all.deb ... Unpacking python3-pkg-resources (68.1.2-2) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../34-python3-lib2to3_3.11.5-1_all.deb ... Unpacking python3-lib2to3 (3.11.5-1) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../35-python3-distutils_3.11.5-1_all.deb ... Unpacking python3-distutils (3.11.5-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../36-python3-setuptools_68.1.2-2_all.deb ... Unpacking python3-setuptools (68.1.2-2) ... Selecting previously unselected package dh-python. Preparing to unpack .../37-dh-python_6.20240401_all.deb ... Unpacking dh-python (6.20240401) ... Selecting previously unselected package libblas3:i386. Preparing to unpack .../38-libblas3_3.12.0-3_i386.deb ... Unpacking libblas3:i386 (3.12.0-3) ... Selecting previously unselected package libgfortran5:i386. Preparing to unpack .../39-libgfortran5_14-20240201-3_i386.deb ... Unpacking libgfortran5:i386 (14-20240201-3) ... Selecting previously unselected package liblapack3:i386. Preparing to unpack .../40-liblapack3_3.12.0-3_i386.deb ... Unpacking liblapack3:i386 (3.12.0-3) ... Selecting previously unselected package liblbfgsb0:i386. Preparing to unpack .../41-liblbfgsb0_3.0+dfsg.4-1+b1_i386.deb ... Unpacking liblbfgsb0:i386 (3.0+dfsg.4-1+b1) ... Selecting previously unselected package libpython3.12-stdlib:i386. Preparing to unpack .../42-libpython3.12-stdlib_3.12.2-1_i386.deb ... Unpacking libpython3.12-stdlib:i386 (3.12.2-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../43-python3.12_3.12.2-1_i386.deb ... Unpacking python3.12 (3.12.2-1) ... Selecting previously unselected package python3-all. Preparing to unpack .../44-python3-all_3.11.6-1_i386.deb ... Unpacking python3-all (3.11.6-1) ... Selecting previously unselected package python3-decorator. Preparing to unpack .../45-python3-decorator_5.1.1-5_all.deb ... Unpacking python3-decorator (5.1.1-5) ... Selecting previously unselected package python3-iniconfig. Preparing to unpack .../46-python3-iniconfig_1.1.1-2_all.deb ... Unpacking python3-iniconfig (1.1.1-2) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../47-python3-numpy_1%3a1.24.2-2_i386.deb ... Unpacking python3-numpy (1:1.24.2-2) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../48-python3-packaging_23.2-1_all.deb ... Unpacking python3-packaging (23.2-1) ... Selecting previously unselected package python3-pluggy. Preparing to unpack .../49-python3-pluggy_1.4.0-1_all.deb ... Unpacking python3-pluggy (1.4.0-1) ... Selecting previously unselected package python3-pytest. Preparing to unpack .../50-python3-pytest_7.4.4-3_all.deb ... Unpacking python3-pytest (7.4.4-3) ... Selecting previously unselected package python3-scipy. Preparing to unpack .../51-python3-scipy_1.11.4-6_i386.deb ... Unpacking python3-scipy (1.11.4-6) ... Selecting previously unselected package python3-six. Preparing to unpack .../52-python3-six_1.16.0-6_all.deb ... Unpacking python3-six (1.16.0-6) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:i386 (1.5.7-1+b2) ... Setting up libicu72:i386 (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... Setting up libmagic-mgc (1:5.45-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libpython3.12-minimal:i386 (3.12.2-1) ... Setting up libmagic1:i386 (1:5.45-2+b1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-2+b1) ... Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Apr 5 13:23:18 UTC 2024. Universal Time is now: Fri Apr 5 13:23:18 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:i386 (3.12.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up autopoint (0.21-14) ... Setting up libgfortran5:i386 (14-20240201-3) ... Setting up autoconf (2.71-3) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:i386 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up libelf1:i386 (0.190-1+b1) ... Setting up readline-common (8.2-3) ... Setting up libxml2:i386 (2.9.14+dfsg-1.3+b2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.12-minimal (3.12.2-1) ... Setting up liblapack3:i386 (3.12.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libreadline8:i386 (8.2-3+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up liblbfgsb0:i386 (3.0+dfsg.4-1+b1) ... Setting up libpython3.12-stdlib:i386 (3.12.2-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:i386 (3.11.8-1) ... Setting up python3.12 (3.12.2-1) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3-stdlib:i386 (3.11.6-1) ... Setting up python3.11 (3.11.8-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.6-1) ... Setting up python3-six (1.16.0-6) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (23.2-1) ... Setting up python3-pluggy (1.4.0-1) ... Setting up python3-lib2to3 (3.11.5-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.11.5-1) ... python3.12: can't get files for byte-compilation Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-pytest (7.4.4-3) ... Setting up python3-all (3.11.6-1) ... Setting up python3-numpy (1:1.24.2-2) ... Setting up dh-python (6.20240401) ... Setting up python3-scipy (1.11.4-6) ... Processing triggers for libc-bin (2.37-15) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/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 i386 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-i686' 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-i686' 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/bar.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/utils_for_testing.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/timeseries.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/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/version.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 copying pymbar/utils.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/gaussian_work.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/exponential_distributions.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_covariance.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_timeseries.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/test_utils.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 copying pymbar/tests/test_mbar.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/bar.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/utils_for_testing.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/timeseries.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/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/version.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 copying pymbar/utils.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/gaussian_work.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/exponential_distributions.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_covariance.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_timeseries.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/test_utils.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 copying pymbar/tests/test_mbar.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 3.12.2, pytest-7.4.4, pluggy-1.4.0 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:69: 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 1264.27s (0:21:04) =========== 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 3.11.8, pytest-7.4.4, pluggy-1.4.0 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:69: 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 1149.30s (0:19:09) =========== 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/bar.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/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/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/__init__.py -> /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__/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__/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__/__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/__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/confidenceintervals.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/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_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_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/__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_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/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_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_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_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__/__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/__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__/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/utils_for_testing.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/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/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/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/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/version.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/__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/utils.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__/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__/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__/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__/__init__.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__/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__/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__/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__/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__ 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/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/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/__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/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/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_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_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/__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_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/utils_for_testing.py to utils_for_testing.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/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/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/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/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/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/__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/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' 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/bar.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/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/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/__init__.py -> /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__/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/__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/confidenceintervals.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/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_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_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/__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_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/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__/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__/__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/__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_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_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_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/utils_for_testing.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/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/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/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/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/version.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/__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/utils.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__/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__/__init__.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__/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__/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__/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__/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__/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__/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__/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__/bar.cpython-311.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ 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/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/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/__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/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/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_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_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/__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_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/utils_for_testing.py to utils_for_testing.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/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/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/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/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/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/__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/utils.py to utils.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_i386.buildinfo dpkg-genchanges --build=binary -O../python-pymbar_3.1.0-4_i386.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/30148 and its subdirectories I: Current time: Fri Apr 5 02:04:24 -12 2024 I: pbuilder-time-stamp: 1712325864 Fri Apr 5 14:04:26 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos6-i386.debian.net. Fri Apr 5 14:04:26 UTC 2024 I: Preparing to do remote build '2' on ionos6-i386.debian.net. Fri Apr 5 14:24:20 UTC 2024 I: Deleting $TMPDIR on ionos6-i386.debian.net. Fri Apr 5 14:24:21 UTC 2024 I: python-pymbar_3.1.0-4_i386.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: ac8fdc73ae70d71d19fa8705039bc26f3af11553 6268 python-pymbar_3.1.0-4_i386.buildinfo 03c4eafef9306ac4b893e7b51a50bfc3ed3847fd 66816 python3-pymbar_3.1.0-4_all.deb Checksums-Sha256: f4dda313ce30e585968f0728ae4322ff705c7a94b57fa103387e02e8fcccfe7c 6268 python-pymbar_3.1.0-4_i386.buildinfo bdfd4d0d1a33667a72c15bf1b0376988eb4176b90eb8fd217664a6b7fd69856a 66816 python3-pymbar_3.1.0-4_all.deb Files: ddc4816a3f88f0e22d282b151b566b2d 6268 science optional python-pymbar_3.1.0-4_i386.buildinfo 6cc43edee9830a30122d13c35aa4a1a7 66816 science optional python3-pymbar_3.1.0-4_all.deb Fri Apr 5 14:24:22 UTC 2024 I: diffoscope 262 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_5-14664.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.RepOT3Zc/python-pymbar_3.1.0-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.RepOT3Zc/python-pymbar_3.1.0-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.RepOT3Zc/python-pymbar_3.1.0-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.RepOT3Zc/b1/python-pymbar_3.1.0-4_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.RepOT3Zc/b2/python-pymbar_3.1.0-4_i386.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: 0.317s) 0.317s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.015s) 0.015s 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: 611ms CPU time consumed: 611ms Fri Apr 5 14:24:23 UTC 2024 I: diffoscope 262 found no differences in the changes files, and a .buildinfo file also exists. Fri Apr 5 14:24:23 UTC 2024 I: python-pymbar from trixie built successfully and reproducibly on i386. Fri Apr 5 14:24:24 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Apr 5 14:24:24 UTC 2024 I: Submitting 8.0K b1/python-pymbar_3.1.0-4_i386.buildinfo.asc Fri Apr 5 14:24:25 UTC 2024 I: Submitting 8.0K b2/python-pymbar_3.1.0-4_i386.buildinfo.asc Fri Apr 5 14:24:25 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Apr 5 14:24:25 UTC 2024 I: Done submitting .buildinfo files. Fri Apr 5 14:24:25 UTC 2024 I: Removing signed python-pymbar_3.1.0-4_i386.buildinfo.asc files: removed './b1/python-pymbar_3.1.0-4_i386.buildinfo.asc' removed './b2/python-pymbar_3.1.0-4_i386.buildinfo.asc'