I: pbuilder: network access will be disabled during build I: Current time: Fri May 17 17:34:45 -12 2024 I: pbuilder-time-stamp: 1716010485 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [python-pymbar_3.1.0-4.dsc] I: copying [./python-pymbar_3.1.0.orig.tar.gz] I: copying [./python-pymbar_3.1.0-4.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Feb 1 09:01:41 2023 -12 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/3342116/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='57a858effdf640ec8e4cbf2d99b54669' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3342116' 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.CW6vudVC/pbuilderrc_pK23 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.CW6vudVC/b1 --logfile b1/build.log python-pymbar_3.1.0-4.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos15-amd64 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Feb 12 2023 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 2023 more -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Feb 12 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/3342116/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: amd64 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 ... 19596 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} libboost-dev{a} libboost1.74-dev{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack3{a} liblbfgsb0{a} libmagic-mgc{a} libmagic1{a} libopenblas-dev{a} libopenblas-pthread-dev{a} libopenblas0{a} libopenblas0-pthread{a} libpipeline1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} libxsimd-dev{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-attr{a} python3-beniget{a} python3-decorator{a} python3-dev{a} python3-distutils{a} python3-gast{a} python3-iniconfig{a} python3-lib2to3{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-ply{a} python3-py{a} python3-pytest{a} python3-pythran{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx python3-pil python3-pygments wget 0 packages upgraded, 85 newly installed, 0 to remove and 0 not upgraded. Need to get 80.7 MB of archives. After unpacking 495 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-2 [76.2 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-2 [131 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 dh-python all 5.20230130 [104 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-20 [9510 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libexpat1-dev amd64 2.5.0-1 [150 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libopenblas0-pthread amd64 0.3.21+ds-4 [6709 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1 [28.9 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libopenblas0 amd64 0.3.21+ds-4 [32.6 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libopenblas-pthread-dev amd64 0.3.21+ds-4 [4971 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libopenblas-dev amd64 0.3.21+ds-4 [44.9 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libpython3.11 amd64 3.11.2-6 [1988 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-dev amd64 3.11.2-6 [4738 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libpython3-dev amd64 3.11.2-1+b1 [9572 B] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libpython3-all-dev amd64 3.11.2-1+b1 [1068 B] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libxsimd-dev amd64 8.1.0-7 [88.8 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B] Get: 66 http://deb.debian.org/debian bookworm/main amd64 python3.11-dev amd64 3.11.2-6 [615 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 python3-dev amd64 3.11.2-1+b1 [26.2 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 python3-all-dev amd64 3.11.2-1+b1 [1072 B] Get: 69 http://deb.debian.org/debian bookworm/main amd64 python3-attr all 22.2.0-1 [65.4 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 python3-gast all 0.5.2-2 [9364 B] Get: 71 http://deb.debian.org/debian bookworm/main amd64 python3-beniget all 0.4.1-3 [9920 B] Get: 72 http://deb.debian.org/debian bookworm/main amd64 python3-decorator all 5.1.1-3 [14.9 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 74 http://deb.debian.org/debian bookworm/main amd64 python3-more-itertools all 8.10.0-2 [53.0 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 23.0-1 [32.5 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 python3-pluggy all 1.0.0+repack-1 [19.7 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 python3-ply all 3.11-5 [65.8 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 python3-py all 1.11.0-1 [89.2 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 python3-pytest all 7.2.1-2 [236 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 python3-pythran amd64 0.11.0+ds-7 [427 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 python3-scipy amd64 1.10.1-2 [15.2 MB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 python3-setuptools all 66.1.1-1 [521 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Fetched 80.7 MB in 1s (85.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (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 ... 19596 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. 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Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... 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 ... 20346 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ... 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Setting up libblas3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libexpat1-dev:amd64 (2.5.0-1) ... Setting up autopoint (0.21-12) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libboost-dev:amd64 (1.74.0.3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.1+b3) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up liblapack3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.21-12) ... Setting up libopenblas0-pthread:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode Setting up libtool (2.4.7-5) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up libopenblas0:amd64 (0.3.21+ds-4) ... Setting up groff-base (1.22.4-10) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1) ... Setting up libopenblas-pthread-dev:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libopenblas-dev:amd64 (0.3.21+ds-4) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libpython3.11:amd64 (3.11.2-6) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up python3-six (1.16.0-4) ... Setting up python3-decorator (5.1.1-3) ... Setting up python3-packaging (23.0-1) ... Setting up libpython3.11-dev:amd64 (3.11.2-6) ... Setting up python3-pluggy (1.0.0+repack-1) ... Setting up python3-lib2to3 (3.11.2-2) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-2) ... Setting up dh-python (5.20230130) ... Setting up python3-more-itertools (8.10.0-2) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-attr (22.2.0-1) ... Setting up libpython3-dev:amd64 (3.11.2-1+b1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-py (1.11.0-1) ... Setting up python3.11-dev (3.11.2-6) ... Setting up python3-pytest (7.2.1-2) ... Setting up python3-ply (3.11-5) ... Setting up python3-gast (0.5.2-2) ... Setting up python3-all (3.11.2-1+b1) ... Setting up python3-beniget (0.4.1-3) ... Setting up libpython3-all-dev:amd64 (3.11.2-1+b1) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up python3-all-dev (3.11.2-1+b1) ... Setting up python3-pythran (0.11.0+ds-7) ... Setting up python3-scipy (1.10.1-2) ... Processing triggers for libc-bin (2.36-8) ... 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/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 amd64 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/python-pymbar-3.1.0' dh_auto_clean I: pybuild base:240: python3.11 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:775: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( 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/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build' (and everything under it) 'build/bdist.linux-x86_64' 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/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:240: python3.11 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:775: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( 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:240: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:775: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( 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/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar copying pymbar/version.py -> /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar copying pymbar/utils_for_testing.py -> /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar copying pymbar/utils.py -> /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar copying pymbar/timeseries.py -> /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar copying pymbar/old_mbar.py -> /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar copying pymbar/mbar_solvers.py -> /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar copying pymbar/mbar.py -> /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar copying pymbar/exp.py -> /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar copying pymbar/confidenceintervals.py -> /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar copying pymbar/bar.py -> /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar copying pymbar/__init__.py -> /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar creating /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems copying pymbar/testsystems/harmonic_oscillators.py -> /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems copying pymbar/testsystems/exponential_distributions.py -> /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems copying pymbar/testsystems/timeseries.py -> /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems copying pymbar/testsystems/gaussian_work.py -> /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems copying pymbar/testsystems/__init__.py -> /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems creating /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests copying pymbar/tests/test_mbar.py -> /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests copying pymbar/tests/test_utils.py -> /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests copying pymbar/tests/test_timeseries.py -> /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests copying pymbar/tests/test_mbar_solvers.py -> /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests copying pymbar/tests/test_covariance.py -> /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests copying pymbar/tests/test_bar.py -> /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests copying pymbar/tests/__init__.py -> /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests debian/rules override_dh_auto_test make[1]: Entering directory '/build/python-pymbar-3.1.0' dh_auto_test -- --test-pytest I: pybuild base:240: cd /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build; python3.11 -m pytest ============================= test session starts ============================== platform linux -- Python 3.11.2, pytest-7.2.1, pluggy-1.0.0+repack rootdir: /build/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/old_mbar.py:2078: DeprecationWarning: invalid escape sequence '\l' """ .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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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, 1445 warnings in 249.51s (0:04:09) =========== make[1]: Leaving directory '/build/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/python-pymbar-3.1.0' dh_auto_install I: pybuild base:240: /usr/bin/python3 setup.py install --root /build/python-pymbar-3.1.0/debian/python3-pymbar /usr/lib/python3/dist-packages/setuptools/dist.py:775: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( 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/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py copying pymbar/version.py -> /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar running install_lib creating /build/python-pymbar-3.1.0/debian/python3-pymbar/usr creating /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib creating /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11 creating /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages creating /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/version.py -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar creating /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/utils_for_testing.cpython-311.pyc -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/old_mbar.cpython-311.pyc -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/exp.cpython-311.pyc -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/bar.cpython-311.pyc -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/mbar_solvers.cpython-311.pyc -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/mbar.cpython-311.pyc -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/version.cpython-311.pyc -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/confidenceintervals.cpython-311.pyc -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/utils.cpython-311.pyc -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/timeseries.cpython-311.pyc -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/__init__.cpython-311.pyc -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ creating /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests creating /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/__pycache__ copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/__pycache__/test_utils.cpython-311-pytest-7.2.1.pyc -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/__pycache__ copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/__pycache__/test_timeseries.cpython-311-pytest-7.2.1.pyc -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/__pycache__ copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/__pycache__/test_mbar_solvers.cpython-311-pytest-7.2.1.pyc -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/__pycache__ copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/__pycache__/test_mbar.cpython-311-pytest-7.2.1.pyc -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/__pycache__ copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/__pycache__/test_covariance.cpython-311-pytest-7.2.1.pyc -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/__pycache__ copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/__pycache__/test_bar.cpython-311-pytest-7.2.1.pyc -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/__pycache__ copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/__pycache__/__init__.cpython-311.pyc -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/__pycache__ copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/__init__.py -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_bar.py -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar_solvers.py -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_timeseries.py -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_utils.py -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests creating /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems creating /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems/__pycache__ copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems/__pycache__/gaussian_work.cpython-311.pyc -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems/__pycache__ copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems/__pycache__/timeseries.cpython-311.pyc -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems/__pycache__ copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems/__pycache__/exponential_distributions.cpython-311.pyc -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems/__pycache__ copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems/__pycache__/harmonic_oscillators.cpython-311.pyc -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems/__pycache__ copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems/__pycache__/__init__.cpython-311.pyc -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems/__pycache__ copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems/__init__.py -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems/gaussian_work.py -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems/timeseries.py -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems/exponential_distributions.py -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems/harmonic_oscillators.py -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__init__.py -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/bar.py -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/confidenceintervals.py -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/exp.py -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar_solvers.py -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/old_mbar.py -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/timeseries.py -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/utils.py -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar copying /build/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/utils_for_testing.py -> /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar byte-compiling /build/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/utils.py to utils.cpython-311.pyc byte-compiling /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/utils_for_testing.py to utils_for_testing.cpython-311.pyc running install_data creating /build/python-pymbar-3.1.0/debian/python3-pymbar/usr/pymbar copying pymbar/_pymbar.c -> /build/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/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/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_amd64.buildinfo dpkg-genchanges --build=binary -O../python-pymbar_3.1.0-4_amd64.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/3342116 and its subdirectories I: Current time: Fri May 17 17:39:54 -12 2024 I: pbuilder-time-stamp: 1716010794