I: pbuilder: network access will be disabled during build I: Current time: Wed May 1 11:10:56 +14 2024 I: pbuilder-time-stamp: 1714511456 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [python-pymbar_3.1.0-4.dsc] I: copying [./python-pymbar_3.1.0.orig.tar.gz] I: copying [./python-pymbar_3.1.0-4.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Feb 1 21:01:41 2023 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./python-pymbar_3.1.0-4.dsc: no acceptable signature found dpkg-source: info: extracting python-pymbar in python-pymbar-3.1.0 dpkg-source: info: unpacking python-pymbar_3.1.0.orig.tar.gz dpkg-source: info: unpacking python-pymbar_3.1.0-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying numpy-1.24.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2685636/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Apr 30 21:11 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2685636/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2685636/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=cbc6e7cd276a4e3d86e7714df9120369 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2685636 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.QaN3MPgf/pbuilderrc_3RpU --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QaN3MPgf/b2 --logfile b2/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-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 22 12:43 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2685636/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 ... 19901 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-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 19.0 MB of archives. After unpacking 73.5 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: dh-python but it is not installable Depends: dh-sequence-python3 which is a virtual package, provided by: - dh-python (6.20240422), but it is not installable Depends: python3-all but it is not installable Depends: python3-numpy but it is not installable Depends: python3-pytest but it is not installable Depends: python3-scipy but it is not installable Depends: python3-setuptools but it is not installable Depends: python3-six but it is not installable The following actions will resolve these dependencies: Remove the following packages: 1) libdb5.3 [5.3.28+dfsg2-4+b1 (now)] 2) libssl3 [3.1.5-1 (now)] Install the following packages: 3) dh-python [6.20240422 (testing)] 4) libblis4-serial [0.9.0-1+b2 (testing)] 5) libdb5.3t64 [5.3.28+dfsg2-7 (testing)] 6) libexpat1 [2.6.2-1 (testing)] 7) libgfortran5 [14-20240330-1 (testing)] 8) liblapack3 [3.12.0-3 (testing)] 9) liblbfgsb0 [3.0+dfsg.4-1+b1 (testing)] 10) libpython3-stdlib [3.11.8-1 (testing)] 11) libpython3.11-minimal [3.11.9-1 (testing)] 12) libpython3.11-stdlib [3.11.9-1 (testing)] 13) libpython3.12-minimal [3.12.3-1 (testing)] 14) libpython3.12-stdlib [3.12.3-1 (testing)] 15) libreadline8t64 [8.2-4 (testing)] 16) libssl3t64 [3.2.1-3 (testing)] 17) media-types [10.1.0 (testing)] 18) netbase [6.4 (testing)] 19) python3 [3.11.8-1 (testing)] 20) python3-all [3.11.8-1 (testing)] 21) python3-decorator [5.1.1-5 (testing)] 22) python3-distutils [3.12.3-1 (testing)] 23) python3-iniconfig [1.1.1-2 (testing)] 24) python3-lib2to3 [3.12.3-1 (testing)] 25) python3-minimal [3.11.8-1 (testing)] 26) python3-numpy [1:1.24.2-2 (testing)] 27) python3-packaging [24.0-1 (testing)] 28) python3-pkg-resources [68.1.2-2 (testing)] 29) python3-pluggy [1.5.0-1 (testing)] 30) python3-pytest [7.4.4-3 (testing)] 31) python3-scipy [1.11.4-6 (testing)] 32) python3-setuptools [68.1.2-2 (testing)] 33) python3-six [1.16.0-6 (testing)] 34) python3.11 [3.11.9-1 (testing)] 35) python3.11-minimal [3.11.9-1 (testing)] 36) python3.12 [3.12.3-1 (testing)] 37) python3.12-minimal [3.12.3-1 (testing)] 38) readline-common [8.2-4 (testing)] 39) tzdata [2024a-3 (testing)] 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} libblis4-serial{a} libdb5.3t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libicu72{a} liblapack3{a} liblbfgsb0{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} libssl3t64{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 will be REMOVED: libdb5.3{a} libssl3{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, 67 newly installed, 2 to remove and 0 not upgraded. Need to get 69.0 MB of archives. After unpacking 308 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-7 [697 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libssl3t64 amd64 3.2.1-3 [2244 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-3 [255 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.3-1 [809 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.3-1 [2139 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-3+b1 [1180 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.39.3-6 [89.4 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.0-3 [1401 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 40 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 python3-distutils all 3.12.3-1 [131 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20240422 [107 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libblis4-serial amd64 0.9.0-1+b2 [5282 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b1 [29.1 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.3-1 [1951 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.3-1 [659 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.11.8-1 [1056 B] Get: 60 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 62 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.24.2-2 [6299 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.0-1 [45.5 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 python3-pytest all 7.4.4-3 [239 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.11.4-6 [19.5 MB] Get: 67 http://deb.debian.org/debian trixie/main amd64 python3-six all 1.16.0-6 [16.3 kB] Fetched 69.0 MB in 2s (42.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libdb5.3:amd64: dependency problems, but removing anyway as you requested: libperl5.38:amd64 depends on libdb5.3. libpam-modules:amd64 depends on libdb5.3. (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 ... 19901 files and directories currently installed.) Removing libdb5.3:amd64 (5.3.28+dfsg2-4+b1) ... Selecting previously unselected package libdb5.3t64: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 ... 19894 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-7_amd64.deb ... Unpacking libdb5.3t64:amd64 (5.3.28+dfsg2-7) ... Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-7) ... dpkg: libssl3:amd64: dependency problems, but removing anyway as you requested: libkrb5-3:amd64 depends on libssl3 (>= 3.0.0). coreutils depends on libssl3 (>= 3.0.0). (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 ... 19900 files and directories currently installed.) Removing libssl3:amd64 (3.1.5-1) ... Selecting previously unselected package libssl3t64:amd64. (Reading database ... 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Setting up libblis4-serial:amd64 (0.9.0-1+b2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blis-serial/libblis.so.4 to provide /usr/lib/x86_64-linux-gnu/libblis.so.4 (libblis.so.4-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/blis-serial/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 file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Apr 30 21:11:58 UTC 2024. Universal Time is now: Tue Apr 30 21:11:58 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up libgfortran5:amd64 (14-20240330-1) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2685636/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2685636/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/python-pymbar-3.1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-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/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-x86_64' 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-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/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/mbar.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar copying pymbar/bar.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar copying pymbar/__init__.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar copying pymbar/confidenceintervals.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/exp.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/utils.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/timeseries.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/__init__.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/harmonic_oscillators.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems copying pymbar/testsystems/timeseries.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems copying pymbar/testsystems/gaussian_work.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems creating /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_utils.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests copying pymbar/tests/test_mbar_solvers.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests copying pymbar/tests/test_covariance.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests copying pymbar/tests/test_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_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/mbar.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar copying pymbar/bar.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar copying pymbar/__init__.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar copying pymbar/confidenceintervals.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/exp.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/utils.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/timeseries.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/__init__.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/harmonic_oscillators.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems copying pymbar/testsystems/timeseries.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems copying pymbar/testsystems/gaussian_work.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems creating /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_utils.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests copying pymbar/tests/test_mbar_solvers.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests copying pymbar/tests/test_covariance.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests copying pymbar/tests/test_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_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 3.12.3, pytest-7.4.4, pluggy-1.5.0 rootdir: /build/reproducible-path/python-pymbar-3.1.0 collected 37 items pymbar/tests/test_bar.py .. [ 5%] pymbar/tests/test_covariance.py ... [ 13%] pymbar/tests/test_mbar.py ................ [ 56%] pymbar/tests/test_mbar_solvers.py .... [ 67%] pymbar/tests/test_timeseries.py ..ss.ss.. [ 91%] pymbar/tests/test_utils.py ... [100%] =============================== warnings summary =============================== pymbar/utils.py:230 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/utils.py:230: SyntaxWarning: invalid escape sequence '\l' """Compute the log of a sum of exponentiated terms exp(a_n) in a numerically-stable manner. pymbar/utils.py:359 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/utils.py:359: SyntaxWarning: invalid escape sequence '\s' 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % pymbar/utils.py:368 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/utils.py:368: SyntaxWarning: invalid escape sequence '\s' 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % pymbar/testsystems/gaussian_work.py:5 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems/gaussian_work.py:5: SyntaxWarning: invalid escape sequence '\e' """Generate samples from forward and reverse Gaussian work distributions. pymbar/mbar.py:381 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:381: SyntaxWarning: invalid escape sequence '\s' """ pymbar/mbar.py:442 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:442: SyntaxWarning: invalid escape sequence '\i' """ pymbar/mbar.py:865 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:865: SyntaxWarning: invalid escape sequence '\s' """ pymbar/mbar.py:1436 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:1436: SyntaxWarning: invalid escape sequence '\s' """ pymbar/mbar.py:1866 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:1866: SyntaxWarning: invalid escape sequence '\l' """ pymbar/bar.py:56 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/bar.py:56: SyntaxWarning: invalid escape sequence '\s' """A function that when zeroed is equivalent to the solution of pymbar/old_mbar.py:957 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/old_mbar.py:957: SyntaxWarning: invalid escape sequence '\i' """Compute estimate of overlap matrix between the states. pymbar/old_mbar.py:1376 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/old_mbar.py:1376: SyntaxWarning: invalid escape sequence '\s' """Compute the free energy of occupying a number of bins. pymbar/old_mbar.py:1864 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/old_mbar.py:1864: SyntaxWarning: invalid escape sequence '\s' 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % pymbar/old_mbar.py:1873 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/old_mbar.py:1873: SyntaxWarning: invalid escape sequence '\s' 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % pymbar/old_mbar.py:2078 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/old_mbar.py:2078: SyntaxWarning: invalid escape sequence '\l' """ pymbar/utils_for_testing.py:29 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/utils_for_testing.py:29: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html from pkg_resources import resource_filename .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_bar.py: 4 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py: 9 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py: 8 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar_solvers.py: 11 warnings /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:561: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. f_i = np.matrix(self.f_k) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_bar.py: 4 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py: 3 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py: 29 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar_solvers.py: 11 warnings /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:1772: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. Ndiag = np.matrix(np.diag(N_k), dtype=np.float64) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_bar.py: 4 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py: 3 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py: 29 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar_solvers.py: 11 warnings /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/mbar.py:1773: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. W = np.matrix(W, dtype=np.float64) .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_bar.py: 40 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_covariance.py: 78 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar.py: 287 warnings .pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar_solvers.py: 99 warnings /usr/lib/python3/dist-packages/numpy/matrixlib/defmatrix.py: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 357.55s (0:05:57) =========== I: pybuild base:311: cd /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build; python3.11 -m pytest ============================= test session starts ============================== platform linux -- Python 3.11.9, pytest-7.4.4, pluggy-1.5.0 rootdir: /build/reproducible-path/python-pymbar-3.1.0 collected 37 items pymbar/tests/test_bar.py .. [ 5%] pymbar/tests/test_covariance.py ... [ 13%] pymbar/tests/test_mbar.py ................ [ 56%] pymbar/tests/test_mbar_solvers.py .... [ 67%] pymbar/tests/test_timeseries.py ..ss.ss.. [ 91%] pymbar/tests/test_utils.py ... [100%] =============================== warnings summary =============================== pymbar/utils.py:230 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/utils.py:230: DeprecationWarning: invalid escape sequence '\l' """Compute the log of a sum of exponentiated terms exp(a_n) in a numerically-stable manner. pymbar/utils.py:359 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/utils.py:359: DeprecationWarning: invalid escape sequence '\s' 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % pymbar/utils.py:368 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/utils.py:368: DeprecationWarning: invalid escape sequence '\s' 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % pymbar/testsystems/gaussian_work.py:5 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/testsystems/gaussian_work.py:5: DeprecationWarning: invalid escape sequence '\e' """Generate samples from forward and reverse Gaussian work distributions. pymbar/mbar.py:381 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:381: DeprecationWarning: invalid escape sequence '\s' """ pymbar/mbar.py:442 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:442: DeprecationWarning: invalid escape sequence '\i' """ pymbar/mbar.py:865 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:865: DeprecationWarning: invalid escape sequence '\s' """ pymbar/mbar.py:1436 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:1436: DeprecationWarning: invalid escape sequence '\s' """ pymbar/mbar.py:1866 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:1866: DeprecationWarning: invalid escape sequence '\l' """ pymbar/bar.py:56 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/bar.py:56: DeprecationWarning: invalid escape sequence '\s' """A function that when zeroed is equivalent to the solution of pymbar/old_mbar.py:957 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/old_mbar.py:957: DeprecationWarning: invalid escape sequence '\i' """Compute estimate of overlap matrix between the states. pymbar/old_mbar.py:1376 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/old_mbar.py:1376: DeprecationWarning: invalid escape sequence '\s' """Compute the free energy of occupying a number of bins. pymbar/old_mbar.py:1864 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/old_mbar.py:1864: DeprecationWarning: invalid escape sequence '\s' 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % pymbar/old_mbar.py:1873 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/old_mbar.py:1873: DeprecationWarning: invalid escape sequence '\s' 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % pymbar/old_mbar.py:2078 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/old_mbar.py:2078: DeprecationWarning: invalid escape sequence '\l' """ pymbar/utils_for_testing.py:29 /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/utils_for_testing.py:29: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html from pkg_resources import resource_filename .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_bar.py: 4 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py: 9 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py: 8 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar_solvers.py: 11 warnings /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:561: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. f_i = np.matrix(self.f_k) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_bar.py: 4 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py: 3 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py: 29 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar_solvers.py: 11 warnings /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:1772: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. Ndiag = np.matrix(np.diag(N_k), dtype=np.float64) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_bar.py: 4 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py: 3 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py: 29 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar_solvers.py: 11 warnings /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/mbar.py:1773: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. W = np.matrix(W, dtype=np.float64) .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_bar.py: 40 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_covariance.py: 78 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar.py: 287 warnings .pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar_solvers.py: 99 warnings /usr/lib/python3/dist-packages/numpy/matrixlib/defmatrix.py: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 332.23s (0:05:32) =========== 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/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/bar.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/__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/confidenceintervals.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/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/exp.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/__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_utils.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests/test_mbar_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_covariance.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_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_bar.cpython-312-pytest-7.4.4.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests/__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_mbar_solvers.cpython-312-pytest-7.4.4.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/tests/__pycache__/test_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/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_mbar.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/mbar_solvers.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__/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__/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__/bar.cpython-312.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/__pycache__/__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__/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__/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__/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__/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.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/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/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/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 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 creating /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems/__pycache__/gaussian_work.cpython-312.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems/__pycache__/harmonic_oscillators.cpython-312.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems/__pycache__/timeseries.cpython-312.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems/__pycache__/exponential_distributions.cpython-312.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.12_pymbar/build/pymbar/testsystems/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/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/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/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/timeseries.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/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/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/__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/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/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/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_utils.py to test_utils.cpython-312.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/tests/test_mbar_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_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_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_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/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/utils.py to utils.cpython-312.pyc /usr/lib/python3.12/dist-packages/pymbar/utils.py:230: SyntaxWarning: invalid escape sequence '\l' /usr/lib/python3.12/dist-packages/pymbar/utils.py:359: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.12/dist-packages/pymbar/utils.py:368: SyntaxWarning: invalid escape sequence '\s' byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems/exponential_distributions.py to exponential_distributions.cpython-312.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/testsystems/harmonic_oscillators.py to harmonic_oscillators.cpython-312.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar/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/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/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/timeseries.py to timeseries.cpython-312.pyc running install_data creating /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/pymbar copying pymbar/_pymbar.c -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/pymbar running install_egg_info running egg_info creating pymbar.egg-info writing pymbar.egg-info/PKG-INFO writing dependency_links to pymbar.egg-info/dependency_links.txt writing top-level names to pymbar.egg-info/top_level.txt writing manifest file 'pymbar.egg-info/SOURCES.txt' reading manifest file 'pymbar.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'pymbar.egg-info/SOURCES.txt' Copying pymbar.egg-info to /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.12/dist-packages/pymbar-3.0.5.egg-info Skipping SOURCES.txt running install_scripts I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar /usr/lib/python3/dist-packages/setuptools/dist.py:744: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) author Levi N. Naden and Michael R. Shirts and John D. Chodera author_emaillevi.naden@choderalab.org, michael.shirts@virginia.edu, john.chodera@choderalab.org data_files [('pymbar', ['pymbar/_pymbar.c'])] descriptionPython implementation of the multistate Bennett acceptance ratio (MBAR) method. download_url http://github.com/choderalab/pymbar ext_modules [] license MIT long_description Pymbar (https://simtk.org/home/pymbar) is a library that provides tools for optimally combining simulations from multiple thermodynamic states using maximum likelihood methods to compute free energies (normalization constants) and expectation values from all of the samples simultaneously. name pymbar package_dir {'pymbar': 'pymbar', 'pymbar.tests': 'pymbar/tests'} packages ['pymbar', 'pymbar.testsystems', 'pymbar.tests'] platforms ['Linux', 'Mac OS X', 'Windows'] requires ['numpy', 'scipy', 'pytest', 'numexpr'] url http://github.com/choderalab/pymbar version 3.0.5 zip_safe False running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py copying pymbar/version.py -> /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar running install_lib creating /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11 creating /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages creating /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/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/bar.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__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/confidenceintervals.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/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/exp.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/__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_utils.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/test_mbar_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_covariance.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_covariance.cpython-311-pytest-7.4.4.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/__pycache__/test_utils.cpython-311-pytest-7.4.4.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/__pycache__/test_timeseries.cpython-311-pytest-7.4.4.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/__pycache__/test_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_mbar_solvers.cpython-311-pytest-7.4.4.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/tests/__pycache__/__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/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_mbar.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/mbar_solvers.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar creating /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/utils.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__/old_mbar.cpython-311.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/exp.cpython-311.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/bar.cpython-311.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/version.cpython-311.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/confidenceintervals.cpython-311.pyc -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/__pycache__ copying /build/reproducible-path/python-pymbar-3.1.0/.pybuild/cpython3_3.11_pymbar/build/pymbar/__pycache__/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__/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__/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__/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/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/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/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 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 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/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/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/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/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/timeseries.py -> /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/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/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/__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/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/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/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_utils.py to test_utils.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/tests/test_mbar_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_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_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_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/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/utils.py to utils.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems/exponential_distributions.py to exponential_distributions.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/testsystems/harmonic_oscillators.py to harmonic_oscillators.cpython-311.pyc byte-compiling /build/reproducible-path/python-pymbar-3.1.0/debian/python3-pymbar/usr/lib/python3.11/dist-packages/pymbar/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/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/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/timeseries.py to timeseries.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_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: user script /srv/workspace/pbuilder/2685636/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2685636/tmp/hooks/B01_cleanup finished 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/2685636 and its subdirectories I: Current time: Wed May 1 11:24:23 +14 2024 I: pbuilder-time-stamp: 1714512263