Diff of the two buildlogs:
--
--- b1/build.log 2025-02-23 18:56:06.464067159 +0000
+++ b2/build.log 2025-02-23 20:05:24.608053928 +0000
@@ -1,6 +1,6 @@
I: pbuilder: network access will be disabled during build
-I: Current time: Sun Feb 23 06:13:39 -12 2025
-I: pbuilder-time-stamp: 1740334419
+I: Current time: Sun Mar 29 15:19:12 +14 2026
+I: pbuilder-time-stamp: 1774747152
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
@@ -28,52 +28,84 @@
dpkg-source: info: applying test_skip_missing_modules.patch
I: Not using root during the build.
I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/3027168/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/283285/tmp/hooks/D01_modify_environment starting
+debug: Running on codethink03-arm64.
+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 Mar 29 01:19 /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/283285/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/283285/tmp/hooks/D02_print_environment starting
I: set
- BUILDDIR='/build/reproducible-path'
- BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
- BUILDUSERNAME='pbuilder1'
- BUILD_ARCH='arm64'
- DEBIAN_FRONTEND='noninteractive'
+ 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]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu")
+ BASH_VERSION='5.2.37(1)-release'
+ BUILDDIR=/build/reproducible-path
+ BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+ BUILDUSERNAME=pbuilder2
+ BUILD_ARCH=arm64
+ DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
- DISTRIBUTION='trixie'
- HOME='/root'
- HOST_ARCH='arm64'
+ DIRSTACK=()
+ DISTRIBUTION=trixie
+ EUID=0
+ FUNCNAME=([0]="Echo" [1]="main")
+ GROUPS=()
+ HOME=/root
+ HOSTNAME=i-capture-the-hostname
+ HOSTTYPE=aarch64
+ HOST_ARCH=arm64
IFS='
'
- INVOCATION_ID='a7b269d692404473bb0a8083b9202bd9'
- LANG='C'
- LANGUAGE='en_US:en'
- LC_ALL='C'
- MAIL='/var/mail/root'
- OPTIND='1'
- PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
- PBCURRENTCOMMANDLINEOPERATION='build'
- PBUILDER_OPERATION='build'
- PBUILDER_PKGDATADIR='/usr/share/pbuilder'
- PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
- PBUILDER_SYSCONFDIR='/etc'
- PPID='3027168'
- PS1='# '
- PS2='> '
+ INVOCATION_ID=732bf15f48db46bb84e9f0f794066918
+ LANG=C
+ LANGUAGE=nl_BE:nl
+ LC_ALL=C
+ MACHTYPE=aarch64-unknown-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=283285
PS4='+ '
- PWD='/'
- SHELL='/bin/bash'
- SHLVL='2'
- SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.qK7ppBaO/pbuilderrc_YoRY --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qK7ppBaO/b1 --logfile b1/build.log mdanalysis_2.8.0-4.dsc'
- SUDO_GID='109'
- SUDO_UID='104'
- SUDO_USER='jenkins'
- TERM='unknown'
- TZ='/usr/share/zoneinfo/Etc/GMT+12'
- USER='root'
- _='/usr/bin/systemd-run'
- http_proxy='http://192.168.101.4:3128'
+ 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.qK7ppBaO/pbuilderrc_0njW --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.qK7ppBaO/b2 --logfile b2/build.log mdanalysis_2.8.0-4.dsc'
+ SUDO_GID=109
+ SUDO_UID=104
+ SUDO_USER=jenkins
+ TERM=unknown
+ TZ=/usr/share/zoneinfo/Etc/GMT-14
+ UID=0
+ USER=root
+ _='I: set'
+ http_proxy=http://192.168.101.4:3128
I: uname -a
- Linux codethink04-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux
+ Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux
I: ls -l /bin
- lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/3027168/tmp/hooks/D02_print_environment finished
+ lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/283285/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
@@ -452,7 +484,7 @@
Get: 275 http://deb.debian.org/debian trixie/main arm64 python3-sphinx-sitemap all 2.6.0-1 [8508 B]
Get: 276 http://deb.debian.org/debian trixie/main arm64 python3-sphinxcontrib.bibtex all 2.6.2-1 [32.4 kB]
Get: 277 http://deb.debian.org/debian trixie/main arm64 python3-tqdm all 4.67.1-2 [91.1 kB]
-Fetched 197 MB in 1s (208 MB/s)
+Fetched 197 MB in 2s (84.5 MB/s)
Preconfiguring packages ...
Selecting previously unselected package fonts-lato.
(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 ... 19919 files and directories currently installed.)
@@ -1346,8 +1378,8 @@
Setting up tzdata (2025a-2) ...
Current default time zone: 'Etc/UTC'
-Local time is now: Sun Feb 23 18:14:19 UTC 2025.
-Universal Time is now: Sun Feb 23 18:14:19 UTC 2025.
+Local time is now: Sun Mar 29 01:21:16 UTC 2026.
+Universal Time is now: Sun Mar 29 01:21:16 UTC 2026.
Run 'dpkg-reconfigure tzdata' if you wish to change it.
Setting up unicode-data (15.1.0-1) ...
@@ -1604,7 +1636,11 @@
Building tag database...
-> Finished parsing the build-deps
I: Building the package
-I: Running cd /build/reproducible-path/mdanalysis-2.8.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../mdanalysis_2.8.0-4_source.changes
+I: user script /srv/workspace/pbuilder/283285/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for trixie
+I: user script /srv/workspace/pbuilder/283285/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/mdanalysis-2.8.0/ && 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 > ../mdanalysis_2.8.0-4_source.changes
dpkg-buildpackage: info: source package mdanalysis
dpkg-buildpackage: info: source version 2.8.0-4
dpkg-buildpackage: info: source distribution unstable
@@ -3193,7 +3229,7 @@
Copying MDAnalysis.egg-info to build/bdist.linux-aarch64/wheel/./MDAnalysis-2.8.0.egg-info
running install_scripts
creating build/bdist.linux-aarch64/wheel/MDAnalysis-2.8.0.dist-info/WHEEL
-creating '/build/reproducible-path/mdanalysis-2.8.0/.pybuild/cpython3_3.12_mdanalysis/.tmp-jbu6k2tu/MDAnalysis-2.8.0-cp312-cp312-linux_aarch64.whl' and adding 'build/bdist.linux-aarch64/wheel' to it
+creating '/build/reproducible-path/mdanalysis-2.8.0/.pybuild/cpython3_3.12_mdanalysis/.tmp-_i2sobyn/MDAnalysis-2.8.0-cp312-cp312-linux_aarch64.whl' and adding 'build/bdist.linux-aarch64/wheel' to it
adding 'MDAnalysis/__init__.py'
adding 'MDAnalysis/authors.py'
adding 'MDAnalysis/due.py'
@@ -5135,7 +5171,7 @@
Copying MDAnalysis.egg-info to build/bdist.linux-aarch64/wheel/./MDAnalysis-2.8.0.egg-info
running install_scripts
creating build/bdist.linux-aarch64/wheel/MDAnalysis-2.8.0.dist-info/WHEEL
-creating '/build/reproducible-path/mdanalysis-2.8.0/.pybuild/cpython3_3.13_mdanalysis/.tmp-m7196qs6/MDAnalysis-2.8.0-cp313-cp313-linux_aarch64.whl' and adding 'build/bdist.linux-aarch64/wheel' to it
+creating '/build/reproducible-path/mdanalysis-2.8.0/.pybuild/cpython3_3.13_mdanalysis/.tmp-78_8y73i/MDAnalysis-2.8.0-cp313-cp313-linux_aarch64.whl' and adding 'build/bdist.linux-aarch64/wheel' to it
adding 'MDAnalysis/__init__.py'
adding 'MDAnalysis/authors.py'
adding 'MDAnalysis/due.py'
@@ -5610,50 +5646,50 @@
parsing bibtex file /build/reproducible-path/mdanalysis-2.8.0/package/doc/sphinx/source/references.bib... parsed 69 entries
locale_dir /build/reproducible-path/mdanalysis-2.8.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist
loading intersphinx inventory 'h5py' from https://docs.h5py.org/en/stable/objects.inv ...
-WARNING: failed to reach any of the inventories with the following issues:
-intersphinx inventory 'https://docs.h5py.org/en/stable/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='docs.h5py.org', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff96bdb230>: Failed to establish a new connection: [Errno 111] Connection refused')))
loading intersphinx inventory 'python' from https://docs.python.org/3/objects.inv ...
loading intersphinx inventory 'scipy' from https://docs.scipy.org/doc/scipy/objects.inv ...
-WARNING: failed to reach any of the inventories with the following issues:
-intersphinx inventory 'https://docs.scipy.org/doc/scipy/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='docs.scipy.org', port=443): Max retries exceeded with url: /doc/scipy/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff96a3cb90>: Failed to establish a new connection: [Errno 111] Connection refused')))
loading intersphinx inventory 'gsd' from https://gsd.readthedocs.io/en/stable/objects.inv ...
WARNING: failed to reach any of the inventories with the following issues:
-intersphinx inventory 'https://gsd.readthedocs.io/en/stable/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='gsd.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff96b7f4d0>: Failed to establish a new connection: [Errno 111] Connection refused')))
+intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff8a53c550>: Failed to establish a new connection: [Errno 111] Connection refused')))
loading intersphinx inventory 'maplotlib' from https://matplotlib.org/stable/objects.inv ...
+loading intersphinx inventory 'griddataformats' from https://mdanalysis.org/GridDataFormats/objects.inv ...
WARNING: failed to reach any of the inventories with the following issues:
-intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff96b7fed0>: Failed to establish a new connection: [Errno 111] Connection refused')))
+intersphinx inventory 'https://matplotlib.org/stable/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='matplotlib.org', port=443): Max retries exceeded with url: /stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff8a680b90>: Failed to establish a new connection: [Errno 111] Connection refused')))
WARNING: failed to reach any of the inventories with the following issues:
-intersphinx inventory 'https://matplotlib.org/stable/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='matplotlib.org', port=443): Max retries exceeded with url: /stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff96b7e210>: Failed to establish a new connection: [Errno 111] Connection refused')))
-loading intersphinx inventory 'griddataformats' from https://mdanalysis.org/GridDataFormats/objects.inv ...
-loading intersphinx inventory 'pmda' from https://mdanalysis.org/pmda/objects.inv ...
-loading intersphinx inventory 'networkx' from https://networkx.org/documentation/stable/objects.inv ...
-loading intersphinx inventory 'numpy' from https://numpy.org/doc/stable/objects.inv ...
-loading intersphinx inventory 'parmed' from https://parmed.github.io/ParmEd/html/objects.inv ...
-loading intersphinx inventory 'rdkit' from https://rdkit.org/docs/objects.inv ...
+intersphinx inventory 'https://docs.scipy.org/doc/scipy/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='docs.scipy.org', port=443): Max retries exceeded with url: /doc/scipy/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff8a53cb90>: Failed to establish a new connection: [Errno 111] Connection refused')))
WARNING: failed to reach any of the inventories with the following issues:
-intersphinx inventory 'https://mdanalysis.org/GridDataFormats/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /GridDataFormats/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff96b7ed50>: Failed to establish a new connection: [Errno 111] Connection refused')))
+intersphinx inventory 'https://gsd.readthedocs.io/en/stable/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='gsd.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff8a680a50>: Failed to establish a new connection: [Errno 111] Connection refused')))
WARNING: failed to reach any of the inventories with the following issues:
-intersphinx inventory 'https://mdanalysis.org/pmda/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /pmda/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff96b7e350>: Failed to establish a new connection: [Errno 111] Connection refused')))
+intersphinx inventory 'https://docs.h5py.org/en/stable/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='docs.h5py.org', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff8a6db230>: Failed to establish a new connection: [Errno 111] Connection refused')))
WARNING: failed to reach any of the inventories with the following issues:
-intersphinx inventory 'https://networkx.org/documentation/stable/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='networkx.org', port=443): Max retries exceeded with url: /documentation/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff96b7e5d0>: Failed to establish a new connection: [Errno 111] Connection refused')))
+intersphinx inventory 'https://mdanalysis.org/GridDataFormats/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /GridDataFormats/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff8a53ccd0>: Failed to establish a new connection: [Errno 111] Connection refused')))
+loading intersphinx inventory 'pmda' from https://mdanalysis.org/pmda/objects.inv ...
+loading intersphinx inventory 'waterdynamics' from https://www.mdanalysis.org/waterdynamics/objects.inv ...
+loading intersphinx inventory 'rdkit' from https://rdkit.org/docs/objects.inv ...
+loading intersphinx inventory 'parmed' from https://parmed.github.io/ParmEd/html/objects.inv ...
+loading intersphinx inventory 'pathsimanalysis' from https://www.mdanalysis.org/PathSimAnalysis/objects.inv ...
WARNING: failed to reach any of the inventories with the following issues:
-intersphinx inventory 'https://parmed.github.io/ParmEd/html/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='parmed.github.io', port=443): Max retries exceeded with url: /ParmEd/html/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff96b7e710>: Failed to establish a new connection: [Errno 111] Connection refused')))
+intersphinx inventory 'https://mdanalysis.org/pmda/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /pmda/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff8a53d450>: Failed to establish a new connection: [Errno 111] Connection refused')))
WARNING: failed to reach any of the inventories with the following issues:
-intersphinx inventory 'https://numpy.org/doc/stable/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='numpy.org', port=443): Max retries exceeded with url: /doc/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff96b7e990>: Failed to establish a new connection: [Errno 111] Connection refused')))
+intersphinx inventory 'https://rdkit.org/docs/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='rdkit.org', port=443): Max retries exceeded with url: /docs/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff8a53d6d0>: Failed to establish a new connection: [Errno 111] Connection refused')))
+loading intersphinx inventory 'networkx' from https://networkx.org/documentation/stable/objects.inv ...
WARNING: failed to reach any of the inventories with the following issues:
-intersphinx inventory 'https://rdkit.org/docs/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='rdkit.org', port=443): Max retries exceeded with url: /docs/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff96b7cb90>: Failed to establish a new connection: [Errno 111] Connection refused')))
-loading intersphinx inventory 'waterdynamics' from https://www.mdanalysis.org/waterdynamics/objects.inv ...
+intersphinx inventory 'https://parmed.github.io/ParmEd/html/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='parmed.github.io', port=443): Max retries exceeded with url: /ParmEd/html/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff8a53d810>: Failed to establish a new connection: [Errno 111] Connection refused')))
WARNING: failed to reach any of the inventories with the following issues:
-intersphinx inventory 'https://www.mdanalysis.org/waterdynamics/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /waterdynamics/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff96a3c190>: Failed to establish a new connection: [Errno 111] Connection refused')))
-loading intersphinx inventory 'pathsimanalysis' from https://www.mdanalysis.org/PathSimAnalysis/objects.inv ...
-loading intersphinx inventory 'mdahole2' from https://www.mdanalysis.org/mdahole2/objects.inv ...
+intersphinx inventory 'https://www.mdanalysis.org/PathSimAnalysis/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /PathSimAnalysis/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff8a53da90>: Failed to establish a new connection: [Errno 111] Connection refused')))
+loading intersphinx inventory 'numpy' from https://numpy.org/doc/stable/objects.inv ...
loading intersphinx inventory 'dask' from https://docs.dask.org/en/stable/objects.inv ...
WARNING: failed to reach any of the inventories with the following issues:
-intersphinx inventory 'https://www.mdanalysis.org/PathSimAnalysis/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /PathSimAnalysis/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff96a3c690>: Failed to establish a new connection: [Errno 111] Connection refused')))
+intersphinx inventory 'https://www.mdanalysis.org/waterdynamics/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /waterdynamics/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff8a53d590>: Failed to establish a new connection: [Errno 111] Connection refused')))
+loading intersphinx inventory 'mdahole2' from https://www.mdanalysis.org/mdahole2/objects.inv ...
+WARNING: failed to reach any of the inventories with the following issues:
+intersphinx inventory 'https://numpy.org/doc/stable/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='numpy.org', port=443): Max retries exceeded with url: /doc/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff8a53df90>: Failed to establish a new connection: [Errno 111] Connection refused')))
+WARNING: failed to reach any of the inventories with the following issues:
+intersphinx inventory 'https://www.mdanalysis.org/mdahole2/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /mdahole2/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff8a53e5d0>: Failed to establish a new connection: [Errno 111] Connection refused')))
WARNING: failed to reach any of the inventories with the following issues:
-intersphinx inventory 'https://www.mdanalysis.org/mdahole2/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /mdahole2/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff96a3c910>: Failed to establish a new connection: [Errno 111] Connection refused')))
+intersphinx inventory 'https://networkx.org/documentation/stable/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='networkx.org', port=443): Max retries exceeded with url: /documentation/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff8a53e490>: Failed to establish a new connection: [Errno 111] Connection refused')))
WARNING: failed to reach any of the inventories with the following issues:
-intersphinx inventory 'https://docs.dask.org/en/stable/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='docs.dask.org', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff96a3ca50>: Failed to establish a new connection: [Errno 111] Connection refused')))
+intersphinx inventory 'https://docs.dask.org/en/stable/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='docs.dask.org', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff8a53e210>: Failed to establish a new connection: [Errno 111] Connection refused')))
locale_dir /build/reproducible-path/mdanalysis-2.8.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist
building [mo]: targets for 0 po files that are out of date
writing output...
@@ -5720,7 +5756,7 @@
Didn't find DistanceMatrix.atoms in MDAnalysis.analysis.diffusionmap
Didn't find DistanceMatrix.results.dist_matrix in MDAnalysis.analysis.diffusionmap
reading sources... [ 6%] documentation_pages/analysis/dihedrals
-Matplotlib created a temporary cache directory at /tmp/matplotlib-twca74gi because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
+Matplotlib created a temporary cache directory at /tmp/matplotlib-uen72pmn because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
Didn't find Dihedral.results.angles in MDAnalysis.analysis.dihedrals
Didn't find Ramachandran.results.angles in MDAnalysis.analysis.dihedrals
Didn't find Janin.results.angles in MDAnalysis.analysis.dihedrals
@@ -26185,8 +26221,8 @@
testsuite/MDAnalysisTests/visualization/test_streamlines.py::test_streamplot_2D_zero_return PASSED [ 99%]
testsuite/MDAnalysisTests/visualization/test_streamlines.py::test_streamplot_3D PASSED [100%]
-= 19099 passed, 558 skipped, 2 deselected, 7 xfailed, 3 xpassed, 170146 warnings in 978.99s (0:16:18) =
-2025-02-23 06:41:15,294 [WARNING] DueCredit internal failure while running <function DueSwitch.dump at 0xffff8219e2a0>: PermissionError(13, 'Permission denied'). Please report to developers at https://github.com/duecredit/duecredit/issues (utils.py:211)
+= 19099 passed, 558 skipped, 2 deselected, 7 xfailed, 3 xpassed, 170146 warnings in 1249.88s (0:20:49) =
+2026-03-29 16:02:50,216 [WARNING] DueCredit internal failure while running <function DueSwitch.dump at 0xffff7bb9e2a0>: PermissionError(13, 'Permission denied'). Please report to developers at https://github.com/duecredit/duecredit/issues (utils.py:211)
DueCredit Report:
- Molecular simulation analysis library / MDAnalysis (v 2.8.0) [1, 2]
@@ -26198,7 +26234,7 @@
- Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.8.0) [8]
- Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel (v 2.8.0) [9]
- LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.8.0) [2]
- - FCA fast correlation algorithm, Mean Squared Displacements with tidynamics / MDAnalysis.analysis.msd (v 2.8.0) [10, 11]
+ - Mean Squared Displacements with tidynamics, FCA fast correlation algorithm / MDAnalysis.analysis.msd (v 2.8.0) [10, 11]
- Cumulative overlap / MDAnalysis.analysis.pca (v 2.8.0) [12]
- Specifications of the H5MD standard, MDAnalysis trajectory reader/writer of the H5MDformat / MDAnalysis.coordinates.H5MD (v 1.1, 2.8.0) [13, 14]
- MMTF Reader / MDAnalysis.coordinates.MMTF (v 2.8.0) [15]
@@ -45891,8 +45927,8 @@
testsuite/MDAnalysisTests/visualization/test_streamlines.py::test_streamplot_2D_zero_return PASSED [ 99%]
testsuite/MDAnalysisTests/visualization/test_streamlines.py::test_streamplot_3D PASSED [100%]
-= 19103 passed, 558 skipped, 2 deselected, 7 xfailed, 3 xpassed, 170226 warnings in 841.45s (0:14:01) =
-2025-02-23 06:55:23,219 [WARNING] DueCredit internal failure while running <function DueSwitch.dump at 0xffff992119e0>: PermissionError(13, 'Permission denied'). Please report to developers at https://github.com/duecredit/duecredit/issues (utils.py:211)
+= 19103 passed, 558 skipped, 2 deselected, 7 xfailed, 3 xpassed, 170226 warnings in 1428.35s (0:23:48) =
+2026-03-29 16:26:46,762 [WARNING] DueCredit internal failure while running <function DueSwitch.dump at 0xffff93a819e0>: PermissionError(13, 'Permission denied'). Please report to developers at https://github.com/duecredit/duecredit/issues (utils.py:211)
DueCredit Report:
- Molecular simulation analysis library / MDAnalysis (v 2.8.0) [1, 2]
@@ -45904,9 +45940,9 @@
- Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.8.0) [8]
- Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel (v 2.8.0) [9]
- LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.8.0) [2]
- - Mean Squared Displacements with tidynamics, FCA fast correlation algorithm / MDAnalysis.analysis.msd (v 2.8.0) [10, 11]
+ - FCA fast correlation algorithm, Mean Squared Displacements with tidynamics / MDAnalysis.analysis.msd (v 2.8.0) [10, 11]
- Cumulative overlap / MDAnalysis.analysis.pca (v 2.8.0) [12]
- - Specifications of the H5MD standard, MDAnalysis trajectory reader/writer of the H5MDformat / MDAnalysis.coordinates.H5MD (v 2.8.0, 1.1) [13, 14]
+ - Specifications of the H5MD standard, MDAnalysis trajectory reader/writer of the H5MDformat / MDAnalysis.coordinates.H5MD (v 1.1, 2.8.0) [13, 14]
- MMTF Reader / MDAnalysis.coordinates.MMTF (v 2.8.0) [15]
- The TNG paper / MDAnalysis.coordinates.TNG (v 2.8.0) [16]
- QCProt implementation / MDAnalysis.lib.qcprot (v 2.8.0) [17, 18]
@@ -45964,8 +46000,8 @@
dh_md5sums -O--buildsystem=pybuild
dh_builddeb -O--buildsystem=pybuild
dpkg-deb: building package 'python3-mdanalysis-dbgsym' in '../python3-mdanalysis-dbgsym_2.8.0-4_arm64.deb'.
-dpkg-deb: building package 'python3-mdanalysis' in '../python3-mdanalysis_2.8.0-4_arm64.deb'.
dpkg-deb: building package 'python-mdanalysis-doc' in '../python-mdanalysis-doc_2.8.0-4_all.deb'.
+dpkg-deb: building package 'python3-mdanalysis' in '../python3-mdanalysis_2.8.0-4_arm64.deb'.
dpkg-genbuildinfo --build=binary -O../mdanalysis_2.8.0-4_arm64.buildinfo
dpkg-genchanges --build=binary -O../mdanalysis_2.8.0-4_arm64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
@@ -45974,12 +46010,14 @@
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/283285/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/283285/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/3027168 and its subdirectories
-I: Current time: Sun Feb 23 06:56:05 -12 2025
-I: pbuilder-time-stamp: 1740336965
+I: removing directory /srv/workspace/pbuilder/283285 and its subdirectories
+I: Current time: Sun Mar 29 16:28:22 +14 2026
+I: pbuilder-time-stamp: 1774751302