Your message dated Thu, 09 Mar 2023 02:34:33 +0000
with message-id <e1pa66z-0058i0...@fasolo.debian.org>
and subject line Bug#1032488: fixed in opendrop 3.3.1-5
has caused the Debian Bug report #1032488,
regarding opendrop: arkode (sundials) error prevents interfacial tension
analysis
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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immediately.)
--
1032488: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1032488
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: opendrop
Version: 3.3.1-4
Severity: grave
Tags: patch upstream
Justification: renders package unusable
debian patch sundials_nvector_API6.patch enabled opendrop to build
against sundials 6.
Nevertheless it still fails when attempting to analysis interfacial
tension measurements:
[ARKODE::ERKStep ERROR] erkStep_FullRHS
At t = inf, the right-hand side routine failed in an unrecoverable manner.
[ARKODE ERROR] ARKODE
At t = 0, the right-hand side routine failed in an unrecoverable manner.
Exception in callback PendantAnalysisJob._ylfit_done(<Future finis...e()
failed.')>)
handle: <GLibSourceHandle PendantAnalysisJob._ylfit_done(<Future
finis...ylfit_done()]>)>
concurrent.futures.process._RemoteTraceback:
"""
Traceback (most recent call last):
File "/usr/lib/python3.11/concurrent/futures/process.py", line 256, in
_process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/opendrop/fit/younglaplace/__init__.py",
line 51, in young_laplace_fit
model.set_params(initial_params)
File "/usr/lib/python3/dist-packages/opendrop/fit/younglaplace/model.py",
line 86, in set_params
dr_dBo, dz_dBo = radius * shape.DBo(s)
^^^^^^^^^^^^
File "opendrop/fit/younglaplace/shape.pyx", line 71, in
opendrop.fit.younglaplace.shape.YoungLaplaceShape.DBo
File "opendrop/fit/younglaplace/shape.pyx", line 89, in
opendrop.fit.younglaplace.shape.YoungLaplaceShape.DBo_array
RuntimeError: ERKStepEvolve() failed.
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/opendrop/vendor/aioglib/_loop.py", line
463, in __call__
self._context.run(self._callback, *self._args)
File "/usr/lib/python3/dist-packages/opendrop/app/ift/services/analysis.py",
line 219, in _ylfit_done
raise e
File "/usr/lib/python3/dist-packages/opendrop/app/ift/services/analysis.py",
line 217, in _ylfit_done
result = fut.result()
^^^^^^^^^^^^
RuntimeError: ERKStepEvolve() failed.
Upstream has prepared a patch to update properly for sundials 6 in
commit cf9d5aa (development branch),
https://github.com/jdber1/opendrop/commit/cf9d5aa2f06d625f306114d001a99934cb913ff0
-- System Information:
Debian Release: 12.0
APT prefers unstable
APT policy: (500, 'unstable'), (1, 'experimental')
merged-usr: no
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 6.1.0-5-amd64 (SMP w/8 CPU threads; PREEMPT)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8),
LANGUAGE=en_AU:en
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
Versions of packages opendrop depends on:
ii gir1.2-gdkpixbuf-2.0 2.42.10+dfsg-1+b1
ii gir1.2-gtk-3.0 3.24.36-4
ii libc6 2.36-8
ii libgcc-s1 12.2.0-14
ii libpython3.11 3.11.2-5
ii libstdc++6 12.2.0-14
ii libsundials-arkode5 6.4.1+dfsg1-3
ii python3 3.11.2-1
ii python3-cairo 1.20.1-5+b1
ii python3-gi 3.42.2-3+b1
ii python3-injector 0.20.1-1
ii python3-matplotlib 3.6.3-1+b1
ii python3-numpy 1:1.24.2-1
ii python3-opencv 4.6.0+dfsg-11
ii python3-scipy 1.10.1-2
opendrop recommends no packages.
Versions of packages opendrop suggests:
ii opendrop-doc 3.3.1-4.1
-- no debconf information
--- End Message ---
--- Begin Message ---
Source: opendrop
Source-Version: 3.3.1-5
Done: Drew Parsons <dpars...@debian.org>
We believe that the bug you reported is fixed in the latest version of
opendrop, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1032...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Drew Parsons <dpars...@debian.org> (supplier of updated opendrop package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Thu, 09 Mar 2023 02:24:59 +0100
Source: opendrop
Architecture: source
Version: 3.3.1-5
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Closes: 1032488
Changes:
opendrop (3.3.1-5) unstable; urgency=medium
.
* debian patch fix_DBo_2f7dc0e.patch applies upstream commit 2f7dc0e
to fix analysis of Interfacial Tension. Closes: #1032488.
* replace debian patch sundials_nvector_API6.patch with
sundials_API6_cf9d5aa.patch applying upstream commit
cf9d5aa (dev branch) to fix build with sundials 6.
* debian patch pygobject_gtk3.patch reduces gui errors by
asserting use of Gtk 3.
* Standards-Version: 4.6.2
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67f18c2c7dbdeaf74a3903a6452ef88d5123b4de 30800 opendrop_3.3.1-5.debian.tar.xz
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opendrop_3.3.1-5.dsc
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opendrop_3.3.1-5.debian.tar.xz
Files:
52b6881f92ff6329b916ab3a186ae541 2614 science optional opendrop_3.3.1-5.dsc
8c412c9cb5e2ac7f45125ac87e29d168 30800 science optional
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--- End Message ---
