Your message dated Thu, 09 Mar 2023 02:34:33 +0000 with message-id <[email protected]> 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 message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 1032488: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1032488 Debian Bug Tracking System Contact [email protected] 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
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--- Begin Message ---Source: opendrop Source-Version: 3.3.1-5 Done: Drew Parsons <[email protected]> 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 [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Drew Parsons <[email protected]> (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 [email protected]) -----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 <[email protected]> Changed-By: Drew Parsons <[email protected]> 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 Checksums-Sha1: 31f7840d7bb431a98576697c62c7d7a4478f1d6c 2614 opendrop_3.3.1-5.dsc 67f18c2c7dbdeaf74a3903a6452ef88d5123b4de 30800 opendrop_3.3.1-5.debian.tar.xz Checksums-Sha256: 7a5babe05f49bb7558b716ef9e0df961a480295cab8f31cbb3a9727843653738 2614 opendrop_3.3.1-5.dsc e2c09d0f25f69ea27358a4ee657c89e4cbd5d10184ca8d6e79eb9c231134959a 30800 opendrop_3.3.1-5.debian.tar.xz Files: 52b6881f92ff6329b916ab3a186ae541 2614 science optional opendrop_3.3.1-5.dsc 8c412c9cb5e2ac7f45125ac87e29d168 30800 science optional opendrop_3.3.1-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEI8mpPlhYGekSbQo2Vz7x5L1aAfoFAmQJOMYACgkQVz7x5L1a Afro3w/9FIBxv4uBsoLSp4ZWWLI6IUA8iuQe8u7waWOpa9jxapglOHKdXMkspH9P chzSC9E7YX8UGsU4gCoB21CiwouAcQ+GIacuLGgSehy/wpUv2enkjGWNqBIbbjhb o9qm1zIp5+jyrLoY//cT5IxqHCz5V5OlAzbewTu6smyxQE8Atb9Fg22HgPQiMemX pXvv/hFO4i63RC7pXsDQZ1+pIdHz1CTS8/D7D5VhM6TdihvpQt75OgCT+2e8iomg 6Gqjtx4DVxZFupL1EAOLFsFuzIlXM1mAaHEA7jbKKxD0QD/ASpG50qkh9QTtg4H0 DOCt63F/1jgO3BzAlA29siPWOkXwX5659fOA/X39UrcIMBSokG4NqaZdugF7HFXa J+fwdARcnqeBa87CyP+WizOzrF/50NmeRMl9NWn1iz0Z9W9bebyAK5PgySDQq8Qz bDoH9BeOSE7Fp5O4vpkG6Fn7icCiPG7bJNhTIgEgfUFovmH4Yz2ckR18uvdUWOwq TcE9lFYK9ybGc/QI4KLfy4yvgPgrbPM50Vc2IUCFtZSTmSrAoD5W/KTdzpSoAYY3 IjhFHFwPzHFcufvxvniF8KGEwgQwtKHfbeUhHzZngATPa4bD0iep/TKrT63g4XqW ycSVL1ku6LTreTNWW8xRTguSr6FuzD+D6sOFBPg6oMBiZw6ma4k= =8+mF -----END PGP SIGNATURE-----
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