Bug#1101686: mpich: triggers test errors: MPII_init_gpu(51)....: gpu_init failed

2025-05-02 Thread Drew Parsons
Package: mpich Followup-For: Bug #1101686 Control: forwarded -1 https://github.com/pmodels/mpich/issues/7399 Post scriptum for this mpich gpu bug, upstream received notice about the problem with gpu support https://github.com/pmodels/mpich/issues/7399 and has now applied a patch https://github.c

Bug#747188: closed by Jeremy Bícha (closing old GNOME Shell bugs)

2025-04-21 Thread Drew Parsons
Thanks. Confirming the bug seems to be fixed in Gnome 48.

Bug#1103427: pymatgen: autopkgtest regression: exit code 5

2025-04-20 Thread Drew Parsons
Source: pymatgen Followup-For: Bug #1103427 Control: severity -1 normal It's a network test, and marked with needs-internet At the particular point in time you saw a failure, online database being accessed was offline. Downgrading severity. This is not an ongoing bug.

Bug#1102612: mpich 4.3 not initialising multiple processes

2025-04-20 Thread Drew Parsons
Package: mpich Version: 4.3.0-5 Followup-For: Bug #1102612 Control: found -1 4.3.0-5 Control: fixed -1 4.3.0-6 Updating tags (the fixed version is in experimental, the version in unstable is not yet updated).

Bug#1103651: superlu-dist: superlu_dist 9 fails to build with CombBLAS

2025-04-20 Thread Drew Parsons
Source: superlu-dist Version: 8.2.1+dfsg1-5 Severity: important Tags: ftbfs Control: forwarded -1 https://github.com/xiaoyeli/superlu_dist/issues/165 Upstream has release superlu-dist 9, but it fails to build against CombBLAS: cd /repositories/superlu-dist/obj-x86_64-linux-gnu/EXAMPLE && /usr/bin

Bug#1102068: libfabric: FTBFS on 32-bit arches: ofi_cma.h: error: passing argument 2 of 'ofi_consume_iov' from incompatible pointer type

2025-04-16 Thread Drew Parsons
Source: libfabric Version: 2.1.0-1 Followup-For: Bug #1102068 Control: tags -1 ftbfs Control: reopen -1 I think that bug closed by mpich 4.3.0-6 was meant to be one of the other mpich bugs (#1102612). 32-bit arches are still failing to build libfabric 2.1.0-1 the same way, so reopening this bug.

Bug#1102612: mpich 4.3 not initialising multiple processes

2025-04-14 Thread Drew Parsons
Package: mpich Followup-For: Bug #1102612 Is this upstream bug related to the problem? https://github.com/pmodels/mpich/issues/7064#issuecomment-2301026290 It suggests the pmix build configuration might be an issue. The timing of that bug doesn't match well, though, it was made in August 2024, be

Bug#1102731: nwchem-mpich and nwchem-openmpi have an undeclared file conflict on /usr/bin/nwchem

2025-04-12 Thread Drew Parsons
Package: nwchem Followup-For: Bug #1102731 Control: tags 1102731 moreinfo Control: severity 1102731 normal Hi Helmut, can you give more information on where you find the file conflict? /usr/bin/nwchem is a symlink to the build for the default MPI for the given architecture. On 64-bit systems op

Bug#1102612: mpich 4.3 not initialising multiple processes

2025-04-11 Thread Drew Parsons
Package: mpich Followup-For: Bug #1102612 There is evidence that libucx0 might be the problem, or a problem, in the ga (libglobalarrays-dev) build logs https://buildd.debian.org/status/fetch.php?pkg=ga&arch=amd64&ver=5.9.1-1&stamp=1744381093&raw=0 e.g. FAIL: global/testing/pgtest copy is OK

Bug#1102612: mpich 4.3 not initialising multiple processes

2025-04-11 Thread Drew Parsons
Package: mpich Version: 4.3.0-5 Followup-For: Bug #1102612 One data point might be relevant. The bug reported here manifests in the amd64 and arm64 tests of armci-mpi. But the armci-mpi tests are passing cleanly on the 32-bit arches, armhf and the others. I note that the build time mpich errors

Bug#1102465: petsc: PETSc was configured with one MPICH/Open MPI mpi.h version but now appears to be compiling using an older version

2025-04-11 Thread Drew Parsons
Source: petsc Followup-For: Bug #1102465 Control: block 1102465 by 1102612 Control: severity 1102465 normal Thinking about it further, I don't think we have a bug here as such, and I'm therefore lowering severity. I don't think any action is needed either. The latest petsc build requires the late

Bug#1102612: mpich 4.3 not initialising multiple processes

2025-04-10 Thread Drew Parsons
Package: mpich Version: 4.3.0-5 Severity: serious Justification: debci I apologise for another serious bug, but mpich 4.3 is doing weird things that we don't want in trixie. I see the problem in mpich test errors in armci-mpi (https://buildd.debian.org/status/fetch.php?pkg=armci-mpi&arch=amd64&ver

Bug#1102465: petsc: PETSc was configured with one MPICH/Open MPI mpi.h version but now appears to be compiling using an older version

2025-04-09 Thread Drew Parsons
Control: block -1 by 1101686 On 2025-04-09 11:15, Adrian Bunk wrote: Source: petsc Version: 3.22.3+dfsg1-1 Issues preventing migration: ∙ ∙ autopkgtest for dolfin/2019.2.0~legacy20240219.1c52e83-18: amd64: Pass, arm64: Pass, armel: Regression or new test ♻ (reference ♻), armhf: Regression or

Bug#1101686: mpich: triggers test errors: MPII_init_gpu(51)....: gpu_init failed

2025-04-08 Thread Drew Parsons
Package: mpich Version: 4.3.0-4 Followup-For: Bug #1101686 Control: reopen 1101686 Alistair, mpich 4.3.0-4 is still triggering gpu errors in armci-mpi, bagel and eztrace. -- System Information: Debian Release: trixie/sid APT prefers unstable-debug APT policy: (500, 'unstable-debug'), (500,

Bug#1096624: fenics-dolfinx: ftbfs with GCC-15

2025-04-05 Thread Drew Parsons
Source: fenics-dolfinx Followup-For: Bug #1096624 Control: tags -1 ftbfs There is a fair change this is not a gcc-15 bug, nor even a bug at all. It's more likely to be a nanobind inconsistency. All nanobind clients need to be rebuilt at the same time to maintain interoperability. cf. dolfinx-mpc

Bug#1101777: xtl: new upstream release

2025-04-05 Thread Drew Parsons
Source: xtl Version: 0.7.7-1 Severity: normal xtl 0.8.0 is now released. It is needed by xtensor 0.26.0. Should we try to get them into trixie?

Bug#1101794: ITP: python-qutip -- QuTiP: Quantum Toolbox in Python

2025-04-04 Thread Drew Parsons
On 2025-04-01 02:08, Dirk Lehmann wrote: Package: wnpp Severity: wishlist Owner: Dirk Lehmann X-Debbugs-Cc: debian-scie...@lists.debian.org * Package name: python-qutip Version : 5.1.1 Upstream Contact: https://github.com/qutip/qutip/discussions * URL : https://githu

Bug#1102068: libfabric: FTBFS on 32-bit arches: ofi_cma.h: error: passing argument 2 of 'ofi_consume_iov' from incompatible pointer type

2025-04-04 Thread Drew Parsons
Source: libfabric Severity: serious Tags: ftbfs Justification: ftbfs X-Debbugs-Cc: debian-am...@lists.debian.org, debian-...@lists.debian.org, debian-h...@lists.debian.org, debian-powe...@lists.debian.org, debian-sup...@lists.debian.org User: debian-...@lists.debian.org Usertags: armel armhf User

Bug#1100943: pipewire: Sporadic audio crackling/distortion with pipewire 1.4.1-1

2025-04-03 Thread Drew Stephens
Package: pipewire Version: 1.4.1-1 Followup-For: Bug #1100943 Also happening on my end with combination of this and fluidsynth. I independently stumbled upon the workaround. As I don't want to get rid of fluidsynth, I've put the workaround in my session startup for now. Thank you for your time.

Bug#1101686: mpich: triggers test errors: MPII_init_gpu(51)....: gpu_init failed

2025-04-01 Thread Drew Parsons
Package: mpich Version: 4.3.0-4 Followup-For: Bug #1101686 Control: affects -1 src:armci-mpi src:bagel src:eztrace It looks like there might have been a problem with the 4.3.0-4 upload. Changelog says it disabled GPU (HIP) support, but looks like the wrong bug numbers might have been given (this

Bug#1101794: ITP: python-qutip -- QuTiP: Quantum Toolbox in Python

2025-04-01 Thread Drew Parsons
On 2025-04-01 03:00, Dirk Lehmann wrote: Hello Drew On 4/1/25 2:56 AM, Drew Parsons wrote: On 2025-04-01 02:08, Dirk Lehmann wrote: Package: wnpp Severity: wishlist Owner: Dirk Lehmann X-Debbugs-Cc: debian-scie...@lists.debian.org * Package name    : python-qutip   Version : 5.1.1

Bug#1101785: ITP: python-qutip-qip-doc -- QuTiP package - Quantum Information Processing (documentation)

2025-03-31 Thread Drew Parsons
for `python3-qutip-qip`. Note that the ITPs are filed for source packages, not binary packages. So only one python-qutip-qip source package is needed. The docs are included in the source, and built alongside the python3-qutip-qip binary package. Drew

Bug#1101766: ITP: python3-qutip-core -- QuTiP: Quantum Toolbox in Python (core)

2025-03-31 Thread Drew Parsons
27;re just reconfiguring the packaging to move the existing contents to a new python3-qutip-core package instead of python3-qutip, and retaining python3-qutip as a dependency package. They're made from the same (existing) source package. Drew

Bug#1101686: mpich: triggers test errors: MPII_init_gpu(51)....: gpu_init failed

2025-03-30 Thread Drew Parsons
Package: mpich Version: 4.3.0-3 Severity: serious Justification: FTBFS The new mpich 4.3.0 is doing something different with GPUs that is causing test failures. mpich itself was affected, Bug#1100880, but 4.3.0-3 hid the problem by disabling GPU support in autopkgtests. That doesn't help other pa

Bug#1096624: fenics-dolfinx: ftbfs with GCC-15

2025-03-29 Thread Drew Parsons
Source: fenics-dolfinx Followup-For: Bug #1096624 Control: tags -1 ftbfs "change" = "chance" in the message above

Bug#1101505: fenics-dolfinx: successful pusimp tests display tested error states

2025-03-28 Thread Drew Parsons
Source: fenics-dolfinx Version: 1:0.9.0-6 Severity: normal The pusimp test in fenics-dolfinx/debian/tests/test-dolfinx-python-pusimp invokes pytest with -s. This means the tested error conditions get displayed, even when the test is successful, e.g. showing ImportError: pusimp has detected the

Bug#1100538: scipy-doc: broken mathjax

2025-03-23 Thread Drew Parsons
Source: scipy Followup-For: Bug #1100538 Control: tags -1 moreinfo How are you accessing the docs? The doc packages are constructed to be accessed locally from the local filesystem, not from a web server, at least that's how I access them i.e. from file:///usr/share/doc/HTML/index.html not h

Bug#1098576: mpi4py: FTBFS: testIMProbe (test_util_pkl5.TestMPISelf.testIMProbe) ... [c7a-large-1740141036:00000] *** An error occurred in PMIx Event Notification

2025-03-22 Thread Drew Parsons
Source: pmix Version: 5.0.7-1 Followup-For: Bug #1098576 Control: tags -1 ftbfs There is some caprice in this bug. I tested mpi4py again with the new versions pmix 5.0.7 and linux 6.12.19. Locally (dpkg-buildpackage) the tests passed without error. So I figured the problem might have been fixed

Bug#1101061: gnome-keyring: After upgrade keyrings expected in .local/share/keyrings but were left in .gnome2/keyrings

2025-03-22 Thread Drew Vogel
Upon further investigation, I think it is very unlikely this misbehavior is due to the gnome-keyring debian package. The relevant code in upstream[1] is very old. It appears to check for the existence of both dirs and prioritizes the new one if both dirs exist. The creation timestamp for the new di

Bug#1101061: gnome-keyring: After upgrade keyrings expected in .local/share/keyrings but were left in .gnome2/keyrings

2025-03-22 Thread Drew Vogel
Package: gnome-keyring Version: 48~beta-3 Severity: important X-Debbugs-Cc: drewpvo...@gmail.com Dear Maintainer, It appears the upgrade of gnome-keyring-daemon does not always account for the existance of keyring files. After upgrading with apt dist-upgrade, I rebooted. After reboot, multiple

Bug#1100833: dipy: FTBFS on s390x: two tests failing

2025-03-22 Thread Drew Parsons
On 2025-03-22 13:22, Santiago Vila wrote: Hi. I've just made a team upload trying to address this. The skips would probably needs to be added to both debian/rules and debian/tests. I was unsure about how to do that, but then I looked at the autopkgtests logs and realized that the tests mark

Bug#1100880: mpich: MPII_init_gpu ... gpu_init failed

2025-03-19 Thread Drew Parsons
Package: mpich Version: 4.3.0-2 Severity: serious Justification: debci Control: affects -1 src:armci-mpi mpich 4.3 is doing something different with gpu support, that is causing tests to fail, both mpich's own tests (on amd64 etc) and build tests in other packages like armci-mpi. For instance, mp

Bug#1100833: dipy: FTBFS on s390x: two tests failing

2025-03-19 Thread Drew Parsons
Source: dipy Version: 1.10.0-2 Severity: serious Tags: ftbfs Justification: FTBFS X-Debbugs-Cc: debian-s...@lists.debian.org User: debian-s...@lists.debian.org Usertags: s390x dipy 1.11 is trying to access a scipy algorithm which is apparently not supported on s390x, ValueError: scipy.sparse doe

Bug#1096535: dolfinx-mpc: ftbfs with GCC-15

2025-03-18 Thread Drew Parsons
Source: dolfinx-mpc Followup-For: Bug #1096535 Control: tags -1 ftbfs Upstream has run a battery of tests. Looks like gcc-15 is not a problem itself. The problem might not be the nanobind version either (sometimes nanobind upgrades will give an ABI conflict, but 2.5 is supposed to be be compatib

Bug#958152: dh-python: improve variables documentation (in particular how to skip tests)

2025-03-15 Thread Drew Parsons
Package: dh-python Followup-For: Bug #958152 Correction, PYBUILD_TEST_PYTEST=1 actually does work. Which proves the point of this bug. How are we supposed to know that is the env variable syntax for --test-pytest, without having to wildly guess it? Please add documentation for the variables.

Bug#958152: dh-python: improve variables documentation (in particular how to skip tests)

2025-03-15 Thread Drew Parsons
Package: dh-python Version: 6.20250308 Followup-For: Bug #958152 I agree with this bug report. The documention does not make it clear how to set the environment variables that control dh's use of pybuild. For instance the pybuild man page says there are options to set which test system is used.

Bug#1100120: libopenmpi-dev: mpi4py spawn tests fail with MPI_ERR_UNKNOWN

2025-03-11 Thread Drew Parsons
Package: libopenmpi-dev Followup-For: Bug #1100120 Control: retitle -1 libopenmpi-dev: mpi4py spawn tests fail with MPI_ERR_UNKNOWN Control: severity -1 normal The OPAL ERROR or libucs segfault at the end of the tests can be avoided by setting OMPI_MCA_btl_tcp_if_include=lo (that's with OMPI_ not

Bug#1100120: libopenmpi-dev: mpi4py spawn tests get OPAL ERROR: Unreachable in file ../../../ompi/runtime/ompi_mpi_finalize.c at line 286

2025-03-11 Thread Drew Parsons
Package: libopenmpi-dev Followup-For: Bug #1100120 We can see the spawn errors in the mpi4py 4.0.3-2 build logs, e.g. https://buildd.debian.org/status/fetch.php?pkg=mpi4py&arch=amd64&ver=4.0.3-2&stamp=1741705221&raw=0 Skipping the test_spawn tests, remaing tests pass but I get the following err

Bug#1100120: libopenmpi-dev: mpi4py spawn tests get OPAL ERROR: Unreachable in file ../../../ompi/runtime/ompi_mpi_finalize.c at line 286

2025-03-11 Thread Drew Parsons
Many.testNoArgs) -- Traceback (most recent call last): File "/home/drew/projects/python/build/mpi4py/test/test_spawn.py", line 175, in testNoArgs child = self.COMM.Spawn( script, None, self.MAXPROCS, info=self.INFO, root=self.ROOT, ) File "src/

Bug#1098576: mpi4py: FTBFS: testIMProbe (test_util_pkl5.TestMPISelf.testIMProbe) ... [c7a-large-1740141036:00000] *** An error occurred in PMIx Event Notification

2025-03-10 Thread Drew Parsons
Source: pmix Followup-For: Bug #1098576 Control: tags -1 ftbfs These PMIx errors seem to be accompanied with kernel errors, including a GPF from libc which doesn't sound good. In /var/log/syslog: 2025-03-10T20:51:04.457486+01:00 debbox kernel: traps: prte[126492] general protection fault ip:7f00

Bug#1096535: dolfinx-mpc: ftbfs with GCC-15

2025-03-10 Thread Drew Parsons
Source: dolfinx-mpc Followup-For: Bug #1096535 Control: tags -1 ftbfs Control: affects -1 src:nanobind Your build log shows the build used package versions gcc-15 15-20250213-1 nanobind 2.5.0-1 dolfinx 1:0.9.0-6+b2 python 3.13.2-1 dolfinx 1:0.9.0-6+b2 was built against nanobind 2.4.0-1 and python

Bug#1096208: dipy: fails tests with scipy 1.15

2025-03-10 Thread Drew Parsons
Source: dipy Followup-For: Bug #1096208 Control: severity -1 serious scipy 1.15 is now uploaded to unstable, so raising to severity: serious

Bug#1098576: mpi4py: FTBFS: testIMProbe (test_util_pkl5.TestMPISelf.testIMProbe) ... [c7a-large-1740141036:00000] *** An error occurred in PMIx Event Notification

2025-03-08 Thread Drew Parsons
Source: pmix Followup-For: Bug #1098576 Control: tags -1 ftbfs It's quite possible the bug is in openmpi, not pmix itself. For instance mpich isn't triggering the error in the mpi4py tests cf. https://tests.reproducible-builds.org/debian/rb-pkg/unstable/armhf/mpi4py.html There was a patch in ope

Bug#1098652: datalab: arm64 failing tests with scipy 1.15

2025-03-06 Thread Drew Parsons
Source: datalab Followup-For: Bug #1098652 Control: forwarded -1 https://github.com/DataLab-Platform/DataLab/issues/117 reported upstream https://github.com/DataLab-Platform/DataLab/issues/117 Upstream says this is a bug in scipy 1.15, https://github.com/scipy/scipy/issues/22586 proposed patch i

Bug#1096208: dipy: fails tests with scipy 1.15

2025-03-06 Thread Drew Parsons
Source: dipy Followup-For: Bug #1096208 numpy 2 is now transitioned to testing. I guess it should be safe to upload the dipy patch now? Drew

Bug#1008296: gdm3: No option to choose between gnome 42 wayland or x11, always goes x11

2025-03-05 Thread Drew Parsons
Package: gdm3 Followup-For: Bug #1008296 Poking the internet around wayland and nvidia, I found that gdm3 is set up to deactivate wayland if it finds nvidia is available but not fully configured. This is why gdm does not show the Wayland option for the Gnome session. It has deliberately been dis

Bug#1098576: mpi4py: FTBFS: testIMProbe (test_util_pkl5.TestMPISelf.testIMProbe) ... [c7a-large-1740141036:00000] *** An error occurred in PMIx Event Notification

2025-02-27 Thread Drew Parsons
Source: mpi4py Followup-For: Bug #1098576 Control: tags -1 ftbfs Control: reassign -1 libpmix-dev Control: affects -1 src:mpi4py I guess this is a problem in the PMIX library, not mpi4py. It might be just a transition mismatch with the recent pmix and openmpi updates. Drew

Bug#1094821: spglib: autopkgtest failure on 32 bits blocking ruby3.3 transition

2025-02-26 Thread Drew Parsons
Source: spglib Followup-For: Bug #1094821 numpy2 is now in testing, and spglib tests are passing. I think we can close this bug now.

Bug#1098805: acpi-call-dkms: dkms kernel module fails to build

2025-02-24 Thread Drew Parsons
Package: acpi-call-dkms Followup-For: Bug #1098805 X-Debbugs-Cc: debian-am...@lists.debian.org User: debian-am...@lists.debian.org Usertags: amd64 Control: tags -1 ftbfs Control: severity -1 normal I was confused by the last update date of acpi-call-dkms (22 Feb) and thought my issue was triggered

Bug#1098805: acpi-call-dkms: dkms kernel module fails to build

2025-02-24 Thread Drew Parsons
Package: acpi-call-dkms Version: 1.2.2-2.1 Severity: serious Tags: ftbfs Justification: FTBFS Upgrading to 1.2.2-2.1, acpi-call-dkms is failing to build kernel modules, complaining about existing source: Setting up acpi-call-dkms (1.2.2-2.1) ... Removing old acpi-call/1.2.2 DKMS files... Loading

Bug#1098652: datalab: arm64 failing tests with scipy 1.15

2025-02-22 Thread Drew Parsons
Source: datalab Version: 0.18.1-1 Severity: normal X-Debbugs-Cc: debian-...@lists.debian.org User: debian-...@lists.debian.org Usertags: arm64 datalab on arm64 is failing tests against scipy 1.15 from experimental. amd64 is passing tests. not clear what the problem is.

Bug#1098454: python3-qutip: Importing 'qutip.qip' requires new Debian 'python3-qutip-qip' package.

2025-02-21 Thread Drew Parsons
Source: qutip Followup-For: Bug #1098454 Control: reassign 1098454 wnpp Control: retitle 1098454 RFP: qutip-qip -- QuTiP quantum information processing Hi Dirk, qutip-qip is a separate package (a plugin addon package for qutip). Its home page is https://github.com/qutip/qutip-qip What you're requ

Bug#1092981: Autopkgtests fail with KeyError: 'l'

2025-02-19 Thread Drew Parsons
The KeyError: 'l' error is no longer triggered. I think it was an issue in one of the other packages, not pymatgen, and now fixed. I think we can close these bugs now unless you're seeing other issues with the package. True, there is some other different error in 32-bit testing. I think again t

Bug#1096176: mdanalysis: autopkgtest failures

2025-02-19 Thread Drew Parsons
mdanalysis 2.8.0-4 is now passing tests. The only change was to run tests verbose, so perhaps the fix was made in numpy2 or multiprocessing. 1096176 may have been fixed by mdanalysis 2.8.0. I think we can close these bugs now, unless you're seeing any other problems. Drew

Bug#1098365: python3-numpy: f2py does not look for fortranobject.c src in multiarch libdir

2025-02-19 Thread Drew Parsons
Package: python3-numpy Version: 1:2.2.3+ds-1 Severity: important For numpy2 files for building numpy extensions have been moved to python3-numpy-dev. As a side effect this has broken f2py. /usr/lib/python3/dist-packages/numpy/f2py/f2py2e.py l.451 accesses fortranobject.c amd .h from the src subd

Bug#1098273: mc: command line subshell becomes nonresponsive after launching a command

2025-02-18 Thread Drew Parsons
Package: mc Version: 3:4.8.33-1 Severity: important The recent mc upgrade appears to have introduced a major regression in behaviour of the command line subshell. I'm referring to the single-line command line appearing near the bottom of the normal mc screen below the list of files, not the full s

Bug#1082816: petsc: enable AMD GPU support

2025-02-18 Thread Drew Parsons
remain operational as they are and automatically gain from the speed up if executed on GPU-supporting hardware? Is the GPU support available for all our CPU architectures? Drew

Bug#1096262: xrayutilities: fails tests with scipy 1.15: cannot import name 'derivative' from 'scipy.misc'

2025-02-17 Thread Drew Parsons
Source: xrayutilities Version: 1.7.8-2 Severity: normal xrayutilities is failing tests with scipy 1.15 from experimental, evidently due to use of deprecated API. Version 1.7.10 has been released upstream and should be compatible. https://ci.debian.net/data/autopkgtest/unstable/amd64/x/xrayutili

Bug#1096252: scikit-learn: fails tests with scipy 1.15

2025-02-17 Thread Drew Parsons
Source: scikit-learn Version: 1.4.2+dfsg-7 Severity: normal scikit-learn is failing tests with scipy 1.15 from experimental https://ci.debian.net/data/autopkgtest/unstable/amd64/s/scikit-learn/57873442/log.gz 256s FAILED ../../../../usr/lib/python3/dist-packages/sklearn/preprocessing/tests/test

Bug#1096208: dipy: fails tests with scipy 1.15

2025-02-17 Thread Drew Parsons
Source: dipy Version: 1.10.0-2 Severity: normal dipy is failing tests with scipy 1.15 from experimental e.g. https://ci.debian.net/packages/d/dipy/unstable/amd64/57839450/ 1756s FAILED reconst/tests/test_csdeconv.py::test_odfdeconv - AssertionError: 1756s FAILED reconst/tests/test_csdeconv.py:

Bug#1096194: python3-cffi: bump priority to Depends: python3-dev

2025-02-17 Thread Drew Parsons
Control: reassign 1096194 python3-ffcx On 2025-02-17 15:18, Stefano Rivera wrote: Hi Drew (2025.02.17_13:15:52_+) python3-cffi has Suggests: python3-dev But when actually using cffi, it needs Python.h and pyconfig.h (included in /usr/lib/python3/dist-packages/cffi/_cffi_include.h) There

Bug#1096194: python3-cffi: bump priority to Depends: python3-dev

2025-02-17 Thread Drew Parsons
Followup-For: Bug #1096194 Control: reassign 1096194 src:scifem No, this was a misdiagnosis. python3-ffcx already does have Depends: python3-dev The issue here is that scifem tests do not explicitly require python3-dev, and then, more to the point, the scifem test is failing with Python 3.12. T

Bug#1096194: python3-cffi: bumpy priority to Depends: python3-dev

2025-02-17 Thread Drew Parsons
Package: python3-cffi Version: 1.17.1-2 Severity: important python3-cffi has Suggests: python3-dev But when actually using cffi, it needs Python.h and pyconfig.h (included in /usr/lib/python3/dist-packages/cffi/_cffi_include.h) That suggests to me the dependency might best be bumped to a strong

Bug#1083172: scipy: python-scipy-doc is broken

2025-02-14 Thread Drew Parsons
Source: scipy Followup-For: Bug #1083172 True, something has gone badly wrong with the doc package for scipy 1.14. In the meantime you may want to try scipy 1.15 from experimental. The scipy 1.15 docs are in place. (the style is broken, which is a different issue as noted in Bug#1088105)

Bug#1095979: autopkgtest: null virt server fails: cannot create /etc/apt/preferences.d/autopkgtest-packages-under-test.pref

2025-02-14 Thread Drew Parsons
Package: autopkgtest Version: 5.44 Severity: normal autopkgtest started failing to start tests today. Previously it was able to launch tests. I'm launching tests using autopkgtest-virt-null, as autopkgtest -B -- null The new error comes from add_apt_preference. I haven't (knowingly) changed an

Bug#1091556: Autopkgtests fail with Python 3.13: KeyError: 'l'

2025-02-13 Thread Drew Parsons
This is a weird error. But pymatgen is successfully building now. I guess the problem was in another package, and has been fixed. When the new build passes debci and is ready to migrate to testing, I'll close these bugs, unless there is any other news to keep them open. Drew

Bug#1095739: mdanalysis FTBFS on i386

2025-02-13 Thread Drew Parsons
Source: mdanalysis Followup-For: Bug #1095739 Yes, I'll add a verbose test flag to armel to help monitor what's troubling it. Upstream marked some distance tests as flaky, but the way they did it broke the tests so it had to be reverted. Drew

Bug#1095739: mdanalysis FTBFS on i386

2025-02-11 Thread Drew Parsons
Source: mdanalysis Followup-For: Bug #1095739 Control: tags -1 ftbfs Thanks. Waiting for build reports from mips64el riscv64 before fixing. Drew

Bug#1094984: python-meshplex: FTBFS with numpy 2.x

2025-02-04 Thread Drew Parsons
Package: python3-meshplex Followup-For: Bug #1094984 Control: tags -1 ftbfs Control: block -1 by 1094985 The bug is effectively in meshio, meshplex is simply accessing a mesh returned by meshio. The problem is that the 2D cell type ("triangle") has no dtype attached to the cell array. Evidently

Bug#1094477: scipy FTBFS on mips64el with numpy 2.2.2: test failures

2025-01-30 Thread Drew Parsons
have been fixed in Numpy 2, but apparently it has gotten worse instead. The workaround is to skip the tests until a proper fix is found. Drew

Bug#1094477: scipy FTBFS on mips64el with numpy 2.2.2: test failures

2025-01-29 Thread Drew Parsons
On 2025-01-29 00:53, Adrian Bunk wrote: Source: scipy Version: 1.14.1-3 Severity: serious Tags: ftbfs X-Debbugs-Cc: Drew Parsons https://buildd.debian.org/status/package.php?p=scipy ... === short test summary info FAILED scipy/special

Bug#1093278: paraview needs a stricter python dependency

2025-01-19 Thread Drew Parsons
e hacked to use the "required" specific version, but I think that wouldn't help anyway to get paraview on the binNMU list for python3 upgrades. The ranged version will do it. Drew

Bug#1093278: paraview needs a stricter python dependency

2025-01-17 Thread Drew Parsons
Package: paraview Followup-For: Bug #1093278 I'd be interested too to know if there's an existing mechanism for this situation. paraview can't be the only package with python extensions that can only be built for the default python. I'd say we'd want Depends: python3.13 rather than Depends: p

Bug#1092354: python3-vtk9: segfault on Python 3.13

2025-01-13 Thread Drew Parsons
On 2025-01-13 21:12, Drew Parsons wrote: Both these patches landed in vtk 9.4, so the simplest fix is to upgrade to the latest upstream release. Well, maybe not the "simplest" fix since it will need new binary package libvtk9.4. But that needs to be done sooner or later.

Bug#1092354: python3-vtk9: segfault on Python 3.13

2025-01-13 Thread Drew Parsons
Package: vtk9 Followup-For: Bug #1092354 Control: forwarded 1092354 https://gitlab.kitware.com/vtk/vtk/-/issues/19466 Reported and fixed upstream, https://gitlab.kitware.com/vtk/vtk/-/merge_requests/11486 Found also in paraview, which shamefully ships its own vtk and needs the same patch. There

Bug#1092347: ITP: scifem -- Scientific Computing Tools for Finite Element Methods

2025-01-07 Thread Drew Parsons
Package: wnpp Severity: wishlist Owner: Drew Parsons X-Debbugs-Cc: debian-de...@lists.debian.org, debian-scie...@lists.debian.org * Package name: scifem Version : 0.3.0 Upstream Contact: Henrik Finsberg * URL : https://scientificcomputing.github.io/scifem * License

Bug#1088865: dolfin: autopkgtests fail

2025-01-03 Thread Drew Parsons
Source: dolfin Followup-For: Bug #1088865 I tested my own legacy code with dolfin on python3.13. It's still running perfectly fine. It looks like the damage here is restricted to the mesh iterators, in MESHITERATOR_MACRO and also mesh.SubsetIterator() If you're not using those iterators, then th

Bug#1088865: dolfin: autopkgtests fail

2025-01-01 Thread Drew Parsons
Source: dolfin Followup-For: Bug #1088865 All of the MESHITERATOR_MACRO functions in python/src/mesh.cpp are affected (cells, facets, faces, edges, vertices) so I guess the problem is somewhere in MESHITERATOR_MACRO: #define MESHITERATOR_MACRO(TYPE, NAME) \ py::class_, \ std::

Bug#1088865: dolfin: autopkgtests fail

2025-01-01 Thread Drew Parsons
Source: dolfin Version: 2019.2.0~legacy20240219.1c52e83-11 Followup-For: Bug #1088865 The mesh itself seems to be fine. >From Francesco's example, both python 3.12 and 3.12 give >>> mesh.cells() array([[0, 1, 4], [0, 3, 4], [1, 2, 5],

Bug#1090393: RM: paraview [ppc64el] -- ROM; FTBFS

2024-12-30 Thread Drew Parsons
stop hindering other packages. Thanks Bas, that's probably best. facet-analyser is a poor victim of paraview upstream's VTK policy, not something we can really fix. Drew

Bug#1091613: python3-adios4dolfinx: test failure: test_original_checkpoint.py usually times out

2024-12-28 Thread Drew Parsons
Package: python3-adios4dolfinx Version: 0.9.0-2 Severity: normal Control: forwarded -1 https://github.com/jorgensd/adios4dolfinx/issues/147 There is some flakiness in test_original_checkpoint.py (test_read_write_P_*). It regularly times out. Perhaps there's some race condition, occasionally it pa

Bug#1091387: nmu: fenicsx-performance-tests_0.9.0-2

2024-12-25 Thread Drew Parsons
Package: release.debian.org Severity: normal X-Debbugs-Cc: fenicsx-performance-te...@packages.debian.org Control: affects -1 + src:fenicsx-performance-tests User: release.debian@packages.debian.org Usertags: binnmu nmu fenicsx-performance-tests_0.9.0-2 . armel armhf i386 m68k sh4 . unstable .

Bug#1090900: fenics-dolfinx: autopkgtest regressions with HDF5 1.14

2024-12-22 Thread Drew Parsons
Source: fenics-dolfinx Followup-For: Bug #1090900 160s Warning! ***HDF5 library version mismatched error*** 160s The HDF5 header files used to compile this application do not match 160s the version used by the HDF5 library to which this application is linked. 160s Data corruption or segmentation f

Bug#1090791: petsc: strict dependency on the mpich version that was used to build

2024-12-22 Thread Drew Parsons
On 2024-12-22 11:33, Emilio Pozuelo Monfort wrote: On Sat, 21 Dec 2024 23:34:42 +0100 Andreas Beckmann wrote: Control: affects -1 + src:slepc src:fenics-dolfinx src:mpich On Sat, 21 Dec 2024 19:19:43 +0200 Drew Parsons wrote: > This is a delicate issue. The strict version test is in

Bug#1090791: petsc: strict dependency on the mpich version that was used to build

2024-12-21 Thread Drew Parsons
Source: petsc Followup-For: Bug #1090791 This is a delicate issue. The strict version test is in the upstream headers. I imagine they have their reasons for making it so.

Bug#1090900: fenics-dolfinx: autopkgtest regressions with HDF5 1.14

2024-12-21 Thread Drew Parsons
Source: fenics-dolfinx Followup-For: Bug #1090900 X-Debbugs-Cc: 1088...@bugs.debian.org There's something wrong here. fenics-dolfinx 1:0.9.0-5+b1 is rebuilt against the new hdf5 1.14, and passing tests in unstable. The tests in testing are still using the old build 1:0.9.0-5 not 1:0.9.0-5+b1, so

Bug#1090393: RM: paraview [ppc64el] -- ROM; FTBFS

2024-12-17 Thread Drew Parsons
Package: ftp.debian.org Severity: normal Tags: ftbfs X-Debbugs-Cc: parav...@packages.debian.org Control: affects -1 + src:paraview User: ftp.debian@packages.debian.org Usertags: remove The VTK componant of paraview no longer builds successfully on ppc64el since paraview version 5.13. In order

Bug#972069: slepc64-dev: enable ARPACK support in 64-bit build

2024-12-11 Thread Drew Parsons
Source: slepc Followup-For: Bug #972069 I don't think we'll be able to resolve this request. 64-bit arpack is now available in libarpack64-2-dev But slepc's arpack configuration uses parpack when MPI support is active 64-bit support in ARPACK is explicitly excluded from PARPACK, see https://gi

Bug#1045230: mirrormagic: Fails to build source after successful build

2024-12-07 Thread Drew Parsons
Package: mirrormagic Followup-For: Bug #1045230 Wait no, the problem is not the deleted orig files, it's the binary executable left in the source dir. That we can fix easily.

Bug#1045230: mirrormagic: Fails to build source after successful build

2024-12-07 Thread Drew Parsons
Package: mirrormagic Version: 3.3.0+dfsg1-1 Followup-For: Bug #1045230 These "orig" files are removed by dh_clean. I guess they should never have been in the upstream tarball in the first place. There's a new upstream release waiting to be processed. Let's see if this bug is fixed (orig files no

Bug#1087784: hypre: FTBFS: Unable to find reachable pairing between local and remote interfaces

2024-12-05 Thread Drew Parsons
Acknowledging it as a known warning is a reasonable workaround. Drew

Bug#1083728: pythran: (build-)depends on deprecated module python3-pkg-resources

2024-12-05 Thread Drew Parsons
Source: pythran Followup-For: Bug #1083728 I'm confused by this bug. pythran does not depend on or refer to pkg-resources anywhere.

Bug#1082552: #1082552: transition: petsc and numerical library stack

2024-12-04 Thread Drew Parsons
On 2024-12-04 20:53, Emilio Pozuelo Monfort wrote: On 04/12/2024 17:52, Drew Parsons wrote: Looks like britney sorted it out eventually anyway. If you mean the autopkgtest, that was Graham scheduling tests with cmake/sid upon my request. Ah, now the pixies behind the music in the garden

Bug#1082552: #1082552: transition: petsc and numerical library stack

2024-12-04 Thread Drew Parsons
On 2024-12-04 17:42, Emilio Pozuelo Monfort wrote: Hi Drew, On 03/12/2024 16:25, Emilio Pozuelo Monfort wrote: On 03/12/2024 14:33, Drew Parsons wrote: All the hypre and petsc uploads for this transition are done, and packages built against the new openmpi 5. Looks like the sundials

Bug#1082552: #1082552: transition: petsc and numerical library stack

2024-12-03 Thread Drew Parsons
All the hypre and petsc uploads for this transition are done, and packages built against the new openmpi 5.

Bug#1087389: gworldclock uploaded to delayed=10

2024-12-03 Thread Drew Parsons
No problem, thanks Andreas. I need time to focus and finish crafting gworldclock's new replacement. Drew

Bug#1088105: python-scipy-doc: Broken style

2024-12-02 Thread Drew Parsons
figure it is better than the alternative of not having any docs at all. Drew

Bug#1088872: RFP: python-jupyterlite-sphinx -- a Sphinx extension that provides utilities for embedding JupyterLite in your docs

2024-12-02 Thread Drew Parsons
Package: wnpp Severity: wishlist X-Debbugs-Cc: debian-pyt...@lists.debian.org, debian-scie...@lists.debian.org Control: block 1088105 by -1 * Package name: python-jupyterlite-sphinx Version : 0.16.5 Upstream Contact: Martin Renou and JupyterLite Contributors * URL : htt

Bug#1088767: ldconfig: Cannot mmap file /lib/x86_64-linux-gnu/libprrte.so.

2024-12-02 Thread Drew Parsons
_type=heads#L34 Is libprrte.so supposed to point at the directory like this, instead of the versioned library? Drew

Bug#1088767: ldconfig: Cannot mmap file /lib/x86_64-linux-gnu/libprrte.so.

2024-12-01 Thread Drew Parsons
Package: libopenmpi-dev Version: 5.0.6-2 Followup-For: Bug #1088767 Control: severity 1088767 serious I get this error too updating to openmpi 5.0.6-2. Looks like some intermediate update got caught in the package updates. libprrte.so is installed by libopenmpi40 5.0.6-2 as /usr/lib/x86_64-linux-

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