Bug#1071722: adios4dolfinx: FTBFS: failing tests

2024-05-26 Thread Drew Parsons
On 2024-05-26 12:44, Santiago Vila wrote: To track that, what does `lscpu` report on your failing system? (the thread,core,socket lines are probably the relevant ones) It's an AWS machine of type m6a.large. These are the most relevant specs. Thread(s) per core: 2 Core(s) per

Bug#1071722: adios4dolfinx: FTBFS: failing tests

2024-05-26 Thread Drew Parsons
On 2024-05-25 18:31, Santiago Vila wrote: El 25/5/24 a las 16:42, Drew Parsons escribió: adios4dolfinx is building cleanly in reproducibility builds. Perhaps the problem was a temporary glitch on your test system? No, this is unlikely to be a temporary glitch: ... My system has 2 CPUs

Bug#1061243: Bug #1061243 FTBFS: needs update for xsimd 12

2024-05-25 Thread Drew Parsons
Control: retitle 1061243 needs update for xsimd 13 Now xsimd 13 is available. -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#1071722: adios4dolfinx: FTBFS: failing tests

2024-05-25 Thread Drew Parsons
Source: adios4dolfinx Followup-For: Bug #1071722 Control: tags -1 ftbfs adios4dolfinx is building cleanly in reproducibility builds. Perhaps the problem was a temporary glitch on your test system? -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net

Bug#1071700: paraview: FTBFS 32-bit arches: xdmf3 invalid conversion ‘long unsigned int*’ to ‘const int*’

2024-05-23 Thread Drew Parsons
Package: paraview Version: 5.12.0+dfsg-4 Severity: important Tags: ftbfs paraview 5.12 has started failing to build on i386. paraview 5.11 previously built on i386. The problem appears to be an implicit conversion from ‘long unsigned int*’ to ‘const int*’ in getArrayType in XdmfArray.cpp

Bug#1071518: paraview: s390x test failure: vtkClientServerStream::Invoke stream_value invalid

2024-05-20 Thread Drew Parsons
Package: paraview Version: 5.11.2+dfsg-7 Severity: important Control: forwarded -1 https://gitlab.kitware.com/paraview/paraview/-/issues/22620 The Debian build of paraview (5.11.2) fails CI tests on the s390x architecture. Test logs can be found at

Bug#900364: paraview: Paraview viewer mishandles fractional Qt screen scaling

2024-05-19 Thread Drew Parsons
Package: paraview Followup-For: Bug #900364 Control: tags 900364 moreinfo Fractional scaling seems to be working now, at least for eDP-1 > 1. Can you confirm if the problem is fixed in paraview 5.11.2 or later? -- debian-science-maintainers mailing list

Bug#842405: paraview: can't load hdf5 file: vtkSISourceProxy: Failed to create vtkXdmfReader

2024-05-19 Thread Drew Parsons
Package: paraview Followup-For: Bug #842405 Control: tags 842405 moreinfo HDF5 is a general data format, it has no natural viewing format. When you load a file into paraview you need to specify which reader you want to open it with. Which reader are you expecting to use with your .h5 file? Your

Bug#820453: paraview: "Help -> ParaView Guide" gives error

2024-05-19 Thread Drew Parsons
Package: paraview Followup-For: Bug #820453 "Help -> ParaView Guide" now (5.11.2) provides a (functioning) url link to https://docs.paraview.org/en/v5.11.2/ which opens normally in the web browser. Not so helpful if you don't have internet access, but at least it's not giving an error now.

Bug#982601: python3-paraview Conflicts: python3-vtk9

2024-05-19 Thread Drew Parsons
Package: paraview Version: 5.11.2+dfsg-6+b9 Followup-For: Bug #982601 X-Debbugs-Cc: Petter Reinholdtsen Petter, paraview might never be aligned with vtk. See https://gitlab.kitware.com/paraview/paraview/-/issues/18751 If facet-analyser needs to be able to work with either (both)

Bug#1070894: slepc: FTBFS: Fatal Error: Cannot open module file ‘slepcmfn.mod’ for reading at (1): No such file or directory

2024-05-17 Thread Drew Parsons
Source: slepc Followup-For: Bug #1070894 Control: tags -1 ftbfs fixed-upstream Control: forwarded -1 https://gitlab.com/slepc/slepc/-/issues/83 Fixed upstream in 3.20.2, https://gitlab.com/slepc/slepc/-/merge_requests/639 -- debian-science-maintainers mailing list

Bug#1069321: FTBFS: [Makefile:163: check] Error 1

2024-05-14 Thread Drew Parsons
Source: hypre Followup-For: Bug #1069321 It's passing in reproducibility rebuilds. Perhaps it was a transitory glitch. -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net

Bug#1069321: FTBFS: [Makefile:163: check] Error 1

2024-05-13 Thread Drew Parsons
Source: hypre Followup-For: Bug #1069321 Control: tags -1 ftbfs hypre is passing debci and reproducibility tests on armhf. Looks like the error reported here was a transitory issue, possibly related to openmpi upgrades. -- debian-science-maintainers mailing list

Bug#1066449: mpi4py: FTBFS: Segmentation fault in tests

2024-05-06 Thread Drew Parsons
Source: mpi4py Followup-For: Bug #1066449 Control: tags -1 ftbfs The bug report stopped scanning at the first "error", which is not an error (it's a check). The last error is the relevant one testIReadIWrite (test_io.TestIOSelf.testIReadIWrite) ... ok testIReadIWriteAll

Bug#1069432: mpi4py: FTBFS on armhf: ld: cannot find -llmpe: No such file or directory

2024-05-05 Thread Drew Parsons
Source: mpi4py Followup-For: Bug #1069432 There have been ongoing issues with OpenMPI on 32-bit architectures, partly related to drop of 32-bit support by pmix. This bug is likely related to that i.e. not a bug in mpi4py itself. -- debian-science-maintainers mailing list

Bug#1070338: FTBFS: libadios2_serial_evpath.so.2.10.0: undefined reference to `cmfabric_add_static_transport'

2024-05-03 Thread Drew Parsons
Source: adios2 Version: 2.10.0+dfsg1-1 Severity: normal Tags: ftbfs Control: forwarded -1 https://github.com/ornladios/ADIOS2/issues/4156 Building the debian package for adios 2.10.0 (in experimental) fails with "libadios2_serial_evpath.so.2.10.0: undefined reference to

Bug#1062405: dolfin: NMU diff for 64-bit time_t transition

2024-04-20 Thread Drew Parsons
Source: dolfin Followup-For: Bug #1062405 Control: severity 1062405 testing Control: tags 1062405 moreinfo This time_t patch was never applied. Is it not needed after all? Can we close this bug now? -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net

Bug#1062587: fenics-dolfinx: NMU diff for 64-bit time_t transition

2024-04-12 Thread Drew Parsons
Source: fenics-dolfinx Followup-For: Bug #1062587 Control: severity 1062587 important Control: tags 1062587 moreinfo This time_t patch was never applied. I presume it's not needed after all and we can close this bug now? -- debian-science-maintainers mailing list

Bug#1068319: armci-mpi: debian-...@lists.debian.org

2024-04-06 Thread Drew Parsons
Source: armci-mpi Followup-For: Bug #1068319 armci-mpi is already building for mpich so the transition should be manageable. Will just need to make sure it switches off the openmpi build cleanly. -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net

Bug#1068464: deal.ii: FTBFS: libgmp not linked, libdeal.ii.g.so.9.5.1: error: undefined reference to '__gmpn_neg'

2024-04-05 Thread Drew Parsons
Source: deal.ii Version: 9.5.1-2 Severity: normal Tags: ftbfs I'm getting an error running deal.ii tests building against petsc 3.20 (from experimental) [100%] Built target dealii_release make -f tests/CMakeFiles/test.dir/build.make tests/CMakeFiles/test.dir/depend make[5]: Entering directory

Bug#1067308: python-meshplex: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.11" --test-args=--ignore-glob=\*test_io\* returned exit code 13

2024-04-02 Thread Drew Parsons
Source: python-meshplex Followup-For: Bug #1067308 Control: tags -1 ftbfs I can't reproduce this error now. It must have been resolved by a separate library transition, or possibly a numpy update. If 0.17.1-3 passes tests successfully then we can close this bug. -- debian-science-maintainers

Bug#1067064: transition: petsc hypre

2024-03-17 Thread Drew Parsons
Package: release.debian.org Severity: normal X-Debbugs-Cc: pe...@packages.debian.org, francesco.balla...@unicatt.it Control: affects -1 + src:petsc User: release.debian@packages.debian.org Usertags: transition The petsc patch for the 64-bit time_t transition was deeply invasive. It makes

Bug#1065323: petsc: bad Provides in libpetsc64-real3.19t64, libpetsc64-complex3.19t64 and libpetsc-real3.19t64

2024-03-04 Thread Drew Parsons
Source: petsc Followup-For: Bug #1065323 petsc has a complex set of symlink farms since it needs to enable multiple alternative build profiles. I'll implement the patch in a way that doesn't let t64 get in the way of updating subsequently (to 3.20 in the near future). Drew --

Bug#894462: paraview: edges are blotted [regression]

2024-02-24 Thread Drew Parsons
On 2024-02-24 12:40, Francesco Poli wrote: On Thu, 04 Jan 2024 12:18:21 +0100 Drew Parsons Can you confirm paraview 5.11 is meeting your image quality expectations? Only if I disable FXAA (which, by the way, is enabled by default, but can luckily be disabled in the settings!). ... Could

Bug#1064280: scikit-learn: armhf tests failing: not giving expected divide-by-zero warning

2024-02-19 Thread Drew Parsons
Source: scikit-learn Version: 1.4.1.post1+dfsg-1 Severity: normal sklearn 1.4 is passing most tests but two remain "failing" on armhf. test_tfidf_no_smoothing and test_qda_regularization are "expected to fail" by emitting a divide-by-zero warning, but they emit no such exception. I guess it's a

Bug#1029701: scikit-learn: tests fail with scipy 1.10

2024-02-15 Thread Drew Parsons
Source: scikit-learn Version: 1.2.1+dfsg-1 Followup-For: Bug #1029701 Control: severity 1029701 serious scipy 1.11 is now uploaded to unstable, so bumping this bug severity to serious. -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net

Bug#1029701: scikit-learn: tests fail with scipy 1.10

2024-02-09 Thread Drew Parsons
Source: scikit-learn Version: 1.2.1+dfsg-1 Followup-For: Bug #1029701 scikit-learn continues to fail with scipy 1.11 from experimental 648s FAILED ../../../../usr/lib/python3/dist-packages/sklearn/linear_model/tests/test_quantile.py::test_incompatible_solver_for_sparse_input[interior-point]

Bug#1062356: adios2: flaky autopkgtest (host dependent): times out on big host

2024-02-06 Thread Drew Parsons
Source: adios2 Followup-For: Bug #1062356 The flakey test is adios2-mpi-examples. debian/tests is building and running them manually, and running on only 3 processors (mpirun -n 3) So the problem can't be overload of the machine. I'll just skip insituGlobalArraysReaderNxN_mpi. For reference,

Bug#1062356: adios2: flaky autopkgtest (host dependent): times out on big host

2024-02-06 Thread Drew Parsons
Source: adios2 Followup-For: Bug #1062356 Can't be quite as simple as just the host machine. https://ci.debian.net/data/autopkgtest/unstable/amd64/a/adios2/41403641/log.gz completed in 9 minutes, while https://ci.debian.net/data/autopkgtest/unstable/amd64/a/adios2/41496866/log.gz failed with

Bug#1061386: libxtensor-dev: Fails to install for arm64 arch on amd64

2024-02-05 Thread Drew Parsons
Package: libxtensor-dev Followup-For: Bug #1061386 Control: fixed 1061386 0.24.7-1 I'm a bit confused why you're installing libxtensor-dev:arm64 on amd64. Wouldn't it make more sense to install libxtensor-dev:amd64? In any case this was fixed in libxtensor-dev 0.24.7 (actually in 0.24.4-1exp1),

Bug#1061357: python3-spglib: spglib python package not identified by dh_python3

2024-01-22 Thread Drew Parsons
Package: python3-spglib Version: 2.2.0-2 Severity: normal We have dh_python3 to help automatically identify python package dependencies when building a package. It's unable to identify spglib, however. For instance a pymatgen build log shows dh_python3 -a -O--buildsystem=pybuild I: dh_python3

Bug#1061263: python3-spglib: fails with python3.12 (extension not built)

2024-01-22 Thread Drew Parsons
On 2024-01-22 09:28, Andrius Merkys wrote: Hi Drew, spglib should be configured to build for all available python versions. In other libraries (e.g. fenics-basix) this is done by building the C library separately from the the python module. Thanks for a pointer, I will give fenics-basix a

Bug#1061263: python3-spglib: fails with python3.12 (extension not built)

2024-01-21 Thread Drew Parsons
Package: python3-spglib Version: 2.2.0-2 Severity: normal python3-spglib fails with python3.12, since the python extension is built only for python3.11. spglib should be configured to build for all available python versions. In other libraries (e.g. fenics-basix) this is done by building the C

Bug#1061243: FTBFS: needs update for xsimd 12

2024-01-21 Thread Drew Parsons
Package: libxtensor-dev Version: 0.24.7-4 Severity: important Tags: upstream Control: forwarded -1 https://github.com/xtensor-stack/xtensor/issues/2769 xtensor 0.24.7 is configured to use xsimd 10. xtensor upstream head supports xsimd 11. But xsimd 12 has been recently released and is required to

Bug#1061063: armhf: h5py's tests expose unaligned memory accesses during the build

2024-01-19 Thread Drew Parsons
Source: h5py Followup-For: Bug #1061063 Control: forwarded 1061063 https://github.com/h5py/h5py/issues/1927 The problem was raised upstream at https://github.com/h5py/h5py/issues/1927 Makes it difficult to test if we can't reproduce it on all armhf environments. A patch was suggested for the

Bug#837796: paraview: segfaults when performing query-based selections

2024-01-04 Thread Drew Parsons
Package: paraview Followup-For: Bug #837796 Control: fixed -1 5.11.0+dfsg-1 I think this problem is now dealt with (paraview 5.11). The query-based selection is not segfaulting now. The values are found as described in the tutorial, and the 3D can image gets highlighting indicated the selection

Bug#894462: paraview: edges are blotted [regression]

2024-01-04 Thread Drew Parsons
Package: paraview Followup-For: Bug #894462 The png generated by the procedure in this bug looks fine to me, using current paraview (5.11). It's slightly blurry but no more than you'd expect for a png file (it's raster image format, not a vector image format, you can't expect to main high

Bug#754968: paraview: cmake crashes when find paraview

2024-01-04 Thread Drew Parsons
Package: paraview Followup-For: Bug #754968 find_package(ParaView) is now operating successfully in cmake. (needs libgdal-dev) That's with paraview-dev 5.11.2+dfsg-4 and cmake 3.28.1-1. Can you confirm paraview is now working for you from cmake, and we can close this bug? --

Bug#959677: paraview: Python calculator does not work

2024-01-04 Thread Drew Parsons
Package: paraview Followup-For: Bug #959677 The calculator seems to be working fine e.g. tutorial steps at https://docs.paraview.org/en/latest/UsersGuide/filteringData.html#python-calculator change the colour of the sphere depending on the value entered in the calculator. Can you confirm you

Bug#753685: dist-packages/paraview/ColorMaps.xml missing

2024-01-04 Thread Drew Parsons
Package: paraview Followup-For: Bug #753685 I suspect the problem with ColorMaps is fixed in paraview 5.11 but can't confirm since paraview.simple has other issues. It wants to use inspect.getargspec, but there's no such function anymore (python 3.11). $ python3 -c "import paraview.simple" (

Bug#688875: paraview: cannot select and copy current time

2024-01-04 Thread Drew Parsons
Package: paraview Followup-For: Bug #688875 I can't see a "Current Time Controls" toolbar in paraview 5.11. Is it the "Time Inspector" tool bar? Are your requirements now met in paraview 5.11? Can we close this bug? -- debian-science-maintainers mailing list

Bug#954329: paraview: opacity incorrectly handled by the debian bullseye(testing) package paraview-5.7

2024-01-04 Thread Drew Parsons
Package: paraview Followup-For: Bug #954329 I can't see a problem with the test file using latest paraview 5.11. It displays a translucent sphere coloured red on one side, blue on the other. Can you confirm this bug has now been fixed? -- debian-science-maintainers mailing list

Bug#1059842: FTBFS: test fails: ZFP lib not compiled with -DBIT_STREAM_WORD_TYPE=uint8

2024-01-02 Thread Drew Parsons
Package: python3-hdf5plugin Version: 4.0.1-3 Severity: serious Justification: FTBFS python3-hdf5plugin has started failing testZfp, causing both FTBFS and debci failure. The error message from debci is 56s ERROR: testZfp (__main__.TestHDF5PluginRW.testZfp) (options={'lossless': False},

Bug#1059791: python3-mpi4py: testPackUnpackExternal alignment error on sparc64

2024-01-01 Thread Drew Parsons
Package: python3-mpi4py Version: 3.1.5-2 Severity: normal Control: forwarded -1 https://github.com/mpi4py/mpi4py/issues/147 sparc64 has started giving a Bus Error (Invalid address alignment) in testPackUnpackExternal (test_pack.TestPackExternal), testProbeRecv

Bug#1058944: transition: petsc

2023-12-18 Thread Drew Parsons
Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: transition X-Debbugs-Cc: pe...@packages.debian.org Control: affects -1 + src:petsc I'd like to upgrade PETSc (and SLEPc, and their python packages) from 3.18 to 3.19. This is expected to fix the

Bug#1057863: slepc4py ftbfs with Python 3.12

2023-12-17 Thread Drew Parsons
Source: slepc4py Followup-For: Bug #1057863 Correction: curexc_traceback is not used in slepc4py 3.19. Maybe it's time to upgrade to PETSc 3.19. -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net

Bug#1057863: slepc4py ftbfs with Python 3.12

2023-12-17 Thread Drew Parsons
Source: slepc4py Followup-For: Bug #1057863 slepc4py does not use curexc_traceback. Perhaps this is a bug in cython? -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#1058353: libadios2-mpi-c-dev: ships headers already shipped in libadios2-common-c-dev

2023-12-13 Thread Drew Parsons
Source: adios2 Followup-For: Bug #1058353 Damn, something went badly wrong in debian/rules. Sorry about that. I'll fix it as soon as possible, in the meantime use the version in testing. Drew -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net

Bug#1058018: libadios2-common-core-dev has an undeclared file conflict on /usr/lib/x86_64-linux-gnu/cmake/adios2/adios2-config.cmake

2023-12-11 Thread Drew Parsons
Source: adios2 Followup-For: Bug #1058018 Control: severity -1 important Call it teething issues. This is a new package, so I'm trying to avoid making debian/control more verbose than it needs to be by not crowding the fields with the strict specifications needed to avoid this error. Once the

Bug#1043240: pandas 1.5 -> 2.1?

2023-12-10 Thread Drew Parsons
On 2023-12-10 21:55, Kingsley G. Morse Jr. wrote: Hi Rebecca, Julian and all science minded pythonistas of debian, great and small! 3.) The following one-liner suggests 44 debian packages might be affected by the breaks Rebecca said would be caused by pandas 2.x: $ for s in augur

Re: paraview_5.11.2+dfsg-2_source.changes REJECTED

2023-12-06 Thread Drew Parsons
On 2023-12-06 08:29, Jochen Sprickerhof wrote: Hi Drew, * Drew Parsons [2023-12-05 10:10]: On 2023-12-05 05:18, Bastian Blank wrote: On Mon, Dec 04, 2023 at 11:27:53PM +0100, Drew Parsons wrote: On 2023-12-04 23:24, Debian FTP Masters wrote: paraview source: lintian output: 'license

Re: paraview_5.11.2+dfsg-2_source.changes REJECTED

2023-12-05 Thread Drew Parsons
On 2023-12-05 05:18, Bastian Blank wrote: On Mon, Dec 04, 2023 at 11:27:53PM +0100, Drew Parsons wrote: On 2023-12-04 23:24, Debian FTP Masters wrote: > paraview source: lintian output: 'license-problem-json-evil > VTK/ThirdParty/fides/vtkfides/thirdparty/rapidjson/fidesrapidjson/licen

Re: paraview_5.11.2+dfsg-2_source.changes REJECTED

2023-12-04 Thread Drew Parsons
On 2023-12-04 23:24, Debian FTP Masters wrote: paraview source: lintian output: 'license-problem-json-evil VTK/ThirdParty/fides/vtkfides/thirdparty/rapidjson/fidesrapidjson/license.txt', automatically rejected package. paraview source: If you have a good reason, you may override this lintian

Bug#1016430: netgen: New upstream version 6.2.2007 available / why is the version overriden with +really?

2023-11-14 Thread Drew Parsons
On 2023-11-13 22:31, Kurt Kremitzki wrote: Hello Drew, ... Debian builds were only succeeding on amd64 but failing on all the other architectures: i386, armel, armhf, arm64, mipsel, mips64el, ppc64el, and s390x. I was able to fix some of the problems by switching to an older version (thus

Bug#1016430: netgen: New upstream version 6.2.2007 available / why is the version overriden with +really?

2023-11-13 Thread Drew Parsons
Package: netgen Followup-For: Bug #1016430 I've prepared netgen 6.2.2305 in experimental. I guess we might as well close this bug when it gets uploaded to unstable. Still, I'd also be interested to hear what the motivation was for the +really6.2.1905 version. -- debian-science-maintainers

Bug#910247: python3-netgen: importing netgen.gui fails due to MPI_Comm_size()

2023-11-09 Thread Drew Parsons
Package: python3-netgen Version: 6.2.2006+really6.2.1905+dfsg-10 Followup-For: Bug #910247 As a workaround, initialise MPI before importing netgen.gui. > from mpi4py import MPI > import netgen.gui -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net

Bug#1054712: ensmallen: FTBFS: adam_test.cpp:17:10: fatal error: catch2/catch.hpp: No such file or directory

2023-10-31 Thread Drew Parsons
Source: ensmallen Followup-For: Bug #1054712 Should be noted that the problem is linked to debian patch 0002-use-system-catch.patch, which disables upstream's local copy of catch in order to use the system catch2 library. So one workaround could be to disable 0002-use-system-catch.patch. --

Bug#1054712: ensmallen: FTBFS: adam_test.cpp:17:10: fatal error: catch2/catch.hpp: No such file or directory

2023-10-31 Thread Drew Parsons
Source: ensmallen Followup-For: Bug #1054712 Control: forwarded 1054712 https://github.com/mlpack/ensmallen/issues/372 This error occurs because of the upgrade of catch2 from v2 to v3. Unfortunately ensmallen upstream don't sound very enthusiastic about dealing with it,

Bug#1054159: paraview: build and provide gmsh plugin

2023-10-18 Thread Drew Parsons
Package: paraview Version: 5.11.0+dfsg-2 Severity: normal paraview offers a GMSH plugin, providing the capability to visualise gmsh meshes. It's not built by default, can it be added to the debian paraview package? Actually there's two of them,

Bug#1053090: libxsimd-dev: arm64 error in xtensor: usage of batch type with unsupported type

2023-10-18 Thread Drew Parsons
Source: xtensor Version: 0.24.7-4 Followup-For: Bug #1053090 Control: severity 1053090 important xsimd support is optional for xtensor. Use of batch is apparently not expected to be routinely used anyway. See further discussion at https://github.com/xtensor-stack/xsimd/issues/945 In summary,

Bug#1053854: xsimd: error: ‘aligned_mode’ in namespace ‘xsimd’ does not name a type

2023-10-12 Thread Drew Parsons
Source: xsimd Version: 10.0.0-3 Severity: important Control: forwarded -1 https://github.com/xtensor-stack/xsimd/issues/954 Control: affects -1 libxtensor-dev xtensor 0.24.7 tests are exposing an error in xsimd 10.0.0 on less common architectures armel, ppc64el and s390x, seen in debian CI tests

Bug#1053314: Depends: python3-h5py-mpi without python3-h5py

2023-10-10 Thread Drew Parsons
On 2023-10-10 09:26, Rafael Laboissière wrote: * Rafael Laboissière [2023-10-09 08:30]: […] At least, I hope that version 3.1.0+dfsg2-5 will really fix Bug#1053314 and the h5py transition will be completed. Unfortunately, it is still not working:

Bug#1053314: Depends: python3-h5py-mpi without python3-h5py

2023-10-09 Thread Drew Parsons
On 2023-10-09 08:30, Rafael Laboissière wrote: Thanks for this detailed explanation, Drew. I released version 3.1.0+dfsg2-5 of the xmds2 package before reading it. I added python3-h5py to Build-Depends and libhdf5-mpi-dev to Depends, as you suggested (even though there is a typo in the

Bug#1053314: Depends: python3-h5py-mpi without python3-h5py

2023-10-08 Thread Drew Parsons
Nilesh explained most of the situation correctly. I can give some more background.It made sense (to me) to have h5py built against hdf5-mpi, since I figured that if you need the complexity of the hdf5 file format then you probably want to use it in an MPI environment. There was a

Bug#1053090: libxsimd-dev: arm64 error in xtensor: usage of batch type with unsupported type

2023-10-03 Thread Drew Parsons
Package: libxsimd-dev Followup-For: Bug #1053090 Control: reassign 1053090 libxtensor-dev Control: forwarded 1053090 https://github.com/xtensor-stack/xtensor/issues/2733 xsimd upstream https://github.com/xtensor-stack/xsimd/issues/945 identified the problem that neon64 does not support bool. A

Bug#1053341: h5py FTBFS on 32-bit archs: OverflowError: Python int too large to convert to C ssize_t

2023-10-02 Thread Drew Parsons
forwarded 1053341 https://github.com/h5py/h5py/issues/2315 thanks I suspect it can be resolved by casting the int returned by addressof to ctypes.c_int. Waiting to hear what upstream thinks. Note it's not quite as simple as "32-bit". sparc64 is also affected. -- debian-science-maintainers

Bug#1053314: Depends: python3-h5py-mpi without python3-h5py

2023-10-01 Thread Drew Parsons
Package: xmds2 Version: 3.1.0+dfsg2-4 Severity: serious Justification: debci xmds2 Depends: python3-h5py-mpi without depending on python3-h5py python3-h5py-mpi only provides the h5py._debian_h5py_mpi namespace, not h5py. Hence tests using h5py without specifying _debian_h5py_mpi fail. This is

Bug#1051781: python3-h5py: where is the egg files

2023-09-29 Thread Drew Parsons
On 2023-09-29 09:28, Stuart Prescott wrote: Control: reopen -1 ... I can't see the fixed files for this dist-info metadata in the updated package: ... BTW a simple test that it is all working is:     python3 -c "from importlib.metadata import distribution; distribution('h5py')" For what

Bug#1049903: petsc: misbuild with gcc-13

2023-09-28 Thread Drew Parsons
Source: petsc Followup-For: Bug #1049903 Control: severity 1049903 important Control: tags 1049903 moreinfo I said previously I'd apply the patch, but I wanted to check the problem first. No problem is showing at https://tests.reproducible-builds.org/debian/rb-pkg/petsc.html even in the

Bug#1051781: python3-h5py: where is the egg files

2023-09-28 Thread Drew Parsons
Source: h5py Followup-For: Bug #1051781 I'm reorganising the package with separate distinfo metadata for the different variants. I think this will fix your problem -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net

Bug#1052748: mpi4py fails test_dynproc.TestDPM.testJoin: socket.gaierror: [Errno -2] Name or service not known

2023-09-28 Thread Drew Parsons
Source: mpi4py Followup-For: Bug #1052748 Control: severity 1052748 important Control: tags 1052748 moreinfo I can't reproduce this error, and debci tests at https://ci.debian.net/packages/m/mpi4py/ continue to pass So I'm downgrading severity. I figure there are two possibilities - it was a

Bug#1052748: mpi4py fails test_dynproc.TestDPM.testJoin: socket.gaierror: [Errno -2] Name or service not known

2023-09-28 Thread Drew Parsons
Source: mpi4py Followup-For: Bug #1052748 Control: retitle 1052748 mpi4py fails test_dynproc.TestDPM.testJoin: socket.gaierror: [Errno -2] Name or service not known The failure was incorrectly identified. The build log says the problem was in testJoin: ERROR: testJoin

Bug#1053140: xtensor: armel failure with clang-16: undefined reference to `__atomic_store_1'

2023-09-27 Thread Drew Parsons
Source: xtensor Version: 0.24.7-1 Severity: normal Control: forwarded -1 https://github.com/xtensor-stack/xtensor/issues/2729 xtensor 0.24.7-1 fails debci test on armel (gnueabi) architecture with clang 16.0.6. The tests pass with g++ 13.2.0, and pass with clang-16 on other architectures. A test

Bug#1052882: xtensor: FTBFS: make[1]: *** [debian/rules:65: override_dh_auto_configure] Error 2

2023-09-27 Thread Drew Parsons
Source: xtensor Followup-For: Bug #1052882 Control: fixed 1052882 0.24.7-1 This bug is weird, in the sense that xtensor 0.24.3-2 in testing failed its test against xsimd 10.0.0-3 from unstable. So why then did the migration daemon allow xsimd to migrate from unstable to testing? --

Bug#1053090: libxsimd-dev: arm64 error in xtensor: usage of batch type with unsupported type

2023-09-26 Thread Drew Parsons
Package: libxsimd-dev Version: 10.0.0-3 Severity: serious Justification: debci libxsimd-dev 10 triggers an error in xtensor tests on arm64 xsimd passes its own tests, and xtensor passes on other arches (except armel which has known issues) The error output from

Bug#1049903: petsc: misbuild with gcc-13

2023-09-11 Thread Drew Parsons
Source: petsc Followup-For: Bug #1049903 Thanks for the clarification. I'll apply the patch. -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#1041480: (python3-h5py: I can't use the debian provided python3-h5py as a dependency in my package because it is called h5py.-debian-h5py-serial)

2023-09-05 Thread Drew Parsons
Hi Tim, I'm not sure if the Debian Bug Tracking System forwarded messages to you from https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1041480 Does it fix your package configuration if you specify Depends: python3-h5py in your debian/control file? Drew -- debian-science-maintainers

Bug#1049903: petsc: misbuild with gcc-13

2023-08-30 Thread Drew Parsons
Source: petsc Followup-For: Bug #1049903 Hi Steve, thanks for the bug report. With patching, wouldn't it be simpler to just add -lstdc++ to CXX_LINKER_FLAGS at configuration time (in debian/rules) rather than hacking the upstream detection code? As you say, hardcoding in the upstream scripts

Bug#1043307: mshr: [ignore test2]

2023-08-10 Thread Drew Parsons
Source: mshr Followup-For: Bug #1043307 [reportbug has not been able to send emails. testing configuration here. Please ignore] -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net

Bug#1043307: [test ignore]

2023-08-10 Thread Drew Parsons
Source: mshr Followup-For: Bug #1043307 [testing reportbug. please ignore] -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#1043313: libsuperlu-dev: Inconsistent declaration of double{C, M}alloc()

2023-08-10 Thread Drew Parsons
Source: superlu Followup-For: Bug #1043313 Upstream has just released a new version to fix it. Apparently it introduced other problems however. Let's see what upstream's response to that is. -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net

Bug#1042560: xtensor autopkg test fails with LLVM-16

2023-08-03 Thread Drew Parsons
Source: xtensor Followup-For: Bug #1042560 Control: forwarded 1042560 https://github.com/xtensor-stack/xtensor/issues/2718#issuecomment-1664157116 Something weird going on here. This is a string comparison not a floating point comparison. The string is supposed to be the type of the values, so

Bug#1041480: python3-h5py: I can't use the debian provided python3-h5py as a dependency in my package because it is called h5py.-debian-h5py-serial

2023-08-03 Thread Drew Parsons
Package: python3-h5py Followup-For: Bug #1041480 If your package does not specifically need the serial or mpi version, then you should just use the common package python3-h5py rather than python3-h5py-serial Depends: python3-h5py Does that fix your configuration? -- debian-science-maintainers

Bug#1040107: h5py: deprecation of Python libraries asyncore and asynchat

2023-08-03 Thread Drew Parsons
Package: python3-h5py Followup-For: Bug #1040107 Control: severity 1040107 normal Control: forwarded 1040107 https://github.com/h5py/h5py/issues/2292 asyncore is only used in the example file swmr_inotify_example.py, so this bug is not really Severity: important -- debian-science-maintainers

Bug#1042003: python3-dolfinx: test_vector_function.py fails with PETSc 3.19

2023-07-31 Thread Drew Parsons
Source: fenics-dolfinx Followup-For: Bug #1042003 Control: tags 1042003 fixed-upstream The issue with PETSc 3.19 has been dealt with upstream by a complete overhaul of the Mesh python wrappers in PR#2611. The patch does not apply cleanly to dolfinx 0.6.0. A large chunk of the patches introduces

Bug#1041372: #1041372 xtensor autopkg tests fail on i386 and s390x

2023-07-26 Thread Drew Parsons
forwarded 1041372 https://github.com/xtensor-stack/xtensor/issues/2718 thanks Evidently triggered by excess precision changes in gcc-13, see https://gcc.gnu.org/gcc-13/porting_to.html -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net

Bug#1042005: transition: mumps hypre2.28.0 superlu combblas

2023-07-25 Thread Drew Parsons
Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: transition X-Debbugs-Cc: mu...@packages.debian.org, debian-scie...@lists.debian.org Control: affects -1 + src:mumps I'd like clear out some transitions in the numerical library stack: combblas:

Bug#1042003: python3-dolfinx: test_vector_function.py fails with PETSc 3.19

2023-07-25 Thread Drew Parsons
Package: python3-dolfinx Version: 1:0.6.0-6 Severity: normal Control: forwarded -1 https://github.com/FEniCS/dolfinx/issues/2736 The python unit test python/test/unit/fem/test_vector_function.py fails after building dolfinx 0.6.0 against PETSc 3.19 $ pytest-3 -v

Bug#1042000: python3-dolfin: test_snes_set_from_options fails with PETSc 3.19

2023-07-25 Thread Drew Parsons
Package: python3-dolfin Version: 2019.2.0~legacy20230609.8b85e9d.ar-3 Severity: normal Control: forwarded -1 https://bitbucket.org/fenics-project/dolfin/issues/1138/ Building dolfin against PETSc 3.19 passes all tests except one, from python/test/unit/nls/test_PETScSNES_solver.py:

Bug#1041705: dolfin: libdolfin needs ABI bump

2023-07-22 Thread Drew Parsons
Source: dolfin Version: 2019.2.0~legacy20230609.8b85e9d.ar-2 Severity: serious Justification: Policy 8.6.2 Control: affects -1 python3-mshr The accumulation of git changes and gcc-13 fixes has apparently introduced an ABI inconsistency in libdolfin.so, such that mshr can no longer be imported in

Bug#1039904: libopenblas64-pthread-dev: 64-bit lapack-openblas.pc needs -lopenblas64

2023-06-29 Thread Drew Parsons
Package: libopenblas64-pthread-dev Version: 0.3.23+ds-2 Severity: important I'm trying to build hypre 2.29.0. It uses lapack+blas, configuring via pkg-config to get the appropriate -llapack -lblas flags. The debian hypre package builds both 32 bit and 64 bit variants of libhypre.so. On my

Bug#1035186: mpi4py-fft: please add autopkgtests (to add coverage for python3-numpy)

2023-06-19 Thread Drew Parsons
Package: python3-mpi4py-fft Version: 2.0.5-1 Followup-For: Bug #1035186 Tests are currently failing inside openmpi libraries. Not sure if it means hdf5 needs to be rebuilt against latest openmpi. Tests should be launched from the tests subdir with H5PY_ALWAYS_USE_MPI=1 ./runtests.sh --

Bug#1036665: unblock: scotch/7.0.3-2

2023-05-24 Thread Drew Parsons
libscotchmetisv5.so +(v5 not v3, to match libmetis), and point libparmetis.so at the +corresponding int-build of libptscotchparmetisv3.so. Likewise for +static .a libraries. Closes: #1036576. + + -- Drew Parsons Tue, 23 May 2023 17:23:49 +0200 + scotch (7.0.3-1) unstable; urgency=medium

Bug#1036576: libscotch{, par}metis-dev: broken symlinks: /usr/lib//*metis-*/lib*metis.* -> ../scotch-*/lib*metis.*

2023-05-23 Thread Drew Parsons
Package: libscotchmetis-dev Version: 7.0.3-1 Followup-For: Bug #1036576 Awkward. Thanks for catching it. -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#1034585: lmfit-py: should use Build-Depends: python3-setuptools-scm instead of patching out scm

2023-04-18 Thread Drew Parsons
Source: lmfit-py Version: 1.1.0-1 Severity: normal lmfit-py 1.1.0-1 introduced debian patch preserve_version.patch to prevent the python package build from introducing a spurious package version. If I correctly understand the way pybuild-plugin-pyproject interacts with setuptools_scm,

Bug#1023820: Re#1023820 hdf5: Dependencies not tight enough

2023-04-17 Thread Drew Parsons
reassign 1023820 src:hdf5 retitle 1023820 hdf5: Dependencies not tight enough affects 1023820 python3-h5py thanks Bug#1023820 reported a failure in h5py: import h5py ... ImportError: /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103: version `HDF5_SERIAL_1.10.7' not found (required by

Bug#1033244: unblock: armci-mpi/0.3.1~beta-7

2023-03-20 Thread Drew Parsons
3.1~beta-7) unstable; urgency=medium + + * Team upload. + * run build-time tests on only 1 process if only 1 CPU is available. +Closes: #1031064. + * debian/tests: don't run mpich tests on s390x. Closes: #1009772. + + -- Drew Parsons Sun, 19 Mar 2023 14:08:54 +0100 + armci-mpi (0.3.1~beta-

Bug#1030775: xtensor: baseline violation: builds with -march=native

2023-02-09 Thread Drew Parsons
Source: xtensor Followup-For: Bug #1030775 Control: tags -1 wontfix moreinfo I think this is not a bug. xtensor is a header-only library. The builds you're seeing with -march=native are in the tests only, not compiled into the binary package. We could make some effort to prevent the tests

Bug#1029701: scikit-learn Re: Are we still trying to do scipy 1.10, given transition freeze?

2023-02-07 Thread Drew Parsons
On 2023-02-07 08:33, Graham Inggs wrote: Hi Drew I think python3-scipy should declare a Breaks on python3-skbio less than the version in unstable (0.5.8-3). This should sort out the autopkgtest regressions of emperor, python-skbio itself, q2-metadata and q2-quality-control, which are all

Bug#1030221: statsmodels: 32 bit arches fail tests using int64

2023-02-01 Thread Drew Parsons
Source: statsmodels Version: 0.13.5+dfsg-4 Severity: serious Justification: debci scipy 1.10 is triggering a problem with tests using int64 on 32 bit arches (armhf, i386, armel) Affected tests are in test_discrete.py: TestDiscretizedGamma.test_basic TestDiscretizedExponential::test_basic

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