Bug#1060318: Could be related to LLVM rather than PoCL: works with LLVM-15
I managed to get the test pass on PoCL v3, v4 and v5 using the same LLVM 15 (on a basis of silx development branch ... on a debian stable base) I suspect the regression is in the version of LLVM more than in PoCL or silx. I will investigate further. Cheers, -- Jérôme Kieffer
Bug#1060318: This is a regression: it used to pass with PoCL3.1
Platform Name Portable Computing Language Platform Vendor The pocl project Platform VersionOpenCL 3.0 PoCL 3.1+debian Linux, None+Asserts, RELOC, SPIR, LLVM 15.0.6, SLEEF, DISTRO, POCL_DEBUG Platform ProfileFULL_PROFILE
Bug#1056471: python-fabio: debdiff with patch from upstream recommendation
This looks good to be. Thanks for your contribution. Cheers, -- Jérôme Kieffer
Bug#1056471: Patch for 3.12
Hi, I am the upstream author of FabIO and indeed, there is a regression in the tests when run for the first time. This is linked to an un-flushed file. This can simply be corrected with this simple patch https://github.com/silx-kit/fabio/pull/550/files It is probably simpler to debian to just apply this patch to the source when packaging instead of making a new release... Cheers, -- Jérôme Kieffer tel +33 476 882 445
Bug#1041443: issue at meson-python
Hi, Apparently this bug comes from the tool used to build the source package: "meson-python" ... it does not set properly timestamps in the source archive. https://github.com/mesonbuild/meson-python/issues/450 Cheers, Jerome
Bug#1039722: [Debian-pan-maintainers] Bug#1039722: pyfai is failing autopkg tests with python 3.11.4
Hi Matthias, I am the upstream developper of pyFAI. This version is >1 year old and I don't have the resources to backport bug-fixes. I develop on a daily basis on debian 12 and python 3.11 and the latest version is OK there. https://pypi.org/project/pyfai/#history How much work would it represent to package the the version from 2023 ? Cheers, Jerome On Wed, 28 Jun 2023 18:41:46 +0200 Matthias Klose wrote: > Package: src:pyfai > Version: 0.21.3+dfsg1-4 > Severity: serious > Tags: sid trixie > > pyfai is failing it's autopkg tests on amd64 with python 3.11.4: > > https://ci.debian.net/data/autopkgtest/testing/amd64/p/pyfai/34908607/log.gz > > 442s == > 442s FAIL: test_count_csr > (pyFAI.test.test_histogram.TestHistogram2d.test_count_csr) > 442s Test that the pixel count and the total intensity is conserved > 442s -- > 442s Traceback (most recent call last): > 442s File "/usr/lib/python3/dist-packages/pyFAI/test/test_histogram.py", > line > 340, in test_count_csr > 442s self.assertTrue(delta == 0, msg="check all pixels were counted") > 442s AssertionError: False is not true : check all pixels were counted > 442s > 442s == > 442s FAIL: test_numpy_vs_cython_vs_csr_2d > (pyFAI.test.test_histogram.TestHistogram2d.test_numpy_vs_cython_vs_csr_2d) > 442s Compare numpy histogram with cython simple implementation > 442s -- > 442s Traceback (most recent call last): > 442s File "/usr/lib/python3/dist-packages/pyFAI/test/test_histogram.py", > line > 375, in test_numpy_vs_cython_vs_csr_2d > 442s self.assertTrue(delta_max <= self.err_max_cnt, "pixel count > difference > numpy/csr : max delta=%s" % delta_max) > 442s AssertionError: False is not true : pixel count difference numpy/csr : > max > delta=8.0 > 442s > 442s -- > 442s Ran 376 tests in 272.476s > 442s > 442s FAILED (failures=2, skipped=9) > 442s 92 > 442s 61 > 442s 33 > 442s autopkgtest [15:28:03]: test command1: ---] > 443s command1 FAIL non-zero exit status 1 > 443s autopkgtest [15:28:04]: test command1: - - - - - - - - - - results - - > - - > - - - - - - > 443s autopkgtest [15:28:04]: summary > 443s command1 FAIL non-zero exit status 1 > > -- > Debian-pan-maintainers mailing list > debian-pan-maintain...@alioth-lists.debian.net > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-pan-maintainers -- Jérôme Kieffer tel +33 476 882 445
Bug#1018811: [Debian-pan-maintainers] Bug#1018811: Three new test issues preventing upload of patch (Was: pyfai: autopkgtest regression on armel and i386)
On Sun, 22 Jan 2023 16:56:46 +0100 Andreas Tille wrote: > Thanks for commenting on this. Would you be able to push the needed changes > to Salsa (and preferably upload)? Hi Andreas, I know a bit about debian packaging and also about the gitlab-CI, but I never used the later for the former. I just re-acetivated my salsa account and forked the project. Now what should I do ? * I guess replace the content of the master branch with the newest release * should I update the content of any other branch ? * then perform a merge-request on the scient-team Maybe (probably) there is a documentation existing, but as usual a quick googling did not provide the adequate answer. Cheers, Jerome
Bug#1018811: Three new test issues preventing upload of patch (Was: pyfai: autopkgtest regression on armel and i386)
Hi Andreas,
Thanks for taking care of the packaging of pyFAI. I had a look at what
the logs and apparently you are packaging the version 0.21.3 ... while
I released the verison 2023.1 last week:
https://pypi.org/project/pyfai/
I just checked on the i386-debian sid chroot I have and none of the 3 test you
found were failing (they are skipped)... but there is another one failing:
==
FAIL: test (pyFAI.test.test_error_model.TestErrorModel.test)
--
Traceback (most recent call last):
File
"/tmp/pyFAI/build/lib/python3/dist-packages/pyFAI/test/test_error_model.py",
line 121, in test
self.assertGreaterEqual(cormap(ref.__getattribute__(array),
res.__getattribute__(array)), epsilon, f"array {array} matches for {k} vs
numpy")
AssertionError: 0 not greater than or equal to 0.002 : array
sum_normalization matches for ('poisson', 'opencl', 'integrate') vs numpy
I double checked and this failure is relative to the PoCL
implemantation used on my i386-chroot. If OpenCL is disabled for the
tests in debian, this test should pass OK.
Cheers,
Jerome
On Fri, 20 Jan 2023 22:20:57 +0100
Andreas Tille wrote:
> Hi Jerome,
>
> I've applied the suggested patch to relax the tests on 32 bit architectures.
> Unfortunately there are new test suite errors as you can see in Salsa CI[1]:
>
>
> ==
> FAIL: test_count_csr
> (pyFAI.test.test_histogram.TestHistogram2d.test_count_csr)
> Test that the pixel count and the total intensity is conserved
> --
> Traceback (most recent call last):
> File
> "/builds/science-team/pyfai/debian/output/source_dir/.pybuild/cpython3_3.11_pyfai/build/pyFAI/test/test_histogram.py",
> line 339, in test_count_csr
> self.assertTrue(delta == 0, msg="check all pixels were counted")
> AssertionError: False is not true : check all pixels were counted
> ==
> FAIL: test_numpy_vs_cython_vs_csr_2d
> (pyFAI.test.test_histogram.TestHistogram2d.test_numpy_vs_cython_vs_csr_2d)
> Compare numpy histogram with cython simple implementation
> --
> Traceback (most recent call last):
> File
> "/builds/science-team/pyfai/debian/output/source_dir/.pybuild/cpython3_3.11_pyfai/build/pyFAI/test/test_histogram.py",
> line 373, in test_numpy_vs_cython_vs_csr_2d
> self.assertTrue(delta_max <= self.err_max_cnt, "pixel count difference
> numpy/csr : max delta=%s" % delta_max)
> AssertionError: False is not true : pixel count difference numpy/csr : max
> delta=8.0
> ==
> FAIL: test_2d_nosplit (pyFAI.test.test_csr.TestCSR.test_2d_nosplit)
> --
> Traceback (most recent call last):
> File
> "/builds/science-team/pyfai/debian/output/source_dir/.pybuild/cpython3_3.11_pyfai/build/pyFAI/test/test_csr.py",
> line 195, in test_2d_nosplit
> self.assertLess(error.mean(), 1e-3, "img are almost the same")
> AssertionError: 244.15215998872887 not less than 0.001 : img are almost the
> same
> ==
>
> Any idea how to fix these?
>
> Kind regards
>Andreas.
>
>
> [1] https://salsa.debian.org/science-team/pyfai/-/jobs/3826387
>
> --
> http://fam-tille.de
Bug#1022440: [Debian-pan-maintainers] Bug#1022440: python-fabio: FTBFS: distutils.errors.DistutilsClassError: command class must subclass Command
Dear Lucas,
I suspect the issue is once again the "numpy.distutils" which enforces
"setuptools<60"...
I have started to port FabIO to the meson-python builder, in a similar
way to what is done for scipy-1.9 (still not packaged for debian).
It is now close to production ready and can release a version as soon
the packaging tools are available in debian.
Best regards,
Jérôme Kieffer
On Sun, 23 Oct 2022 15:37:18 +0200
Lucas Nussbaum wrote:
> Source: python-fabio
> Version: 0.14.0+dfsg-1
> Severity: serious
> Justification: FTBFS
> Tags: bookworm sid ftbfs
> User: lu...@debian.org
> Usertags: ftbfs-20221023 ftbfs-bookworm
>
> Hi,
>
> During a rebuild of all packages in sid, your package failed to build
> on amd64.
>
>
> Relevant part (hopefully):
> > fakeroot debian/rules clean
> > dh clean --buildsystem=pybuild
> >dh_auto_clean -O--buildsystem=pybuild
> > I: pybuild base:240: python3.10 setup.py clean
> > /<>/setup.py:49: DeprecationWarning: The distutils package is
> > deprecated and slated for removal in Python 3.12. Use setuptools or check
> > PEP 632 for potential alternatives
> > from distutils.command.clean import clean as Clean
> > /usr/lib/python3/dist-packages/_distutils_hack/__init__.py:18: UserWarning:
> > Distutils was imported before Setuptools, but importing Setuptools also
> > replaces the `distutils` module in `sys.modules`. This may lead to
> > undesirable behaviors or errors. To avoid these issues, avoid using
> > distutils directly, ensure that setuptools is installed in the traditional
> > way (e.g. not an editable install), and/or make sure that setuptools is
> > always imported before distutils.
> > warnings.warn(
> > /usr/lib/python3/dist-packages/_distutils_hack/__init__.py:33: UserWarning:
> > Setuptools is replacing distutils.
> > warnings.warn("Setuptools is replacing distutils.")
> > INFO: Disabling color, you really want to install colorlog.
> > INFO:pythran:Disabling color, you really want to install colorlog.
> > INFO:fabio.setup:Use setuptools with cython
> > INFO:fabio.setup:Use setuptools.setup
> > Traceback (most recent call last):
> > File "/<>/setup.py", line 1118, in
> > setup_package()
> > File "/<>/setup.py", line 1114, in setup_package
> > setup(**setup_kwargs)
> > File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 87, in
> > setup
> > return distutils.core.setup(**attrs)
> > File "/usr/lib/python3/dist-packages/setuptools/_distutils/core.py", line
> > 172, in setup
> > ok = dist.parse_command_line()
> > File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line
> > 474, in parse_command_line
> > args = self._parse_command_opts(parser, args)
> > File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 1107, in
> > _parse_command_opts
> > nargs = _Distribution._parse_command_opts(self, parser, args)
> > File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line
> > 540, in _parse_command_opts
> > raise DistutilsClassError(
> > distutils.errors.DistutilsClassError: command class > '__main__.CleanCommand'> must subclass Command
> > E: pybuild pybuild:379: clean: plugin distutils failed with: exit code=1:
> > python3.10 setup.py clean
> > dh_auto_clean: error: pybuild --clean -i python{version} -p 3.10 returned
> > exit code 13
> > make: *** [debian/rules:7: clean] Error 25
>
>
> The full build log is available from:
> http://qa-logs.debian.net/2022/10/23/python-fabio_0.14.0+dfsg-1_unstable.log
>
> All bugs filed during this archive rebuild are listed at:
> https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20221023;users=lu...@debian.org
> or:
> https://udd.debian.org/bugs/?release=na=ign=7=7=only=ftbfs-20221023=lu...@debian.org=1=1=1=1#results
>
> A list of current common problems and possible solutions is available at
> http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
>
> If you reassign this bug to another package, please marking it as
> 'affects'-ing
> this package. See https://www.debian.org/Bugs/server-control#affects
>
> If you fail to reproduce this, please provide a build log and diff it with
> mine
> so that we can identify if something relevant changed in the meantime.
>
> --
> Debian-pan-maintainers mailing list
> debian-pan-maintain...@alioth-lists.debian.net
> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-pan-maintainers
--
Jérôme Kieffer
tel +33 476 882 445
Bug#1020073: [Debian-pan-maintainers] Bug#1020073: pyfai: FTBFS: distutils.errors.DistutilsError: Command '['/usr/bin/python3.10', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w
Hi Lucas,
All my packages (and probably many more) are marked for removal because of this
bug.
I believe this bugs comes from a specificity of Debian which does not
install python3-pip together with python3. If python3-pip is now needed by
pybuild it should be a build dependency.
Cheers,
Jerome
On Sun, 18 Sep 2022 08:31:39 +0200
Lucas Nussbaum wrote:
> Source: pyfai
> Version: 0.21.3+dfsg1-1
> Severity: serious
> Justification: FTBFS
> Tags: bookworm sid ftbfs
> User: lu...@debian.org
> Usertags: ftbfs-20220917 ftbfs-bookworm
>
> Hi,
>
> During a rebuild of all packages in sid, your package failed to build
> on amd64.
>
>
> Relevant part (hopefully):
> > fakeroot debian/rules clean
> > dh clean --buildsystem=pybuild
> >dh_auto_clean -O--buildsystem=pybuild
> > install -d
> > /<>/pyfai-0.21.3\+dfsg1/debian/.debhelper/generated/_source/home
> > pybuild --clean -i python{version} -p 3.10
> > I: pybuild base:240: python3.10 setup.py clean
> > /<>/setup.py:43: DeprecationWarning: The distutils package is
> > deprecated and slated for removal in Python 3.12. Use setuptools or check
> > PEP 632 for potential alternatives
> > from distutils.command.clean import clean as Clean
> > /usr/lib/python3/dist-packages/_distutils_hack/__init__.py:18: UserWarning:
> > Distutils was imported before Setuptools, but importing Setuptools also
> > replaces the `distutils` module in `sys.modules`. This may lead to
> > undesirable behaviors or errors. To avoid these issues, avoid using
> > distutils directly, ensure that setuptools is installed in the traditional
> > way (e.g. not an editable install), and/or make sure that setuptools is
> > always imported before distutils.
> > warnings.warn(
> > /usr/lib/python3/dist-packages/_distutils_hack/__init__.py:33: UserWarning:
> > Setuptools is replacing distutils.
> > warnings.warn("Setuptools is replacing distutils.")
> > INFO: Disabling color, you really want to install colorlog.
> > INFO:pythran:Disabling color, you really want to install colorlog.
> > INFO:pyFAI.setup:Use setuptools with cython
> > INFO:pyFAI.setup:Use setuptools.setup
> > /usr/lib/python3/dist-packages/setuptools/installer.py:27:
> > SetuptoolsDeprecationWarning: setuptools.installer is deprecated.
> > Requirements should be satisfied by a PEP 517 installer.
> > warnings.warn(
> > /usr/lib/python3/dist-packages/setuptools/installer.py:34: UserWarning:
> > Unbuilt egg for pyFAI [unknown version] (/<>)
> > pkg_resources.get_distribution('wheel')
> > WARNING: The wheel package is not available.
> > /usr/lib/python3/dist-packages/setuptools/installer.py:60: UserWarning:
> > Unbuilt egg for pyFAI [unknown version] (/<>)
> > environment = pkg_resources.Environment()
> > /usr/bin/python3.10: No module named pip
> > Traceback (most recent call last):
> > File "/usr/lib/python3/dist-packages/setuptools/installer.py", line 82,
> > in fetch_build_egg
> > subprocess.check_call(cmd)
> > File "/usr/lib/python3.10/subprocess.py", line 369, in check_call
> > raise CalledProcessError(retcode, cmd)
> > subprocess.CalledProcessError: Command '['/usr/bin/python3.10', '-m',
> > 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w',
> > '/tmp/tmpymrbi1ta', '--quiet', 'setuptools<60.0.0']' returned non-zero exit
> > status 1.
> >
> > The above exception was the direct cause of the following exception:
> >
> > Traceback (most recent call last):
> > File "/<>/setup.py", line 1137, in
> > setup_package()
> > File "/<>/setup.py", line 1133, in setup_package
> > setup(**setup_kwargs)
> > File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 86, in
> > setup
> > _install_setup_requires(attrs)
> > File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 80, in
> > _install_setup_requires
> > dist.fetch_build_eggs(dist.setup_requires)
> > File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 875, in
> > fetch_build_eggs
> > resolved_dists = pkg_resources.working_set.resolve(
> > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line
> > 789, in resolve
> > dist = best[req.key] = env.best_match(
> > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line
> > 1075, in best_match
> > return self.obtain(req, installer)
> > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line
> > 1087, in obtain
> > return installer(requirement)
> > File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 945, in
> > fetch_build_egg
> > return fetch_build_egg(self, req)
> > File "/usr/lib/python3/dist-packages/setuptools/installer.py", line 84,
> > in fetch_build_egg
> > raise DistutilsError(str(e)) from e
> > distutils.errors.DistutilsError: Command '['/usr/bin/python3.10', '-m',
> > 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w',
> > '/tmp/tmpymrbi1ta', '--quiet', 'setuptools<60.0.0']' returned non-zero exit
>
Bug#1018820: [Debian-pan-maintainers] Bug#1018820: fabio-viewer: crash during file opening
Dear Martin, Thanks for reporting the bug. I have opened another at github: https://github.com/silx-kit/fabio/issues/491 It should be fairly easy to fix. Best regards, Jerome On Wed, 31 Aug 2022 11:57:45 +0200 Martin Lutz via Debian-pan-maintainers wrote: > Package: fabio-viewer > Version: 0.14.0+dfsg-1 > Severity: normal > > Dear Maintainer, > > when opening a file with the script fabio_viewer a crash occurs. (Tried on cbf > and Bruker sfrm images). The progress bar expects an integer value but the > routine returns a float value. > > Traceback (most recent call last): > File "/usr/lib/python3/dist-packages/fabio/app/viewer.py", line 192, in > open_data_series > self.progressBar.setValue(float(iid + 1) / (total) * 100.) > TypeError: setValue(self, int): argument 1 has unexpected type 'float' > Aborted > > Reading the files interactively in python and display with matplotlib works as > expected. > > > > -- System Information: > Debian Release: bookworm/sid > APT prefers testing > APT policy: (500, 'testing') > Architecture: amd64 (x86_64) > > Kernel: Linux 5.18.0-4-amd64 (SMP w/8 CPU threads; PREEMPT) > Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE, > TAINT_UNSIGNED_MODULE > Locale: LANG=C, LC_CTYPE=C.UTF-8 (charmap=UTF-8), LANGUAGE=en_US:en > Shell: /bin/sh linked to /usr/bin/dash > Init: systemd (via /run/systemd/system) > LSM: AppArmor: enabled > > Versions of packages fabio-viewer depends on: > ii python33.10.6-1 > ii python3-fabio 0.14.0+dfsg-1+b1 > ii python3-numpy 1:1.21.5-1+b1 > > fabio-viewer recommends no packages. > > fabio-viewer suggests no packages. > > -- no debconf information > > -- > Debian-pan-maintainers mailing list > debian-pan-maintain...@alioth-lists.debian.net > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-pan-maintainers
Bug#1018811: [Debian-pan-maintainers] Bug#1018811: pyfai: autopkgtest regression on armel and i386
Hi Graham, Thanks for making me aware ... this is probably related to this PR which was just accepted upstream: https://github.com/silx-kit/pyFAI/pull/1729 Apparently, Michael Hudson-Doyle is from Ubuntu and the bugs addressed are exactly those... Unfortunately, there is no release planed in the foreseeable future ... Cheers, Jerome (upstream author of pyFAI) On Wed, 31 Aug 2022 08:35:02 +0200 Graham Inggs wrote: > Source: pyfai > Version: 0.21.3+dfsg1-1 > Severity: important > User: debian...@lists.debian.org > Usertags: regression > > Hi Maintainer > > The autopkgtests of pyfai have regressed on armel and i386 [1][2], > where they passed previously (see results of e.g. 0.20.0+dfsg1-3). I > have copied what I hope is the relevant part of the log below. > > These test failures are known upstream, as can be seen in the > following code snippets. > > pyFAI/test/test_histogram.py: > @unittest.skipIf(UtilsTest.low_mem, "test unreliable on 32bits processor") > def test_count_csr(self): > > pyFAI/test/test_histogram.py: > @unittest.skipIf(UtilsTest.low_mem, "test unreliable on 32bits processor") > def test_numpy_vs_cython_vs_csr_2d(self): > > pyFAI/test/test_csr.py: > @unittest.skipIf(UtilsTest.low_mem, "test unreliable on 32bits processor") > def test_2d_nosplit(self): > > This was noticed in Ubuntu, when the upload of glibc 2.36 caused the > same tests to start failing on armhf. > > Regards > Graham > > > [1] https://ci.debian.net/packages/p/pyfai/unstable/armel/ > [2] https://ci.debian.net/packages/p/pyfai/unstable/i386/ > > > == > FAIL: test_count_csr (pyFAI.test.test_histogram.TestHistogram2d) > Test that the pixel count and the total intensity is conserved > -- > Traceback (most recent call last): > File "/usr/lib/python3/dist-packages/pyFAI/test/test_histogram.py", > line 339, in test_count_csr > self.assertTrue(delta == 0, msg="check all pixels were counted") > AssertionError: False is not true : check all pixels were counted > > == > FAIL: test_numpy_vs_cython_vs_csr_2d > (pyFAI.test.test_histogram.TestHistogram2d) > Compare numpy histogram with cython simple implementation > -- > Traceback (most recent call last): > File "/usr/lib/python3/dist-packages/pyFAI/test/test_histogram.py", > line 373, in test_numpy_vs_cython_vs_csr_2d > self.assertTrue(delta_max <= self.err_max_cnt, "pixel count > difference numpy/csr : max delta=%s" % delta_max) > AssertionError: False is not true : pixel count difference numpy/csr : > max delta=8.0 > > == > FAIL: test_2d_nosplit (pyFAI.test.test_csr.TestCSR) > -- > Traceback (most recent call last): > File "/usr/lib/python3/dist-packages/pyFAI/test/test_csr.py", line > 195, in test_2d_nosplit > self.assertLess(error.mean(), 1e-3, "img are almost the same") > AssertionError: 244.15215998872887 not less than 0.001 : img are almost the > same > > -- > Ran 376 tests in 285.382s > > FAILED (failures=3, skipped=10) > > -- > Debian-pan-maintainers mailing list > debian-pan-maintain...@alioth-lists.debian.net > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-pan-maintainers -- Jérôme Kieffer tel +33 476 882 445
Bug#1011752: [Debian-pan-maintainers] Bug#1011752: freesas: please make the build reproducible
Hi Chris, This patch looks good to me. Thanks for the fix -- Jérôme Kieffer upstream author of FreeSAS
Bug#1008465: [Debian-pan-maintainers] Bug#1008465: python-fabio: FTBFS: Could not import extension nbsphinx (exception: No module named 'ipython_genutils')
Hi Lucas,
Thanks for the report. This looks like a bug I recently fixed in pyFAI ... I'll
have a look tomorrow. Probably just a missing dependency like in
https://github.com/silx-kit/pyFAI/commit/7bcb6dd7419b48580d97cd91a28d05f86b301f1c
Cheers,
Jerome
On Sat, 26 Mar 2022 22:57:37 +0100
Lucas Nussbaum wrote:
> Source: python-fabio
> Version: 0.13.0+dfsg-1
> Severity: serious
> Justification: FTBFS
> Tags: bookworm sid ftbfs
> User: lu...@debian.org
> Usertags: ftbfs-20220326 ftbfs-bookworm
>
> Hi,
>
> During a rebuild of all packages in sid, your package failed to build
> on amd64.
>
>
> Relevant part (hopefully):
> > make[1]: Entering directory '/<>'
> > dh_auto_build
> > I: pybuild base:237: /usr/bin/python3.10 setup.py build
> > /<>/setup.py:49: DeprecationWarning: The distutils package is
> > deprecated and slated for removal in Python 3.12. Use setuptools or check
> > PEP 632 for potential alternatives
> > from distutils.command.clean import clean as Clean
> > INFO:fabio.setup:Use setuptools with cython
> > INFO:fabio.setup:Install requires: numpy >=1.21.5
> > running build
> > running build_py
> > running build_ext
> > I: pybuild base:237: /usr/bin/python3 setup.py build
> > INFO:fabio.setup:Use setuptools with cython
> > INFO:fabio.setup:Install requires: numpy >=1.21.5
> > running build
> > running build_py
> > running build_ext
> > dh_auto_build -- -s custom --build-args="PYTHONPATH={build_dir} xvfb-run -a
> > --server-args=\"-screen 0 1024x768x24\" {interpreter} setup.py build_man"
> > I: pybuild base:237:
> > PYTHONPATH=/<>/.pybuild/cpython3_3.10_fabio/build xvfb-run -a
> > --server-args="-screen 0 1024x768x24" python3.10 setup.py build_man
> > /<>/setup.py:49: DeprecationWarning: The distutils package is
> > deprecated and slated for removal in Python 3.12. Use setuptools or check
> > PEP 632 for potential alternatives
> > from distutils.command.clean import clean as Clean
> > INFO:fabio.setup:Use setuptools with cython
> > INFO:fabio.setup:Install requires: numpy >=1.21.5
> > running build_man
> > INFO:fabio.setup:Build man for entry-point target 'fabio-convert'
> > INFO:fabio.setup:Build man for entry-point target 'eiger2cbf'
> > ERROR:eiger2cbf:Numexpr is needed to interpret formula ...
> > INFO:fabio.setup:Build man for entry-point target 'eiger2crysalis'
> > ERROR:eiger2crysalis:Numexpr is needed to interpret formula ...
> > INFO:fabio.setup:Build man for entry-point target 'densify-Bragg'
> > INFO:fabio.setup:Build man for entry-point target 'fabio_viewer'
> > I: pybuild base:237:
> > PYTHONPATH=/<>/.pybuild/cpython3_3.9_fabio/build xvfb-run -a
> > --server-args="-screen 0 1024x768x24" python3.9 setup.py build_man
> > INFO:fabio.setup:Use setuptools with cython
> > INFO:fabio.setup:Install requires: numpy >=1.21.5
> > running build_man
> > INFO:fabio.setup:Build man for entry-point target 'fabio-convert'
> > INFO:fabio.setup:Build man for entry-point target 'eiger2cbf'
> > ERROR:eiger2cbf:Numexpr is needed to interpret formula ...
> > INFO:fabio.setup:Build man for entry-point target 'eiger2crysalis'
> > ERROR:eiger2crysalis:Numexpr is needed to interpret formula ...
> > INFO:fabio.setup:Build man for entry-point target 'densify-Bragg'
> > INFO:fabio.setup:Build man for entry-point target 'fabio_viewer'
> > dh_auto_build -- -s custom --build-args="cd doc && PYTHONPATH={build_dir}
> > http_proxy='127.0.0.1:9' {interpreter} -m sphinx -N -bhtml source
> > build/html"
> > I: pybuild base:237: cd doc &&
> > PYTHONPATH=/<>/.pybuild/cpython3_3.10_fabio/build
> > http_proxy='127.0.0.1:9' python3.10 -m sphinx -N -bhtml source build/html
> > Running Sphinx v4.3.2
> >
> > Extension error:
> > Could not import extension nbsphinx (exception: No module named
> > 'ipython_genutils')
> > E: pybuild pybuild:367: build: plugin custom failed with: exit code=2: cd
> > doc && PYTHONPATH=/<>/.pybuild/cpython3_3.10_fabio/build
> > http_proxy='127.0.0.1:9' python3.10 -m sphinx -N -bhtml source build/html
> > I: pybuild base:237: cd doc &&
> > PYTHONPATH=/<>/.pybuild/cpython3_3.9_fabio/build
> > http_proxy='127.0.0.1:9' python3.9 -m sphinx -N -bhtml source build/html
> > Running Sphinx v4.3.2
> >
> > Extension error:
> > Could not import extension nbsphinx (exception: No module named
> > 'ipython_genutils')
> > E: pybuild pybuild:367: build: plugin custom failed with: exit code=2: cd
> > doc && PYTHONPATH=/<>/.pybuild/cpython3_3.9_fabio/build
> > http_proxy='127.0.0.1:9' python3.9 -m sphinx -N -bhtml source build/html
> > dh_auto_build: error: pybuild --build -i python{version} -p "3.10 3.9" -s
> > custom "--build-args=cd doc && PYTHONPATH={build_dir}
> > http_proxy='127.0.0.1:9' {interpreter} -m sphinx -N -bhtml source
> > build/html" returned exit code 13
> > make[1]: *** [debian/rules:21: override_dh_auto_build-indep] Error 25
>
>
> The full build log is available from:
> http://qa-logs.debian.net/2022/03/26/python-fabio_0.13.0+dfsg-1_unstable.log
>
> A list of
Bug#1008119: [Debian-pan-maintainers] Bug#1008119: src:pyfai: fails to migrate to testing for too long: autopkgtest regression
Dear Paul, I am the upstream author of pyFAI and the release 0.21.1 is a bugfix for the regressions spotted by the debian CI on a couple of 32-bit computer architectures (thanks to debian for that). Thus I don't understand why the migration from unstable to testing is blocked, especially that the tests passes on all architectures now. Best regards, Jerome Nota, a version 0.21.2 was released with some documentation improvements. On Tue, 22 Mar 2022 20:34:35 +0100 Paul Gevers wrote: > Source: pyfai > Version: 0.20.0+dfsg1-4.1 > Severity: serious > Control: close -1 0.21.1+dfsg1-1 > Tags: sid bookworm > User: release.debian@packages.debian.org > Usertags: out-of-sync > Control: block -1 by 1004509 > > Dear maintainer(s), > > The Release Team considers packages that are out-of-sync between testing > and unstable for more than 60 days as having a Release Critical bug in > testing [1]. Your package src:pyfai has been trying to migrate for 61 > days [2]. Hence, I am filing this bug. > > If a package is out of sync between unstable and testing for a longer > period, this usually means that bugs in the package in testing cannot be > fixed via unstable. Additionally, blocked packages can have impact on > other packages, which makes preparing for the release more difficult. > Finally, it often exposes issues with the package and/or > its (reverse-)dependencies. We expect maintainers to fix issues that > hamper the migration of their package in a timely manner. > > This bug will trigger auto-removal when appropriate. As with all new > bugs, there will be at least 30 days before the package is auto-removed. > > I have immediately closed this bug with the version in unstable, so if > that version or a later version migrates, this bug will no longer affect > testing. I have also tagged this bug to only affect sid and bookworm, so > it doesn't affect (old-)stable. > > If you believe your package is unable to migrate to testing due to > issues beyond your control, don't hesitate to contact the Release Team. > > Paul > > [1] https://lists.debian.org/debian-devel-announce/2020/02/msg5.html > [2] https://qa.debian.org/excuses.php?package=pyfai > -- Jérôme Kieffer tel +33 476 882 445
Bug#1004509: [Debian-pan-maintainers] Bug#1004509: pyfai: autopkgtest regression on armhf: images have different dimensions
Dear Paul, Dear Fred. Those 3-broken tests are exactly the same as the one reported by Fred Picca on i386 with Python3.10. I tried to reproduce them manually on a Zen computer with an i386 debian system installed on it, without success. I will try to reproduce the bug on an ARM system: I own a Tinkerboard to perform this test. What puzzles me is that it shows of only with Py3.10 The 2GB limit per process can be hit with even moderate size problems in pyFAI and I wonder if it makes sense to package pyFAI for 32-bits systems. That said, I could easily release a 0.21.1 with those 3 tests disables on 32-bits systems. Cheers, Jerome developer of pyFAI On Sat, 29 Jan 2022 19:21:38 +0100 Paul Gevers wrote: > Source: pyfai > Version: 0.21.0+dfsg1-1 > X-Debbugs-CC: debian...@lists.debian.org > Severity: serious > User: debian...@lists.debian.org > Usertags: regression > > Dear maintainer(s), > > With a recent upload of pyfai the autopkgtest of pyfai fails in testing > when that autopkgtest is run with the binary packages of pyfai from > unstable. It passes when run with only packages from testing. In tabular > form: > > passfail > pyfai from testing0.21.0+dfsg1-1 > all others from testingfrom testing > > I copied some of the output at the bottom of this report. > > Currently this regression is blocking the migration to testing [1]. Can > you please investigate the situation and fix it? > > More information about this bug and the reason for filing it can be found on > https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation > > Paul > > [1] https://qa.debian.org/excuses.php?package=pyfai > > https://ci.debian.net/data/autopkgtest/testing/armhf/p/pyfai/18797397/log.gz > > == > FAIL: test_count_csr (pyFAI.test.test_histogram.TestHistogram2d) > Test that the pixel count and the total intensity is conserved > -- > Traceback (most recent call last): >File "/usr/lib/python3/dist-packages/pyFAI/test/test_histogram.py", > line 337, in test_count_csr > self.assertTrue(delta == 0, msg="check all pixels were counted") > AssertionError: False is not true : check all pixels were counted > > == > FAIL: test_numpy_vs_cython_vs_csr_2d > (pyFAI.test.test_histogram.TestHistogram2d) > Compare numpy histogram with cython simple implementation > -- > Traceback (most recent call last): >File "/usr/lib/python3/dist-packages/pyFAI/test/test_histogram.py", > line 370, in test_numpy_vs_cython_vs_csr_2d > self.assertTrue(delta_max <= self.err_max_cnt, "pixel count > difference numpy/csr : max delta=%s" % delta_max) > AssertionError: False is not true : pixel count difference numpy/csr : > max delta=8.0 > > == > FAIL: test_2d_nosplit (pyFAI.test.test_csr.TestCSR) > -- > Traceback (most recent call last): >File "/usr/lib/python3/dist-packages/pyFAI/test/test_csr.py", line > 193, in test_2d_nosplit > self.assertLess(error.mean(), 1e-3, "img are almost the same") > AssertionError: 244.15215998872887 not less than 0.001 : img are almost > the same > > -- > Ran 375 tests in 138.562s > > FAILED (failures=3, skipped=9) > 60 > 44 > 23 > autopkgtest [08:17:51]: test command1 >
Bug#679905: RFP: cctbx -- Computational Crystallography Toolbox
Hi Recently (last summer), Fred Picca told me he advanced quite a bit on this package and finally got something working. Using non standart packaging system is really a pain ... Cheers, Jérôme On Wed, 6 Oct 2021 14:28:06 +0200 Baptiste Carvello wrote: > Hi, > > thanks for caring about Debian packaging efforts! This one is an old > one, it must have been 2012 or 2013, and salsa was called alioth :-) > > What I remember was a rather inflexible packaging system, that forced us > to duplicate existing code. And an effort that, well, slowly lost steam. > Then I lost track of it due to real life commitments (my first child was > born 2014). > > I also gratefully remember that Luc Bourhis was very helpful from the > upstream side. I wouldn't want to bother him again, though, until we > have something concrete to put on the table. > > Best regards, > Baptiste > > Le 06/10/2021 à 10:13, Andreas Tille a écrit : > > Hi, > > > > I've got a hint about cctbx and realised that there is an RFP (degraded > > from ITP) as well as a salsa repository[1]. I took the freedom to > > inject the latest upstream source and updated *parts* of the packaging > > to recent standards. I have no idea whether this might give some new > > inspiration for those who want to catch up with this package, which is > > interesting for several teams (in CC). So I simply make some noise for > > anybody who might want to continue from here. > > > > Kind regards > > > > Andreas. > > > > [1] https://salsa.debian.org/science-team/cctbx > > > >
Bug#971829: python3-pyopencl: Random runtime error in the C++ layer (crash the program)
Package: python3-pyopencl Version: 2019.1.1-1 Severity: critical Tags: upstream Justification: causes serious data loss Dear Maintainer, We are using pyopencl to perform GPU computing in Python workflows. Since we deployed Ubuntu 20.04 (which is using the same version as Debian 10 (and newer), we encounter various crashes of the server with the following error message: ``` terminate called after throwing an instance of 'std::runtime_error' what(): pybind11_object_dealloc(): Tried to deallocate unregistered instance! ``` As thoses server are managing HDF5, this causes (lots of) data corruption. The good piece of news is that the bug is known and has been fixed by this patch: https://github.com/inducer/pyopencl/commit/1dd0183dba05c17d0c21e3f9b3d73d0fee257a2d Moreover there has been a 5 releases since then which include the fix. The easiest would probably be to upgrade the package in debian. Conda based system with recent version of pyopencl are not subject to this kind of crashes. Thanks for your help, Jerome Kieffer -- System Information: Debian Release: 10.6 APT prefers stable APT policy: (800, 'stable'), (500, 'stable-updates') Architecture: amd64 (x86_64) Foreign Architectures: i386, armhf Kernel: Linux 4.19.0-11-amd64 (SMP w/4 CPU cores) Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_WARN, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=fr_FR.UTF8, LC_CTYPE=fr_FR.UTF8 (charmap=UTF-8), LANGUAGE=fr_FR.UTF8:fr:en_GB.UTF8:en (charmap=UTF-8) Shell: /bin/sh linked to /bin/bash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages python3-pyopencl depends on: ii amd-opencl-icd [opencl-icd] 1:15.9-4~deb8u2 ii libc6 2.28-10 ii libgcc1 1:8.3.0-6 ii libstdc++6 8.3.0-6 ii nvidia-opencl-icd [opencl-icd] 450.66-1~bpo10+1 ii ocl-icd-libopencl1 [libopencl1] 2.2.12-2 ii pocl-opencl-icd [opencl-icd]1.2-5 ii python3 3.7.3-1 ii python3-appdirs 1.4.3-1 ii python3-decorator 4.3.0-1.1 ii python3-numpy [python3-numpy-abi9] 1:1.16.2-1 ii python3-pkg-resources 40.8.0-1 ii python3-pytools 2019.1-1 ii python3-six 1.12.0-1 Versions of packages python3-pyopencl recommends: ii python-pyopencl-doc 2019.1.1-1 ii python3-mako 1.0.7+ds1-1 Versions of packages python3-pyopencl suggests: pn python3-imaging-tk ii python3-matplotlib3.0.2-2 ii python3-opengl3.1.0+dfsg-2 ii python3-pyopencl-dbg 2019.1.1-1 ii python3-pytest3.10.1-2 -- no debconf information
Bug#954352: pymca: Missing dependency "python3-scipy", probably in "python3-silx"
Package: pymca Version: 5.4.3+dfsg-1 Severity: grave Justification: renders package unusable Dear Maintainer, I installed "pymca" on a debian 10 system, this draggs the dependencies: * python3-pymca5 * python3-silx The package python3-silx apparently requires python3-scipy, the graphical user interface does not load and crashed at start up. Cheers, Jerpme -- System Information: Debian Release: 10.3 APT prefers stable APT policy: (800, 'stable'), (500, 'stable-updates') Architecture: amd64 (x86_64) Foreign Architectures: i386, armhf Kernel: Linux 4.19.0-8-amd64 (SMP w/8 CPU cores) Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=fr_FR.utf8, LC_CTYPE=fr_FR.utf8 (charmap=UTF-8), LANGUAGE=fr_FR.UTF8:fr:en_GB.UTF8:en (charmap=UTF-8) Shell: /bin/sh linked to /bin/bash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages pymca depends on: ii python3 3.7.3-1 ii python3-numpy 1:1.16.2-1 ii python3-pymca5 5.4.3+dfsg-1 pymca recommends no packages. pymca suggests no packages. -- no debconf information
Bug#946422: Fw: pocl and silx
Thanks Fred for the time spent on this. It looks like it is a very deep problem ! Concerning the code: This medfilt code never properly worked on POCL CPU-thread version while it works as expected on CUDA (POCL+CUDA) or other drivers. There is a huge amount of shared memory involved which may be the root of the problem (?) But about the interference I mainly see specfile (the C-library) which is our "first" guess inside "silx.io". This legacy code is far from our current standards ... Other point, pyopencl.array.zeros_like() is calling the opencl enfillBuffer function which caused me also issues in (POCL+CUDA). Creating a work-around on the silx side is an option as it has been done many times. I opened a bug on our side: https://github.com/silx-kit/silx/issues/2848 Cheers Begin forwarded message: Date: Thu, 19 Dec 2019 10:08:49 + From: PICCA Frederic-Emmanuel To: "kief...@esrf.fr" Subject: pocl and silx Salut Jerome, on est en train d'essayer de demerder le problème avec pocl. On a mis les info la https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=946422 est-ce que cela te dis quelque choses. C'est vrai que si l'on import silxs.io avant silxs.opencl dans le petit snipset de test, ca change fondamentalement la done... Amicalement Fred -- Jérôme Kieffer tel +33 476 882 445
Bug#937436: pyfai: Python2 removal in sid/bullseye
On Thu, 5 Sep 2019 19:58:14 -0400 Sandro Tosi wrote: > i've pushed to pyfai git repo a few commits, most importantly to drop > the python2 packages; i'm really not familiar with the package (but it > build fine in a pbuilder chroot), so i'm writing to you: could you > have a look at the latest changes and possibly upload the package? > ideally we should target unstable for this upload. > > pyfai currently depends on several python2 packages, which cant be > dropped until their reverse-depends count goes to 0. Hi, The latest pyFAI uses python3 for the application instead of python2, at least on the master. I did not check if it was the case for the release. In the worse case, one would just have to wait for the next release which is planed later this year. Anyhow, I recently fixed a bug related to the documentation which was generated using the python2 build systsem. Cheers, Jerome
Bug#926019: RM: clsparse -- ROM; dead upstream
On Sat, 30 Mar 2019 14:34:05 +0100 ghisv...@gmail.com wrote: > Package: ftp.debian.org > Severity: normal > X-Debbugs-CC: debian-scie...@lists.debian.org > Control: affects -1 clsparse > > Please remove "clsparse" from "unstable". > > This package is dead upstream and currently affected by two RC bugs. It > has got no rdpends and should be safe to remove. This is a sad piece of news :( -- Jérôme Kieffer
Bug#916292: Kahan summation not working on i386
Hi, This FBFS bug comes down to the POCL on i386 which is not able to perform calculation as described by the OpenCL spec. It is likely a numerical optimization at the wrong place as those tests ensures the calculation are performed as expected. This is described in: https://en.wikipedia.org/wiki/Kahan_summation_algorithm#Possible_invalidation_by_compiler_optimization If I find some time I could have a look at it, but on the other hand, pyFAI does not support 32bits architecture as it requires often more than 2GB of memory for real scientific application. -- Jérôme Kieffer: core dev of pyFAI.
Bug#861640: f2fs-tools: buffer overflow detected: fsck.f2fs terminated
Package: f2fs-tools Version: 1.7.0-1.1~bpo8+1 Severity: important Tags: newcomer Dear Maintainer, I formated a complete SSD (Samsung 940evo, 250GB) interfaced in USB3 with F2FS on a debian stretch computer. 76GB of data were copied to it (mainly images and videos) After 4 days, only 217MB of data remained. Running manually fsck on the volume crashed. Apparently this imay be related to: https://www.mail-archive.com/linux-f2fs- de...@lists.sourceforge.net/msg05070.html The version 1.8 (compiled from sources) was able to run on the volume (while unable to retrieve the lost data). root@mac13:/media/kieffer# du -h . [...] 217M./SSD940evo 217M. root@mac13:/media/kieffer# df -h Filesystem Size Used Avail Use% Mounted on [...] /dev/sdb1 233G 76G 156G 33% /media/kieffer/SSD940evo root@mac13:/media/kieffer# fsck /dev/sdb1 fsck from util-linux 2.29.2 Info: Segments per section = 1 Info: Sections per zone = 1 Info: sector size = 512 Info: total sectors = 488395120 (238474 MB) Info: MKFS version "Linux version 4.9.0-1-amd64 (debian-ker...@lists.debian.org) (gcc version 6.3.0 20170124 (Debian 6.3.0-5) ) #1 SMP Debian 4.9.6-3 (2017-01-28)" Info: FSCK version from "Linux version 4.9.0-1-amd64 (debian-ker...@lists.debian.org) (gcc version 6.3.0 20170124 (Debian 6.3.0-5) ) #1 SMP Debian 4.9.6-3 (2017-01-28)" to "Linux version 4.9.0-1-amd64 (debian-ker...@lists.debian.org) (gcc version 6.3.0 20170124 (Debian 6.3.0-5) ) #1 SMP Debian 4.9.6-3 (2017-01-28)" Info: superblock features = 0 : Info: superblock encrypt level = 0, salt = Info: total FS sectors = 488395120 (238474 MB) Info: CKPT version = 732 Info: checkpoint state = 41 : unmount [ASSERT] (fsck_chk_data_blk:1459) --> SIT bitmap is 0x0. blk_addr[0x187] [ASSERT] (fsck_chk_data_blk:1459) --> SIT bitmap is 0x0. blk_addr[0x2000200] [ASSERT] (fsck_chk_data_blk:1459) --> SIT bitmap is 0x0. blk_addr[0x338f8ba] [ASSERT] (fsck_chk_data_blk:1459) --> SIT bitmap is 0x0. blk_addr[0x2000600] [ASSERT] (fsck_chk_data_blk:1459) --> SIT bitmap is 0x0. blk_addr[0x2000700] [ASSERT] (fsck_chk_data_blk:1447) --> blkaddress is not valid. [0xffcf] [ASSERT] (fsck_chk_data_blk:1447) --> blkaddress is not valid. [0xfff] [is_valid_ssa_data_blk: 282] summary_entry.nid [0x2f8] [is_valid_ssa_data_blk: 284] summary_entry.version [0x0] [is_valid_ssa_data_blk: 286] summary_entry.ofs_in_node [0x284] [is_valid_ssa_data_blk: 288] parent nid[0x9] [is_valid_ssa_data_blk: 289] version from nat [0x0] [is_valid_ssa_data_blk: 291] idx in parent node[0x9] [is_valid_ssa_data_blk: 293] Target data block addr[0x9] [ASSERT] (is_valid_ssa_data_blk: 294) --> Invalid data seg summary [ASSERT] (fsck_chk_data_blk:1454) --> summary data block is not valid. [0x9] [ASSERT] (fsck_chk_data_blk:1447) --> blkaddress is not valid. [0x1] [ASSERT] (fsck_chk_data_blk:1447) --> blkaddress is not valid. [0x2] [ASSERT] (fsck_chk_data_blk:1447) --> blkaddress is not valid. [0x300] [is_valid_ssa_data_blk: 282] summary_entry.nid [0x4] [is_valid_ssa_data_blk: 284] summary_entry.version [0x0] [is_valid_ssa_data_blk: 286] summary_entry.ofs_in_node [0xd] [is_valid_ssa_data_blk: 288] parent nid[0x9] [is_valid_ssa_data_blk: 289] version from nat [0x0] [is_valid_ssa_data_blk: 291] idx in parent node[0xd] [is_valid_ssa_data_blk: 293] Target data block addr[0x2000200] [ASSERT] (is_valid_ssa_data_blk: 294) --> Invalid data seg summary [ASSERT] (fsck_chk_data_blk:1454) --> summary data block is not valid. [0x9] [ASSERT] (fsck_chk_data_blk:1447) --> blkaddress is not valid. [0xbd58856d] [is_valid_ssa_data_blk: 282] summary_entry.nid [0x389] [is_valid_ssa_data_blk: 284] summary_entry.version [0x0] [is_valid_ssa_data_blk: 286] summary_entry.ofs_in_node [0x171] [is_valid_ssa_data_blk: 288] parent nid[0x9] [is_valid_ssa_data_blk: 289] version from nat [0x0] [is_valid_ssa_data_blk: 291] idx in parent node[0xf] [is_valid_ssa_data_blk: 293] Target data block addr[0xa1ae1] [ASSERT] (is_valid_ssa_data_blk: 294) --> Invalid data seg summary [ASSERT] (fsck_chk_data_blk:1454) --> summary data block is not valid. [0x9] [ASSERT] (fsck_chk_data_blk:1447) --> blkaddress is not valid. [0x1d020008] [ASSERT] (fsck_chk_data_blk:1447) --> blkaddress is not valid. [0xe2acacbd] [ASSERT] (fsck_chk_data_blk:1447) --> blkaddress is not valid. [0x8000a1a] [ASSERT] (fsck_chk_data_blk:1447) --> blkaddress is not valid. [0xe13d0200] [ASSERT] (fsck_chk_data_blk:1447) --> blkaddress is not valid. [0x1f1d37fb] [is_valid_ssa_data_blk: 282] summary_entry.nid [0x4cc] [is_valid_ssa_data_blk: 284] summary_entry.version [0x0] [is_valid_ssa_data_blk: 286] summary_entry.ofs_in_node [0x250] [is_valid_ssa_data_blk: 288] parent nid[0x9] [is_valid_ssa_data_blk: 289] version from nat [0x0]
Bug#784709: os-prober prevent the upgrade to jessie
Package: os-prober Version: 1.65 Severity: critical Tags: newcomer Justification: breaks the whole system Dear Maintainer, During the upgrade (apt-get dist-upgrade) of a computer from debian7 (Wheezy) to Debian8 (Jessie) the system still runs the kernel 3.2 from Wheezy; but the os-prober version used by update-grub is already the one from Jessie... and hang. According to: https://lists.debian.org/debian-boot/2013/05/msg00077.html (and related bugs at maegia), the new os-prober (from Jessie) is unable to scan a hard-drive containing Extended partitions (like sdb4 hereafter) and locks forever (at least 90mn), locking the debian system in the middle of a dist- upgrade. Disque /dev/sdb : 1,8 TiB, 2000398934016 octets, 3907029168 secteurs Unités : secteur de 1 × 512 = 512 octets Taille de secteur (logique / physique) : 512 octets / 512 octets taille d'E/S (minimale / optimale) : 512 octets / 512 octets Type d'étiquette de disque : dos Identifiant de disque : 0x9a2578f7 Device Boot StartEndSectors Size Id Type /dev/sdb1 63 33575849 33575787 16G 82 Linux swap / Solaris /dev/sdb2 33575850 243304424 209728575 100G 83 Linux /dev/sdb3243304425 453032999 209728575 100G 83 Linux /dev/sdb4453033000 3907024064 3453991065 1,6T 5 Extended /dev/sdb5453033063 557905319 104872257 50G 83 Linux /dev/sdb6557905383 662777639 104872257 50G 83 Linux /dev/sdb766203 767649959 104872257 50G 83 Linux /dev/sdb8767650023 872522279 104872257 50G 83 Linux /dev/sdb9872522343 1082250854 209728512 100G 83 Linux /dev/sdb10 1082250918 3907024064 2824773147 1,3T 83 Linux The system was fully occupied by a mount process trying to mount /dev/sdb4. This process was uninteruptable (kill -9 being ineffective) and forced to reboot exactly at the stage grub was updating. The only solution found was to boot an external device with a rescue system and a recent kernel (3.16) to finish the dist-upgrade. One solution may have been to upgrade first the kernel via wheezy-backports packages before upgrading to Jessie. Best regards, Jerome Kieffer -- System Information: Debian Release: 8.0 APT prefers stable APT policy: (800, 'stable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 3.16.0-4-amd64 (SMP w/8 CPU cores) Locale: LANG=fr_FR.UTF8, LC_CTYPE=fr_FR.UTF8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/bash Init: systemd (via /run/systemd/system) Versions of packages os-prober depends on: ii libc6 2.19-18 os-prober recommends no packages. os-prober suggests no packages. -- no debconf information -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#783084: debian packaging ...
Most of the packaging is done in: https://github.com/kif/clFFT/tree/debian the issues remaining are especially related to the test program Client -- Jérôme Kieffer Data analysis unit - ESRF -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#783084: ITP: clfft -- OpenCL FFT library
Package: wnpp Severity: wishlist Owner: Jerome Kieffer jerome.kief...@esrf.fr * Package name: clfft Version : 2.4.0 Upstream Author : Kent Knox kent.k...@amd.com * URL : https://github.com/clMathLibraries/clFFT * License : Apache 2 Programming Lang: C++, Python Description : clFFT is an OpenCL FFT library clFFT is a software library containing FFT functions written in OpenCL. In addition to GPU devices, the libraries also support running on CPU devices to facilitate debugging and heterogeneous programming. -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#672868: intel-opencl-sdk: changing from ITP to RFP
Hi Lucas, I did this packaging ... actually many times as Intel released multiple version of their SDK. I did not manage to define clearly if those repackaged RPM could be distributed or not. Knowing the Debian policy ... you know this story better than me :) This is somehow linked to the Xeon Phi story discussed on the Debian Science list. Cheers, -- Jerome Kieffer jerome.kief...@terre-adelie.org -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#735432: new upstream
Hi, The new upstream version (0.14) will include a debian-friendly source tree which includes test images (this makes the source package 100MB) and exclude all auto-generated files like from cython, sphinx, pylint, epydoc, ... to keep it compatible with debian rules. Once upon a time I read upstream packages should not be tailored for Debian ... but that was a long time ago. -- Jérôme Kieffer tel +33 476 882 445 -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#697348: Patch to correct this bug
Dear Debian Python Modules Team, Could you please have python-qt4 recompiled for Debian6-Squeeze including this patch to fix bug #697348. Thanks in advance, With by best regards. -- Jérôme Kieffer Data analysis unit - ESRF python-qt4_4.7.3-1.dsc Description: Binary data python-qt4_4.7.3-1.debian.tar.gz Description: Binary data
Bug#697348: [Python-modules-team] Patch to correct this bug
On Sat, 31 Aug 2013 10:47:18 -0400 Scott Kitterman deb...@kitterman.com wrote: On Saturday, August 31, 2013 16:25:16 Jerome Kieffer wrote: Dear Debian Python Modules Team, Could you please have python-qt4 recompiled for Debian6-Squeeze including this patch to fix bug #697348. Are you sure that's right? At least I am sure it fixes this bug. Maybe the str is double shouting. It looks like the bg_i18n lost this string attribute recently. The patch I sent you is in production on many computers for 6 months. I don't know that the extra str() matters, but I think it's better to match upstream's change unless there's a good reason not to. Could you please check that it works for you without the str()? I just recompiled everything and it works without the str. Cheers, -- Jérôme Kieffer Data analysis unit - ESRF -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#711554: RE : Bug#711554: ITP: pyhst -- High Speed Tomographic reconstruction controled from Python
On Sat, 8 Jun 2013 06:54:29 + PICCA Frédéric-Emmanuel frederic-emmanuel.pi...@synchrotron-soleil.fr wrote: if you want I can sponsorise this package :) The code was just (officially) freed ... but I am sure there is still plenty of work on the packaging side. Cheers, -- Jérôme Kieffer Data analysis unit - ESRF -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#711554: ITP: pyhst -- High Speed Tomographic reconstruction controled from Python
Package: wnpp Severity: wishlist Owner: Jerome Kieffer jerome.kief...@esrf.fr Package name: pyhst Version : 2.0. Upstream Author : Alessandro Mirone mir...@esrf.fr URL : https://forge.epn-campus.eu/projects/pyhst2 License : GPL Programming Lang: C, Python, CUDA Description : High Speed Tomographic reconstruction controled from Python The PyHST2 code is in service at ESRF for phase-contrast and absorption tomography. This code has been engineered to sustain the high data flow typical of the third generation synchrotron facilities by adopting a distributed and pipelined architecture. The code implements, beside a default filtered backprojection reconstruction, iterative reconstruction techniques with a-priori knowledge. These latter are used to improve the reconstruction quality or in order to reduce the required data volume and reach a given quality goal. The implemented a-priori knowledge techniques are based on the total variation penalisation and a new recently found convex functional which is based on overlapping patches. -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#710121: work ongoing
One can follow the development of the debian package on: https://github.com/kif/pyFAI_debian -- Jérôme Kieffer Data analysis unit - ESRF -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#710121: pyfai: Please package the latest pyFAI
On Tue, 28 May 2013 15:42:54 +0200 Frederic-Emmanuel PICCA pi...@synchrotron-soleil.fr wrote: Package: pyfai Version: 0.3.5-1 Severity: normal Dear Maintainer, Hello, now that wheezy is out, it would be nice to upload the lastest pyFAI. so we could use it on the beamlines with the official packaging. Hello Frédéric, We are currently in a beta phase of pyFAI ... It should last for a couple of weeks before the release of v0.9 There are a couple of bugs reported by the user I would like to fix before releasing. Cheers, -- Jérôme Kieffer On-Line Data analysis / Software Group ISDD / ESRF tel +33 476 882 445 -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#697348: python-qt4: uic.loadUi crashed with AttributeError in createWidget() when RadioButtons
Package: python-qt4 Version: 4.7.3-1+b1 Severity: normal Tags: upstream Maybe this bug could be rated critical as it makes unrelated software on the system break ... This bug apprears when a group of RadioButtons is defined in a UIC file, see attached example. It has already been fixed in newer version of upstream (absent in wheezy) and in Ubuntu: https://bugs.launchpad.net/ubuntu/+source/python-qt4/+bug/514796 Here is an example of patch: diff /usr/lib/pymodules/python2.6/PyQt4/uic/uiparser.py uiparser.py 184,188c184,185 try: bg_name = bg_i18n.string except AttributeError: print(Error detected %s%bg_i18n) bg_name = str(bg_i18n) --- bg_name = bg_i18n.string -- System Information: Debian Release: 6.0.6 APT prefers stable APT policy: (500, 'stable') Architecture: amd64 (x86_64) Kernel: Linux 2.6.32-5-amd64 (SMP w/4 CPU cores) Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Versions of packages python-qt4 depends on: ii libc6 2.11.3-4 Embedded GNU C Library: Shared lib ii libgcc1 1:4.4.5-8 GCC support library ii libpython2.6 2.6.6-8+b1 Shared Python runtime library (ver ii libqt4-assistant 4:4.6.3-4+squeeze1 Qt 4 assistant module ii libqt4-designer 4:4.6.3-4+squeeze1 Qt 4 designer module ii libqt4-help 4:4.6.3-4+squeeze1 Qt 4 help module ii libqt4-network4:4.6.3-4+squeeze1 Qt 4 network module ii libqt4-script 4:4.6.3-4+squeeze1 Qt 4 script module ii libqt4-scripttools4:4.6.3-4+squeeze1 Qt 4 script tools module ii libqt4-svg4:4.6.3-4+squeeze1 Qt 4 SVG module ii libqt4-test 4:4.6.3-4+squeeze1 Qt 4 test module ii libqt4-webkit 4:4.6.3-4+squeeze1 Qt 4 WebKit module ii libqt4-xml4:4.6.3-4+squeeze1 Qt 4 XML module ii libqt4-xmlpatterns4:4.6.3-4+squeeze1 Qt 4 XML patterns module ii libqtcore44:4.6.3-4+squeeze1 Qt 4 core module ii libqtgui4 4:4.6.3-4+squeeze1 Qt 4 GUI module ii libstdc++64.4.5-8The GNU Standard C++ Library v3 ii python2.6.6-3+squeeze7 interactive high-level object-orie ii python-sip [sip-api-7 4.10.2-1 Python/C++ bindings generator runt ii python-support1.0.10 automated rebuilding support for P python-qt4 recommends no packages. Versions of packages python-qt4 suggests: pn python-qt4-dbgnone (no description available) -- no debconf information -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#697348: Acknowledgement (python-qt4: uic.loadUi crashed with AttributeError in createWidget() when RadioButtons)
Example of test-case with just 2 radiobuttons
--
Jérôme Kieffer
On-Line Data analysis / Software Group
ISDD / ESRF
tel +33 476 882 445
#!/usr/bin/python
import sys
from PyQt4 import QtCore, QtGui, uic
class AIWidget(QtGui.QWidget):
def __init__(self):
QtGui.QWidget.__init__(self)
uic.loadUi('buggy.ui', self)
if __name__ == __main__:
app = QtGui.QApplication(sys.argv)
window = AIWidget()
window.show()
sys.exit(app.exec_())
buggy.ui
Description: Binary data
Bug#672868: On the grill
Hello, I already made a package that is compatible with other OpenCL vendors but I admitted the SDK was redistributable. Have you advanced on that subject ? Cheers, -- Jérôme Kieffer On-Line Data analysis / Software Group ISDD / ESRF tel +33 476 882 445 -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#664993: python-rfoo and remote-tty: error when trying to install together
On Thu, 22 Mar 2012 08:12:00 +0100 Treinen trei...@free.fr wrote: Package: remote-tty,python-rfoo Version: remote-tty/4.0-13 Version: python-rfoo/1.3.0-1 Severity: serious User: trei...@debian.org Usertags: edos-file-overwrite Thanks Ralf for the bug report, the fault is on our side. I contacted the upstream author to let him choose the name of the new script in /usr/bin. Cheers, -- Jérôme Kieffer On-Line Data analysis / Software Group ISDD / ESRF tel +33 476 882 445 -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#663706: ITP: python-rfoo -- Fast RPC package for Python (and a remote console)
Package: wnpp Severity: wishlist Owner: Jerome KIEFFER jerome.kief...@esrf.fr * Package name: python-rfoo Version : 1.3.0 Upstream Author : Nir Aides n...@winpdb.org * URL : http://code.google.com/p/rfoo/ * License : BSD Programming Lang: Python Description : Fast RPC package for Python (and a remote console) rfoo (remote foo) is a fast Python RPC package which can do 160,000 RPC calls per second on a regular PC. It includes a fast serialization module called rfoo.marsh which extends the Python built in marshal module by eliminating serialization of code objects and protecting against bad input. The result is a safe to use ultra fast serializer. . Included with rfoo is rconsole, a remote Python console with auto completion, which can be used to inspect and modify the namespace of a running script. -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#656633: ITP: pyfai -- python library for Fast Azimuthal Integration
Package: wnpp Severity: wishlist Owner: Jerome KIEFFER jerome.kief...@esrf.fr * Package name: pyfai Version : 0.3.5 Upstream Author : Jerome Kieffer jerome.kief...@esrf.fr * URL : http://forge.epn-campus.eu/projects/azimuthal * License : GPL Programming Lang: Python Description : python library for Fast Azimuthal Integration PyFAI is a Python library for azimuthal integration; it allows the conversion of diffraction images taken with 2D detectors like CCD cameras into X-Ray powder patterns that can be used by other software like Rietveld refinement tools (i.e. FullProf), phase analysis or texture analysis. As PyFAI is a library, its main goal is to be integrated in other tools like PyMca, LiMa or EDNA. To perform online data analysis, the precise description of the experimental setup has to be known. This is the reason why PyFAI includes geometry optimization code working on powder rings of reference samples. Alternatively, PyFAI can also import geometries fitted with other tools like Fit2D. PyFAI has been designed to work with any kind of detector with any geometry (transmission, reflection, off-axis, ...). It uses the Python library FabIO to read most images taken by diffractometer. -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#651697: ITP: python-fftw -- FFTW bindings for python
Package: wnpp Severity: wishlist Owner: Jerome Kieffer jerome.kief...@esrf.fr Package name: python-fftw Version : 0.2.2 Upstream Author : Jochen Schroedercycoma...@gmail.com URL : https://launchpad.net/pyfftw License : GPL Programming Lang: Python Description : Python bindings to the FFTW3 C-library for computing discrete Fourier transforms. Python bindings to the FFTW3 Fastest Fourier Transform in the West. C-library (http://www.fftw.org/) for computing discrete Fourier transforms. PyFFTW are python bindings for the FFTW3 C-routines, using numpy and ctypes. It includes a somewhat pythonic interface to the FFTW routines, but leaves the concept of creating plans and executing these plans intact. -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#649008: ITP: python-fabio -- I/O library for images produced by 2D X-ray detector
Package: wnpp Severity: wishlist Owner: Jerome KIEFFER jerome.kief...@esrf.fr Package name: python-fabio Version : 0.0.8 Upstream Author : Erik Knudsen erik.knud...@risoe.dk URL : http://sourceforge.net/apps/trac/fable/wiki/fabio License : GPL Programming Lang: Python Description : I/O library for images produced by 2D X-ray detector FabIO is an I/O library for images produced by 2D X-ray detectors and written in python. FabIO support images detectors from a dozen of companies (including Mar, Dectris, ADSC, Hamamatsu, Oxford, ...), for a total of 20 different file formats (like CBF, EDF, TIFF, ...) and offers an unified interface to their headers (as a python dictionary) and datasets (as a numpy ndarray of integers or floats) -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#649009: ITP: python-fabio -- I/O library for images produced by 2D X-ray detector
Package: wnpp Severity: wishlist Owner: Jerome KIEFFER jerome.kief...@esrf.fr Package name: python-fabio Version : 0.0.8 Upstream Author : Erik Knudsen erik.knud...@risoe.dk URL : http://sourceforge.net/apps/trac/fable/wiki/fabio License : GPL Programming Lang: Python Description : I/O library for images produced by 2D X-ray detector FabIO is an I/O library for images produced by 2D X-ray detectors and written in python. FabIO support images detectors from a dozen of companies (including Mar, Dectris, ADSC, Hamamatsu, Oxford, ...), for a total of 20 different file formats (like CBF, EDF, TIFF, ...) and offers an unified interface to their headers (as a python dictionary) and datasets (as a numpy ndarray of integers or floats) -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#644518: ITP: spd -- Synchrotron image corrections and azimuthal integration
Package: wnpp Severity: wishlist Owner: Jerome Kieffer jerome.kief...@esrf.fr * Package name: spd Version : 1.3 Upstream Author : Peter Boesecke boese...@esrf.fr * URL : http://forge.epn-campus.eu/projects/azimuthal * License : LGPL Programming Lang: C Description : Synchrotron image corrections and azimuthal integration SPD stands for SPatial Distortion. Written in C language, this command-line driven program deals with images coming from X-ray diffusion/diffraction experiments. It does subsequently: *intensity corrections (dark current, flat field correction, ...), *geometry corrections using spline files or a pair of distortion arrays, *azimuthal integration in 2D or 1D after maskin defective pixels. SPD was originally written by Jorg Klora for ESRF and was re-written by Peter Boesecke from ESRF/ID02. Maintenance and packaging of the program are provided by Rainer Wilcke and Jerome Kieffer from Scisoft at ESRF. -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
