Bug#946752: intel-opencl-icd: Depends on libigdgmm5, which no longer exists

2019-12-15 Thread Rebecca N. Palmer
Package: intel-opencl-icd Version: 19.29.13530-1 Severity: serious Justification: makes package uninstallable This package's debian/control hardcodes a dependency on libigdgmm5. As this library has changed soname to libigdgmm11, this makes it uninstallable. Changing the dependency may well

Bug#945389: Tried to upgrade skimage to see whether #945389 is fixed but failed

2019-12-05 Thread Rebecca N. Palmer
Stefan van der Walt wrote: One possibility is that NumPy was compiled with an older version of Cython:[...] Do you know how I can check the source files for the NumPy 1.17 build that is used here? Source: https://sources.debian.org/src/numpy/1:1.17.4-3/ Build log:

Bug#945263: numpy FTBFS on all

2019-12-14 Thread Rebecca N. Palmer
Probably because the arch:all build doesn't build python3-numpy (only python-numpy-doc), and hence the ls [0] providing the filename for that >> evaluates to empty. The obvious fix (though I haven't tested it) is to wrap this in an "only if building arch:any / python3-numpy" conditional.

Bug#943732: pandas: test failures on non-Intel

2019-10-28 Thread Rebecca N. Palmer
Package: python3-pandas Version: 0.25.2+dfsg-1 Severity: serious Control: notfound -1 0.23.3+dfsg-8 (Filed as RC to make sure I don't forget about these: actual severity to be decided.) - Several datetime-related failures on arm* and mips64el. - Several convert-to-records failures on s390x

Bug#943732: pandas: test failures on non-Intel

2019-10-29 Thread Rebecca N. Palmer
and 14 on riscv64, not investigated yet.

Bug#942235: dask: autopkgtest needs update for new version of pytest

2019-10-28 Thread Rebecca N. Palmer
Assuming we're talking about https://salsa.debian.org/python-team/modules/dask/blob/experimental/debian/patches/use-local-intersphinx.patch I think the actual problem is on the numpy line: it adds the local inventory but doesn't remove the online one, so the tuple is too long. (I haven't

Bug#945501: python-statsmodels-doc: unhandled symlink to directory conversion: /usr/share/doc/python-statsmodels-doc/examples

2019-11-26 Thread Rebecca N. Palmer
Control: tags -1 pending This happened when python-statsmodels was removed in 0.10.1-1, and the documentation was hence moved from /usr/share/doc/python-statsmodels to /usr/share/doc/python-statsmodels-doc. 0.10.2-1 (in salsa) includes your suggested fix. 0.9.0-5 -> 0.10.2-1 works, but

Bug#940679: pandas: random test crashes

2019-09-25 Thread Rebecca N. Palmer
Control: tags -1 - patch That's not the problem: cdef classes _can_ have non-cdef class (not instance) attributes. https://github.com/cython/cython/issues/3154 On further inspection, the actual problem is that we have a Timedelta (full Python class, has a dict) allocated in a memory space

Bug#949767: libgpuarray pocl out-of-order queues

2020-01-26 Thread Rebecca N. Palmer
Control: reassign -1 src:libgpuarray,src:pocl Control: retitle -1 wrong results in gemm(batch) in out-of-order queues libgpuarray checks whether the device supports out-of-order queues, and requests one if it does (src/gpuarray_buffer_opencl.c:155,185). pocl 1.3 says it doesn't support

Bug#949767: clblas: *gemm wrong answers in out-of-order queues

2020-01-27 Thread Rebecca N. Palmer
Control: retitle -1 clblas: *gemm wrong answers in out-of-order queues Control: reassign -1 src:clblas Control: found -1 2.12-1 I think I've found the actual bug, in clblas src/library/blas/xgemm.cc: clblasGemm (with a single command queue) enqueues up to 4 kernels and returns an event that

Bug#950098: patsy: exceptions in documentation, FTBFS with new ipython

2020-01-28 Thread Rebecca N. Palmer
in example + +Author: Rebecca N. Palmer +Bug-Debian: https://bugs.debian.org/ +Forwarded: no + +--- patsy-0.5.1.orig/doc/spline-regression.rst patsy-0.5.1/doc/spline-regression.rst +@@ -179,7 +179,7 @@ marginal spline bases patterns can be ob + :{"x1": x1.ravel(), &quo

Bug#950101: python-xarray-doc: FTBFS with new ipython

2020-01-28 Thread Rebecca N. Palmer
Package: python-xarray-doc Version: 0.14.1-2 Severity: serious Control: tags -1 patch ipython_directive examples are executed at build time. xarray has some examples that fail without optional dependencies Debian doesn't have (e.g. h5netcdf) and/or downloaded data. This used to put the error

Bug#950087: statsmodels: FTBFS with new ipython

2020-01-28 Thread Rebecca N. Palmer
Package: python-statsmodels-doc Severity: serious Control: tags -1 patch (only tested in 0.11, but believed to exist earlier) Some documentation examples (e.g. contrasts.rst) fail in a Debian build because they need to download data. This has been the case for some time, but only became an

Bug#950695: seaborn: FTBFS test failure in TestFacetGrid.test_set_ticklabels

2020-02-04 Thread Rebecca N. Palmer
Package: python3-seaborn Version: 0.9.0-2 Severity: serious Found during statsmodels transition testing, but also occurs without statsmodels. I have not investigated further. __ TestFacetGrid.test_set_ticklabels ___ self = def

Bug#949464: local intersphinx

2020-01-31 Thread Rebecca N. Palmer
Control: reassign -1 python3-sphinx-astropy Control: tags -1 patch (untested) (If reading this in the bug, see https://lists.debian.org/debian-mentors/2020/01/msg00295.html.) An intersphinx_mapping can specify multiple alternatives for where to find the inventory referred to, and these can

Bug#949767: causes autopkgtest regression in libgpuarray

2020-01-24 Thread Rebecca N. Palmer
Source: libffi Version: 3.3-3 Severity: serious (This is a "block migration while I investigate" bug: it may well be downgraded or reassigned when I know more.) https://ci.debian.net/packages/libg/libgpuarray/unstable/amd64/ libffi is one of the few that changed:

Bug#949767: causes autopkgtest regression in libgpuarray

2020-01-25 Thread Rebecca N. Palmer
(The above debci log is misleading due to #764081; pocl also changed, and the failure goes away on using the old pocl.) It looks like this fails because it is reading the result before the computation has finished: - On a failure, the np.asarray(gr) passed to assert_allclose doesn't match cr

Bug#953970: python-boto: autopkgtest failure with Python 3.8 as default

2020-04-09 Thread Rebecca N. Palmer
This might fix the remaining errors (but has not been tested): https://docs.python.org/3/library/hmac.html#hmac.new --- tests/unit/utils/test_utils.py~ 2020-04-09 11:02:26.967201681 +0100 +++ tests/unit/utils/test_utils.py 2020-04-09 11:02:26.991202140 +0100 @@ -85,7 +85,7 @@ class

Bug#956512: node-unicode-data: autopkgtest requires outdated version

2020-04-12 Thread Rebecca N. Palmer
Package: node-unicode-13.0.0 Version: 0~20200315+gitfc57d75a-2 Severity: serious Tags: patch The autopkgtest includes the versioned package name (in both debian/tests/control and debian/tests/require). As these were not updated when this changed from 12 to 13, the autopkgtest fails as

Bug#956503: node-lodash-reevaluate: mis-spelled test dependency

2020-04-12 Thread Rebecca N. Palmer
Package: node-lodash-reevaluate Version: 3.0.0-1 Severity: serious Tags: patch debian/tests/control has a stray . in the package name. As there is no package with this name, this causes the test to fail as uninstallable.

Bug#956507: pegjs: stray Provides: nodejs

2020-04-12 Thread Rebecca N. Palmer
Package: pegjs Version: 0.10.0-1 Tags: patch Severity: serious debian/control lists a Provides: nodejs. This is obviously wrong, and also causes the autopkgtest to fail by not installing the real nodejs.

Bug#956517: node-rw: missing test-depends on node-d3-queue

2020-04-12 Thread Rebecca N. Palmer
Package: node-rw Version: 1.3.3-1 Severity: serious Tags: patch One of this package's upstream tests (encoding-async) requires (node-)d3-queue. It build-depends on this, but does not test-depend on it (debian/tests/control last test), so the autopkgtest fails.

Bug#954647: pandas - maybe fixed but can't build now

2020-03-31 Thread Rebecca N. Palmer
Control: tags -1 pending Control: block -1 by 955399 I just pushed what I think is a fix to salsa, but pandas is currently BD-Uninstallable due to xvfb (#955399), so it has not been tested.

Bug#955471: theano: test failures

2020-04-01 Thread Rebecca N. Palmer
Package: python3-theano Version: 1.0.4-1 Severity: serious Justification: at least one looks like a silently wrong answer The tests passed (at least on amd64) when 1.0.4-1 was first uploaded, but 9 tests failed when it was rebuilt as 1.0.4-1+b1 (for Python 3.8, but I suspect the actual cause

Bug#955471: theano: test failures

2020-04-02 Thread Rebecca N. Palmer
Control: severity -1 normal Control: tags -1 upstream patch pending Control: forwarded -1 https://github.com/Theano/theano/pull/6749 On closer inspection, this isn't a "silently wrong answer" bug after all, so lowering the severity. Some parts of it appear to be caused by numpy 1.17 and some

Bug#958700: pocl: nested(?) dlopen fails

2020-04-26 Thread Rebecca N. Palmer
Control: retitle -1 pocl: nested(?) dlopen fails Control: reassign -1 libpocl2 1.5-2 Control: affects -1 src:libgpuarray python3-pyopencl ocl-icd-libopencl1 dlopen()s ICDs (at https://sources.debian.org/src/ocl-icd/2.2.12-4/ocl_icd_loader.c/#L184). With pocl 1.5, this dlopen() fails in some

Bug#956882: statsmodels: FTBFS on armel

2020-04-23 Thread Rebecca N. Palmer
Control: tags -1 patch The failed tests are expecting an 0/0 warning from numpy, which it produces on amd64 but not armel: amd64$ python3 Python 3.8.2 (default, Apr 1 2020, 15:52:55) [GCC 9.3.0] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import numpy

Bug#958531: pandas: broken by NaT/isnan changes in numpy 1.18

2020-04-23 Thread Rebecca N. Palmer
Package: python3-pandas Version: 0.25.3+dfsg-9 Severity: serious Tags: fixed-upstream patch numpy 1.18 includes two behaviour changes that affect pandas, causing a CI fail / presumed FTBFS. Both are fixed in pandas 1.0 (in experimental, but moving that to unstable causes other issues, see

Bug#959615: theano: FTBFS: make[2]: pegjs: Command not found

2020-05-03 Thread Rebecca N. Palmer
This is because /usr/bin/pegjs exists in node-pegjs 0.7 but not 0.10. (/usr/share/nodejs/bin/pegjs exists instead; I have not yet checked whether it works.) pegjs maintainer: is this an intentional change or a mistake? The upstream documentation still mentions the command:

Bug#959758: theano: FTBFS with pegjs 0.10

2020-05-04 Thread Rebecca N. Palmer
Package: python3-theano Version: 1.0.4+dfsg-2 Severity: serious #graphlib-dot.js make -C debian/missing-source/graphlib-dot --always-make dist make[2]: Entering directory '/build/theano-1.0.4+dfsg/debian/missing-source/graphlib-dot' pegjs -e 'module.exports' src/dot-grammar.pegjs

Bug#959597: python-schema-salad FTBFS: python-rdflib-jsonld too new

2020-05-11 Thread Rebecca N. Palmer
Control: retitle -1 schema-salad FTBFS: python-rdflib-jsonld too new Control: tags -1 fixed-upstream patch This explicit version check was relaxed (without other changes) in the next upstream commit, though I haven't tested this change:

Bug#954647: pandas - that's not the actual problem

2020-03-24 Thread Rebecca N. Palmer
Control: retitle -1 pandas FTBFS: deprecations/improvements fail tests The message on the old title is just a warning, but there are 6 other tests that fail. I think these are all bugs in the tests not the actual package, i.e. using our current pandas is fine. Deprecation warnings in

Bug#968210: statsmodels: still broken on armel

2020-09-10 Thread Rebecca N. Palmer
Control: severity -1 important Control: retitle -1 statsmodels: on armel may give wrong answer or crash This bug is no longer an FTBFS as the tests are now ignored on armel, but still exists. (At least as a crash; we stopped using --forked, so don't know if there are still also wrong

Bug#959136: close this bug?

2020-10-13 Thread Rebecca N. Palmer
The linked upstream report says this went away in numpy 1.18.4, and the tests in question now pass on debci.

Bug#972033: Bug#969650: Bug#972033: python3.9, dask, pandas 1.1

2020-10-16 Thread Rebecca N. Palmer
Control: tags -1 - pending The package currently in Salsa doesn't work. test_statsmodels is probably a circular dependency that should be ignored for now; TestHDFStore is under investigation. === FAILURES ===

Bug#972015: Bug#972033: python3.9 pandas

2020-10-17 Thread Rebecca N. Palmer
Control: tags -1 patch The underlying cause (and reason this is 3.9-specific) appears to be the mostly-removal of ast.Index and its replacement by a bare value. This appears to fix it, though I'm not yet sure if it's a good idea: --- a/pandas/core/computation/pytables.py +++

Bug#972015: Bug#972033: python3.9 pandas

2020-10-17 Thread Rebecca N. Palmer
This bug is not specific to DateTimeIndexes, and the immediate cause is the index being passed to numpy as a pandas.core.computation.pytables.Constant instead of an int: $ python3.9 Python 3.9.0+ (default, Oct 16 2020, 17:57:59) [GCC 10.2.0] on linux Type "help", "copyright", "credits" or

Bug#969648: dask, pandas 1.1

2020-10-19 Thread Rebecca N. Palmer
The upstream patch doesn't even apply as-is; this version does, but I don't have time right now to actually test it. There's also a circular dependency problem, as dask indirectly build-depends on itself and my new pandas makes it uninstallable. Description: pandas 1.1 compatibility Origin:

Bug#972469: joblib: TerminatedWorkerError, AttributeError: '_SafeQueue' object has no attribute '_notempty' with Python 3.9

2020-10-18 Thread Rebecca N. Palmer
Package: python3-joblib Tags: fixed-upstream Control: affects -1 scikit-learn statsmodels Control: block 966426 by -1 Severity: serious Justification: causes other packages to FTBFS Our current version of joblib is incompatible with Python 3.9, which was recently added to the supported versions

Bug#972015: Bug#972033: python3.9 pandas

2020-10-18 Thread Rebecca N. Palmer
Control: tags -1 pending Control: forwarded -1 https://github.com/pandas-dev/pandas/issues/37217 This appears to fix it, though I'm not yet sure if it's a good idea I was trying to find upstream's fix and use that instead, but it now looks like they don't have one, and probably didn't know

Bug#972033: python3.9, dask, pandas 1.1

2020-10-14 Thread Rebecca N. Palmer
Control: severity 969648 serious Control: tags 969650 pending Control: tags 972033 pending Python 3.9 related breakage has been declared RC, so if nobody objects, I intend to upload pandas 1.1 to unstable (possibly tonight, but it probably won't build before numpy and matplotlib are binNMUd

Bug#969648: dask, pandas 1.1

2020-10-19 Thread Rebecca N. Palmer
2020-02-26 21:01:52.000000000 +0000 +++ dask-2.11.0+dfsg/debian/changelog 2020-10-19 08:38:20.0 +0100 @@ -1,3 +1,10 @@ +dask (2.11.0+dfsg-1.1) UNRELEASED; urgency=medium + + * Non-maintainer upload. + * Fix test failures with pandas 1.1 (Closes: #969648) + + -- Rebecca N. Palmer M

Bug#969648: dask, pandas 1.1

2020-10-19 Thread Rebecca N. Palmer
Or maybe not an actual regression...it's a ~5e-7 difference and one of the things the patch does (at around dask/dataframe/tests/test_rolling.py:270) is _tighten_ the tolerance on that test. I have filed a separate bug (#972516) for the fsspec issues.

Bug#969648: dask, pandas 1.1

2020-10-19 Thread Rebecca N. Palmer
On 19/10/2020 20:07, Stefano Rivera wrote: Hi Rebecca (2020.10.19_11:51:33_-0700) Or maybe not an actual regression...it's a ~5e-7 difference and one of the things the patch does (at around dask/dataframe/tests/test_rolling.py:270) is _tighten_ the tolerance on that test. Hrm, I didn't see

Bug#969648: marked as pending in dask

2020-10-19 Thread Rebecca N. Palmer
sorry, not any more. On 19/10/2020 19:57, Rebecca N. Palmer wrote: That looks like my earlier version, which fails with NameError.

Bug#969648: marked as pending in dask

2020-10-19 Thread Rebecca N. Palmer
That looks like my earlier version, which fails with NameError.

Bug#969648: BD-Uninstallable Re: dask, pandas 1.1

2020-10-19 Thread Rebecca N. Palmer
A bot wrote: Dependency installability problem for dask on all: dask build-depends on: - python3-pandas:amd64 (>= 0.19.0) dask build-depends on: - python3-distributed:amd64 python3-distributed depends on: - python3-dask:amd64 (>= 2.9.0) python3-pandas conflicts with: - python3-dask:amd64 (<

Bug#968210: statsmodels: arm* test failures/crashes

2020-08-18 Thread Rebecca N. Palmer
Using --forked revealed that the above is one of 21 test crashes on armel, and that there are also 2 wrong answers. The ones I have tried (the wrong answers and most of the crashes) are not reproducible on qemu-armel.

Bug#969050: pytest-asyncio: AttributeError: type object 'Function' has no attribute 'from_parent' with our current pytest

2020-08-26 Thread Rebecca N. Palmer
Package: python3-pytest-asyncio Version: 0.14.0-1 Severity: serious Control: affects -1 src:pandas pytest-asyncio 0.14 tries to use pytest Function.from_parent (e.g. at pytest_asyncio/plugin.py:39), which does not exist in the archive's current version of pytest (4.6). This causes at least

Bug#969050: pytest-asyncio: AttributeError: type object 'Function' has no attribute 'from_parent' with our current pytest

2020-08-26 Thread Rebecca N. Palmer
This bug can happen even if the tests being run don't actually use pytest_asyncio (e.g. see pandas 1.0.5+dfsg-2); to avoid it one needs to not have it installed, i.e. remove the build/test-dependency. This suggests that the current pytest-asyncio package is totally unusable without a more

Bug#959558: this fix breaks things

2020-05-30 Thread Rebecca N. Palmer
This fix causes Sphinx to fail if documenting an object whose __getattr__ fails, e.g. flask.request. This causes at least snakemake to FTBFS. Details and fix: https://github.com/sphinx-doc/sphinx/pull/7520 A workaround in failing packages is to add autodoc_default_options =

Bug#966393: pandas: FTBFS: TypeError: use() got an unexpected keyword argument 'warn'

2020-07-29 Thread Rebecca N. Palmer
Control: found -1 0.25.3+dfsg2-3 Control: tags -1 fixed-upstream patch (untested) Probably matplotlib 3.3: https://github.com/pandas-dev/pandas/pull/35323

Bug#968210: statsmodels: arm* test failures/crashes

2020-08-12 Thread Rebecca N. Palmer
This doesn't crash when just that test file is run in statsmodels 0.11.1-3 qemu-armel, but this isn't 100% proof that -4 (rather than a dependency) caused it. -4 (built locally in qemu) doesn't crash that way either, which suggests this bug doesn't show up in qemu, and (given the lack of

Bug#966393: pandas: FTBFS with matplotlib 3.3

2020-07-30 Thread Rebecca N. Palmer
Control: tags -1 - patch That's not enough by itself: it does fix that particular error, but exposes 16 other failures, some of the form ValueError: The number of FixedLocator locations (8), usually from a call to set_ticks, does not match the number of ticklabels (4). and some datetime

Bug#968210: statsmodels: arm* test failures/crashes

2020-08-10 Thread Rebecca N. Palmer
Package: python3-statsmodels Version: 0.11.1-4 Severity: serious arm64 fail in TestZeroInflatedModel_probit.test_fit_regularized: https://buildd.debian.org/status/fetch.php?pkg=statsmodels=arm64=0.11.1-4=1597051632=0 https://ci.debian.net/packages/s/statsmodels/testing/arm64/ From the CI

Bug#968208: pandas: TestMoments.test_rolling_quantile_interpolation_options fails on i386 - rounding issue

2020-08-10 Thread Rebecca N. Palmer
Package: python3-pandas Version: 0.25.3+dfsg2-4 Severity: serious One test fails on i386 with a 1-in-last-place difference, probably due to different rounding (x87 extra precision?). https://buildd.debian.org/status/fetch.php?pkg=pandas=i386=0.25.3%2Bdfsg2-4=1597048961=0

Bug#963817: Breaks?

2020-06-29 Thread Rebecca N. Palmer
On 29/06/2020 20:59, Paul Gevers wrote: Does this mean that numpy should add a Breaks relation on the old pandas version to avoid upgrading numpy but not pandas on user systems? Not really - the constant was replaced by its value, so the only 1.19-related change outside of tests is the

Bug#954554: python-asynctest: FTBFS, maybe-RM

2020-06-29 Thread Rebecca N. Palmer
Is the above intended as a proposal to remove asynctest? The rdeps in Debian are hypercorn, python-aioresponses, and (for autopkgtest only) python-fakeredis. hypercorn upstream have stopped using it: https://gitlab.com/pgjones/hypercorn/-/commit/80e2ad5db107c42d42471ea64764d2b42202349c The

Bug#962335: FTBFS: new upstream version available with bug fixes

2020-06-08 Thread Rebecca N. Palmer
Control: fixed -1 0.25.3+dfsg2-2 Control: tags -1 patch This is fixed in unstable, and in Salsa's experimental branch. I didn't consider it worth the buildd resources to upload in experimental, without also doing some work on other issues such as #877419. (1.0 is in experimental and not

Bug#968210: statsmodels: arm* test failures/crashes

2020-08-16 Thread Rebecca N. Palmer
The TestZeroInflatedModel_probit issue appears to be a failure to converge: as it does trigger warnings of that, and it's already skipped on i386, I intend to ignore it. qemu-arm64: >>> a object at 0x4000d31130> >>> a.res1.params Traceback (most recent call last): File "", line 1, in

Bug#979621: pandas: autopkgtest regression in testing: No tables found

2021-01-11 Thread Rebecca N. Palmer
Control: tags -1 fixed-upstream pending The trigger was a change in the outside world, not Debian testing: the tests (of HTML table parsing) were trying to access a web page that no longer exists. Fixed in Salsa.

Bug#975931: [Pkg-opencl-devel] Bug#975931: pocl breaks libgpuarray autopkgtest on armhf: segmentation fault

2020-11-27 Thread Rebecca N. Palmer
Existing discussion (in what was originally a different bug): https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=974797#28 This bug might also be in llvm or clblas.

Bug#976573: pandas: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.8 3.9" returned exit code 13

2020-12-06 Thread Rebecca N. Palmer
On 05/12/20 at 13:47 +0100, Lucas Nussbaum wrote: Tags: bullseye sid ftbfs Usertags: ftbfs-20201205 ftbfs-bullseye Does this imply that it was also tested and failed in bullseye? The log is marked unstable, and the test failures in it are #976620, which is probably unstable-only.

Bug#976620: xlrd: if defusedxml installed, AttributeError: 'ElementTree' object has no attribute 'getiterator'

2020-12-09 Thread Rebecca N. Palmer
I have applied this workaround to pandas. However, this only makes pandas use xlrd less; this bug still exists in other users of xlrd when defusedxml is installed. By default this includes python3-glue (the original reason for upgrading xlrd), via the Recommends/Depends chain python3-glue ->

Bug#972246: numba, python3.9, dolfinx

2020-11-02 Thread Rebecca N. Palmer
Control: affects -1 + pynpoint python-loompy umap-learn Control: affects -1 + dolfinx python-numpy-groupies As this bug cannot immediately be fixed, numba may be removed from testing to unblock the python3.9 transition (#966426). (If any of the failed tests are silently wrong answers, please

Bug#973115: cfgrib FTBFS

2020-11-05 Thread Rebecca N. Palmer
Confirmed, still exists in pandas 1.1.4, not obviously known upstream. #969648 was also a datetime issue that appeared during the pandas 1.0 -> 1.1 transition, but I don't know if they're related. (cfgrib wasn't tested as part of that transition because it doesn't directly depend on pandas.)

Bug#973115: cfgrib FTBFS

2020-11-05 Thread Rebecca N. Palmer
Control: tags -1 upstream cfgrib's upstream CI is failing, and started failing when it started using pandas 1.1.x.

Bug#988142: pandas FTBFS in buster: test failures

2021-05-09 Thread Rebecca N. Palmer
This is _probably_ the same issue that 0.23.3+dfsg-3 has had since it was new: some tests run in all installed locales, and on reproducible-builds (but not buildds without a locales-all dependency) this includes a few with no text encoding. The underlying issue is in Python stdlib, and is an

Bug#992681: scipy breaks statsmodels autopkgtest: place: mask and data must be the same size

2021-08-22 Thread Rebecca N. Palmer
Control: reassign -1 src:statsmodels Control: tags -1 fixed-upstream Appears to be these (but not yet tested in Debian): https://github.com/statsmodels/statsmodels/issues/7371 https://github.com/statsmodels/statsmodels/issues/7453

Bug#992673: libgpuarray: autopkgtest depends on libclblas-dev which is not in testing *and* has skip-not-installable

2021-08-22 Thread Rebecca N. Palmer
clblas has been replaced by clblast, so I tried switching to that, but doing so makes a varying number of cases of test_gemv fail, e.g. == FAIL: pygpu.tests.test_blas.test_gemv((128, 50), 'float32', 'c', True, False, 2, True,

Bug#993107: theano: autopkgtest depends on libclblas-dev which is not in testing *and* has skip-not-installable

2021-08-29 Thread Rebecca N. Palmer
Control: tags -1 pending This is the same underlying problem as #992673, but for this one it looks like switching to clblast is enough to pass the tests we actually run. (Which isn't all of them because the GPU part of theano has never fully worked under OpenCL, but we already warn the user

Bug#992673: libgpuarray: *gemv broken on libclblast

2021-08-30 Thread Rebecca N. Palmer
There's also this test failure on arm64 (which is at least a crash not a wrong answer), again with clblast not clblas. It probably isn't a new problem either: the tests were previously run with clblas only. (The "regression" on ppc64el is that the test has never been installable there and

Bug#992673: libgpuarray: *gemv broken on libclblast

2021-08-30 Thread Rebecca N. Palmer
Control: retitle -1 libgpuarray: *gemv broken on libclblast For now I have disabled *gemv when used with libclblast, to make this bug an explicit error rather than a silently wrong answer. These functions are still available with clblas, but that has enough other issues

Bug#974792: beignet FTBFS with llvm-toolchain-11

2021-09-30 Thread Rebecca N. Palmer
I'm not aware of a fix for this, and beignet is abandoned upstream and mostly useful for old hardware (on newer hardware it is replaced by intel-opencl-icd). However, I may look at it more later (and at least try llvm-toolchain-12, though I'd expect that to be worse if anything). Hence, I'm

Bug#994833: [Pkg-opencl-devel] Bug#994833: OpenCL programs abort when intel-opencl-icd is installed

2021-09-22 Thread Rebecca N. Palmer
On 22/09/2021 07:32, Andreas Beckmann wrote: We will proably still run into problems if different ICDs built against different LLVM versions are going to be loaded at the same time (e.g. pocl/llvm9 and intel/llvm1x) because the different llvm versions seem to stomp on each others internal

Bug#997081: statsmodels FTBFS - tests fail

2021-10-24 Thread Rebecca N. Palmer
Reproduced here; not obviously known upstream. Autopkgtest says it started between 2021-08-30 and 2021-09-14 in unstable, between 2021-10-10 and 2021-10-18 in testing. It might be easiest to upgrade to 0.13.0 (if it fixes this - I haven't checked yet), given that we should do that anyway at

Bug#997382: theano FTBFS - sphinx 4.2?

2021-10-24 Thread Rebecca N. Palmer
Control: tags -1 patch This looks similar to #997026, and the same fix appears to work.

Bug#992673: libgpuarray *gemv, *ger test fails

2021-10-26 Thread Rebecca N. Palmer
Control: tags -1 pending (fixed in Salsa, as far as I consider it my bug) It looks like both of these originate further down the stack, not in libgpuarray: The *ger error code is an OpenCL compile failure from inside clblast, so likely either pocl or clblast. The *gemv problem appears to

Bug#1052454: numexpr: unnecessarily disables security check

2023-09-22 Thread Rebecca N. Palmer
Package: python3-numexpr Version: 2.8.6-2 Severity: serious Justification: block testing migration of a known security hole Tags: patch numexpr 2.8.5 introduced a security check, which was initially buggy enough to break pyfai and pandas (#1049326). Fixes for this were sent upstream, but only

Bug#1053672: Apple copyright notices in test .xlsx files

2023-10-08 Thread Rebecca N. Palmer
Source: openpyxl Version: 3.0.9-2 Severity: serious licensecheck -r --copyright . on openpyxl finds these: ./openpyxl/formatting/tests/data/conditional-formatting.xlsx: UNKNOWN [Copyright: 2007 Apple Inc.] ./openpyxl/reader/tests/data/complex-styles.xlsx: UNKNOWN [Copyright: 2007 Apple

Bug#1033907: numba crashes on non-x86

2023-08-19 Thread Rebecca N. Palmer
numba also crashes on mips64el, mipsel and armhf (and s390x but that was already known; not amd64, i386 or ppc64el). However, I agree that arm64 is a good place to start trying to fix this, given how common it is. For examples, see the pandas 2.0.3+dfsg-3 / 1.5.3+dfsg-5 build logs. Given the

Bug#1049326: pandas FTBFS with numexpr 2.8.5

2023-08-17 Thread Rebecca N. Palmer
On further thought, both of those probably should be fixed in numexpr - I have pushed them to fix1049326. With those changes to numexpr, the new pandas (1.5.3+dfsg-5) should build; pytables will still also need its upstream fix.

Bug#1049326: pandas FTBFS with numexpr 2.8.5

2023-08-17 Thread Rebecca N. Palmer
stringToExpression() in this numexpr patch needs a default of True for sanitize (like the others already have), because pytables calls that directly: https://salsa.debian.org/science-team/pandas/-/jobs/4571451/raw (The other failure in there is one I plan to fix.) The two pytables tests with

Bug#1049326: pandas FTBFS with numexpr 2.8.5

2023-08-15 Thread Rebecca N. Palmer
Numexpr upstream have what they think is a fix for the exception issue (though not the overflow change), but it hasn't been tested yet: https://github.com/pydata/numexpr/issues/442

Bug#1049326: pandas FTBFS with numexpr 2.8.5

2023-08-16 Thread Rebecca N. Palmer
I pushed this fix to Salsa as the 'fix1049326' branch - it isn't enough to fix pandas by itself, but is plausibly an improvement.

Bug#1049326: pandas FTBFS with numexpr 2.8.5

2023-08-17 Thread Rebecca N. Palmer
Given that this is a security feature and we hence want it in quickly, I'd consider that patch enough to xfail/disable the remaining issues in pandas, but discussions with upstream are ongoing. (It also won't do anything about the pytables breakage, known upstream as #1044.)

Bug#1049326: pandas FTBFS with numexpr 2.8.5

2023-08-14 Thread Rebecca N. Palmer
Package: python3-numexpr Version: 2.8.5-1 Severity: serious Control: forwarded -1 https://github.com/pandas-dev/pandas/issues/54449 (actually they found it first) I only have actual logs for 2.0.x, but I suspect 1.5.x is also affected. As a short term fix, it may be possible to disable pandas'

Bug#1020060: statsmodels: FTBFS: make[1]: *** [debian/rules:105: override_dh_auto_test] Error 1

2022-09-19 Thread Rebecca N. Palmer
This is the same test as #1014278 / upstream 8341, but now on amd64. From the upstream discussion, it may be a numerically unstable test. It doesn't fail everywhere: a test build on Salsa CI passed, as did the last debci runs. (reproducible-builds FTBFS on the second build, on amd64/sid

Bug#1028373: pandas: test-failing warnings with numpy 1.24

2023-01-10 Thread Rebecca N. Palmer
Package: python3-pandas Version: 1.5.2+dfsg-4 Severity: serious Looks like the numpy 1.24 issues I knew about weren't the only ones. Fix in progress in Salsa.

Bug#1026539: theano FTBFS

2023-01-03 Thread Rebecca N. Palmer
Please do *not* upload theano 1.12 to unstable - it's the Aesara version, which may seriously break backward compatibility. I haven't had time to properly look at this bug yet.

Bug#1027254: dask and pandas 1.5

2023-01-09 Thread Rebecca N. Palmer
To get the new upstream version to work, dask_sphinx-theme, dask and dask.distributed all need to be updated, in that order. Tests here: https://launchpad.net/~rebecca-palmer/+archive/ubuntu/dask2022p12v2/+packages dask didn't run its tests (PPAs only build, not autopkgtest), and

Bug#1027254: dask and pandas 1.5

2023-01-09 Thread Rebecca N. Palmer
(I meant to send that to the dask/pandas bug, which is #1025393, but both of them are potential reasons to update dask.) The intake issue is now https://github.com/dask/dask/issues/9813 (They're planning to fix it in intake rather than dask, but we might not be allowed to do that after the

Bug#1028359: pygpu: fails to import in numpy 1.24

2023-01-09 Thread Rebecca N. Palmer
Package: python3-pygpu Version: 0.7.6-12 Severity: grave numpy 1.24 no longer has np.bool, which makes pygpu fail to import: pygpu/dtypes.py:74: in _fill_dtype_registry register_dtype(np.bool, ["ga_bool", "bool"]) numpy/__init__.py:284: in __getattr__ raise AttributeError("module {!r}

Bug#1024906: apparently fixed Re: dask autopkgtest fail with python 3.11

2022-12-03 Thread Rebecca N. Palmer
This combination stopped failing on 2022-11-22/23 (without a dask upload, suggesting it was fixed somewhere other than dask itself). Hence, I suggest closing this bug.

Bug#1000922: llvmlite: uninstallable due to llvm-11 removal

2022-11-27 Thread Rebecca N. Palmer
Control: severity -1 grave Control: merge -1 1024795 Control: retitle -1 llvmlite: uninstallable due to llvm-11 removal It looks like closing and reopening this removed its "blocks" relationship to 1000941 (the llvm-11 removal request). Hence, llvm-11 has now been removed, making llvmlite

Bug#1027215: How much do we lose if we remove theano (+keras, deepnano, invesalius)?

2023-01-14 Thread Rebecca N. Palmer
theano has been mostly abandoned upstream since 2018. (The Aesara fork is not abandoned, but includes interface changes including the import name, so would break reverse dependencies not specifically altered for it.) Its reverse dependencies are keras, deepnano and invesalius. It is

Bug#1028667: dask BD-Uninstallable

2023-01-14 Thread Rebecca N. Palmer
Control: retitle -1 dask: B-D on python-numpy-doc which no longer exists Control: tags -1 pending The python-numpy-doc error is because that package no longer exists. This build-dependency has already been removed in Salsa. However, that version doesn't build the dask documentation due to

Bug#1029232: dask.distributed: broken by version mismatch with dask

2023-01-20 Thread Rebecca N. Palmer
Package: python3-distributed Version: 2022.02.0+ds1-3 Severity: serious dask.distributed has been failing its autopkgtests since dask was upgraded to 2022.12.1. This is the expected result of upgrading one but not the other: I'd seen the same in my test PPA, and the upstream

Bug#1029251: pandas: FTBFS: tests failed

2023-01-21 Thread Rebecca N. Palmer
Control: tags -1 pending Looks like rounding error in a test; ignored in Salsa.

Bug#1029232: dask.distributed: broken by version mismatch with dask

2023-01-20 Thread Rebecca N. Palmer
Would you like some help? If so, please push what you currently have to Salsa so we can see it. (No promises - #1029251 doesn't look like a big job but I might be wrong about that.)

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