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Bug#956512: node-unicode-data: autopkgtest requires outdated version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

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#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 #95

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 a

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&arch=i386&ver=0.25.3%2Bdfsg2-4&stamp=1597048961&raw=0

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&arch=arm64&ver=0.11.1-4&stamp=1597051632&raw=0 https://ci.debian.net/packages/s/statsmodels/testing/arm64/

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 relev

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 Attri

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 fail-o

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 wa

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 pan

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 rece

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 answers.)

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 be

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 test_set_ticklabe

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: 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 fo

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 === T

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 "lice

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 +++ b/pandas/core/com

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#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 iss

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 = {'exclude-members'

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 unst

Bug#839357: [pkg-fgfs-crew] Bug#839357: fgrun: FTBFS: wizard_funcs.cxx:1202:51: error: no matching function for call to 'readProperties(const char*, SGPropertyNode*)'

2016-10-01 Thread Rebecca N. Palmer
Control: tags -1 fixed-upstream https://sourceforge.net/p/flightgear/fgrun/ci/312a8de41336cfe6d85336e8909b517e0c590c0c/ (We might need the next commit as well; given how little has changed, probably easiest to take the whole upstream release)

Bug#840107: beignet: FTBFS with libdrm-intel 2.4.71

2016-10-08 Thread Rebecca N. Palmer
Source: beignet Severity: serious Control: tags -1 upstream patch beignet started using drm_intel_get_pooled_eu and drm_intel_get_min_eu_in_pool if available early in their development, before their interface was finalized, and hence does not build with the released version (libdrm-intel 2.4.7

Bug#839327: pandas: FTBFS: tests failures

2016-10-09 Thread Rebecca N. Palmer
The tests in question are checking that numexpr and numpy give the same answers (by default, pandas uses numexpr if available for large arrays but numpy for small ones), and require integers to match exactly. The failing values are all 15**15, which is 437893890380859375 in exact arithmetic bu

Bug#1056828: Severity / marking of "uses cython3-legacy" bugs

2024-01-03 Thread Rebecca N. Palmer
pandas and statsmodels are currently using cython3-legacy. I left their cython 3.0 bugs open when I made this change, as I do want to actually switch them to cython 3.x at some point. These bugs have now been raised to RC. Is this an intentional attempt to remove cython3-legacy (which seems

Bug#1068104: pandas: FTBFS on 32-bit architectures with -D_TIME_BITS=64

2024-04-01 Thread Rebecca N. Palmer
Thanks - I plan to look at this tomorrow.

Bug#1068422: can't import dask.dataframe - TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object

2024-04-04 Thread Rebecca N. Palmer
Package: python3-dask Version: 2023.12.1+dfsg-2 Severity: serious Control: affects -1 src:pandas Control: block 1068104 by -1 Importing dask.dataframe currently fails with the error TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object amd64 https://salsa.de

Bug#1068349: nbsphinx/nbconvert broken by lxml 5.2: lxml.html.clean

2024-04-07 Thread Rebecca N. Palmer
Control: unblock 1068104 by -1 Control: unblock 1068104 by 1068422 To avoid being blocked by this bug, the pandas version I just uploaded temporarily disables the documentation. This is also an option for any other affected packages that urgently need to be uploaded. (I don't know whether th

Bug#1076925: snakemake: FTBFS failing tests

2024-07-31 Thread Rebecca N. Palmer
The initial error appears to be "SQLite objects created in a thread can only be used in that same thread." with a traceback pointing to pytools/persistent_dict.py, and the timing matches pytools 2024.1.1 -> 2024.1.6. I intend to look into this more later.

Bug#1076925: snakemake: FTBFS failing tests

2024-07-31 Thread Rebecca N. Palmer
Control: retitle -1 pytools.persistent_dict fails in multithread Control: reassign -1 python3-pytools Control: affects -1 snakemake Control: tags -1 fixed-upstream Control: severity -1 normal (for pytools - it's still RC for snakemake) This was probably introduced when pytools.persistent_dict sta

Bug#1068422: possibly caused by python 3.12.3 Re: Bug#1068422: can't import dask.dataframe - TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object

2024-04-21 Thread Rebecca N. Palmer
This bug is not *obviously* known to dask upstream, but their CI is failing and I haven't checked why. It happens only in Python 3.12, not 3.11: https://ci.debian.net/packages/d/dask/unstable/amd64/45013666/ and still doesn't happen in testing, but does happen in mostly-testing with src:python

Bug#1069608: topplot: missing test-depends on python3-all

2024-04-21 Thread Rebecca N. Palmer
Source: topplot Version: 0.2.2+repack-1 Tags: patch Severity: serious Justification: blocks testing migration of other packages topplot tries to run its autopkgtest in all versions of Python (which is good), but does not test-depend on all those versions of Python. This previously worked becau

Bug#1050854: xarray test failure on amd64

2023-11-19 Thread Rebecca N. Palmer
This bug is now a crash (not the original error message): https://ci.debian.net/data/autopkgtest/testing/amd64/p/python-xarray/39962554/log.gz I don't know whether the same patch still works. The Salsa repository now appears to be up to date. You probably also want to include the fixes for the o

Bug#1053700: xarray test failure on s390x

2023-11-19 Thread Rebecca N. Palmer
Control: tags -1 patch These all come from xarray/tests/test_coding_times.py, and are probably fixable by replacing both instances of ("M8[ns]" if sys.byteorder=='big' else "haven't actually tried that.

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 Inc.]

Bug#1066801: pandas: FTBFS: /usr/lib/python3/dist-packages/dateutil/zoneinfo/__init__.py:26: UserWarning: I/O error(2): No such file or directory

2024-03-14 Thread Rebecca N. Palmer
Control: retitle -1 pandas: test-failing warning with new xarray This is a warning being treated as an error, but the one in test_to_xarray (probably due to the new version of xarray), not the zoneinfo one. This is a FutureWarning, so it should be OK to *use* the current pandas with the new x

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' n

Bug#1049326: pandas FTBFS with numexpr 2.8.5

2023-08-14 Thread Rebecca N. Palmer
Control: forwarded -1 https://github.com/pandas-dev/pandas/issues/54546 Control: affects -1 python3-pandas There's actually *two* bugs here: an exception in eval/query, https://github.com/pandas-dev/pandas/issues/54449, and a changed result with integer overflow, https://github.com/pandas-dev/p

Bug#1049326: pandas FTBFS with numexpr 2.8.5

2023-08-14 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

2023-08-17 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

2023-08-17 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#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#1042043: pandas: FTBFS: failed tests

2023-07-25 Thread Rebecca N. Palmer
Control: tags -1 fixed-upstream patch This is probably caused by the new fsspec version, and is also seen in autopkgtest: https://ci.debian.net/data/autopkgtest/testing/amd64/p/pandas/36146393/log.gz Upstream fix: https://github.com/pandas-dev/pandas/commit/ce9e3d658d6efa3600a4563ca7a00e7a15b8

Bug#1043048: openblas: gives wrong results on mips64el, ignores test failures

2023-08-05 Thread Rebecca N. Palmer
Package: libopenblas0-pthread Version: 0.3.23+ds-2 Control: affects -1 src:statsmodels Severity: serious Justification: the default BLAS should NOT silently give wrong answers (i.e. if there's no easy way to actually fix this, please switch the default on mips64el back to atlas, and consider remo

Bug#1043048: openblas: gives wrong results on mips64el, ignores test failures

2023-08-05 Thread Rebecca N. Palmer
The most obviously relevant change between those is that the installed BLAS changed from atlas to openblas. It looks like this wasn't a change of default, but that experimental uses libatlas and unstable uses libopenblas. (I don't know why, as the obvious dependency chain is src:statsmodels -

Bug#1043048: openblas: gives wrong results on mips64el, ignores test failures

2023-08-05 Thread Rebecca N. Palmer
Control: tags -1 upstream Upstream CI's mips64 qemu test has what look like the same FATAL ERRORs, in MIPS64_GENERIC but not SICORTEX, but is still listed as passing. Which suggests that they also have both parts of this bug (wrong answers on mips64el, and errors not actually failing the buil

Bug#1043048: Please give back statsmodels on mips64el Re: (Bug#1043048: fixed in openblas 0.3.23+ds-3)

2023-08-07 Thread Rebecca N. Palmer
This does seem to have worked: the openblas build log no longer contains FATAL ERROR. Hence, please give back statsmodels on mips64el. (DMs aren't allowed to use the self-service link.)

Bug#1068422: can't import dask.dataframe - TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object

2024-05-04 Thread Rebecca N. Palmer
Control: forwarded -1 https://github.com/dask/dask/pull/11035 Control: tags -1 fixed-upstream patch Thanks and probably yes (but I haven't tested that fix myself), as while it didn't happen in 3.11.8, it *does* happen in 3.11.9: https://ci.debian.net/packages/d/dask/unstable/amd64/46185892/

Bug#1058160: tqdm and pandas 2.1 / python 3.12

2024-01-28 Thread Rebecca N. Palmer
Control: retitle 1058160 tqdm: tests failing/hanging in Python 3.12 That works for #1053946 (pandas 2.x), but #1058160 (python 3.12) is more than a single hanging test, and it's not immediately obvious what should be done. Attempted fix (caution, currently just skips the hanging test) and fa

Bug#1053946: tqdm and pandas 2.1 / python 3.12

2024-01-29 Thread Rebecca N. Palmer
That turned out to be easier than it looked - fixing the easy one also made the others go away. Please upload this: https://salsa.debian.org/rnpalmer-guest/tqdm

Bug#1044076: influxdb-python and pandas 2.1

2024-01-29 Thread Rebecca N. Palmer
Some looking through the code suggests that the precision is user-set and hence constant within a single query, and hence that this fix is OK, but I'm not entirely certain of that. There are ways to make pandas 2.x accept mixed time format, but I think they're 2.x _only_ and/or slow.

Bug#1044076: influxdb-python and pandas 2.1

2024-01-30 Thread Rebecca N. Palmer
Note that this uncertainty is only around whether this is a complete fix - even in the case where it's not, it *wouldn't* be actively worse than doing nothing, though it would be hiding the problem.

Bug#1044057: python-ulmo and pandas 2

2024-02-18 Thread Rebecca N. Palmer
lmo's tests.Description: Don't fail on malformed or changed test data CDEC has malformed lines that pandas 1.4+ errors out on (I'm not sure why earlier pandas didn't do the same); GHCN has simply changed at the source. Author: Rebecca N. Palmer (but upstream independently came up w

Bug#1063274: pydevd: autopkgtest-failing warning with pandas 2.1

2024-02-19 Thread Rebecca N. Palmer
This has been merged but not uploaded - is there a reason it shouldn't be, or have you just not had time?

Bug#1063274: pydevd: autopkgtest-failing warning with pandas 2.1

2024-02-19 Thread Rebecca N. Palmer
Thank you for caring about not breaking other packages, and yes, that's a good reason to not upload that new upstream for now. Does just the patch (not the new upstream) also break debugpy? (It shouldn't be able to, since it only touches test code.)

Bug#1063274: pydevd: autopkgtest-failing warning with pandas 2.1

2024-02-20 Thread Rebecca N. Palmer
Is that a yes to>> Does just the patch (not the new upstream) also break debugpy?or have you not tried specifically that? (I'm looking for a quick fix for the autopkgtest fail to unblock the pandas 2.x transition. I agree that upgrading to a new upstream is a good idea in the long run.) th

Bug#1063273: seaborn: autopkgtest fail on i386 - probable rounding error

2024-02-05 Thread Rebecca N. Palmer
Package: python3-seaborn Version: 0.13.2-1 Severity: serious seaborn's autopkgtest failed on i386, with differences small enough that they are plausibly rounding error (i.e. should be ignored, by using *almost_equal instead of exact comparisons), but I haven't looked carefully.

Bug#1063274: pydevd: autopkgtest-failing warning with pandas 2.1

2024-02-05 Thread Rebecca N. Palmer
Source: pydevd Severity: serious Tags: patch A pydevd test uses DataFrame.applymap(), and fails because this now raises a FutureWarning. Replacing it with DataFrame.map() as this message suggests would probably fix it.

Bug#1063435: geopandas: test fail with pandas 2.x on 32 bit - int32 vs int64 mismatch

2024-02-07 Thread Rebecca N. Palmer
Package: python3-geopandas Version: 0.14.3-1 Severity: serious Control: block 1043240 by -1 In pandas 2.x (now in unstable), there are a few places where geopandas uses native-size int but the plain pandas objects used as test references are always int64, failing the test: https://ci.debian.n

Bug#1063273: seaborn: autopkgtest fail on i386 - probable rounding error

2024-02-08 Thread Rebecca N. Palmer
Control: tags -1 pending This appears to be fixed in Salsa (before I reported it) - is there any reason not to upload this now?

Bug#1061761: marked as pending in snakemake

2024-02-08 Thread Rebecca N. Palmer
Control: tag -1 pending Hello, Bug #1061761 in snakemake reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/snakemake/-/commit/607bd710a51b77502c641443cf6

Bug#1063274: pandas 2.x fixes

2024-02-08 Thread Rebecca N. Palmer
Control: tags -1 patch See the Salsa merge request.

Bug#1044071: feather and pandas 2.0

2024-02-08 Thread Rebecca N. Palmer
Control: tags -1 patch It does sometimes happen that fixing "can't import the tests" reveals "the tests fail". Fixed in the Salsa merge request.

Bug#1050854: xarray test failure on amd64

2023-11-21 Thread Rebecca N. Palmer
I have added what should be fixes for #1053700 and #1044869, but they are currently untested as salsa-ci only runs the autopkgtest on amd64. #1050854 appears to have been fixed (or at least xfailed - it passed on salsa-ci but they say it's flaky) by upstream.

Bug#1053700: xarray test failure on s390x

2023-11-25 Thread Rebecca N. Palmer
This fix worked but the new upstream version added another similar issue, so s390x failed again. I have pushed a fix for this, and enabled allow-stderr to fix armel (error output from an already-xfailed test). I don't know what's causing the hang on arm64, so please do _not_ upload this just

Bug#1053700: xarray test failure on s390x

2023-11-25 Thread Rebecca N. Palmer
I retried the arm64 test and it passed, so it's probably just a random hang (I've seen those before in pytest). Hence, I now _do_ suggest uploading current Salsa.

Bug#1055801: pandas: test failures with Python 3.12

2023-12-07 Thread Rebecca N. Palmer
Control: unblock -1 by 1043240 The remaining test failures (all pytables-related) exist in both pandas 1.5 and 2.1, and do not appear to be known upstream. If they are all crashes rather than wrong answers (which I think they are), I intend to ignore them for now to unblock this, but still c

Bug#1055801: pandas: test failures with Python 3.12

2023-12-08 Thread Rebecca N. Palmer
Control: severity -1 normal Control: retitle -1 pandas/pytables: ignored test fails with Python 3.12 Control: found -1 2.1.3+dfsg-1 Control: tags 1057805 pending In 1.5.3+dfsg-8, these are ignored, so are no longer an FTBFS but are still a bug. I don't know whether they're a pandas bug or a pyt

Bug#1031414: Proposed RM: libgpuarray - abandoned, RC-buggy

2023-12-10 Thread Rebecca N. Palmer
libgpuarray has been de facto abandoned upstream since 2018, and is currently unused in Debian. (Its original user was theano, which was removed in #1042574.) It currently has what may or may not be a wrong-answer bug (#1031414), and two broken-by-transition bugs. (The latter two _might_ be

Bug#1056504: python-sparse in Python 3.12

2023-12-10 Thread Rebecca N. Palmer
Control: tags -1 fixed-upstream This was fixed upstream by https://github.com/pydata/sparse/commit/266af7307b5232a37daa1d7659f02faf6a42e46e . It still exists here because debian/patches/fix-test-fails-on-i386.patch effectively reverses that fix, possibly by accident.

Bug#1055847: python-sparse crash on arm64 (and possibly other non-x86)

2023-12-10 Thread Rebecca N. Palmer
At least on arm64, this appears to be a crash in a @numba.jit function. Given numba's known issues on non-x86 (e.g. #1033907), this suggests that actually fixing it _may_ not be reasonable. In pandas I don't recommend/build/test-depend on numba on the problem architectures, but python-sparse h

Bug#1055848: cfgrib failing to find eccodes

2023-12-10 Thread Rebecca N. Palmer
Control: retitle -1 cfgrib: test failure - can't find eccodes Because we now enforce that build-depends of testing must be in testing, this bug is blocking python-xarray and hence pandas from testing, so is more important than this package's popcon would suggest. I consider it likely that the

Bug#1044076: influxdb-python and pandas 2.1

2024-02-03 Thread Rebecca N. Palmer
My fixes are pushed to Salsa, but they're in a fork because this isn't a debian-science package: https://salsa.debian.org/rnpalmer-guest/influxdb-python

Bug#1044073: python-altair and pandas 2.0

2024-02-03 Thread Rebecca N. Palmer
Please don't skip/xfail tests - my suggestion above is an actual fix: https://salsa.debian.org/rnpalmer-guest/python-altair/-/tree/fix1044073?ref_type=heads (In a fork because, despite its description, this is not actually a debian-science package. The Salsa CI "fail" is because the *old* ver

Bug#1061761: snakemake issues with Python 3.12

2024-02-03 Thread Rebecca N. Palmer
It looks like this is at least two issues: - Tests mix tabs and spaces, which is no longer allowed = upstream 2459 - Assumes f-strings are not tokenized, which they now are = upstream 2485/2588/2649 Fix in progress on the debian-v7 branch. (The main branch has 8.x, which doesn't work due to m

Bug#1044073: Sorry Re: python-altair and pandas 2.0

2024-02-03 Thread Rebecca N. Palmer
On 03/02/2024 22:01, Andreas Tille wrote: The point I was making in my mail was that I had trouble running the tests in **latest** upstream version (5.2.0). Sorry - I'd misread your previous message as you having tried 5.x, found that it didn't work due to the missing dependency, and decided t

Bug#768090: beignet: pow/erf/tgamma, GBE_DEBUG, constants bug

2014-11-07 Thread Rebecca N. Palmer
Fix committed to Alioth. This fix has been accepted upstream; they found that it exposed another bug that compare and type-convert don't properly handle constants (http://lists.freedesktop.org/archives/beignet/2014-November/004387.html), so I included the fix for that as well. My own testing

Bug#766251: flightgear fails to start with *** stack smashing detected ***

2014-10-21 Thread Rebecca N. Palmer
Package: flightgear-data-base Version: 3.0.0-1 Severity: grave Justification: renders package unusable Control: tags -1 patch A fresh install (no .fgfs) of amd64 flightgear in current jessie or current sid fails to start: Program received signal SIGABRT, Aborted. 0x71d6f077 in __GI_rai

Bug#765818: simgear: FTBFS[kfreebsd]: wrong usage of GL/glxext.h

2014-10-22 Thread Rebecca N. Palmer
Control: reassign -1 src:simgear Control: found -1 3.0.0-5 Control: merge -1 765932 These are both the same kfreebsd FTBFS; this (#765818) patch looks better, but I haven't tried either. -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of "unsubscribe". Troub

Bug#766251: flightgear fails to start with *** stack smashing detected ***

2014-10-22 Thread Rebecca N. Palmer
ebian/changelog @@ -1,3 +1,10 @@ +flightgear-data (3.0.0-2) UNRELEASED; urgency=medium + + * Fix type mismatch crash. Closes: #766251. + * Downgrade -ai, -aircrafts to Recommends. + + -- Rebecca N. Palmer Wed, 22 Oct 2014 18:27:01 +0100 + flightgear-data (3.0.0-1) unstable; urgency=low

Bug#766251: patch line endings

2014-10-27 Thread Rebecca N. Palmer
dpkg-source --commit produced a patch with all Unix line endings, which failed; running that through unix2dos gave a patch with all DOS line endings, which also failed, with (Stripping trailing CRs from patch; use --binary to disable.) patching file Effects/model-combined-transparent.eff Hunk #

Bug#764930: beignet: FTBFS - uses versioned llvm commands, but unversioned build dependency

2014-10-28 Thread Rebecca N. Palmer
4-04-19 18:54:55.0 +0100 +++ beignet-0.8/debian/patches/versioned-llvm-tools 2014-10-28 12:17:01.0 + @@ -1,9 +1,20 @@ Description: Use versioned LLVM tools -Author: Simon Richter -Last-Update: 2014-04-19 +Description: +Author: Simon Richter , Rebecca N. Palmer

Bug#767384: libjogl2-java: non-DFSG file in test suite

2014-10-30 Thread Rebecca N. Palmer
Source: libjogl2-java Version: 2.2.4-1 Severity: serious Justification: Policy 2.1 Control: found -1 2.1.5-2 src/test/com/jogamp/opengl/test/junit/jogl/demos/es2/shader/landscape.fp has a NonCommercial license, which is not allowed in Debian (even if the file isn't actually used: https://releas

Bug#767387: beignet: Non-free files in test suite

2014-10-30 Thread Rebecca N. Palmer
Package: beignet Version: 0.8-1.1 Severity: serious Justification: Policy 2.1 Control: tags -1 patch upstream X-Debbugs-CC: pkg-opencl-de...@lists.alioth.debian.org The beignet test suite contains three images derived from Lenna ( kernels/lenna128x128.bmp kernels/compiler_box_blur_float_ref.bmp

Bug#764930: [Pkg-opencl-devel] Bug#764930: beignet: FTBFS - uses versioned llvm commands, but unversioned build dependency

2014-10-30 Thread Rebecca N. Palmer
I'm just wondering where the build failure in late August with exactly those dependencies came from and why the change fixed them? during compilation clang was called but could not be found: [...] Only the clang metapackage but not the clang-some.version package provides /usr/bin/clang. Agre

Bug#767387: beignet: Non-free files in test suite

2014-10-31 Thread Rebecca N. Palmer
Control: forwarded -1 http://lists.freedesktop.org/archives/beignet/2014-October/004343.html I have reported this upstream; they have agreed it's a problem and are in the process of removing the first group and investigating the second. To deal with this problem in the meantime, we will need to

Bug#767387: [Pkg-opencl-devel] Bug#767387: beignet: Non-free files in test suite

2014-10-31 Thread Rebecca N. Palmer
*mandelbrot* were included in this report by mistake, and are actually OK to keep. Now it FTBFS (it was working before the dfsg changes), tail of buildlog: I get the same error with git-buildpackage, but success with dpkg-buildpackage (as root in cowbuilder --login chroot; not cowbuilder --bu

Bug#764930: [Pkg-opencl-devel] Bug#764930: beignet: FTBFS - uses versioned llvm commands, but unversioned build dependency

2014-10-31 Thread Rebecca N. Palmer
You have my blessing to change the maintainer field if you like, as I won't be able to do as much as is needed in the next days. It would probably make sense for the pkg-opencl-devel list to own this package; I'm willing to be named as uploader, but will need a sponsor to actually upload anyth

Bug#767387: beignet 0.8+dfsg-1

2014-11-01 Thread Rebecca N. Palmer
.4, update versioned-llvm-tools.patch. +(Closes: #764930) + * State in the description what hardware this supports. + + -- Rebecca N. Palmer Sat, 01 Nov 2014 14:01:26 + + beignet (0.8-1.1) unstable; urgency=medium * Non-maintainer upload. diff -Nru beignet-0.8/debian/control beigne

Bug#768090: beignet: pow(n), erf(c), tgamma give wrong results

2014-11-04 Thread Rebecca N. Palmer
if f[0] in ("pow(a[i],c[i])","powr(a[i],c[i])"): d0=f[1](c,c) elif f[0] in ("pown(a[i],d[i])",): d0=f[1](c,ci) else: d0=f[1](c) print(dCL.get(),"\n",d0) Description: TODO: Put a short sum

Bug#769191: #769072,#769191: nvidia-opencl-icd breaking non-nvidia systems

2014-11-22 Thread Rebecca N. Palmer
I think the trigger is nvidia-opencl-icd adding a new dependency on libcuda1 (changelog: Add libcuda1 dependency to libraries that seem to be capable of doing dlopen("libcuda.so") or dlopen("libcuda.so.1").), which pulls in the rest of nvidia-* as libcuda1 Recommends: nvidia-kernel-dkms which R

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