Bug#1030096: #1030096 dask.distributed autopkgtest fail

2023-02-04 Thread Rebecca N. Palmer
I have an attempt to fix this in Salsa now (in my fork), but it hasn't had time to run the tests yet, so I don't know whether it works. Note the above mention that if we lose dask.distributed then we lose Spyder, which makes this a bigger issue than I initially thought.

Bug#1030327: science-numericalcomputation: please stop recommending python3-theano as it is being removed

2023-02-02 Thread Rebecca N. Palmer
Package: science-numericalcomputation Severity: minor theano is abandoned upstream and is broken by numpy 1.24 (#1027215). It is hence being removed from testing/next-stable, and probably from unstable as well. Hence, please stop listing it in this metapackage.

Bug#1030326: astro-python3: please stop recommending python3-theano as it is being removed

2023-02-02 Thread Rebecca N. Palmer
Package: astro-python3 Severity: minor theano is abandoned upstream and is broken by numpy 1.24 (#1027215). It is hence being removed from testing/next-stable, and probably from unstable as well. Hence, please stop listing it in this metapackage.

Bug#1030208: Acknowledgement (statsmodels: FTBFS with scipy 1.10 on 32-bit: int64 -> int32 cast)

2023-02-01 Thread Rebecca N. Palmer
Control: merge -1 1030210 1030221 Not obviously known upstream. It's due to the test passing an int64 array to np.bincount (which casts to native-size int). Hence, we can probably get it to pass by explicitly casting to int32 in the test code, but I haven't tried that yet. I don't know exac

Bug#1030208: statsmodels: FTBFS with scipy 1.10 on 32-bit: int64 -> int32 cast

2023-01-31 Thread Rebecca N. Palmer
Package: python3-statsmodels Version: 0.13.5+dfsg-4 Severity: serious Since scipy 1.10, some statsmodels tests fail on 32-bit with a message that int64 -> int32 casting is unsafe. I haven't yet had time to investigate further.

Bug#1017573: patch Re: ulmo broken by pandas 1.4+

2023-01-28 Thread Rebecca N. Palmer
Control: tags -1 patch Control: unblock -1 by 1011225 (Block possibly added by mistake - these don't look related.) This patch is now available as a Salsa merge request, and passed build+autopkgtest there.

Bug#1027244: scikit-learn Re: Are we still trying to do scipy 1.10, given transition freeze?

2023-01-26 Thread Rebecca N. Palmer
Control: tags 1029701 fixed-upstream Full log: https://ci.debian.net/data/autopkgtest/unstable/amd64/s/scikit-learn/30693526/log.gz There appear to be at least 2 separate failures here, both known and probably fixed upstream. So yes, 'new upstream version' is the first thing to try, but we'

Bug#1004869: python-xarray autopkgtest fail on i386

2023-01-23 Thread Rebecca N. Palmer
Control: reopen -1 Control: found -1 2023.01.0-1 This patch was dropped in the next upload (probably by accident), and hence this bug has reappeared. It is currently listed as blocking pandas from testing, though I'm not sure why (it isn't obvious why pandas and xarray would have to go togeth

Bug#1022571: transition: pandas 1.3 -> 1.5

2023-01-23 Thread Rebecca N. Palmer
The remaining autopkgtest failures blocking pandas are: - dipy/amd64 and snakemake/i386 look like random flakiness: please retry them. (I think DMs can't use the self-service interface.) Or for dipy, see #1029533 for a possible fix. - python-xarray/i386 looks like xarray not pandas: see #1004

Bug#1029533: python3-dipy: autopkgtest measures wall-clock time, causing random failures

2023-01-23 Thread Rebecca N. Palmer
Package: python3-dipy Version: 1.5.0-6 Tags: patch test_mapmri_isotropic_static_scale_factor measures wall-clock time to check which of two methods is faster, which is flaky on a shared autopkgtest server. (Known instances of it failing are https://ci.debian.net/data/autopkgtest/testing/amd64

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.)

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 setup.py/requirem

Bug#1027244: Are we still trying to do scipy 1.10, given transition freeze?

2023-01-18 Thread Rebecca N. Palmer
Control: tags -1 fixed-upstream patch Control: forwarded -1 https://github.com/scipy/scipy/pull/17033 This "broken by numpy 1.24" bug looks to me like 17033, not 17630. This has what looks like a trivially-backportable patch, though I haven't actually tried that: https://github.com/scipy/scip

Bug#1028667: dask BD-Uninstallable

2023-01-16 Thread Rebecca N. Palmer
On 16/01/2023 07:22, Diane Trout wrote: On Sun, 2023-01-15 at 14:42 -0800, Diane Trout wrote: On Sun, 2023-01-15 at 18:16 +, Rebecca N. Palmer wrote: Probably fixed - see my merge request on Salsa. I'd tried to build versions of dask from 2022.03 - 2022.06 and they all failed

Bug#1028667: dask BD-Uninstallable

2023-01-15 Thread Rebecca N. Palmer
Probably fixed - see my merge request on Salsa.

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 othe

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 currently

Bug#1022571: pandas 1.5 now in unstable

2023-01-12 Thread Rebecca N. Palmer
Control: severity 1025393 serious Control: severity 1024820 serious The autopkgtest fails (except statsmodels, which I just fixed) are packages that are test-uninstallable because pandas 1.5 Breaks: current dask. (This is #1025393, but some of its discussion was accidentally sent to #1027254

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#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} ha

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 12th

Bug#1017573: ulmo fails in pandas 1.4+

2023-01-09 Thread Rebecca N. Palmer
Control: forwarded -1 https://github.com/ulmo-dev/ulmo/pull/214 Control: severity -1 serious Untested patch at the above link. pandas 1.5 should be uploaded to unstable today, making this RC.

Bug#1022571: transition: pandas 1.3 -> 1.5

2023-01-09 Thread Rebecca N. Palmer
skbio is fixed, ulmo is maybe fixed but untested. dask is unclear (see #1027254 for details): it looks like it's probably fixable, but I don't have an actual working fix yet. There has been no response from its maintainers.

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 dask.distribu

Bug#1022571: transition: pandas 1.3 -> 1.5

2023-01-07 Thread Rebecca N. Palmer
On 06/01/2023 09:16, Nilesh Patra wrote: The version of dask is same since few months. What do you mean by new dask? Current Debian dask (2022.02) fails its tests with pandas 1.5 (#1025393), and the obvious way to fix that (and #1027254) is to update it to current upstream dask (2022.12), but

Bug#1027254: dask: fail with numpy 1.24

2023-01-06 Thread Rebecca N. Palmer
Control: tags -1 fixed-upstream Those are all from bcolz, which upstream dask has stopped using: https://github.com/dask/dask/pull/9479 (Upstream also mention numpy 1.24 in https://github.com/dask/dask/pull/9777 which hasn't been in a release yet, but that one looks like it's only suppressing w

Bug#1022571: transition: pandas 1.3 -> 1.5

2023-01-06 Thread Rebecca N. Palmer
Should this go ahead before the freeze? I think yes if the new dask works, but am open to disagreement. Issues this would fix: python3.11 #1023965: We're currently ignoring these test failures. Mystery autopkgtest failure (fails without any listed individual test failure, started 2022-11-13)

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#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#1025393: dask: autopkgtest fail with pandas 1.5

2022-12-03 Thread Rebecca N. Palmer
Package: python3-dask Version: 2022.02.0+dfsg-2 Tags: fixed-upstream Control: block 1022571 by -1 With pandas 1.5 (currently in experimental), the dask autopkgtest fails: https://ci.debian.net/data/autopkgtest/unstable/amd64/d/dask/28842796/log.gz This appears to be fixed upstream, but I haven't

Bug#1017573: python3-ulmo: autopkgtest fail with pandas 1.4

2022-11-30 Thread Rebecca N. Palmer
Control: reopen -1 On 13/11/2022 15:02, Rebecca N. Palmer wrote: It looks like this has been fixed somewhere other than the ulmo package (I don't know where), as the autopkgtest now passes with pandas 1.4/1.5. No it doesn't - it's being run with pandas 1.3 because pandas

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 (and

Bug#1022571: pandas 1.5

2022-11-25 Thread Rebecca N. Palmer
Control: severity -1 wishlist Control: retitle -1 transition: pandas 1.3/1.4 -> 1.5 Control: tags -1 fixed-in-experimental pandas 1.5.1 is now in experimental. It appears to break emperor, q2templates and statsmodels. (Compared to 1.4; also python-skbio (#1017574) compared to 1.3.) statsmodel

Bug#1017574: python3-skbio: FTBFS/autopkgtest fail with pandas 1.4/1.5

2022-11-25 Thread Rebecca N. Palmer
Control: block 1022571 by -1 This still fails with pandas 1.5. Build log: https://launchpadlibrarian.net/633830773/buildlog_ubuntu-lunar-amd64.python-skbio_0.5.6-6build2_BUILDING.txt.gz Autopkgtest log: https://ci.debian.net/data/autopkgtest/unstable/amd64/p/python-skbio/28542505/log.gz

Bug#1024821: q2templates: FTBFS/autopkgtest fail with pandas 1.5

2022-11-25 Thread Rebecca N. Palmer
Package: q2templates Version: 2022.8.0+ds-1 Control: block 1022571 by -1 Tests fail with pandas 1.5 (currently in experimental). Build log: https://launchpadlibrarian.net/633830688/buildlog_ubuntu-lunar-amd64.q2templates_2022.8.0+ds-1_BUILDING.txt.gz Autopkgtest log: https://ci.debian.net/data/a

Bug#1024820: emperor: FTBFS/autopkgtest fail with pandas 1.5

2022-11-25 Thread Rebecca N. Palmer
Package: python3-emperor Version: 1.0.3+ds-4 Control: block 1022571 by -1 Tests fail with pandas 1.5 (currently in experimental). Build log: https://launchpadlibrarian.net/633828020/buildlog_ubuntu-lunar-amd64.emperor_1.0.3+ds-4_BUILDING.txt.gz Autopkgtest log: https://ci.debian.net/data/autopkg

Bug#1020060: statsmodels sometimes FTBFS

2022-11-13 Thread Rebecca N. Palmer
It also doesn't fail on the buildds. (The failed binNMU of statsmodels for Python 3.11 is instead the expected result of trying to build statsmodels on a Python version without pandas - pandas failed due to #1023965.) Is there anything special about the mass-rebuild environment that might ex

Bug#1023965: pandas FTBFS with Python 3.11 as supported version

2022-11-13 Thread Rebecca N. Palmer
Control: block 1021984 by -1 Control: tags -1 fixed-upstream fixed-in-experimental There's more than just those 2[0]. Some are tests that expect an error and check the message (not just the type), and fail because the message has been reworded - these should be trivial to fix. The 2 in test_nul

Bug#1023986: parso: too old to parse Python 3.11

2022-11-13 Thread Rebecca N. Palmer
Package: python3-parso Version: 0.8.1-1 Tags: fixed-upstream Control: block 1023965 1021984 by -1 Attempting to use parso on Python 3.11 gives an error that this is not supported. (e.g. some pandas tests do this - https://launchpadlibrarian.net/631797785/buildlog_ubuntu-lunar-amd64.pandas_1.3

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 only,

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 b

Bug#997908: pocl: Assertion `td->printf_buffer != NULL' failed on armel/armhf

2021-10-26 Thread Rebecca N. Palmer
Source: pocl Version: 1.8-1 (Filing this as something to refer to when I disable those tests; it may or may not actually be worth fixing.) Since some time in August, all the packages that use pocl for their autopkgtests have been failing on armel/armhf (but not arm64) with either Assertion `

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#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 s

Bug#963041: Lagging behind several versions for snakemake - lots of failed tests in latest version

2021-10-17 Thread Rebecca N. Palmer
On 15/10/2021 14:46, Andreas Tille wrote: Hi Rebecca and whoever might care. As usual snakemake is troublesome to upgrade. I have injected the latest version into Git but there are lots of failed tests. It would be great if someone could care about this. Kind regards Andreas. I had

Bug#995415: unblock: theano/1.0.5+dfsg-3 - not really a regression

2021-09-30 Thread Rebecca N. Palmer
Package: release.debian.org User: release.debian@packages.debian.org Usertags: unblock Severity: normal theano 1.0.5+dfsg-3 is currently held in unstable for an autopkgtest "regression" on armhf. The test in question (smoketestgpu) is currently skipped in plain testing because it depends

Bug#974789: 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 f

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 bits.

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 we'

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 (https://bugs.debian.o

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 a

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, F

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#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 e

Bug#983328: scipy 1.6.1 breaks sparse (COO) matrix construction

2021-03-02 Thread Rebecca N. Palmer
Fine by me, thanks.

Bug#983328: scipy 1.6.1 breaks sparse (COO) matrix construction

2021-03-02 Thread Rebecca N. Palmer
What, if any, action are you proposing before bullseye? Or is this a request for an up-to-date pandas in experimental? That workaround just disables the affected test, i.e. it will probably fix the FTBFS but do nothing to the underlying problem. As noted in #983404, a real scipy fix also exi

Bug#983328: pandas: sparse test_from_coo fails with scipy 1.6.1

2021-02-22 Thread Rebecca N. Palmer
On 22/02/2021 12:44, Drew Parsons wrote: v1.2.2 is the latest pandas release Has this error in test_from_coo been fixed in that latest release? Not obviously, but I haven't tried actually running that. Is scipy 1.6.1 intended for bullseye?

Bug#982947: clinfo reports fatal error

2021-02-17 Thread Rebecca N. Palmer
On 17/02/2021 10:00, Andreas Beckmann wrote: Note to self: `reportbug clinfo` should report all installed ICDs Feel free to borrow beignet-opencl-icd.bug-script

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#977743: packages.debian.org: "list of files" fails on sid/testing arch:all packages - not processing Contents-all.gz ?

2020-12-19 Thread Rebecca N. Palmer
Package: www.debian.org On the packages.d.o pages of arch:all packages from sid, bullseye or experimental, the "list of files" link gives the error message "No such package in this suite on this architecture." This does not affect arch:any packages, or packages from stable. e.g. fails - http

Bug#888733: RM: hyantesite

2020-12-18 Thread Rebecca N. Palmer
Control: retitle -1 RM: hyantesite -- RoM; behaviour does not match documentation, upstream/uploader inactive The patches above and regenerating the test references would probably fix the FTBFS, but that still leaves the code for amortized_disk and pareto not matching the documentation. It wou

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

2020-12-06 Thread Rebecca N. Palmer
Control: severity -1 serious Control: affects -1 pandas This breaks the default form of pandas.read_excel(). A workaround for this is to use pandas.read_excel(engine='openpyxl'), and pandas upstream have made this the default: https://github.com/pandas-dev/pandas/pull/35029/files I intend to

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'

2020-12-05 Thread Rebecca N. Palmer
Package: python3-xlrd Version: 1.2.0-1 Tags: patch xlrd 1.2.0 started using defusedxml if available. As defusedxml.cElementTree does not have a top-level ElementTree attribute, Element_has_iter gets set to False (https://sources.debian.org/src/python-xlrd/1.2.0-1/xlrd/xlsx.py/#L59). However,

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#974797: pocl: Please upgrade to llvm-toolchain-11

2020-11-19 Thread Rebecca N. Palmer
(libgpuarray maintainer) This isn't testable in a qemu-armhf chroot, as pocl doesn't work there. Do all the non-clblas tests pass? (This can be checked by uninstalling libclblas-dev then running the tests - this will "error" the clblas tests but should at least not crash them.) On 19/11/202

Bug#974792: [Pkg-opencl-devel] Bug#974792: beignet: Please upgrade to llvm-toolchain-11

2020-11-16 Thread Rebecca N. Palmer
https://lists.freedesktop.org/archives/beignet/2020-January/009251.html With that partial patch, the errors are LLVM 10: builtin_acos_float()clang (LLVM option parsing): for the --pgo-warn-misexpect option: may only occur zero or one times! LLVM 11: In file included from /build/beignet-1.3.2

Bug#973854: debian/patches/i386_loosen_test_tolerances.patch not Multi-Arch safe

2020-11-06 Thread Rebecca N. Palmer
Control: severity -1 minor Control: retitle -1 imperfect/non-upstreamable architecture detection The sys.maxsize check should catch amd64 vs i386; the directory check is mostly to catch other-32-bit vs i386. All this patch does is allow more rounding error in some tests (because i386 registers

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#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#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 d

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 (< 2.11

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 th

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#972516: dask: fsspec API changes / new aiohttp dependency

2020-10-19 Thread Rebecca N. Palmer
Package: python3-dask Version: 2.11.0+dfsg-1 Some of fsspec's functionality now requires python3-aiohttp, including parts used in dask autopkgtests: https://ci.debian.net/data/autopkgtest/testing/amd64/d/dask/7549002/log.gz Some of these work if I add a test-dependency, but 2 continue to fail

Bug#969648: dask, pandas 1.1

2020-10-19 Thread Rebecca N. Palmer
ertionError diff -Nru dask-2.11.0+dfsg/debian/changelog dask-2.11.0+dfsg/debian/changelog --- dask-2.11.0+dfsg/debian/changelog 2020-02-26 21:01:52.0 + +++ 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=me

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 th

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#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#964791: [Pkg-opencl-devel] Bug#964791: Bug#964791: libclc-amdgcn: OpenCL fails to start

2020-10-16 Thread Rebecca N. Palmer
The error message has gone for me as well, but I don't have the hardware to tell whether mesa-opencl-icd actually works. Have you checked this? I agree that this is probably the same bug as #964973, which is marked as fixed.

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#969648: 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#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#969648: python3.9 Re: dask, pandas 1.1

2020-10-11 Thread Rebecca N. Palmer
Control: block 972033 by 969650 This is now the only bug blocking pandas 1.1. Is there something wrong with the above fix, or have you just not had time to try it? Upgrading dask to a newer upstream version is also an option, but I haven't checked if it would break anything else. Python 3.

Bug#972033: pandas ftbfs with python3.9 as supported python version

2020-10-11 Thread Rebecca N. Palmer
There's a 1.1.3 package in Salsa, but it hasn't been tested. (With python3-all-dev from experimental, it fails because numpy doesn't have a 3.9 build yet.)

Bug#972033: pandas ftbfs with python3.9 as supported python version

2020-10-11 Thread Rebecca N. Palmer
Control: merge -1 972015 Control: found -1 1.0.5+dfsg-3 Control: forwarded -1 https://github.com/pandas-dev/pandas/issues/36296 Control: tags -1 fixed-upstream pandas 1.1.3 may fix this, but moving to 1.1.x triggers #969648.

Bug#924036: partly fixed

2020-10-06 Thread Rebecca N. Palmer
Most of these tests no longer fail in 0.11.1-5 (current Ubuntu) and 0.12.0-2 (current Debian), but 3 still do: two variants of varmax test_bse_oim, and test_pickle_fit_sarimax.

Bug#963041: python3-pulp 2.x

2020-10-06 Thread Rebecca N. Palmer
Control: affects -1 snakemake Upstream snakemake have now moved to pulp 2.x - but went straight from 1.x only to 2.x only, i.e. they need to be upgraded together.

Bug#970555: libncurses upgrade fails in cowbuilder chroots

2020-09-27 Thread Rebecca N. Palmer
Jessica Clarke wrote: It seems to me like dpkg has done a very dodgy sequence of events that have resulted in the system being broken for a short period and, whilst most don't notice, cowdancer does. Why is this not a dpkg (or apt) bug? It should be possible to do that sequence in a way that pres

Bug#963041: python3-pulp: maybe API break Re: New upstream

2020-09-13 Thread Rebecca N. Palmer
This _might_ be an API break. The reverse dependencies are snakemake and congress. snakemake recently started declaring a <=1.6.8 version restriction: https://github.com/snakemake/snakemake/commits/a7ac40c96d6e2af47102563d0478a2220e2a2ab7 However, their reason seems to be that pulp 2.x doesn't

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#969650: transition: pandas 1.0 -> 1.1

2020-09-06 Thread Rebecca N. Palmer
Package: python3-pandas Version: 1.0.5+dfsg-3 Severity: wishlist Control: block -1 by 969648 969649 pandas 1.1.x is currently in experimental. The upstream description suggests this is not supposed to be an API break, but does have new warnings. Packages tested with it (build + autopkgtest):

Bug#969649: skbio: FTBFS/test fail with pandas 1.1

2020-09-06 Thread Rebecca N. Palmer
Package: python3-skbio Version: 0.5.6-2 With pandas 1.1 from experimental, python-skbio fails 3 of its tests. Log: https://ci.debian.net/data/autopkgtest/unstable/amd64/p/python-skbio/6900486/log.gz

Bug#969648: dask: autopkgtest fail with pandas 1.1 - datetime issues

2020-09-06 Thread Rebecca N. Palmer
Package: python3-dask Version: 2.11.0+dfsg-1 Tags: fixed-upstream With pandas 1.1.x from experimental, dask fails 8 of its tests, at least mostly datetime-related. Log: https://ci.debian.net/data/autopkgtest/unstable/amd64/d/dask/6900447/log.gz Upstream fix (untested): https://github.com/da

Bug#790925: not Re: appears to be fixed

2020-09-03 Thread Rebecca N. Palmer
Control: reopen -1 Looks like pytest --forked --runxfail doesn't work properly (probably related to https://github.com/pytest-dev/pytest-forked/pull/34#discussion_r436140456), so that wasn't a valid test.

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

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