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#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#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#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#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#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#881507: dar: par2 option broken - bad path in /etc/darrc

2017-11-12 Thread Rebecca N. Palmer
/dar_par.dcf): No such file or directory Author: Rebecca N. Palmer Bug-Debian: https://bugs.debian.org/ Forwarded: not-needed --- a/doc/samples/Makefile.in +++ b/doc/samples/Makefile.in @@ -465,7 +465,7 @@ install-data-hook: $(INSTALL) -m 0644 $(NO_EXE_SAMPLES) $(DESTDIR)$(pkgdatadir)/samples

Bug#893050: (no subject)

2018-03-22 Thread Rebecca N. Palmer
Control: tags -1 patch Looks like the problem is the "-i pythonX.Y" at https://sources.debian.org/src/pyopencl/2018.1.1-1/debian/rules/#L38 : that's not valid input to pybuild, and (probably since pybuild commit https://anonscm.debian.org/cgit/dh-python/dh-python.git/commit/?id=fa7caff4ee25228

Bug#893656: transition: theano 0.9 -> 1.0 - please update lasagne

2018-03-22 Thread Rebecca N. Palmer
lasagne - 3 test failures; fixed upstream by https://github.com/Lasagne/Lasagne/pull/836 Latest upstream (37ca134; only packaging change was to drop remove-deprecated.patch) doesn't have these failures. There is a warning that cuda_convnet is no longer available with Theano 1.0, but that has

Bug#893050: pyopencl test failures

2018-03-23 Thread Rebecca N. Palmer
Control: tags -1 patch The failing tests also happen with the current version installed, so are probably nothing to do with this fix. 9 tests fail or crash for me, of which 5 are things my hardware isn't expected to be able to do: test_coarse_grain_svm - needs OpenCL 2.0 test_scan InclusiveS

Bug#878596: theano: FTBFS on big-endian systems - test_pooling_with_tensor_vars fails

2017-10-14 Thread Rebecca N. Palmer
Package: python-theano Version: 0.9.0+dfsg-1 Severity: serious Suspect the problem is theano/theano/tensor/signal/pool.py:650, which effectively does int32 = *(int64 *)(pointer_to_some_int_type) - if some_int_type is int32, that works on little-endian but not big-endian.

Bug#878596: fixed in Alioth

2017-10-19 Thread Rebecca N. Palmer
Control: tags -1 patch fixed-upstream pending Ready for upload (the GPU tests again haven't been run, but this shouldn't touch those parts).

Bug#882486: unnecessarily scary warning under Wayland

2018-01-10 Thread Rebecca N. Palmer
Control: tags -1 fixed-upstream patch Upstream agree that this is expected under Wayland. The warning can be disabled with https://cgit.freedesktop.org/beignet/commit/?id=d1b99a1da56757971753288986419f1b8b9d55f4

Bug#869271: flightgear-data-base: relative vs absolute symlinks

2018-05-06 Thread Rebecca N. Palmer
This has previously come up in another large game [0], and it was there noted that while Debian Policy discourages absolute links within a top-level directory [1], it does not forbid them. That discussion led to the -X option of dh_link, but note that this only disables relative/absolute conve

Bug#895332: flightgear: FTBFS on armel and armhf - GLES related?

2018-05-06 Thread Rebecca N. Palmer
This looks like a GL vs GLES incompatibility: libqt5opengl uses OpenGL ES on armel+armhf, simgear/flightgear use full OpenGL on all architectures, and the two can't be mixed. simgear+flightgear probably can't switch to OpenGL ES because they use legacy OpenGL functions that aren't in ES. (The

Bug#897159: flightgear: missing qml dependencies

2018-05-06 Thread Rebecca N. Palmer
This is known upstream: https://sourceforge.net/p/flightgear/mailman/flightgear-devel/thread/96b69154-ebd9-166f-9be5-d4971ee4ab05%40numericable.com/#msg36224500 Upstream keep a dependency list in https://sourceforge.net/p/flightgear/fgmeta/ci/next/tree/download_and_compile.sh (lines ~330), but i

Bug#898126: theano: memory leak

2018-05-07 Thread Rebecca N. Palmer
Package: python-theano Version: 1.0.1+dfsg-2 Severity: serious (Filing this as RC to give myself time to investigate: I may downgrade it later.) Memory usage increases over theano's tests, to ~6GB by the end of the python2 set (6981 tests) in Debian sid amd64, and enough to fail the Ubuntu a

Bug#898126: theano: memory leak

2018-05-11 Thread Rebecca N. Palmer
Control: severity -1 normal This is not a new problem (I'm not sure if it's got worse per test, or just got noticed because the test suite got longer), so removing the migration block. The largest (but not only) leaks are test_pickle_big_fusion (theano.tensor.tests.test_opt.test_fusion) test_

Bug#745688: libjs-d3: SyntaxError due to non-ASCII variable names

2017-09-29 Thread Rebecca N. Palmer
Control: severity -1 minor Control: affects -1 src:theano Control: retitle -1 libjs-d3: SyntaxError - non-ASCII variable names This actually does have practical consequences: because d3's source contains Greek-alphabet variable names (e.g. in http://sources.debian.net/src/d3/3.5.17-2/src/math/t

Bug#877316: clblas: Crashes on single-precision-only hardware, due to double-precision literals

2017-09-30 Thread Rebecca N. Palmer
Package: libclblas2 Version: 2.12-1 Control: tags -1 upstream Control: affects -1 beignet-opencl-icd Some clblas operations use '0.0' (a double-precision literal) not '0.0f' (a single-precision literal) even when processing single-precision arrays. This causes it to crash on GPUs that don't su

Bug#877359: clang: precompiled headers are not reproducible

2017-09-30 Thread Rebecca N. Palmer
Package: clang-4.0 Version: 1:4.0.1-5 Severity: wishlist User: reproducible-bui...@lists.alioth.debian.org Usertags: toolchain randomness Control: affects -1 beignet-opencl-icd liboclgrind-16.10 X-Debbugs-Cc: reproducible-b...@lists.alioth.debian.org Generating a .pch precompiled header with clan

Bug#852138: theano 0.9 ready for upload

2017-10-01 Thread Rebecca N. Palmer
On 01/10/17 08:38, Ghislain Vaillant wrote: I thought Theano v0.9.x would require libgpuarray 0.7.x? Or is that for the future (and probably last) 1.0 version? The documentation for theano stable (0.9.0, this package) says 0.6.2: http://www.deeplearning.net/software/theano/install_ubuntu.html#

Bug#852138: theano 0.9 ready for upload

2017-10-01 Thread Rebecca N. Palmer
They have now said libgpuarray 0.6 for Theano 0.9 (i.e. what we currently have is fine) and libgpuarray 0.7 for Theano 0.10. https://github.com/Theano/Theano/issues/6454 (#877316 is a separate problem.)

Bug#877419: pandas FTBFS on !x86/ppc64el: test failures

2017-10-03 Thread Rebecca N. Palmer
This is actually at least three problems: - (arm*, mips*el) datetime issues, at least mostly inconsistency in whether casting NaN to datetime gives NaT. - (armel, armhf) SystemError in JSON processing. Known upstream as https://github.com/pandas-dev/pandas/issues/14852 , but they don't have

Bug#877316: clblas: Crashes on single-precision-only hardware, due to double-precision literals

2017-10-03 Thread Rebecca N. Palmer
I intend to file this upstream after investigating further (with a patch if I can); the main purpose of this Debian bug is to explain why I can't fully test the theano package I recently pushed.

Bug#877359: clang: precompiled headers are not reproducible

2017-10-05 Thread Rebecca N. Palmer
Possible workarounds for beignet: - Remove the .pch files entirely. This slows down compiling (which is a run-time operation in OpenCL): 263sec instead of 90sec for the 540-kernel test suite = ~0.3sec extra per kernel compile. At a guess, that's unlikely but not impossible to matter in pract

Bug#877359: clang: precompiled headers are not reproducible

2017-10-07 Thread Rebecca N. Palmer
SION_TYPES reproducible Author: Rebecca N. Palmer Bug-Debian: https://bugs.debian.org/877359 Forwarded: no --- llvm-toolchain-5.0-5.0.orig/clang/lib/Serialization/ASTWriter.cpp +++ llvm-toolchain-5.0-5.0/clang/lib/Serialization/ASTWriter.cpp @@ -4153,9 +4153,13 @@ void ASTWriter::WriteOpenCLExtensionType

Bug#877359: clang: precompiled headers are not reproducible

2017-10-07 Thread Rebecca N. Palmer
The problems with current beignet look to be: - file timestamps in INPUT_FILES_BLOCK (some of beignet's .h files are script-generated). This part can be fixed in beignet. - build path captured in ORIGINAL_PCH_DIR. _Might_ be fixable in beignet by using clang (...) > /path/to/beignet.pch ins

Bug#877359: clang: precompiled headers are not reproducible

2017-10-07 Thread Rebecca N. Palmer
On 07/10/17 14:09, Rebecca N. Palmer wrote: The problems with current beignet look to be: - file timestamps in INPUT_FILES_BLOCK (some of beignet's .h files are script-generated).  This part can be fixed in beignet. That works (COMMAND touch -d '@$ENV{SOURCE_DATE_EPOCH}' $

Bug#896220: using theano without $HOME

2018-04-25 Thread Rebecca N. Palmer
It's trying to create a cache directory. You can tell it to do this somewhere else with the THEANO_FLAGS variable (as we do for the test suite - https://sources.debian.org/src/theano/0.9.0+dfsg-2/debian/rules/#L34 ).

Bug#942106: (some kind of) transition: add python3.8 as a supported python3 version

2019-10-26 Thread Rebecca N. Palmer
What should be done with modules where Python 3.8 compatibility requires moving to a new upstream release that doesn't support Python 2, but the Python 2 package still has dependencies (so can't be removed yet under existing rules)? - Split them into two source packages with different upstream

Bug#942106: (some kind of) transition: add python3.8 as a supported python3 version

2019-10-26 Thread Rebecca N. Palmer
On 26/10/2019 22:50, Matthias Klose wrote: Ubuntu already dropped python-pandas, I wasn't involved with that. This seems to have been done by the "let things break" approach that isn't allowed in Debian, e.g. they can no longer build python-matplotlib: https://bugs.debian.org/cgi-bin/bugreport.

Bug#942106: (some kind of) transition: add python3.8 as a supported python3 version

2019-10-27 Thread Rebecca N. Palmer
Detailed discussion of pandas has moved to #931557 / debian-science. Summary: - python-pandas removal looks feasible, but there is one item that needs ftpmaster or release team authorization: either let pypubsub out of NEW (preferred), or give us permission to break tnseq-transit. - 0.23 -> 0

Bug#931557: pandas: Python 2 removal, 0.23 -> 0.25 transition

2019-10-27 Thread Rebecca N. Palmer
Python 3.8 is being added (#942106). pandas <0.25 does not support Python 3.8[0] (when Ubuntu tried they got 268 test failures [1]), while pandas>=0.25 does not support Python 2. Hence, our options are: (a) Remove python-pandas and upgrade pandas to 0.25 (b) Split pandas into two source package

Bug#936870: theano: remove python2

2019-10-28 Thread Rebecca N. Palmer
On 28/10/2019 06:30, Mo Zhou wrote: Hi Rebecca, Theano is a leaf package No it isn't: deepnano Depends on it. (If you used my checker - not finding this is bug https://lists.debian.org/debian-python/2019/10/msg00106.html ) blocking python2 removal. What's the blocker for the pending comm

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 actua

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 an

Bug#931557: transition: pandas 0.23 -> 0.25

2019-10-29 Thread Rebecca N. Palmer
Control: retitle -1 transition: pandas 0.23 -> 0.25 I now have pandas 0.25.2 in experimental, with these autopkgtest failures: pandas itself: probably I forgot to add a dependency (it passed locally, but in the same chroot as the build) statsmodels: looks like a reappearance of #923707 and some

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

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

Bug#931557: transition: pandas 0.23 -> 0.25

2019-10-31 Thread Rebecca N. Palmer
Control: block -1 by 937236 (0.25 is Python 3 only) I have now done a build test with the new python3-pandas installed: Success: bcbio caffe cnvkit dask dask.distributed drms igdiscover lmfit-py matplotlib mirtop nbsphinx partd patsy poliastro pynwb python-airr python-apptools python-biom-form

Bug#943923: python-apptools: please stop build-depending on python-pandas

2019-10-31 Thread Rebecca N. Palmer
+ + * Stop build-depending on python-pandas, +and fix resulting test issues. + + -- Rebecca N. Palmer Thu, 31 Oct 2019 21:42:13 + + python-apptools (4.4.0-3) unstable; urgency=medium * Fixing broken links in python-apptools-doc diff -Nru python-apptools-4.4.0/debian/control python-apptools

Bug#943924: matplotlib2: please stop build-depending on python-pandas

2019-10-31 Thread Rebecca N. Palmer
Package: python-matplotlib Version: 2.2.4-2 Control: block 937296 by -1 Control: tags -1 patch pandas upstream dropped Python 2 support in 0.25 (before adding Python 3.8 support). As further discussed in #937296, the Debian package python-pandas is currently part of a big tangle of circular (

Bug#943925: python-feather-format: FTBFS with pandas 0.25

2019-10-31 Thread Rebecca N. Palmer
Package: python3-feather-format Version: 0.3.1+dfsg1-2 Control: block 931557 by -1 With python3-pandas 0.25, the build fails with these test failures: == ERROR: test_boolean_object_nulls (feather.tests.test_reader.TestFeatherR

Bug#877754: NaN -> datetime = 0 (not NaT) on arm*

2019-11-02 Thread Rebecca N. Palmer
Control: retitle -1 NaN -> datetime = 0 (not NaT) on arm* Control: tag -1 - fixed-upstream Control: reassign -1 python3-numpy Control: affects -1 python3-pandas Control: forwarded -1 https://github.com/numpy/numpy/issues/8325 The underlying issue is that datetime/timedelta are internally ints, an

Bug#943732: pandas: test fails/crashes on mipsel

2019-11-02 Thread Rebecca N. Palmer
Control: retitle -1 pandas: test fails/crashes on mipsel arm* = new tests hitting the already-known issue #877754 (which I don't like having open with no user-level warning, but blocking the transition over it doesn't actually help) s390x/ppc64 = bug in the tests, not the library riscv64 = look

Bug#944041: cnvkit: autopkgtest fail with pandas 0.25

2019-11-03 Thread Rebecca N. Palmer
Source: cnvkit Version: 0.9.6-1 Control: block 931557 by -1 https://ci.debian.net/data/autopkgtest/unstable/amd64/c/cnvkit/3322951/log.gz

Bug#944042: python3-skbio: FTBFS and autopkgtest fail with pandas 0.25

2019-11-03 Thread Rebecca N. Palmer
Package: python3-skbio Version: 0.5.5-2 Control: block 931557 by -1 https://ci.debian.net/data/autopkgtest/unstable/amd64/p/python-skbio/3322971/log.gz Also fails to build; I suspect (but haven't checked) that these are the same problem.

Bug#944043: q2-types: autopkgtest fail with pandas 0.25

2019-11-03 Thread Rebecca N. Palmer
Source: q2-types Version: 2019.7.0-1 Control: block 931557 by -1 https://ci.debian.net/data/autopkgtest/unstable/amd64/q/q2-types/3322976/log.gz

Bug#944054: statsmodels: ignored test failures on at least ppc64el

2019-11-03 Thread Rebecca N. Palmer
Package: python3-statsmodels Version: 0.10.1-1 Control: fixed -1 0.9.0-6 Severity: serious While making statsmodels clean up after its tests, I accidentally also made it ignore failed tests. Some tests did fail on at least ppc64el and s390x; I don't yet know if these are actually a serious pr

Bug#944054: statsmodels: ignored test failures on at least ppc64el

2019-11-03 Thread Rebecca N. Palmer
The test failures are: armhf: 86, probably all #924036 i386: 1, TestDFM_Approx.test_smoothed_measurement_disturbance out of tolerance: suspect rounding error (x87 extra precision). arm64, ppc64el, s390x: the same 3, base.tests.test_penalized.TestPenalizedPoissonOraclePenalized2*: looks like

Bug#943732: pandas: high RAM usage in test suite

2019-11-06 Thread Rebecca N. Palmer
Control: retitle -1 pandas: high RAM usage in test suite Control: severity -1 normal The ones I've tried (~half the affected ones) pass on qemu-mipsel when run in smaller batches. Memory usage for the whole test suite (on amd64) starts at nearly 1GB just for *collecting* the tests and continu

Bug#944054: statsmodels: ignored test failures on at least ppc64el

2019-11-06 Thread Rebecca N. Palmer
Control: severity -1 important (mostly for ignoring failures, not the actual ones that happened) After further testing, it looks like base.tests.test_penalized.TestPenalizedPoissonOraclePenalized2* is on a convergence edge: if the random seed isn't fixed, it sometimes finds all 4 and sometimes

Bug#933034: Should we stop reassigning py2removals?

2019-11-07 Thread Rebecca N. Palmer
The Python 2 removal checklist currently says that on uploading a package as Python 3 only, one should reassign the removal bug to ftp.debian.org for removal of the old binary, not close it: https://wiki.debian.org/Python/2Removal Scott Kitterman wrote (in #938661): The python-theano binary wa

Bug#936190: pandas needs 0.25 for Python 3.8

2019-11-07 Thread Rebecca N. Palmer
Control: severity -1 important Python 3.8 is being added to unstable's supported versions (#942106). As discussed in #931557, pandas in sid (0.23) doesn't support Python 3.8. pandas in experimental (0.25) does, but contains some API breaks and doesn't support Python 2, triggering these bugs.

Bug#937250: patsy: circular py2removal dependency

2019-11-07 Thread Rebecca N. Palmer
Control: severity -1 important (blocks pandas 0.23 -> 0.25 transition, and hence python3.8 support) patsy, pandas and statsmodels form a circular dependency, so they will all need to drop python2 support at once. As discussed in #942106 and #931557, this can't happen right now but may be happ

Bug#936999: pandas needs 0.25 for Python 3.8

2019-11-10 Thread Rebecca N. Palmer
Control: severity -1 important Python 3.8 is being added to unstable's supported versions (#942106). As discussed in #931557, pandas in sid (0.23) doesn't support Python 3.8. pandas in experimental (0.25) does, but contains some API breaks and doesn't support Python 2, triggering these bugs.

Bug#942106: python3.8 / pandas py2removal

2019-11-10 Thread Rebecca N. Palmer
Matthias Klose wrote: yes, please do [raise pandas 0.25 blocking bugs to "important"] Done, but only 2 of them have been fixed since. This leaves 13: has patch or Ubuntu fix: matplotlib2 patsy python-apptools scikit-learn may need more extensive work: cnvkit python-feather-format python-skbio

Bug#942106: python3.8 / pandas py2removal

2019-11-10 Thread Rebecca N. Palmer
mdp isn't in testing either, but if you're using a policy of "no py2removals that break packages in testing", tnseq-transit (Depends: statsmodels) and possibly stimfit (Recommends: pandas) need to be done as well. Those are both thought to need new upstream versions. (patsy isn't a leaf packa

Bug#938444: pymvpa2: Python2 removal in sid/bullseye

2019-11-10 Thread Rebecca N. Palmer
On 10/11/2019 13:45, Matthias Klose wrote: I'm preparing a NMU for scikit-learn, based on the new subminor upstream release 0.20.3 I don't know why Ubuntu has 0.20.3 and Debian only .2, but it doesn't look related to either python3.8 or py2removal: https://scikit-learn.org/0.20/whats_new.html

Bug#942106: python3.8 / pandas py2removal

2019-11-10 Thread Rebecca N. Palmer
I have uploaded pandas and statsmodels. On 10/11/2019 14:18, Matthias Klose wrote: https://people.debian.org/~doko/tmp/ The patsy one has a bug: as debian/tests/nosetests3 was a symlink to nosetests2, it should have deleted this link and renamed nosetests2 to nosetests3, not deleted nosetest

Bug#943923: it no longer exists Re: please stop build-depending on python-pandas

2019-11-10 Thread Rebecca N. Palmer
Control: severity -1 serious python-pandas has now been removed, so these packages are now BD-Uninstallable.

Bug#943924: pandas2?

2019-11-10 Thread Rebecca N. Palmer
Matthias disagrees: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=942106#73 It should be technically straightforward to make a pandas2 package (start from the debian-v023 branch and drop the python2 part), but you'd have to upload it because DMs can't upload NEW packages. (Only pandas wou

Bug#943925: patch - feather / pandas 0.25

2019-11-11 Thread Rebecca N. Palmer
0.25 Author: Rebecca N. Palmer Bug-Debian: https://bugs.debian.org/943925 Forwarded: not-needed (upstream have switched to pyarrow) --- python-feather-format-0.3.1+dfsg1.orig/feather/api.py +++ python-feather-format-0.3.1+dfsg1/feather/api.py @@ -15,6 +15,7 @@ import six from distutils.version

Bug#943924: reducing matplotlib2 build-depends.

2019-11-12 Thread Rebecca N. Palmer
By itself, removing those dependencies reduces the big tangle [0] from 148 packages to 141, the freed ones being: ipywidgets pyqt5 pep8 autopep8 xcffib xlwt cairocffi. (Note that "not in a tangle" means "no *circular* dependencies", *not* "leaf / can be removed immediately".) There may also b

Bug#937330: Remove pyoptical from Debian, [or?] upgrade psychopy to latest upstream to enable Pandas migration

2019-11-13 Thread Rebecca N. Palmer
psychopy isn't blocking pandas' testing migration because psychopy already isn't in testing (for reasons unrelated to py2removal). Upstream say it's now Python 3 compatible [0], but I haven't tried to fix its other problems. The ones that are blocking pandas [1] are python-skbio, python-feath

Bug#944042: broken with pandas 0.25

2019-11-13 Thread Rebecca N. Palmer
Control: severity -1 serious pandas 0.25 is now in unstable. The explicit Breaks: (causing the current "badpkg" status) end on the next upload of these packages, but the underlying issues (see above log) also need to be dealt with.

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

2019-11-14 Thread Rebecca N. Palmer
Ubuntu have dask 2.6.0 and fsspec, but still have a few autopkgtest failures: https://people.canonical.com/~ubuntu-archive/proposed-migration/update_excuses.html dask itself - looks like trying to use a nonexistent temporary directory pyfftw - looks like a test treating a new (unexpected) warni

Bug#926215: dune-pdelab: FTBFS with gcc 8.3

2019-05-05 Thread Rebecca N. Palmer
Control: tags -1 moreinfo It works for me, in both sid and buster cowbuilder chroots. Has it been fixed (the version of dune-pdelab hasn't changed, but the bug may have been elsewhere), or is it hardware/setup dependent?

Bug#888733: hyantesite: test failures on most architectures

2019-05-05 Thread Rebecca N. Palmer
Control: found -1 1.3.0-1.1 Control: retitle -1 hyantesite: test failures on most architectures At least on i386, this *isn't* just -0 vs +0 and last-digit rounding errors: in test 'family' (which applies a cone smoother to a regularly spaced set of spikes), centre points drop from highest to 0

Bug#926180: scilab: FTBFS on all

2019-05-05 Thread Rebecca N. Palmer
Control: tags -1 moreinfo I don't see this in a DIST=sid cowbuilder --build scilab_6.0.1-9.dsc --binary-indep build: has it been fixed (the -8 to -9 changelog suggests not), or does my setup allow enough graphics access to not have it? If the bug does still exist, can someone affected try add

Bug#927808: gmsh: FTBFS in buster (/usr/include/occt/Standard_Version.hxx cannot be read)

2019-05-05 Thread Rebecca N. Palmer
I agree that this is probably fixed in unstable, but as we're in freeze and unstable has a new upstream version, that won't fix it in buster. The fix was probably removing the line -DOCC_INC:STRING="/usr/include/occt" \ from debian/rules (commit 3556b0a, but please don't include the reformattin

Bug#919216: lrslib: Tree truncated at depth -1 on i386

2019-05-05 Thread Rebecca N. Palmer
As a fixed version is now in unstable and testing, I suggest closing this bug.

Bug#926047: octave: missing licenses

2019-05-05 Thread Rebecca N. Palmer
Control: found -1 4.4.1-5 The /etc/fonts/* issue (but not the out-of-date year) also applies to testing/unstable. As they appear to be an already-unused embedded copy from fonts-freefont (GPL-3 + font exception), and are the .otf not the preferred source .sfd, it may be best to repack the so

Bug#888733: hyantesite: test failures on most architectures

2019-05-05 Thread Rebecca N. Palmer
Control: tags -1 upstream (probably - I haven't actually tried) The missing centre points (0 instead of max at distance=0) are probably due to rounding error in the great circle distance (src/hyantes_run.c:80): equal coordinates should give tmp=acos(1)=0, but rounding error might make it acos(

Bug#888733: hyantesite: test failures on most architectures

2019-05-05 Thread Rebecca N. Palmer
However, the "obvious" fix seems to break ra_pareto, for unknown reasons. It's not this change that breaks ra_pareto: it was _already_ totally broken on i386 (all-0s output). Not using the name 'tmp' for two different variables gives some nonzero output: --- a/src/hyantes.c +++ b/src/hyant

Bug#888733: hyantesite: test failures on most architectures

2019-05-06 Thread Rebecca N. Palmer
It looks like ra_pareto was also broken on amd64 (probably for the same "two variables with the same name" reason, though I haven't tested this), giving a constant output within its range circle, and the ra_pareto.out reference used that broken version (it's identical to ra_disk.out). Hence,

Bug#925555: linux-image-4.19.0-4-amd64: [regression] No graphics on some IvyBridge / Haswell systems

2019-05-06 Thread Rebecca N. Palmer
Control: forcemerge -1 926193 Control: tags -1 upstream patch Control: retitle -1 linux-image-4.19.0-4-amd64: [regression] No graphics on some IvyBridge / Haswell systems Control: forwarded -1 https://bugs.freedesktop.org/show_bug.cgi?id=109806 (Summary of the merged bugs - I haven't tried any of

Bug#926180: scilab: FTBFS on all - baseline violation?

2019-05-13 Thread Rebecca N. Palmer
Given that the error is "Illegal instruction", and reproducibly happens on x86-bm-01 and not the other machines we've tried, could it be something assuming CPU features more recent than the amd64 baseline? If so, it's not obvious where: scilab does contain some C/C++ code (as well as Java), bu

Bug#927808: gmsh: FTBFS in buster (/usr/include/occt/Standard_Version.hxx cannot be read)

2019-05-17 Thread Rebecca N. Palmer
I think this should be a t-p-u upload not a +really, but I'd wait for release team to decide (see #929108). https://www.debian.org/doc/manuals/developers-reference/ch05.en.html#t-p-u

Bug#888733: hyantesite: test failures on most architectures

2019-05-20 Thread Rebecca N. Palmer
On 19/05/2019 18:15, Andreas Tille wrote: So what is the plan to fix this bug? Create new references to craft a valid test or ignore these tests? ...or decide that something that's abandoned and doesn't follow its documentation (even after the above fixes) doesn't belong in Debian stable and

Bug#926180: scilab: FTBFS on all

2019-05-20 Thread Rebecca N. Palmer
Control: found -1 6.0.1-10 (I suggest opening a new bug for the 6.0.2 issues: as noted above, that probably won't be accepted for buster even if we do get it to build.) Running what I think is the relevant step in a debugger: * Go to the top level directory of a _built_ source tree (i.e. one t

Bug#926180: scilab: FTBFS on all

2019-05-23 Thread Rebecca N. Palmer
* valgrind: reports a _lot_ of invalid memory accesses, It now looks like these are actually "valgrind doesn't understand Java memory allocation" - 'valgrind jdb' and 'valgrind jar' also report large numbers of "invalid" accesses. However, the segfaults are still evidence that this is memory

Bug#926180: scilab: FTBFS on all

2019-05-25 Thread Rebecca N. Palmer
On 23/05/2019 22:35, Rebecca N. Palmer wrote: It now looks like these are actually "valgrind doesn't understand Java memory allocation" The Valgrind documentation says --smc-check=all should fix this, but it doesn't. Ubuntu has a 6.0.2 package that builds in Debian, b

Bug#948563: beignet: some operations crash with LLVM 8+

2020-01-10 Thread Rebecca N. Palmer
Package: beignet-opencl-icd Version: 1.3.2-7 Severity: important Control: block 947435 by -1 (The above version only exists in Salsa; earlier versions won't build at all with LLVM 8+.) When beignet is built with LLVM 8+, some operations assert-fail: compiler_rotate()ASSERTION FAILED: Unsuppor

Bug#948563: beignet and LLVM 8+

2020-01-11 Thread Rebecca N. Palmer
Progress so far: compiler_rotate()ASSERTION FAILED: Unsupported intrinsics The intrinsic in question is an fshl (funnel shift left). I suspect this issue appeared because LLVM started optimizing rotates to this intrinsic: https://github.com/llvm/llvm-project/commit/654e6aabb9f25d0d0fbad19

Bug#948563: [PATCH 3/3] Fix rotate and subgroup crashes with LLVM 8+

2020-01-12 Thread Rebecca N. Palmer
Block rotate to fshl optimization, as we don't implement fshl. Set reg for physical registers to avoid out-of-range index crash. Signed-off-by: Rebecca N. Palmer --- (where patches 1 and 2 are the LLVM 8/9 ones from https://svnweb.freebsd.org/ports/head/lang/beignet/files/ ; see also

Bug#790925: not fixed - pandas: HDF I/O crashes on armhf - bus error

2020-03-01 Thread Rebecca N. Palmer
Control: reopen -1 Control: found -1 0.25.3+dfsg-6 Control: retitle -1 pandas: HDF I/O crashes on armhf - bus error test_append_frame_column_oriented does still exist - it was being silently skipped by -m "not single". Having removed that, it again crashes on armhf, as do TestHDFStore.test_enc

Bug#877419: pandas: some I/O tests (hdf5, Stata) fail on non-x86

2020-03-01 Thread Rebecca N. Palmer
Re-enabling these tests found that this bug (which is probably actually multiple bugs) _does_ still exist, on big-endian systems and _possibly_ others. pandas now (0.25.3+dfsg-7) warns the user when these are used on any non-x86 system. ** Stata format - All big-endian (s390x, hppa, ppc64):

Bug#953014: grep-dctrl -w without -F misses the last package of each field

2020-03-02 Thread Rebecca N. Palmer
Package: dctrl-tools Version: 2.24-3 Control: tags -1 patch Example: grep-dctrl -w -s Package "python3-pandas" /var/lib/apt/lists/*_debian_dists_sid_main_source_Sources doesn't find influxdb-python, jsonpickle, poretools and tqdm, while the same without the -w does. (This caused me to be unawa

Bug#950430: more rdeps testing

2020-03-03 Thread Rebecca N. Palmer
These packages were missing from my old packages-to-test list due to #953014: influxdb-python jsonpickle psychopy tqdm They have now been tested: jsonpickle - OK influxdb-python (#950063), tqdm - already broken (probably by the 0.23 -> 0.25 transition, where the same bug left them off the to-te

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. [0]

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 wo

Bug#946761: llvm-9-dev: symlinks to but doesn't depend on libclang-cpp9

2019-12-15 Thread Rebecca N. Palmer
Package: llvm-9-dev Version: 1:9.0.0-4 Control: tags -1 patch llvm-9-dev provides symlinks for both libclang-cpp.so (libclang-cpp9) and libclang.so (libclang1-9), but depends on libclang1-9 and not libclang-cpp9.

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 dep

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 FTB

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

2020-01-28 Thread Rebecca N. Palmer
ax 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(),

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#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#950429: transition: statsmodels 0.10 -> 0.11

2020-02-01 Thread Rebecca N. Palmer
Package: python3-statsmodels Version: 0.10.2-1 Severity: wishlist The upstream release notes https://www.statsmodels.org/stable/release/version0.11.html don't specifically list API breaks. The one item that is _obviously_ an API break (removal of DynamicVAR) is something codesearch says we don'

<    2   3   4   5   6   7   8   9   10   11   >