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

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

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

2019-11-26 Thread Rebecca N. Palmer
Control: tags -1 pending This happened when python-statsmodels was removed in 0.10.1-1, and the documentation was hence moved from /usr/share/doc/python-statsmodels to /usr/share/doc/python-statsmodels-doc. 0.10.2-1 (in salsa) includes your suggested fix. 0.9.0-5 -> 0.10.2-1 works, but 0.9.

Bug#909439: version mismatch, the other way

2019-11-23 Thread Rebecca N. Palmer
On 23/11/2019 20:35, Paul Gevers wrote: Hi Rebecca, On 23-11-2019 15:33, Rebecca N. Palmer wrote: https://ci.debian.net/data/autopkgtest/testing/amd64/p/python-feather-format/3483361/log.gz appears to have the opposite problem: it finds the new source (-3), but as this had not yet been built

Bug#909439: version mismatch, the other way

2019-11-23 Thread Rebecca N. Palmer
https://ci.debian.net/data/autopkgtest/testing/amd64/p/python-feather-format/3483361/log.gz appears to have the opposite problem: it finds the new source (-3), but as this had not yet been built, it used the old binary (-2). The testing excuses pages for both pandas and python-feather-format c

Bug#942106: python3.8 / pandas py2removal

2019-11-22 Thread Rebecca N. Palmer
On 22/11/2019 17:06, Graham Inggs wrote: I scheduled statsmodels there, but it still fails. The error message points to joblib, which has just been uploaded (#942899): try again when the new version is available?

Bug#937330: Help with upgrading psychopy needed

2019-11-21 Thread Rebecca N. Palmer
This incompatibility is known upstream as https://github.com/psychopy/psychopy/issues/2189 but has no activity beyond declaring the version restriction. https://docs.pytest.org/en/latest/deprecations.html#pytest-namespace has a suggested replacement.

Bug#942106: python3.8 / pandas py2removal

2019-11-19 Thread Rebecca N. Palmer
The binNMUs (to add python3.8 support) of pandas and statsmodels failed. I think this will make them work (but haven't tried it): - Apply the (existing) #943418 fix to python-xlrd. - Build matplotlib, pandas and statsmodels in that order. (ben can't work this out because the declared dependen

Bug#942235: Adding Python 3.8 as a supported Python3 version

2019-11-18 Thread Rebecca N. Palmer
On 18/11/2019 07:07, Matthias Klose wrote: On 18.11.19 07:52, Alastair McKinstry wrote: So I've uploaded a python-xarray 0.14.0-2 which passes on python3.7. Its failing on python 3.8 but apparently due to pandas not ready on 3.8, so it should be ok to pass as the transition completes. I think

Bug#937657: Issue with numpy under Python 3.8

2019-11-16 Thread Rebecca N. Palmer
I think that just means "numpy hasn't yet been rebuilt for Python 3.8". (In Python modules that include a C extension, the .py files are shared but the C part is compiled separately for each Python version.) As there are ~500 modules requiring such a rebuild (https://release.debian.org/transit

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#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#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#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#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: 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#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#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#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
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#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#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#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#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#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#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#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

2019-11-03 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#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#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#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#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#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#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#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#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#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#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#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

2019-10-29 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

2019-10-28 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#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#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#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#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#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

2019-10-26 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#943169: this is already py3k-only

2019-10-24 Thread Rebecca N. Palmer
Control: retitle -1 matplotlib: has Python 2 Testsuite-Triggers A bot wrote: matplotlib 3.0.2-2 ['Testsuite-Triggers->python-matplotlib', 'Testsuite-Triggers->python-matplotlib-dbg', 'Testsuite-Triggers->python-numpy', 'Testsuite-Triggers->python-numpy-dbg', 'Testsuite-Triggers->python-qt4',

Bug#936870: libgpuarray: Python2 removal in sid/bullseye

2019-10-20 Thread Rebecca N. Palmer
On 20/10/2019 14:25, Drew Parsons wrote: http://sandrotosi.me/debian/py2removal/index.html, where src:libgpuarray shows with no dependencies, The 0 there is in the forward Depends column, not reverse depends (maybe the column order should be changed, given that the reverse depends column is

Bug#936870: libgpuarray: Python2 removal in sid/bullseye

2019-10-20 Thread Rebecca N. Palmer
The libgpuarray dependency chain is python-lasagne Depends python-theano Recommends python-pygpu (src:libgpuarray), and none of those have been uploaded recently. Did you mean to post this to a different package, or are you using a checking tool that assumes binary name = python-sourcename and

Bug#941309: node-browserify-lite: unreproducible dependency map order

2019-09-29 Thread Rebecca N. Palmer
Control: forwarded -1 https://github.com/andrewrk/browserify-lite/pull/13 Upstream pointed out that this doesn't escape special characters in file names; corrected version follows. Subject: Ease reproducible build author: Rebecca N. Palmer" Sort module list and dependency lists in o

Bug#941309: node-browserify-lite: unreproducible dependency map order

2019-09-28 Thread Rebecca N. Palmer
test was *not* done, as reprotest/disorderfs fails on my system (I apparently don't have a fuse group even though the fuse package is installed; I don't know why). Description: Ease reproducible build Sort module list and dependency lists in order to be reproducible Author: Re

Bug#940679: cython3: generated code does out of bounds reads in with-dict (subclass of) cdef class

2019-09-27 Thread Rebecca N. Palmer
Control: reassign -1 cython3 Control: affects -1 python3-pandas python3-skimage Control: tags -1 fixed-upstream Control: retitle -1: cython3: generated code does out of bounds reads in with-dict (subclass of) cdef class No, it is a proper Timedelta-sized space (144 bytes, not a _Timedelta's 128)

Bug#940679: pandas: random test crashes

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

Bug#940679: pandas: random test crashes

2019-09-23 Thread Rebecca N. Palmer
There's also a few more of these: https://salsa.debian.org/science-team/pandas/commit/c6fc5d5ccbec7ca833ca6d2556ab7013aff4b065 However, the above fix doesn't work: cdef attributes can't have default values.

Bug#940679: pandas: random test crashes

2019-09-22 Thread Rebecca N. Palmer
Control: tags -1 patch Running the test suite (of -7) under gdb a few times produced a crash in pandas/tests/indexes/interval/test_astype.py::TestDatetimelikeSubtype::test_astype_category[index4] (4 not 3). The trace points to Cython-generated C from _Timedelta._has_ns, which (among other th

Bug#940679: pandas: random test crashes

2019-09-21 Thread Rebecca N. Palmer
The ppc64 failure was this bug, specifically the pandas/tests/indexes/interval/test_astype.py::TestDatetimelikeSubtype::test_astype_category[index3] version. It was retried successfully. (The hppa failure is something else.) The "Build environment" section of the build log (i.e. the versions

Bug#940873: sphinx-gallery: circular Python 2 build-dependencies

2019-09-21 Thread Rebecca N. Palmer
Source: sphinx-gallery Version: 0.2.0-1 Control: tags -1 patch Control: block 934852 by -1 seaborn, matplotlib2 and sphinx-gallery form a cycle of Python 2 build-dependencies, which makes it impossible to drop Python 2 packages one at a time without breaking anything. (I am about to start a d

Bug#851525: RFP: pandas-datareader

2019-09-20 Thread Rebecca N. Palmer
Control: reassign -1 wnpp Control: retitle -1 RFP: pandas-datareader Control: severity -1 wishlist Control: affects -1 src:pandas You are correct; moving this to the standard place for new package requests. In the meantime, it can be installed from PyPI with: apt-get install python3-pip pip3 ins

Bug#940679: pandas: random test crashes

2019-09-20 Thread Rebecca N. Palmer
Control: tags -1 unreproducible Running just the affected test files (in installed -6) produced no failures in ~350 attempts. The build of -7 succeeded on amd64; it failed on ppc64, but as the log isn't available yet, I don't know if it's this bug. While both tests involve time-related dtyp

Bug#940679: pandas: FTBFS on amd64 - TestDatetimelikeSubtype::test_astype_category[index3] crash

2019-09-19 Thread Rebecca N. Palmer
Control: retitle -1 pandas: random test crashes You're right that there are multiple issues here. --- Random test crashes (this bug): tests/indexes/interval/test_astype.py::TestDatetimelikeSubtype::test_astype_category[index3] on amd64; worked when retried, also works here tests/reshape/test_t

Bug#940679: pandas: FTBFS on amd64 - TestDatetimelikeSubtype::test_astype_category[index3] crash

2019-09-18 Thread Rebecca N. Palmer
Source: pandas Version: 0.23.3+dfsg-6 Severity: serious https://buildd.debian.org/status/fetch.php?pkg=pandas&arch=amd64&ver=0.23.3%2Bdfsg-6&stamp=1568839095&raw=0 Was your local build on a different architecture, or must this be something random / hardware-or-environment-dependent / a very rec

Bug#937485: pymvpa2 Python 3

2019-09-14 Thread Rebecca N. Palmer
Upstream say Python 3 is supposed to work but that they don't test this: https://github.com/PyMVPA/PyMVPA/blob/master/doc/source/installation.rst#must-have This package has been RC-buggy (for unrelated reasons) for over a year without response, but is quite popular for a scientific package (popc

Bug#939303: matplotlib2: FTBFS unsatisfied b-d

2019-09-10 Thread Rebecca N. Palmer
Control: tags -1 patch The dependency chain involved is matplotlib2 -> python-mpltoolkits.basemap -> python-pyproj, python-pyshp where all but the first no longer exist as Python 2 packages (and pyproj has also moved to a Python 3 only new upstream version). Searching the code suggests that

Bug#938949: statsmodels: test failures on some architectures

2019-08-30 Thread Rebecca N. Palmer
Package: statsmodels Version: 0.9.0-3 Severity: serious Control: notfound -1 0.8.0-9 https://buildd.debian.org/status/package.php?p=statsmodels&suite=experimental This might actually be more than one bug. Some of the armhf ones look like #924036, but not all of them. This may be reduced to n

Bug#932664: gobby.debian.org: mismatched character encoding

2019-07-21 Thread Rebecca N. Palmer
Package: gobby Nonsense characters instead of (probably) bullet points in https://gobby.debian.org/export/debconf19/bof/Python

Bug#932629: piuparts.debian.org: stable2sid broken by buster release

2019-07-21 Thread Rebecca N. Palmer
Package: piuparts.debian.org Since the buster release, stable2sid seems to be failing everything with E: Repository 'http://mirror-ubc.debian.org/debian buster InRelease' changed its 'Suite' value from 'testing' to 'stable' e.g. https://piuparts.debian.org/stable2sid/fail/python3-statsmodels

Bug#932411: lintian: duplicate-files could suggest how to fix it

2019-07-18 Thread Rebecca N. Palmer
Package: lintian Version: 2.16.0 Severity: wishlist Control: tags -1 patch Based on https://wiki.debian.org/dedup.debian.net#Tips_for_reducing_duplication_in_packages How: jdupes is simpler, but rdfind+symlinks is currently more popular (8 vs 42 according to codesearch). This may be because

Bug#931540: transition: statsmodels 0.8 -> 0.9 or 0.10

2019-07-11 Thread Rebecca N. Palmer
0.9 in salsa is now buildable (but _not_ ready for upload). With this version installed: seaborn, tnseq-transit: build successful pymvpa2: the same FTBFS as with 0.8 (#931888) pandas only build-depends on statsmodels for documentation examples (run during build), and the others import (somewhe

Bug#931888: pymvpa2 FTBFS: test_assert_objectarray_equal / test_vector_alignment_find_rotation_illegal_inputs

2019-07-11 Thread Rebecca N. Palmer
Source: pymvpa2 Version: 2.6.5-1 Severity: serious This package FTBFS in sid (plain dpkg-buildpackage) with these test failures (which are different from the ones in #906399, but the same as the ones in reproducible-builds). This bug was found during statsmodels 0.9 transition testing, but al

Bug#931557: transition: pandas 0.23 -> 0.24

2019-07-07 Thread Rebecca N. Palmer
Source: pandas Version: 0.23.3+dfsg-3 Severity: wishlist (Posting here rather than debian-release as that is generally not used for interpreted language modules) Upstream have released 0.24.2. They are likely to release 0.25 soon, but I do *not* intend to go straight to that as it drops Pyth

Bug#931540: transition: statsmodels 0.8 -> 0.9 or 0.10

2019-07-07 Thread Rebecca N. Palmer
Source: statsmodels Version: 0.8.0-9 Severity: wishlist (Posting here rather than debian-release as that is generally not used for interpreted language modules) Upstream have released statsmodels 0.10.0. I am not yet sure whether to go straight for that or do 0.9.x first. The upstream rele

Bug#926180: scilab: FTBFS on all

2019-06-04 Thread Rebecca N. Palmer
Some more testing: * When run normally, or in gdb with "handle SIGSEGV nostop pass", 6.0.1 has the IllegalStateExceptions and undocumented macro warnings, 6.0.2 does not; both finish. * valgrind --smc-check=all crashes at about the same place as this bug (but with a segmentation fault instea

Bug#926180: scilab: FTBFS on all

2019-05-30 Thread Rebecca N. Palmer
Some further searching suggests that Java triggers and catches SIGSEGVs as part of normal operation, and hence is expected to not work under gdb without "handle SIGSEGV nostop pass". With this, both 6.0.1 and 6.0.2 don't crash in gdb, i.e. the crash in gdb probably isn't this bug. This sugges

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#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

2019-05-20 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#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#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#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#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#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#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

2019-05-05 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#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#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#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#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#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#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#924840: highwayhash: FTBFS - symbol missing

2019-04-07 Thread Rebecca N. Palmer
I do see this bug in both sid and mostly-buster (I haven't tried creating a new buster chroot). If only some people see this bug, but who sees it is reproducible, that could be a sign of another problem such as the package doing build-time hardware detection. (https://sources.debian.org/src/hi

Bug#924036: statsmodels: KalmanFilter wrong results on armhf

2019-03-10 Thread Rebecca N. Palmer
Control: retitle -1 statsmodels: KalmanFilter wrong results on armhf Control: found -1 0.9.0-2 Control: found -1 0.8.0-7 This is not a regression - it only looks new because the upstream tests weren't previously run. Also reported as https://bugs.launchpad.net/ubuntu/+source/statsmodels/+bug/1

Bug#923771: unblock: pandas/0.23.3+dfsg-3

2019-03-07 Thread Rebecca N. Palmer
Control: tags -1 - moreinfo Built on every release architecture, autopkgtest good. As discussed, please also give back statsmodels, as the new pandas should allow it to build.

Bug#923771: unblock pre-approval: pandas/0.23.3+dfsg-3

2019-03-06 Thread Rebecca N. Palmer
ataFrame. (Closes: #923707) + * Revert "Add documentation examples dependencies" to comply with +freeze policy. + + -- Rebecca N. Palmer Mon, 04 Mar 2019 21:59:43 + + pandas (0.23.3+dfsg-2) unstable; urgency=medium * Team upload. diff --git a/debian/control b/debian/control

Bug#923803: age: gdk-pixbuf/2.38.1+dfsg-1

2019-03-05 Thread Rebecca N. Palmer
(Not release team) Iain Lane wrote: I should have uploaded this with a higher urgency probably That wouldn't have done anything: urgencies have been ignored since soft freeze. some quite nice fixes Are any of them Important or higher? https://release.debian.org/buster/freeze_policy.html

Bug#923708: pandas: np.array @ Series acts the wrong way round

2019-03-04 Thread Rebecca N. Palmer
Source: pandas Version: 0.23.3+dfsg-2 Severity: important Control: tags -1 fixed-upstream patch np.array @ Series actually calculates Series @ np.array, which is an error for nonsquare matrices and a *wrong answer* for square matrices. Fixed upstream by https://github.com/pandas-dev/pandas/pu

Bug#923707: statsmodels FTBFS: array |= frame now returns frame

2019-03-03 Thread Rebecca N. Palmer
Source: pandas Version: 0.23+dfsg-2 Severity: serious Control: affects -1 src:statsmodels Control: tags -1 patch The fix for #918206 (setting __array_priority__ to make np.array @ DataFrame work) is technically API breaking: in-place operators arr = np.array(...) df = pd.DataFrame(...) arr +=

Bug#804552: Pandas documentation package is empty

2019-02-26 Thread Rebecca N. Palmer
Also changing the ipython dependency to ipython3 fixes this. The documentation so built does contain some error messages in its example output (the examples are run during build), including attempts to download data (not allowed in Debian package builds), and attempts to use modules we don't b

Bug#804552: Pandas documentation package is empty

2019-02-25 Thread Rebecca N. Palmer
The build log ( https://launchpadlibrarian.net/412630196/buildlog_ubuntu-disco-amd64.pandas_0.23.3-1fakesync1ubuntu3_BUILDING.txt.gz ) suggests this is due to passing a PYTHONPATH to the just-built python-pandas, but not -lib or python3-, causing a failed import. However, the obvious way to fi

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