python-nipy failed to build from source in Fedora rawhide https://koji.fedoraproject.org/koji/taskinfo?taskID=28223023 For details on the mass rebuild see: https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild Please fix python-nipy at your earliest convenience and set the bug's status to ASSIGNED when you start fixing it. If the bug remains in NEW state for 8 weeks, python-nipy will be orphaned. Before branching of Fedora 30, python-nipy will be retired, if it still fails to build. For more details on the FTBFS policy, please visit: https://fedoraproject.org/wiki/Fails_to_build_from_source
Created attachment 1466483 [details] build.log
Created attachment 1466484 [details] root.log file root.log too big, will only attach last 32768 bytes
Created attachment 1466485 [details] state.log
(This is a mass bug update. Forgive me if things are not 100% accurate for this one.) At this moment, your package still requires Python 3.6. This will cause broken upgrades to Fedora 29. Please prioritize this rebuild. Let me know if you need help from the Python maintenance team figuring out why the package FTBFS. Consider orphaning the package if you don't have time for it. Consider retiring the package if upstream is dead and nothing depends on it in Fedora. If you are blocked by other packages (I've recently tried to set the Bugzilla metadata to reflect that), consider helping there as well. Thank you.
Not much to do here until nibabel is ready.
Note that I requested an approval from FESCo to retire leaf packages that still require Python 3.6 at beta freeze and their bugs are in NEW state. (This package might not necessarily be leaf at this moment, but I'm updating all the bugs in case the dependencies change in the meantime.) More info at https://pagure.io/fesco/issue/1965
Another bulk reminder. Please take action. Your package doesn't install on Fedora 29. Fix it or retire it.
(In reply to Miro Hrončok from comment #7) > Another bulk reminder. Please take action. Your package doesn't install on > Fedora 29. Fix it or retire it. So this is the one which needs update & also some workarounds for de-bundling. If you have time, I would appreciate if you fix this package. If not, I will get to this within a week or so.
I'm looking at this.
This bug appears to have been reported against 'rawhide' during the Fedora 29 development cycle. Changing version to '29'.
====================================================================== ERROR: nipy.algorithms.statistics.formula.tests.test_formula.test_nonlin1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3.7/site-packages/sympy/utilities/lambdify.py", line 750, in _subexpr expr = sympify(expr).xreplace(dummies_dict) AttributeError: 'list' object has no attribute 'xreplace' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/python3.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/builddir/build/BUILD/nipy-0.4.2/build/lib.linux-x86_64-3.7/nipy/algorithms/statistics/formula/tests/test_formula.py", line 422, in test_nonlin1 A = f.design(n, p) File "/builddir/build/BUILD/nipy-0.4.2/build/lib.linux-x86_64-3.7/nipy/algorithms/statistics/formula/formulae.py", line 838, in design self._setup_design() File "/builddir/build/BUILD/nipy-0.4.2/build/lib.linux-x86_64-3.7/nipy/algorithms/statistics/formula/formulae.py", line 774, in _setup_design self._f = lambdify(newparams + newterms, d, ("numpy")) File "/usr/lib/python3.7/site-packages/sympy/utilities/lambdify.py", line 456, in lambdify funcstr = funcprinter.doprint(funcname, args, expr) File "/usr/lib/python3.7/site-packages/sympy/utilities/lambdify.py", line 661, in doprint argstrs, expr = self._preprocess(args, expr) File "/usr/lib/python3.7/site-packages/sympy/utilities/lambdify.py", line 732, in _preprocess expr = self._subexpr(expr, {arg: dummy}) File "/usr/lib/python3.7/site-packages/sympy/utilities/lambdify.py", line 761, in _subexpr expr = [sub_expr(sympify(a), dummies_dict) for a in expr] File "/usr/lib/python3.7/site-packages/sympy/utilities/lambdify.py", line 761, in <listcomp> expr = [sub_expr(sympify(a), dummies_dict) for a in expr] NameError: name 'sub_expr' is not defined ====================================================================== ERROR: nipy.algorithms.statistics.formula.tests.test_formula.test_nonlin2 ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3.7/site-packages/sympy/utilities/lambdify.py", line 750, in _subexpr expr = sympify(expr).xreplace(dummies_dict) AttributeError: 'list' object has no attribute 'xreplace' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/python3.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/builddir/build/BUILD/nipy-0.4.2/build/lib.linux-x86_64-3.7/nipy/algorithms/statistics/formula/tests/test_formula.py", line 438, in test_nonlin2 assert_raises(ValueError, f.design, dz, p) File "/usr/lib64/python3.7/unittest/case.py", line 760, in assertRaises return context.handle('assertRaises', args, kwargs) File "/usr/lib64/python3.7/unittest/case.py", line 195, in handle callable_obj(*args, **kwargs) File "/builddir/build/BUILD/nipy-0.4.2/build/lib.linux-x86_64-3.7/nipy/algorithms/statistics/formula/formulae.py", line 838, in design self._setup_design() File "/builddir/build/BUILD/nipy-0.4.2/build/lib.linux-x86_64-3.7/nipy/algorithms/statistics/formula/formulae.py", line 774, in _setup_design self._f = lambdify(newparams + newterms, d, ("numpy")) File "/usr/lib/python3.7/site-packages/sympy/utilities/lambdify.py", line 456, in lambdify funcstr = funcprinter.doprint(funcname, args, expr) File "/usr/lib/python3.7/site-packages/sympy/utilities/lambdify.py", line 661, in doprint argstrs, expr = self._preprocess(args, expr) File "/usr/lib/python3.7/site-packages/sympy/utilities/lambdify.py", line 732, in _preprocess expr = self._subexpr(expr, {arg: dummy}) File "/usr/lib/python3.7/site-packages/sympy/utilities/lambdify.py", line 761, in _subexpr expr = [sub_expr(sympify(a), dummies_dict) for a in expr] File "/usr/lib/python3.7/site-packages/sympy/utilities/lambdify.py", line 761, in <listcomp> expr = [sub_expr(sympify(a), dummies_dict) for a in expr] NameError: name 'sub_expr' is not defined ====================================================================== FAIL: nipy.modalities.fmri.tests.test_aliases.test_implemented_function ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/builddir/build/BUILD/nipy-0.4.2/build/lib.linux-x86_64-3.7/nipy/modalities/fmri/tests/test_aliases.py", line 47, in test_implemented_function assert_true(hasattr(func, '_imp_')) AssertionError: False is not true ---------------------------------------------------------------------- Should be fixed by: https://src.fedoraproject.org/rpms/sympy/pull-request/2
https://src.fedoraproject.org/rpms/sympy/pull-request/2 https://src.fedoraproject.org/rpms/python-nipy/pull-request/2
Rawhide built. F29 fails on s390x but it didn't before, so I'm just gonna try couple of scratch builds to see if this is random or not.
OK, the failure is consistent. Here's what different on f29 and f30: -annobin.s390x 8.23-1.fc29 +annobin.s390x 8.24-1.fc30 -libssh.s390x 0.8.1-2.fc29 +libssh.s390x 0.8.1-3.fc30 -openblas.s390x 0.3.2-2.fc29 +openblas.s390x 0.3.2-1.fc29 -python3-sympy.noarch 1.2-2.fc29 +python3-sympy.noarch 1.2-2.fc30 -redhat-rpm-config.noarch 117-1.fc29 +redhat-rpm-config.noarch 118-1.fc30 The failure: ====================================================================== FAIL: nipy.algorithms.statistics.tests.test_utils.test_mahalanobis2 ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/builddir/build/BUILD/nipy-0.4.2/build/lib.linux-s390x-3.7/nipy/algorithms/statistics/tests/test_utils.py", line 41, in test_mahalanobis2 assert_almost_equal(mah, f_mah) File "/usr/lib64/python3.7/site-packages/numpy/testing/_private/utils.py", line 584, in assert_almost_equal raise AssertionError(_build_err_msg()) AssertionError: Arrays are not almost equal to 7 decimals ACTUAL: 7.404667856592318 DESIRED: 195.70625366732543 ====================================================================== FAIL: nipy.algorithms.utils.tests.test_pca.test_2D ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/builddir/build/BUILD/nipy-0.4.2/build/lib.linux-s390x-3.7/nipy/algorithms/utils/tests/test_pca.py", line 146, in test_2D assert_array_almost_equal((rimgs * rmse) + data_mean, data) File "/usr/lib64/python3.7/site-packages/numpy/testing/_private/utils.py", line 964, in assert_array_almost_equal precision=decimal) File "/usr/lib64/python3.7/site-packages/numpy/testing/_private/utils.py", line 780, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not almost equal to 6 decimals (mismatch 100.0%) x: array([-1.352913e+31, -8.484429e+29, -3.576206e+31, ..., 3.994668e+30, 3.352649e+30, 3.485307e+30]) y: array([0.71618 , 0.873804, 0.951521, ..., 0.189184, 0.386872, 0.361009]) ====================================================================== FAIL: nipy.modalities.fmri.fmristat.tests.test_FIAC.test_agreement ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/builddir/build/BUILD/nipy-0.4.2/build/lib.linux-s390x-3.7/nipy/modalities/fmri/fmristat/tests/test_FIAC.py", line 283, in test_agreement assert_true(np.greater(np.abs(cmax), 0.999)) AssertionError: False is not true ---------------------------------------------------------------------- Back to ASSIGNED.
I have no idea. skip that tests on s390x for now?
Proposed as a Freeze Exception for 29-beta by Fedora user churchyard using the blocker tracking app because: System with the old version installed cannot update to F29.
> skip that tests on s390x for now? working on that.
Could be related to the openblas change, -1 had z13-based kernel by mistake, we need the generic one (fixed in -2). With the latest upstream change also the generic kernel should provide the same results as the z13 (optimized) one.
Thanks. I've excluded the affected tests for now to build this. Building in https://koji.fedoraproject.org/koji/taskinfo?taskID=29366783
python-nipy-0.4.2-1.fc29 has been submitted as an update to Fedora 29. https://bodhi.fedoraproject.org/updates/FEDORA-2018-87d9b0eb0a
python-nipy-0.4.2-1.fc29 has been pushed to the Fedora 29 testing repository. If problems still persist, please make note of it in this bug report. See https://fedoraproject.org/wiki/QA:Updates_Testing for instructions on how to install test updates. You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2018-87d9b0eb0a
The originally excluded nipy tests are passing on s390x with the fixed openblas-0.3.2-5.fc30 - https://koji.fedoraproject.org/koji/taskinfo?taskID=29375941
Discussed at 2018-09-10 freeze exception review meeting: https://meetbot-raw.fedoraproject.org/fedora-blocker-review/2018-09-10/f29-blocker-review.2018-09-10-16.01.html . Accepted (under the block vote at the end of the meeting) as a freeze exception issue as this can prevent upgrades working without the potentially-dangerous --allowerasing , and upgrades typically run without updates-testing so there is a benefit to pushing this stable for folks trying to upgrade at present. (Note: the openblas thing worries me a bit. Should we fix openblas for f29 too?)
python-nipy-0.4.2-1.fc29 has been pushed to the Fedora 29 stable repository. If problems still persist, please make note of it in this bug report.