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pythonPackages.h5py: 2.7.1 -> 2.8.0 #41581

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merged 1 commit into from Jun 7, 2018

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jluttine
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@jluttine jluttine commented Jun 6, 2018

Motivation for this change

Upgrade h5py.

(I'm running the nox-review at the moment but I guess it can take a very long time.)

Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
  • Built on platform(s)
    • NixOS
    • macOS
    • other Linux distributions
  • Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
  • Tested compilation of all pkgs that depend on this change using nix-shell -p nox --run "nox-review wip"
  • Tested execution of all binary files (usually in ./result/bin/)
  • Fits CONTRIBUTING.md.

@lsix
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lsix commented Jun 6, 2018

Looks good to me. Lets see how the build goes.

@GrahamcOfBorg build pythonPackages.h5py python3Packages.h5py

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Success on x86_64-linux (full log)

Attempted: pythonPackages.h5py, python3Packages.h5py

Partial log (click to expand)

./h5py/api_types_ext.pxd: cannot find cimported module 'mpi4py.MPI'
/build/h5py-2.8.0/h5py/h5p.pyx: cannot find cimported module 'mpi4py.libmpi'
/build/h5py-2.8.0/h5py/h5p.pyx: cannot find cimported module 'mpi4py.mpi_c'
....................................s................x.........................s.........................................x....................................s...s......ss.........................sss.....................................................ss....................ssssss...................................................................x....x.........................x......x.................................................ssss.....s............
----------------------------------------------------------------------
Ran 457 tests in 0.676s

OK (skipped=22, expected failures=6)
/nix/store/66qzf441sb63nnfq8jv5lf4prm4qsj5z-python2.7-h5py-2.8.0
/nix/store/vw4mds5q0d957acwjssvfwnm1bfiz8ji-python3.6-h5py-2.8.0

@jluttine
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jluttine commented Jun 6, 2018

I ran nox-review but some packages failed to build. Not sure if they were failing anyway before this change...

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Failure on aarch64-linux (full log)

Attempted: pythonPackages.h5py, python3Packages.h5py

Partial log (click to expand)

khavkine1.cpp: In function ‘PyObject* __pyx_f_9khavkine1___pyx_unpickle_T__set_state(__pyx_obj_9khavkine1_T*, PyObject*)’:
khavkine1.cpp:1914:7: warning: ‘__pyx_t_2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   int __pyx_t_2[1];
       ^~~~~~~~~
==============================
building of '/nix/store/n3pfmiijz0b0gz8kv518ns8k9hmp32j2-python2.7-Cython-0.28.2.drv' timed out after 3600 seconds
building of '/nix/store/zv7lw4zimiab12abjx26c7l6djv037mq-python3.6-Cython-0.28.2.drv' timed out after 3600 seconds
cannot build derivation '/nix/store/fxjqw37jvzhf2qj4b1l8clib5xmn7swv-python2.7-h5py-2.8.0.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/m9b6z19p9aj8rx47yhm88szv4pcsymab-python3.6-h5py-2.8.0.drv': 1 dependencies couldn't be built
error: build of '/nix/store/fxjqw37jvzhf2qj4b1l8clib5xmn7swv-python2.7-h5py-2.8.0.drv', '/nix/store/m9b6z19p9aj8rx47yhm88szv4pcsymab-python3.6-h5py-2.8.0.drv' failed

@@ -30,18 +30,13 @@ in buildPythonPackage rec {

preBuild = if mpiSupport then "export CC=${mpi}/bin/mpicc" else "";

checkInputs = optional (isPy26 || isPy27) unittest2;
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isPy26 test is obsolete, we don't have python26 in nixpkgs anymore.

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Ok, removed.

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xeji commented Jun 7, 2018

@GrahamcOfBorg build pythonPackages.h5py python3Packages.h5py

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Success on x86_64-darwin (full log)

Attempted: pythonPackages.h5py, python3Packages.h5py

Partial log (click to expand)

./h5py/api_types_ext.pxd: cannot find cimported module 'mpi4py.MPI'
/private/tmp/nix-build-python3.6-h5py-2.8.0.drv-0/h5py-2.8.0/h5py/h5p.pyx: cannot find cimported module 'mpi4py.libmpi'
/private/tmp/nix-build-python3.6-h5py-2.8.0.drv-0/h5py-2.8.0/h5py/h5p.pyx: cannot find cimported module 'mpi4py.mpi_c'
.....................................................x.........................s.........................................x....................................s...s......ss.......................................................................................................ssssss...................................................................x....x.........................x......x.................................................ssss.....s............
----------------------------------------------------------------------
Ran 457 tests in 0.605s

OK (skipped=16, expected failures=6)
/nix/store/fh3rafkb5m1jzlkzgn5adk2ww8y0072c-python2.7-h5py-2.8.0
/nix/store/d5lkd0gjrch95vd75nf3c84zycj06b95-python3.6-h5py-2.8.0

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Success on x86_64-linux (full log)

Attempted: pythonPackages.h5py, python3Packages.h5py

Partial log (click to expand)

./h5py/api_types_ext.pxd: cannot find cimported module 'mpi4py.MPI'
/build/h5py-2.8.0/h5py/h5p.pyx: cannot find cimported module 'mpi4py.libmpi'
/build/h5py-2.8.0/h5py/h5p.pyx: cannot find cimported module 'mpi4py.mpi_c'
....................................s................x.........................s.........................................x....................................s...s......ss......................ss.sss.....................................................ss..........................sss................................................................x....x.........................x......x.................................................ssss.....s............
----------------------------------------------------------------------
Ran 457 tests in 0.575s

OK (skipped=21, expected failures=6)
/nix/store/66qzf441sb63nnfq8jv5lf4prm4qsj5z-python2.7-h5py-2.8.0
/nix/store/vw4mds5q0d957acwjssvfwnm1bfiz8ji-python3.6-h5py-2.8.0

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Failure on aarch64-linux (full log)

Attempted: pythonPackages.h5py, python3Packages.h5py

Partial log (click to expand)

                 from /nix/store/mw19w3iwk7dnww2m5qfnhzcm227nzbba-python2.7-numpy-1.14.3/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from extension_type_memoryview.cpp:580:
/nix/store/mw19w3iwk7dnww2m5qfnhzcm227nzbba-python2.7-numpy-1.14.3/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^~~~~~~
building of '/nix/store/29h5im265mc174afsf4qza8iqzv0svq0-python2.7-Cython-0.28.2.drv' timed out after 3600 seconds
cannot build derivation '/nix/store/cazda0cldk3bndp7gvylh059v9qazrqy-python2.7-h5py-2.8.0.drv': 1 dependencies couldn't be built
building of '/nix/store/zh4vgh550i8iypbhi305wavx1xdkcrv2-python3.6-Cython-0.28.2.drv' timed out after 3600 seconds
cannot build derivation '/nix/store/2d8q1xfkixzxqkizz0zpwm7xxbrwqw52-python3.6-h5py-2.8.0.drv': 1 dependencies couldn't be built
error: build of '/nix/store/2d8q1xfkixzxqkizz0zpwm7xxbrwqw52-python3.6-h5py-2.8.0.drv', '/nix/store/cazda0cldk3bndp7gvylh059v9qazrqy-python2.7-h5py-2.8.0.drv' failed

@dotlambda
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Edward and tflearn were broken before.

@dotlambda dotlambda merged commit 0b41fa3 into NixOS:master Jun 7, 2018
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5 participants