Control: tag -1 + moreinfo unreproducible On Sat, Aug 04, 2018 at 03:11:17PM +0000, Lumin wrote: > Package: autopkgtest > Version: 5.4.2 > Severity: serious > > the "su" command from util-linux breaks autopkgtest. The previous > working one comes from shadow. > > python-h5py-dbg is already the newest version (2.8.0-1). > python-h5py-dbg set to manually installed. > python-h5py is already the newest version (2.8.0-1). > python-h5py set to manually installed. > 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. > (Reading database ... 13709 files and directories currently installed.) > Removing autopkgtest-satdep (0) ... > autopkgtest [16:38:33]: test command1: set -e ; for py in $(pyversions -r > 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c > "import h5py; h5py.run_tests()" ; echo "Testing with $py-dbg:" ; $py-dbg -c > "import h5py; h5py.run_tests()" ; done > autopkgtest [16:38:33]: test command1: [----------------------- > su: user does not exist > autopkgtest [16:38:33]: test command1: -----------------------] > Unexpected error: > Traceback (most recent call last): > File "/usr/share/autopkgtest/lib/VirtSubproc.py", line 717, in mainloop > command() > File "/usr/share/autopkgtest/lib/VirtSubproc.py", line 646, in command > r = f(c, ce) > File "/usr/share/autopkgtest/lib/VirtSubproc.py", line 584, in cmd_copyup > copyupdown(c, ce, True) > File "/usr/share/autopkgtest/lib/VirtSubproc.py", line 469, in copyupdown > copyupdown_internal(ce[0], c[1:], upp) > File "/usr/share/autopkgtest/lib/VirtSubproc.py", line 494, in > copyupdown_internal > copyup_shareddir(sd[0], sd[1], dirsp, downtmp_host) > File "/usr/share/autopkgtest/lib/VirtSubproc.py", line 408, in > copyup_shareddir > shutil.copy(tb, host) > File "/usr/lib/python3.5/shutil.py", line 241, in copy > copyfile(src, dst, follow_symlinks=follow_symlinks) > File "/usr/lib/python3.5/shutil.py", line 120, in copyfile > with open(src, 'rb') as fsrc: > FileNotFoundError: [Errno 2] No such file or directory: > '/var/run/schroot/mount/unstable-amd64-debomatic-98e10886-4014-46ea-a35e-37ffe71bdcf3/tmp/autopkgtest.mZ5fp7/command1-stdout' > autopkgtest [16:38:34]: ERROR: testbed failure: unexpected eof from the > testbed
Are you sure you saw this with autopkgtest 5.4.2? This bug was present 5.4.1, but explicitly fixed in 5.4.2. See the attached log for an attempt I just made at reproducing this. The tests fail but autopkgtest itself works as expected.
autopkgtest [13:26:52]: version 5.4.2 autopkgtest [13:26:52]: host lemur; command line: /usr/bin/autopkgtest --apt-upgrade --log-file /tmp/log -B h5py -- lxc --sudo autopkgtest-unstable-amd64 autopkgtest: WARNING: running as root in testbed, because no normal user could be determined autopkgtest [13:27:04]: @@@@@@@@@@@@@@@@@@@@ test bed setup Get:1 http://deb.debian.org/debian unstable InRelease [233 kB] Get:2 http://deb.debian.org/debian unstable/non-free Sources.diff/Index [27.8 kB] Get:3 http://deb.debian.org/debian unstable/main Sources.diff/Index [27.9 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:5 http://deb.debian.org/debian unstable/contrib amd64 Packages.diff/Index [27.8 kB] Get:6 http://deb.debian.org/debian unstable/non-free Sources 2018-08-03-2013.11.pdiff [1,306 B] Get:7 http://deb.debian.org/debian unstable/non-free Sources 2018-08-04-0814.44.pdiff [665 B] Get:8 http://deb.debian.org/debian unstable/main Sources 2018-08-02-1416.04.pdiff [5,521 B] Get:7 http://deb.debian.org/debian unstable/non-free Sources 2018-08-04-0814.44.pdiff [665 B] Get:9 http://deb.debian.org/debian unstable/main Sources 2018-08-02-2015.39.pdiff [10.3 kB] Get:10 http://deb.debian.org/debian unstable/main Sources 2018-08-03-0208.52.pdiff [3,145 B] Get:11 http://deb.debian.org/debian unstable/main Sources 2018-08-03-0811.08.pdiff [15.6 kB] Get:12 http://deb.debian.org/debian unstable/main Sources 2018-08-03-1408.50.pdiff [39.5 kB] Get:13 http://deb.debian.org/debian unstable/main Sources 2018-08-03-2013.11.pdiff [8,876 B] Get:14 http://deb.debian.org/debian unstable/main Sources 2018-08-04-0211.02.pdiff [5,928 B] Get:15 http://deb.debian.org/debian unstable/main Sources 2018-08-04-0814.44.pdiff [11.7 kB] Get:16 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [55.3 kB] Get:17 http://deb.debian.org/debian unstable/main Sources 2018-08-04-1411.17.pdiff [12.2 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 Packages 2018-08-02-1416.04.pdiff [27.6 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 Packages 2018-08-02-2015.39.pdiff [16.0 kB] Get:17 http://deb.debian.org/debian unstable/main Sources 2018-08-04-1411.17.pdiff [12.2 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 Packages 2018-08-03-0208.52.pdiff [2,583 B] Get:21 http://deb.debian.org/debian unstable/main amd64 Packages 2018-08-03-0811.08.pdiff [13.7 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 Packages 2018-08-03-1408.50.pdiff [43.3 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 Packages 2018-08-03-2013.11.pdiff [33.6 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 Packages 2018-08-04-0211.02.pdiff [4,425 B] Get:25 http://deb.debian.org/debian unstable/main amd64 Packages 2018-08-04-0814.44.pdiff [20.5 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 Packages 2018-08-04-1411.17.pdiff [9,739 B] Get:27 http://deb.debian.org/debian unstable/contrib amd64 Packages 2018-08-04-0211.02.pdiff [460 B] Get:26 http://deb.debian.org/debian unstable/main amd64 Packages 2018-08-04-1411.17.pdiff [9,739 B] Get:27 http://deb.debian.org/debian unstable/contrib amd64 Packages 2018-08-04-0211.02.pdiff [460 B] Get:28 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [111 kB] Get:29 http://incoming.debian.org/debian-buildd buildd-unstable/main amd64 Packages [153 kB] Fetched 950 kB in 2s (491 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: bsdutils dbus fdisk gcc-8-base libblkid1 libdbus-1-3 libfdisk1 libgcc1 libmount1 libpcre3 libsmartcols1 libstdc++6 libuuid1 make mount util-linux 16 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 4,013 kB of archives. After this operation, 38.9 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian unstable/main amd64 bsdutils amd64 1:2.32-0.4 [117 kB] Get:2 http://deb.debian.org/debian unstable/main amd64 libuuid1 amd64 2.32-0.4 [77.6 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libblkid1 amd64 2.32-0.4 [190 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libfdisk1 amd64 2.32-0.4 [229 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libmount1 amd64 2.32-0.4 [201 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 libsmartcols1 amd64 2.32-0.4 [146 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 fdisk amd64 2.32-0.4 [168 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 util-linux amd64 2.32-0.4 [974 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 mount amd64 2.32-0.4 [164 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 gcc-8-base amd64 8.2.0-3 [186 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libstdc++6 amd64 8.2.0-3 [393 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libgcc1 amd64 1:8.2.0-3 [40.7 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 libpcre3 amd64 2:8.39-11 [341 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 dbus amd64 1.12.10-1 [233 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.12.10-1 [211 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 make amd64 4.2.1-1.2 [341 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 4,013 kB in 1s (7,975 kB/s) (Reading database ... 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Processing triggers for libc-bin (2.27-5) ... Processing triggers for systemd (239-7) ... Setting up libdbus-1-3:amd64 (1.12.10-1) ... Setting up dbus (1.12.10-1) ... A reboot is required to replace the running dbus-daemon. Please reboot the system when convenient. Processing triggers for libc-bin (2.27-5) ... autopkgtest [13:27:09]: rebooting testbed after setup commands that affected boot autopkgtest [13:27:29]: testbed running kernel: Linux 4.17.0-1-amd64 #1 SMP Debian 4.17.8-1 (2018-07-20) autopkgtest [13:27:29]: testbed dpkg architecture: amd64 autopkgtest [13:27:29]: @@@@@@@@@@@@@@@@@@@@ apt-source h5py Get:1 http://deb.debian.org/debian unstable/main h5py 2.7.1-2 (dsc) [2,668 B] Get:2 http://deb.debian.org/debian unstable/main h5py 2.7.1-2 (tar) [264 kB] Get:3 http://deb.debian.org/debian unstable/main h5py 2.7.1-2 (diff) [7,756 B] gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Mon 11 Sep 2017 10:14:27 AM UTC gpgv: using RSA key 8F58342BEABE1EF4379551FBB193770C186A1C7D gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./h5py_2.7.1-2.dsc autopkgtest [13:27:30]: testing package h5py version 2.7.1-2 autopkgtest [13:27:30]: build not needed autopkgtest [13:27:30]: test command1: preparing testbed Reading package lists... Building dependency tree... Reading state information... Correcting dependencies...Starting pkgProblemResolver with broken count: 0 Starting 2 pkgProblemResolver with broken count: 0 Done Done Starting pkgProblemResolver with broken count: 0 Starting 2 pkgProblemResolver with broken count: 0 Done The following additional packages will be installed: libaec0 libblas3 libgfortran5 libhdf5-100 liblapack3 libpython-all-dbg libpython-dbg libpython-stdlib libpython2-dbg libpython2-stdlib libpython2.7-dbg libpython2.7-minimal libpython2.7-stdlib libquadmath0 libsz2 mime-support python python-all python-all-dbg python-dbg python-h5py python-h5py-dbg python-minimal python-numpy python-numpy-dbg python-six python2 python2-dbg python2-minimal python2.7 python2.7-dbg python2.7-minimal Suggested packages: python2.7-gdbm-dbg python2.7-tk-dbg python-doc python-tk python-h5py-doc gcc gfortran python-dev python-nose python-numpy-doc python2-doc python2.7-doc python-gdbm-dbg python-tk-dbg binfmt-support Recommended packages: file The following NEW packages will be installed: libaec0 libblas3 libgfortran5 libhdf5-100 liblapack3 libpython-all-dbg libpython-dbg libpython-stdlib libpython2-dbg libpython2-stdlib libpython2.7-dbg libpython2.7-minimal libpython2.7-stdlib libquadmath0 libsz2 mime-support python python-all python-all-dbg python-dbg python-h5py python-h5py-dbg python-minimal python-numpy python-numpy-dbg python-six python2 python2-dbg python2-minimal python2.7 python2.7-dbg python2.7-minimal 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. 1 not fully installed or removed. Need to get 38.4 MB of archives. After this operation, 133 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian unstable/main amd64 libpython2.7-minimal amd64 2.7.15-3 [393 kB] Get:2 http://deb.debian.org/debian unstable/main amd64 python2.7-minimal amd64 2.7.15-3 [1,358 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 python2-minimal amd64 2.7.15-3 [41.3 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 python-minimal amd64 2.7.15-3 [20.9 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 mime-support all 3.61 [37.1 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 libpython2.7-stdlib amd64 2.7.15-3 [1,904 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 python2.7 amd64 2.7.15-3 [298 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 libpython2-stdlib amd64 2.7.15-3 [20.7 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 libpython-stdlib amd64 2.7.15-3 [20.7 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 python2 amd64 2.7.15-3 [41.5 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 python amd64 2.7.15-3 [22.7 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 python-all amd64 2.7.15-3 [1,044 B] Get:13 http://deb.debian.org/debian unstable/main amd64 libpython2.7-dbg amd64 2.7.15-3 [4,889 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 libpython2-dbg amd64 2.7.15-3 [20.8 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 libpython-dbg amd64 2.7.15-3 [20.7 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 libpython-all-dbg amd64 2.7.15-3 [1,184 B] Get:17 http://deb.debian.org/debian unstable/main amd64 python2.7-dbg amd64 2.7.15-3 [9,536 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 python2-dbg amd64 2.7.15-3 [1,268 B] Get:19 http://deb.debian.org/debian unstable/main amd64 python-dbg amd64 2.7.15-3 [1,252 B] Get:20 http://deb.debian.org/debian unstable/main amd64 python-all-dbg amd64 2.7.15-3 [1,068 B] Get:21 http://deb.debian.org/debian unstable/main amd64 libquadmath0 amd64 8.2.0-3 [133 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 8.2.0-3 [583 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.8.0-1+b1 [148 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.8.0-1+b1 [2,112 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 python-numpy amd64 1:1.14.5-1+b1 [2,005 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 python-six all 1.11.0-2 [15.1 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.0.2-1 [20.1 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.0.2-1 [6,676 B] Get:29 http://deb.debian.org/debian unstable/main amd64 libhdf5-100 amd64 1.10.0-patch1+docs-4+b2 [1,266 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 python-h5py amd64 2.7.1-2 [683 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 python-numpy-dbg amd64 1:1.14.5-1+b1 [8,059 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 python-h5py-dbg amd64 2.7.1-2 [4,762 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 38.4 MB in 0s (125 MB/s) Selecting previously unselected package libpython2.7-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12101 files and directories currently installed.) Preparing to unpack .../0-libpython2.7-minimal_2.7.15-3_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.15-3) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../1-python2.7-minimal_2.7.15-3_amd64.deb ... Unpacking python2.7-minimal (2.7.15-3) ... Selecting previously unselected package python2-minimal. 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Preparing to unpack .../8-libpython-stdlib_2.7.15-3_amd64.deb ... Unpacking libpython-stdlib:amd64 (2.7.15-3) ... Setting up libpython2.7-minimal:amd64 (2.7.15-3) ... Setting up python2.7-minimal (2.7.15-3) ... Setting up python2-minimal (2.7.15-3) ... Selecting previously unselected package python2. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12885 files and directories currently installed.) Preparing to unpack .../python2_2.7.15-3_amd64.deb ... Unpacking python2 (2.7.15-3) ... Setting up python-minimal (2.7.15-3) ... Selecting previously unselected package python. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12918 files and directories currently installed.) Preparing to unpack .../00-python_2.7.15-3_amd64.deb ... Unpacking python (2.7.15-3) ... Selecting previously unselected package python-all. Preparing to unpack .../01-python-all_2.7.15-3_amd64.deb ... Unpacking python-all (2.7.15-3) ... 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Setting up libblas3:amd64 (3.8.0-1+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up python2.7-dbg (2.7.15-3) ... Setting up libpython2-stdlib:amd64 (2.7.15-3) ... Setting up liblapack3:amd64 (3.8.0-1+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libpython2-dbg:amd64 (2.7.15-3) ... Setting up python2 (2.7.15-3) ... Setting up libpython-stdlib:amd64 (2.7.15-3) ... Setting up libpython-dbg:amd64 (2.7.15-3) ... Setting up libpython-all-dbg:amd64 (2.7.15-3) ... Setting up python (2.7.15-3) ... Setting up python2-dbg (2.7.15-3) ... Setting up python-numpy (1:1.14.5-1+b1) ... Setting up python-six (1.11.0-2) ... Setting up python-dbg (2.7.15-3) ... Setting up python-all (2.7.15-3) ... Setting up python-h5py (2.7.1-2) ... Setting up python-numpy-dbg:amd64 (1:1.14.5-1+b1) ... Setting up python-all-dbg (2.7.15-3) ... Setting up python-h5py-dbg (2.7.1-2) ... Setting up autopkgtest-satdep (0) ... Processing triggers for libc-bin (2.27-5) ... (Reading database ... 13867 files and directories currently installed.) Removing autopkgtest-satdep (0) ... autopkgtest [13:27:37]: test command1: set -e ; for py in $(pyversions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import h5py; h5py.run_tests()" ; echo "Testing with $py-dbg:" ; $py-dbg -c "import h5py; h5py.run_tests()" ; done autopkgtest [13:27:37]: test command1: [----------------------- Testing with python2.7: /usr/lib/python2.7/dist-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters .....................................................x...................................................................x....................................s...s......ss.....................ss...................................................................................sss...........................F..................................x....x........................x.....x.................................................ssss.........F.... ====================================================================== FAIL: test_out_of_order_offsets (h5py.tests.old.test_h5t.TestCompound) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.7/dist-packages/h5py/tests/old/test_h5t.py", line 61, in test_out_of_order_offsets self.assertEqual(tid.dtype, expected_dtype) AssertionError: dtype({'names':['f1','f3','f2'], 'formats':['<f4','<f8','<i4'], 'offsets':[0,8,16], 'itemsize':20}) != dtype({'names':['f1','f2','f3'], 'formats':['<f4','<i4','<f8'], 'offsets':[0,16,8], 'itemsize':20}) ====================================================================== FAIL: test_out_of_order_offsets (h5py.tests.hl.test_datatype.TestOffsets) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.7/dist-packages/h5py/tests/hl/test_datatype.py", line 198, in test_out_of_order_offsets self.assertArrayEqual(fd['data'], data) File "/usr/lib/python2.7/dist-packages/h5py/tests/common.py", line 124, in assertArrayEqual "Dtype mismatch (%s vs %s)%s" % (dset.dtype, arr.dtype, message) AssertionError: Dtype mismatch ({'names':['f1','f3','f2'], 'formats':['<f4','<f8','<i4'], 'offsets':[0,8,16], 'itemsize':20} vs {'names':['f1','f2','f3'], 'formats':['<f4','<i4','<f8'], 'offsets':[0,16,8], 'itemsize':20}) ---------------------------------------------------------------------- Ran 446 tests in 0.617s FAILED (failures=2, skipped=13, expected failures=6) Testing with python2.7-dbg: /usr/lib/python2.7/dist-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters .....................................................x...................................................................x....................................s...s......ss.....................ss...................................................................................sss...........................F..................................x....x........................x.....x.................................................ssss.........F.... ====================================================================== FAIL: test_out_of_order_offsets (h5py.tests.old.test_h5t.TestCompound) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.7/dist-packages/h5py/tests/old/test_h5t.py", line 61, in test_out_of_order_offsets self.assertEqual(tid.dtype, expected_dtype) AssertionError: dtype({'names':['f1','f3','f2'], 'formats':['<f4','<f8','<i4'], 'offsets':[0,8,16], 'itemsize':20}) != dtype({'names':['f1','f2','f3'], 'formats':['<f4','<i4','<f8'], 'offsets':[0,16,8], 'itemsize':20}) ====================================================================== FAIL: test_out_of_order_offsets (h5py.tests.hl.test_datatype.TestOffsets) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.7/dist-packages/h5py/tests/hl/test_datatype.py", line 198, in test_out_of_order_offsets self.assertArrayEqual(fd['data'], data) File "/usr/lib/python2.7/dist-packages/h5py/tests/common.py", line 124, in assertArrayEqual "Dtype mismatch (%s vs %s)%s" % (dset.dtype, arr.dtype, message) AssertionError: Dtype mismatch ({'names':['f1','f3','f2'], 'formats':['<f4','<f8','<i4'], 'offsets':[0,8,16], 'itemsize':20} vs {'names':['f1','f2','f3'], 'formats':['<f4','<i4','<f8'], 'offsets':[0,16,8], 'itemsize':20}) ---------------------------------------------------------------------- Ran 446 tests in 0.896s FAILED (failures=2, skipped=13, expected failures=6) autopkgtest [13:27:39]: test command1: -----------------------] autopkgtest [13:27:39]: test command1: - - - - - - - - - - results - - - - - - - - - - command1 PASS autopkgtest [13:27:39]: test command2: preparing testbed autopkgtest [13:27:54]: @@@@@@@@@@@@@@@@@@@@ test bed setup Get:1 http://deb.debian.org/debian unstable InRelease [233 kB] Get:2 http://deb.debian.org/debian unstable/non-free Sources.diff/Index [27.8 kB] Get:3 http://deb.debian.org/debian unstable/main Sources.diff/Index [27.9 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:5 http://deb.debian.org/debian unstable/contrib amd64 Packages.diff/Index [27.8 kB] Get:6 http://deb.debian.org/debian unstable/non-free Sources 2018-08-03-2013.11.pdiff [1,306 B] Get:7 http://deb.debian.org/debian unstable/non-free Sources 2018-08-04-0814.44.pdiff [665 B] Get:8 http://deb.debian.org/debian unstable/main Sources 2018-08-02-1416.04.pdiff [5,521 B] Get:9 http://deb.debian.org/debian unstable/main Sources 2018-08-02-2015.39.pdiff [10.3 kB] Get:10 http://deb.debian.org/debian unstable/main Sources 2018-08-03-0208.52.pdiff [3,145 B] Get:11 http://deb.debian.org/debian unstable/main Sources 2018-08-03-0811.08.pdiff [15.6 kB] Get:12 http://deb.debian.org/debian unstable/main Sources 2018-08-03-1408.50.pdiff [39.5 kB] Get:13 http://deb.debian.org/debian unstable/main Sources 2018-08-03-2013.11.pdiff [8,876 B] Get:14 http://deb.debian.org/debian unstable/main Sources 2018-08-04-0211.02.pdiff [5,928 B] Get:15 http://deb.debian.org/debian unstable/main Sources 2018-08-04-0814.44.pdiff [11.7 kB] Get:16 http://deb.debian.org/debian unstable/main Sources 2018-08-04-1411.17.pdiff [12.2 kB] Get:7 http://deb.debian.org/debian unstable/non-free Sources 2018-08-04-0814.44.pdiff [665 B] Get:16 http://deb.debian.org/debian unstable/main Sources 2018-08-04-1411.17.pdiff [12.2 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 Packages 2018-08-02-1416.04.pdiff [27.6 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 Packages 2018-08-02-2015.39.pdiff [16.0 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 Packages 2018-08-03-0208.52.pdiff [2,583 B] Get:20 http://deb.debian.org/debian unstable/main amd64 Packages 2018-08-03-0811.08.pdiff [13.7 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 Packages 2018-08-03-1408.50.pdiff [43.3 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 Packages 2018-08-03-2013.11.pdiff [33.6 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 Packages 2018-08-04-0211.02.pdiff [4,425 B] Get:24 http://deb.debian.org/debian unstable/main amd64 Packages 2018-08-04-0814.44.pdiff [20.5 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 Packages 2018-08-04-1411.17.pdiff [9,739 B] Get:26 http://deb.debian.org/debian unstable/contrib amd64 Packages 2018-08-04-0211.02.pdiff [460 B] Get:26 http://deb.debian.org/debian unstable/contrib amd64 Packages 2018-08-04-0211.02.pdiff [460 B] Get:25 http://deb.debian.org/debian unstable/main amd64 Packages 2018-08-04-1411.17.pdiff [9,739 B] Get:27 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [55.3 kB] Get:28 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [111 kB] Get:29 http://incoming.debian.org/debian-buildd buildd-unstable/main amd64 Packages [153 kB] Fetched 950 kB in 1s (958 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: bsdutils dbus fdisk gcc-8-base libblkid1 libdbus-1-3 libfdisk1 libgcc1 libmount1 libpcre3 libsmartcols1 libstdc++6 libuuid1 make mount util-linux 16 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 4,013 kB of archives. After this operation, 38.9 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian unstable/main amd64 bsdutils amd64 1:2.32-0.4 [117 kB] Get:2 http://deb.debian.org/debian unstable/main amd64 libuuid1 amd64 2.32-0.4 [77.6 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libblkid1 amd64 2.32-0.4 [190 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libfdisk1 amd64 2.32-0.4 [229 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libmount1 amd64 2.32-0.4 [201 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 libsmartcols1 amd64 2.32-0.4 [146 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 fdisk amd64 2.32-0.4 [168 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 util-linux amd64 2.32-0.4 [974 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 mount amd64 2.32-0.4 [164 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 gcc-8-base amd64 8.2.0-3 [186 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libstdc++6 amd64 8.2.0-3 [393 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libgcc1 amd64 1:8.2.0-3 [40.7 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 libpcre3 amd64 2:8.39-11 [341 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 dbus amd64 1.12.10-1 [233 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.12.10-1 [211 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 make amd64 4.2.1-1.2 [341 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 4,013 kB in 0s (96.0 MB/s) (Reading database ... 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Processing triggers for libc-bin (2.27-5) ... Processing triggers for systemd (239-7) ... Setting up libdbus-1-3:amd64 (1.12.10-1) ... Setting up dbus (1.12.10-1) ... A reboot is required to replace the running dbus-daemon. Please reboot the system when convenient. Processing triggers for libc-bin (2.27-5) ... autopkgtest [13:27:58]: rebooting testbed after setup commands that affected boot autopkgtest [13:28:11]: testbed dpkg architecture: amd64 Reading package lists... Building dependency tree... Reading state information... Correcting dependencies...Starting pkgProblemResolver with broken count: 0 Starting 2 pkgProblemResolver with broken count: 0 Done Done Starting pkgProblemResolver with broken count: 0 Starting 2 pkgProblemResolver with broken count: 0 Done The following additional packages will be installed: dh-python libaec0 libblas3 libgfortran5 libhdf5-100 liblapack3 libmpdec2 libpython3-all-dbg libpython3-dbg libpython3-stdlib libpython3.6-dbg libpython3.6-stdlib libpython3.7-dbg libpython3.7-minimal libpython3.7-stdlib libquadmath0 libsz2 mime-support python3 python3-all python3-all-dbg python3-dbg python3-distutils python3-h5py python3-h5py-dbg python3-lib2to3 python3-numpy python3-numpy-dbg python3-six python3.6 python3.6-dbg python3.7 python3.7-dbg python3.7-minimal Suggested packages: python3-doc python3-tk python3-venv python-h5py-doc gcc gfortran python-numpy-doc python3-dev python3-nose python3.6-venv python3.6-doc python3-gdbm-dbg python3-tk-dbg python3.7-venv python3.7-doc binfmt-support Recommended packages: file gdb The following NEW packages will be installed: dh-python libaec0 libblas3 libgfortran5 libhdf5-100 liblapack3 libmpdec2 libpython3-all-dbg libpython3-dbg libpython3-stdlib libpython3.6-dbg libpython3.6-stdlib libpython3.7-dbg libpython3.7-minimal libpython3.7-stdlib libquadmath0 libsz2 mime-support python3 python3-all python3-all-dbg python3-dbg python3-distutils python3-h5py python3-h5py-dbg python3-lib2to3 python3-numpy python3-numpy-dbg python3-six python3.6 python3.6-dbg python3.7 python3.7-dbg python3.7-minimal 0 upgraded, 34 newly installed, 0 to remove and 0 not upgraded. 1 not fully installed or removed. Need to get 104 MB of archives. After this operation, 357 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian unstable/main amd64 mime-support all 3.61 [37.1 kB] Get:2 http://deb.debian.org/debian unstable/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libpython3.6-stdlib amd64 3.6.6-1 [1,709 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 python3.6 amd64 3.6.6-1 [234 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.6.6-1 [19.8 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.6.6-1 [47.5 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 python3-lib2to3 all 3.6.6-1 [79.1 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 python3-distutils all 3.6.6-1 [144 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 dh-python all 3.20180723 [94.2 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libpython3.7-minimal amd64 3.7.0-4 [590 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 python3.7-minimal amd64 3.7.0-4 [1,727 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libpython3.7-stdlib amd64 3.7.0-4 [1,733 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 python3.7 amd64 3.7.0-4 [309 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.6.6-1 [1,060 B] Get:15 http://deb.debian.org/debian unstable/main amd64 libpython3.6-dbg amd64 3.6.6-1 [10.8 MB] Get:16 http://deb.debian.org/debian unstable/main amd64 libpython3-dbg amd64 3.6.6-1 [19.8 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libpython3.7-dbg amd64 3.7.0-4 [11.6 MB] Get:18 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dbg amd64 3.6.6-1 [1,064 B] Get:19 http://deb.debian.org/debian unstable/main amd64 python3.6-dbg amd64 3.6.6-1 [14.9 MB] Get:20 http://deb.debian.org/debian unstable/main amd64 python3-dbg amd64 3.6.6-1 [1,292 B] Get:21 http://deb.debian.org/debian unstable/main amd64 python3.7-dbg amd64 3.7.0-4 [16.1 MB] Get:22 http://deb.debian.org/debian unstable/main amd64 python3-all-dbg amd64 3.6.6-1 [1,068 B] Get:23 http://deb.debian.org/debian unstable/main amd64 libquadmath0 amd64 8.2.0-3 [133 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 8.2.0-3 [583 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.8.0-1+b1 [148 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.8.0-1+b1 [2,112 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:1.14.5-1+b1 [2,216 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 python3-six all 1.11.0-2 [15.2 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.0.2-1 [20.1 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.0.2-1 [6,676 B] Get:31 http://deb.debian.org/debian unstable/main amd64 libhdf5-100 amd64 1.10.0-patch1+docs-4+b2 [1,266 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 python3-h5py amd64 2.7.1-2 [1,020 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dbg amd64 1:1.14.5-1+b1 [26.2 MB] Get:34 http://deb.debian.org/debian unstable/main amd64 python3-h5py-dbg amd64 2.7.1-2 [10.2 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 104 MB in 16s (6,614 kB/s) Selecting previously unselected package mime-support. 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Preparing to unpack .../32-python3-numpy-dbg_1%3a1.14.5-1+b1_amd64.deb ... Unpacking python3-numpy-dbg:amd64 (1:1.14.5-1+b1) ... Selecting previously unselected package python3-h5py-dbg. Preparing to unpack .../33-python3-h5py-dbg_2.7.1-2_amd64.deb ... Unpacking python3-h5py-dbg (2.7.1-2) ... Setting up libquadmath0:amd64 (8.2.0-3) ... Setting up libaec0:amd64 (1.0.2-1) ... Setting up mime-support (3.61) ... Setting up libpython3.7-minimal:amd64 (3.7.0-4) ... Setting up python3.7-minimal (3.7.0-4) ... Processing triggers for libc-bin (2.27-5) ... Setting up libgfortran5:amd64 (8.2.0-3) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up libsz2:amd64 (1.0.2-1) ... Setting up libpython3.6-stdlib:amd64 (3.6.6-1) ... Setting up libpython3.7-stdlib:amd64 (3.7.0-4) ... Setting up python3.6 (3.6.6-1) ... Setting up libhdf5-100:amd64 (1.10.0-patch1+docs-4+b2) ... Setting up python3.7 (3.7.0-4) ... Setting up libpython3.7-dbg:amd64 (3.7.0-4) ... Setting up libblas3:amd64 (3.8.0-1+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up python3.7-dbg (3.7.0-4) ... Setting up libpython3.6-dbg:amd64 (3.6.6-1) ... Setting up libpython3-stdlib:amd64 (3.6.6-1) ... Setting up python3 (3.6.6-1) ... Setting up liblapack3:amd64 (3.8.0-1+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up python3-six (1.11.0-2) ... Setting up python3.6-dbg (3.6.6-1) ... Setting up libpython3-dbg:amd64 (3.6.6-1) ... Setting up libpython3-all-dbg:amd64 (3.6.6-1) ... Setting up python3-dbg (3.6.6-1) ... Setting up python3-lib2to3 (3.6.6-1) ... Setting up python3-distutils (3.6.6-1) ... Setting up python3-numpy (1:1.14.5-1+b1) ... Setting up dh-python (3.20180723) ... Setting up python3-h5py (2.7.1-2) ... Setting up python3-numpy-dbg:amd64 (1:1.14.5-1+b1) ... Setting up python3-h5py-dbg (2.7.1-2) ... Setting up python3-all (3.6.6-1) ... Setting up python3-all-dbg (3.6.6-1) ... Setting up autopkgtest-satdep (0) ... Processing triggers for libc-bin (2.27-5) ... (Reading database ... 14834 files and directories currently installed.) Removing autopkgtest-satdep (0) ... autopkgtest [13:28:40]: test command2: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import h5py; h5py.run_tests()" ; echo "Testing with $py-dbg:" ; $py-dbg -c "import h5py; h5py.run_tests()" ; done autopkgtest [13:28:40]: test command2: [----------------------- Testing with python3.7: Traceback (most recent call last): File "<string>", line 1, in <module> File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 26, in <module> from . import _errors ImportError: cannot import name '_errors' from 'h5py' (/usr/lib/python3/dist-packages/h5py/__init__.py) autopkgtest [13:28:40]: test command2: -----------------------] autopkgtest [13:28:40]: test command2: - - - - - - - - - - results - - - - - - - - - - command2 FAIL non-zero exit status 1 autopkgtest [13:28:40]: @@@@@@@@@@@@@@@@@@@@ summary command1 PASS command2 FAIL non-zero exit status 1
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