Package: python-scipy
Version: 0.9.0+dfsg1-1+b2
Severity: serious
Justification: fails to build from source (but built successfully in the past)
I have ran into this while building pymvpa2 packages. on mips and mipsel it
times out.
I have troubleshooted it on gabrielli and I believe the following snippet
should reproduce it (warns but returns fine after all on my laptop
amd64):
$> cat scipy-fit.py
#!/usr/bin/python
from numpy import array
from scipy.stats.distributions import ksone
print ksone.fit(array([ 0.14328729, 0.25490644, 0.13804094, 0.49698268,
0.1380734 ,
0.42811492, -0.1115938 , -0.31843031, 0.09982475, -0.2468207 ,
-0.18507596, 0.38959311, 0.1849186 , -0.18565553, 0.06733078,
-0.17673704, 0.00511101, -0.22497416, 0.3387749 , 0.14232358,
0.43253836, 0.02236981, -0.0588139 , -0.1195712 , 0.04046193,
0.04705898, -0.08171521, -0.10318616, 0.20083469, -0.4830056 ,
-0.14728118, 0.0365655 , -0.26662431, 0.16725666, -0.36558027,
-0.09645765, 0.12076468, 0.30362135, -0.09133471, -0.26500672,
-0.08376685, -0.0062318 , 0.26514818, -0.32202921, 0.2390966 ,
-0.1353733 , -0.0616442 , 0.15498897]))
here is how it looks in gdb:
(gdb) bt 10
#0 __ieee754_pow (x=nan(0x7ffffffffffff), y=-1716592327) at
../sysdeps/ieee754/dbl-64/e_pow.c:74
#1 0x2adb2860 in __pow (x=nan(0x7ffffffffffff), y=-1716592327) at w_pow.c:34
#2 0x2beb413c in cephes_smirnov () from
/usr/lib/python2.6/dist-packages/scipy/special/_cephes.so
#3 0x2be91fac in PyUFunc_dd_d_As_id_d () from
/usr/lib/python2.6/dist-packages/scipy/special/_cephes.so
#4 0x2b15fddc in _ftext () from
/usr/lib/pymodules/python2.6/numpy/core/umath.so
#5 0x2b131190 in ?? () from
/usr/lib/pymodules/python2.6/numpy/core/multiarray.so
warning: GDB can't find the start of the function at 0x2b13118e.
GDB is unable to find the start of the function at 0x2b13118e
and thus can't determine the size of that function's stack frame.
This means that GDB may be unable to access that stack frame, or
the frames below it.
This problem is most likely caused by an invalid program counter or
stack pointer.
However, if you think GDB should simply search farther back
from 0x2b13118e for code which looks like the beginning of a
function, you can increase the range of the search using the `set
heuristic-fence-post' command.
(gdb) finish
Run till exit from #0 __ieee754_pow (x=nan(0x7ffffffffffff), y=-1716592327) at
../sysdeps/ieee754/dbl-64/e_pow.c:74
0x2adb2860 in __pow (x=nan(0x7ffffffffffff), y=-1716592327) at w_pow.c:34
34 w_pow.c: No such file or directory.
in w_pow.c
Value returned is $1 = nan(0x8000000000000)
(gdb) finish
Run till exit from #0 0x2adb2860 in __pow (x=nan(0x7ffffffffffff),
y=-1716592327) at w_pow.c:34
0x2beb413c in cephes_smirnov () from
/usr/lib/python2.6/dist-packages/scipy/special/_cephes.so
Value returned is $2 = nan(0x8000000000000)
(gdb) finish
Run till exit from #0 0x2beb413c in cephes_smirnov () from
/usr/lib/python2.6/dist-packages/scipy/special/_cephes.so
^C
Program received signal SIGINT, Interrupt.
0x2beb414c in cephes_smirnov () from
/usr/lib/python2.6/dist-packages/scipy/special/_cephes.so
(gdb) print "it stalled for more than a day and never returned from this
function"
-- System Information:
Debian Release: wheezy/sid
APT prefers testing
APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100,
'stable')
Architecture: amd64 (x86_64)
Kernel: Linux 3.0.0-1-amd64 (SMP w/2 CPU cores)
Locale: LANG=en_US, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/bash
Versions of packages python-scipy depends on:
ii libamd2.2.0 1:3.4.0-2
ii libatlas3gf-base [liblapack.so.3gf] 3.8.3-27
ii libblas3gf [libblas.so.3gf] 1.2.20110419-2
ii libc6 2.13-18
ii libgcc1 1:4.6.1-4
ii libgfortran3 4.6.1-4
ii liblapack3gf [liblapack.so.3gf] 3.3.1-1
ii libstdc++6 4.6.1-4
ii libumfpack5.4.0 1:3.4.0-2
ii python 2.7.2-9
ii python-numpy 1:1.5.1-3
ii python2.6 2.6.7-3
ii python2.7 2.7.2-8
Versions of packages python-scipy recommends:
ii g++ [c++-compiler] 4:4.6.1-2
ii g++-4.3 [c++-compiler] 4.3.5-4
ii g++-4.4 [c++-compiler] 4.4.6-8
ii g++-4.6 [c++-compiler] 4.6.1-4
Versions of packages python-scipy suggests:
ii python [python-profiler] 2.7.2-9
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