Discussion:
[MacPorts] #57699: py-astropy: segfault in astropy.wcs.WCS
MacPorts
2018-11-29 13:23:46 UTC
Permalink
#57699: py-astropy: segfault in astropy.wcs.WCS
----------------------+------------------------
Reporter: lpsinger | Owner: (none)
Type: defect | Status: new
Priority: Normal | Milestone:
Component: ports | Version:
Keywords: | Port: py-astropy
----------------------+------------------------
I get a segmentation fault when attempting to read almost any WCS header.
Here's an example using one of the test files from the
astropy/wcs/tests/data.

{{{
$ python -c 'from astropy.io import fits; from astropy import wcs;
wcs.WCS(fits.open("j94f05bgq_flt.fits")[0])'
WARNING: FITSFixedWarning: The WCS transformation has more axes (2) than
the image it is associated with (0) [astropy.wcs.wcs]
Segmentation fault: 11
}}}

I am using Python 3.7 on macOS 10.14.1, py37-astropy @3.0.5_0, and wcslib
@6.2_0.
--
Ticket URL: <https://trac.macports.org/ticket/57699>
MacPorts <https://www.macports.org/>
Ports system for macOS
MacPorts
2018-11-29 13:26:27 UTC
Permalink
#57699: py-astropy: segfault in astropy.wcs.WCS
-------------------------+--------------------
Reporter: lpsinger | Owner: (none)
Type: defect | Status: new
Priority: Normal | Milestone:
Component: ports | Version:
Resolution: | Keywords:
Port: py-astropy |
-------------------------+--------------------

Comment (by lpsinger):

Here's the stack trace:

{{{
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libsystem_platform.dylib 0x00007fff7c8f5712
_platform_strlen + 18
1 org.python.python 0x000000010611c089
PyUnicode_FromString + 14
2 org.python.python 0x00000001060f8ab4
PyDict_SetItemString + 24
3 _wcs.cpython-37m-darwin.so 0x000000010915b344 PyWcsprm_fix +
1300
4 org.python.python 0x00000001060d6b88
_PyMethodDef_RawFastCallKeywords + 545
5 org.python.python 0x00000001060db4f2
_PyMethodDescr_FastCallKeywords + 82
6 org.python.python 0x000000010616c02c call_function +
801
7 org.python.python 0x00000001061646a8
_PyEval_EvalFrameDefault + 4751
8 org.python.python 0x000000010616c88e
_PyEval_EvalCodeWithName + 1835
9 org.python.python 0x00000001060d60b8
_PyFunction_FastCallKeywords + 225
10 org.python.python 0x000000010616bffc call_function +
753
11 org.python.python 0x00000001061647d6
_PyEval_EvalFrameDefault + 5053
12 org.python.python 0x000000010616c88e
_PyEval_EvalCodeWithName + 1835
13 org.python.python 0x00000001060d5d21
_PyFunction_FastCallDict + 441
14 org.python.python 0x00000001060d6e51
_PyObject_Call_Prepend + 150
15 org.python.python 0x0000000106114798 slot_tp_init +
80
16 org.python.python 0x0000000106111464 type_call + 178
17 org.python.python 0x00000001060d5f59
_PyObject_FastCallKeywords + 359
18 org.python.python 0x000000010616bff5 call_function +
746
19 org.python.python 0x00000001061646c1
_PyEval_EvalFrameDefault + 4776
20 org.python.python 0x000000010616c88e
_PyEval_EvalCodeWithName + 1835
21 org.python.python 0x0000000106163391 PyEval_EvalCode
+ 42
22 org.python.python 0x0000000106191b15 run_mod + 54
23 org.python.python 0x0000000106190c5b
PyRun_StringFlags + 120
24 org.python.python 0x0000000106190bb2
PyRun_SimpleStringFlags + 69
25 org.python.python 0x00000001061a78ed pymain_main +
4134
26 org.python.python 0x00000001061a850b _Py_UnixMain +
75
27 libdyld.dylib 0x00007fff7c70f08d start + 1

Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x000000010a2257b0 rbx: 0x0000000000000000 rcx:
0x0000000000000000 rdx: 0x0000000000000000
rdi: 0x0000000000000000 rsi: 0x0000000000000000 rbp:
0x00007ffee9b4a650 rsp: 0x00007ffee9b4a650
r8: 0x65676e616863206f r9: 0x000000000000000f r10:
0x0000000106698cd8 r11: 0x00000000010c425f
r12: 0x00007fc5d5962410 r13: 0x0000000109119808 r14:
0x000000010a2257b0 r15: 0x000000010932b2d0
rip: 0x00007fff7c8f5712 rfl: 0x0000000000010246 cr2:
0x0000000000000000

Logical CPU: 0
Error Code: 0x00000004
Trap Number: 14


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0x7fff7ad49000 - 0x7fff7ad4afff liblangid.dylib (128.15.1)
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0x7fff7bf86000 - 0x7fff7c15dfe7 libsqlite3.dylib (274.20)
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0x7fff7c260000 - 0x7fff7c2adfff libssl.44.dylib (22.200.4)
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0x7fff7c3ea000 - 0x7fff7c3edffb libutil.dylib (51.200.4)
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0x7fff7c50d000 - 0x7fff7c51fffb libz.1.dylib (70.200.4)
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0x7fff7c595000 - 0x7fff7c59fff3 libcommonCrypto.dylib
(60118.220.1) <1099E427-6E81-3059-87AF-6F5FD81CA998>
/usr/lib/system/libcommonCrypto.dylib
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<A4D9CF37-D076-3CE9-95F1-DA89DA1601B6>
/usr/lib/system/libcompiler_rt.dylib
0x7fff7c5a8000 - 0x7fff7c5b1ff3 libcopyfile.dylib (146.200.3)
<4BCDADBF-79F5-3829-B47D-64DA0D44BCBF> /usr/lib/system/libcopyfile.dylib
0x7fff7c5b2000 - 0x7fff7c636fdf libcorecrypto.dylib (602.220.6)
<E1046E01-A2FD-35B4-B018-ACC372F3880E> /usr/lib/system/libcorecrypto.dylib
0x7fff7c6bd000 - 0x7fff7c6f7ff7 libdispatch.dylib (1008.220.2)
<D8B56783-152A-34A8-94E9-8E6BAE049384> /usr/lib/system/libdispatch.dylib
0x7fff7c6f8000 - 0x7fff7c727fff libdyld.dylib (635.2) <1B79A5CE-
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0x7fff7c728000 - 0x7fff7c728ffb libkeymgr.dylib (30)
<A73AA788-C35C-3284-BFCA-95B1BBDF0CF3> /usr/lib/system/libkeymgr.dylib
0x7fff7c729000 - 0x7fff7c735ff7 libkxld.dylib (4903.221.2)
<16D75C5C-584A-3848-84C0-3BFB312AEB92> /usr/lib/system/libkxld.dylib
0x7fff7c736000 - 0x7fff7c736ff7 liblaunch.dylib (1336.220.5)
<95EB6EAF-2DC5-344F-BADB-CA4E35E4E503> /usr/lib/system/liblaunch.dylib
0x7fff7c737000 - 0x7fff7c73cfff libmacho.dylib (921) <ECC4E97C-
575E-3A08-8191-BF02D7D4E637> /usr/lib/system/libmacho.dylib
0x7fff7c73d000 - 0x7fff7c73fffb libquarantine.dylib (86.220.1)
<6AE5AEEC-A9FD-3CF8-92DD-12B5AFBE12DE> /usr/lib/system/libquarantine.dylib
0x7fff7c740000 - 0x7fff7c741ff3 libremovefile.dylib (45.200.2)
<D74A307B-3DC7-3992-B16C-DACB8207BE13> /usr/lib/system/libremovefile.dylib
0x7fff7c742000 - 0x7fff7c759ff3 libsystem_asl.dylib (356.200.4)
<EC9D8AD4-E5CB-3765-804A-9E1E9DC045D2> /usr/lib/system/libsystem_asl.dylib
0x7fff7c75a000 - 0x7fff7c75afff libsystem_blocks.dylib (73)
<26419398-C30C-30F1-B656-A92AFA9560F6>
/usr/lib/system/libsystem_blocks.dylib
0x7fff7c75b000 - 0x7fff7c7e3fff libsystem_c.dylib (1272.200.26)
<3DEEE96E-6DF6-35AD-8654-D69AC26B907B> /usr/lib/system/libsystem_c.dylib
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(963.200.27) <02CC3996-B34E-333C-8806-AE2699D34424>
/usr/lib/system/libsystem_configuration.dylib
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<254B6849-2C8F-302C-8616-B8324A11AB30>
/usr/lib/system/libsystem_coreservices.dylib
0x7fff7c7ec000 - 0x7fff7c7f2ffb libsystem_darwin.dylib
(1272.200.26) <974E9EF7-DE72-34B7-B056-0A81C10DF8EB>
/usr/lib/system/libsystem_darwin.dylib
0x7fff7c7f3000 - 0x7fff7c7f9ff7 libsystem_dnssd.dylib
(878.200.35) <FFC665AA-B257-35AD-BD8B-32FD42C2EEC1>
/usr/lib/system/libsystem_dnssd.dylib
0x7fff7c7fa000 - 0x7fff7c846ff3 libsystem_info.dylib (517.200.9)
<0707C387-D7DE-372E-8FF1-3DE5C91932D6>
/usr/lib/system/libsystem_info.dylib
0x7fff7c847000 - 0x7fff7c86eff7 libsystem_kernel.dylib
(4903.221.2) <0E882078-7330-3B49-AA5D-3CDB5645A4E5>
/usr/lib/system/libsystem_kernel.dylib
0x7fff7c86f000 - 0x7fff7c8baff7 libsystem_m.dylib (3158.200.7)
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0x7fff7c8bb000 - 0x7fff7c8dfff7 libsystem_malloc.dylib
(166.220.1) <3B196122-4E0D-3E3F-AA3E-5115B976DE26>
/usr/lib/system/libsystem_malloc.dylib
0x7fff7c8e0000 - 0x7fff7c8ebff3 libsystem_networkextension.dylib
(767.220.1) <C54EB8F6-F305-3452-8DB1-F7DA6859AF8C>
/usr/lib/system/libsystem_networkextension.dylib
0x7fff7c8ec000 - 0x7fff7c8f3fff libsystem_notify.dylib
(172.200.21) <BCCB222F-DC64-3954-A836-DCCE6659CA5A>
/usr/lib/system/libsystem_notify.dylib
0x7fff7c8f4000 - 0x7fff7c8fdfef libsystem_platform.dylib
(177.200.16) <B75B04AD-69FE-3ADE-84D2-C17972FC8F49>
/usr/lib/system/libsystem_platform.dylib
0x7fff7c8fe000 - 0x7fff7c908fff libsystem_pthread.dylib
(330.220.2) <4958273C-4273-3501-8137-E44249E10D9C>
/usr/lib/system/libsystem_pthread.dylib
0x7fff7c909000 - 0x7fff7c90cff7 libsystem_sandbox.dylib
(851.220.9) <4D6433A8-C703-3ED9-82EB-B9E481A0FD2F>
/usr/lib/system/libsystem_sandbox.dylib
0x7fff7c90d000 - 0x7fff7c90fff3 libsystem_secinit.dylib
(30.220.1) <6C681113-8C48-3256-BEF6-0C3723DEB926>
/usr/lib/system/libsystem_secinit.dylib
0x7fff7c910000 - 0x7fff7c917ff7 libsystem_symptoms.dylib
(820.227.2) <3147D594-F41F-35FD-BF0B-6B8B66A407DE>
/usr/lib/system/libsystem_symptoms.dylib
0x7fff7c918000 - 0x7fff7c92dff7 libsystem_trace.dylib (906.220.1)
<D5045DC5-A165-3238-A470-1796F12BF84F>
/usr/lib/system/libsystem_trace.dylib
0x7fff7c92f000 - 0x7fff7c934ffb libunwind.dylib (35.4)
<41222EF6-2233-3CF4-947A-15D48CB8C030> /usr/lib/system/libunwind.dylib
0x7fff7c935000 - 0x7fff7c965fff libxpc.dylib (1336.220.5)
<B2137772-E202-3656-A089-F6DD517007D5> /usr/lib/system/libxpc.dylib
}}}
--
Ticket URL: <https://trac.macports.org/ticket/57699#comment:1>
MacPorts <https://www.macports.org/>
Ports system for macOS
MacPorts
2018-11-29 13:30:09 UTC
Permalink
#57699: py-astropy: segfault in astropy.wcs.WCS
-------------------------+------------------------
Reporter: lpsinger | Owner: robitaille
Type: defect | Status: assigned
Priority: Normal | Milestone:
Component: ports | Version:
Resolution: | Keywords:
Port: py-astropy |
-------------------------+------------------------
Changes (by lpsinger):

* owner: (none) => robitaille
* status: new => assigned
--
Ticket URL: <https://trac.macports.org/ticket/57699#comment:2>
MacPorts <https://www.macports.org/>
Ports system for macOS
MacPorts
2018-11-29 13:34:45 UTC
Permalink
#57699: py-astropy: segfault in astropy.wcs.WCS
-------------------------+------------------------
Reporter: lpsinger | Owner: robitaille
Type: defect | Status: assigned
Priority: Normal | Milestone:
Component: ports | Version:
Resolution: | Keywords:
Port: py-astropy |
-------------------------+------------------------

Comment (by lpsinger):

A similar segfault is reported in
https://github.com/astropy/astropy/issues/7929.
--
Ticket URL: <https://trac.macports.org/ticket/57699#comment:3>
MacPorts <https://www.macports.org/>
Ports system for macOS
MacPorts
2018-12-07 05:06:02 UTC
Permalink
#57699: py-astropy: segfault in astropy.wcs.WCS
-------------------------+------------------------
Reporter: lpsinger | Owner: robitaille
Type: defect | Status: closed
Priority: Normal | Milestone:
Component: ports | Version:
Resolution: fixed | Keywords:
Port: py-astropy |
-------------------------+------------------------
Changes (by lpsinger):

* status: assigned => closed
* resolution: => fixed


Comment:

In [changeset:"b3320de6a3f38ea2416e0c448213b58cf236342b/macports-ports"
b3320de6a3f38ea2416e0c448213b58cf236342b/macports-ports] (master):
{{{
#!ConfigurableCommitTicketReference repository="macports-ports"
revision="b3320de6a3f38ea2416e0c448213b58cf236342b"
py-astropy: update to 3.1/2.0.10

Fixes https://trac.macports.org/ticket/57699.
}}}
--
Ticket URL: <https://trac.macports.org/ticket/57699#comment:4>
MacPorts <https://www.macports.org/>
Ports system for macOS
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