[reportlab-users] Python 3.x progress

Peter Cock p.j.a.cock at googlemail.com
Thu Jan 9 06:58:18 EST 2014

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On Thu, Jan 9, 2014 at 11:25 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

>

> Is this expected to work on Mac OS X yet? Or, does it require a

> specific revision of Python 3.3 - as I'm running into some problems:

>

> Mac OS X, using hg from Mercurial-2.8.2-py2.7-macosx10.9.zip

> and Apple Xcode from App Store, using a self compiled Python

> version 3.3.0 under $HOME/bin,

>

> $ hg clone ssh://hg@bitbucket.org/rptlab/reportlab

> $ cd reportlab

> $ hg checkout py33

> $ hg log -b py33 | head

> changeset: 3972:b5870c0f3eb4

> branch: py33

> tag: tip

> user: robin

> date: Wed Jan 08 17:56:06 2014 +0000

> summary: patches from Matthias Klose

>

> ...

>

> So far so good, although there are some unicode related glitches

> causing failures in the Biopython unit tests using ReportLab, which

> I will look into (they may be problems on the Biopython side).

One issue was clearly bytes versus strings on the Biopython side,
provisionally fixed:
https://github.com/biopython/biopython/commit/cfc38cecd5ef71c81b7ce1e59fb4ca3a3188aa3d

The second problem is curious - a TypeError under Python 3.3
(self compiled) but a segmentation fault in _rl_accel.so under
Python 2.7 (provided by Apple):

$ python3 test_GraphicsChromosome.py
test_add_count (__main__.ChromosomeCountTest)
...
test_simple_organism_ps (__main__.OrganismGraphicTest)
Output a simple organism to a postscript file. ... ERROR
test_simple_organism_svg (__main__.OrganismGraphicTest)
...
======================================================================
ERROR: test_simple_organism_ps (__main__.OrganismGraphicTest)
Output a simple organism to a postscript file.
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_GraphicsChromosome.py", line 195, in test_simple_organism_ps
self._simple_organism("organism.eps", "ps")
File "test_GraphicsChromosome.py", line 190, in _simple_organism
test_organism.draw(test_file, "Test organism")
File "/Users/peterjc/lib/python3.3/site-packages/Bio/Graphics/BasicChromosome.py",
line 164, in draw
return _write(cur_drawing, output_file, self.output_format)
File "/Users/peterjc/lib/python3.3/site-packages/Bio/Graphics/__init__.py",
line 80, in _write
return drawmethod.drawToFile(drawing, output_file)
File "/Users/peterjc/lib/python3.3/site-packages/reportlab/graphics/renderPS.py",
line 879, in drawToFile
c.save(fn)
File "/Users/peterjc/lib/python3.3/site-packages/reportlab/graphics/renderPS.py",
line 155, in save
file.write(self._sep.join(self.code))
TypeError: 'str' does not support the buffer interface

----------------------------------------------------------------------
Ran 13 tests in 1.001s

FAILED (errors=1)

Versus:

$ python2.7 test_GraphicsChromosome.py
test_add_count (__main__.ChromosomeCountTest)
...
test_simple_organism_ps (__main__.OrganismGraphicTest)
Output a simple organism to a postscript file. ... Segmentation fault: 11

This popped up a crash report window - although on repeat runs
Apple isn't showing me this, the log is available via the console
application - details below.

Peter

-----------------------------------------------------------------------------

Details from the (Apple provided) Python 2.7 segmentation fault,

Process: Python [72211]
Path:
/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Identifier: Python
Version: 2.7.5 (2.7.5)
Code Type: X86-64 (Native)
Parent Process: bash [72086]
Responsible: Terminal [72078]
User ID: 501

PlugIn Path: /Library/Python/2.7/site-packages/reportlab/lib/_rl_accel.so
PlugIn Identifier: _rl_accel.so
PlugIn Version: ??? (0)

Date/Time: 2014-01-09 11:54:36.795 +0000
OS Version: Mac OS X 10.9.1 (13B42)
Report Version: 11
Anonymous UUID: 55310509-E3DE-B551-C6D9-E3F0B5EDE396

Sleep/Wake UUID: 3F1DF29E-343A-4FD5-9D4F-12900619F30D

Crashed Thread: 0 Dispatch queue: com.apple.main-thread

Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000008

VM Regions Near 0x8:
-->
__TEXT 000000010e9a7000-000000010e9a8000 [ 4K]
r-x/rwx SM=COW
/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 org.python.python 0x000000010e9e5470 PyModule_GetDict + 9
1 _rl_accel.so 0x000000010f09811e _add_TB + 29
(_rl_accel.c:470)
2 _rl_accel.so 0x000000010f09706b unicode2T1 +
1844 (_rl_accel.c:637)
3 org.python.python 0x000000010ea2f14d PyEval_EvalFrameEx + 8080
4 org.python.python 0x000000010ea33864 0x10e9ad000 + 551012
5 org.python.python 0x000000010ea304d4 PyEval_EvalFrameEx + 13079
6 org.python.python 0x000000010ea2d093 PyEval_EvalCodeEx + 1641
7 org.python.python 0x000000010ea338c8 0x10e9ad000 + 551112
8 org.python.python 0x000000010ea304d4 PyEval_EvalFrameEx + 13079
9 org.python.python 0x000000010ea33864 0x10e9ad000 + 551012
10 org.python.python 0x000000010ea304d4 PyEval_EvalFrameEx + 13079
11 org.python.python 0x000000010ea33864 0x10e9ad000 + 551012
12 org.python.python 0x000000010ea304d4 PyEval_EvalFrameEx + 13079
13 org.python.python 0x000000010ea33864 0x10e9ad000 + 551012
14 org.python.python 0x000000010ea304d4 PyEval_EvalFrameEx + 13079
15 org.python.python 0x000000010ea33864 0x10e9ad000 + 551012
16 org.python.python 0x000000010ea304d4 PyEval_EvalFrameEx + 13079
17 org.python.python 0x000000010ea33864 0x10e9ad000 + 551012
18 org.python.python 0x000000010ea304d4 PyEval_EvalFrameEx + 13079
19 org.python.python 0x000000010ea33864 0x10e9ad000 + 551012
20 org.python.python 0x000000010ea304d4 PyEval_EvalFrameEx + 13079
21 org.python.python 0x000000010ea2d093 PyEval_EvalCodeEx + 1641
22 org.python.python 0x000000010ea338c8 0x10e9ad000 + 551112
23 org.python.python 0x000000010ea304d4 PyEval_EvalFrameEx + 13079
24 org.python.python 0x000000010ea2d093 PyEval_EvalCodeEx + 1641
25 org.python.python 0x000000010ea338c8 0x10e9ad000 + 551112
26 org.python.python 0x000000010ea304d4 PyEval_EvalFrameEx + 13079
27 org.python.python 0x000000010ea2d093 PyEval_EvalCodeEx + 1641
28 org.python.python 0x000000010ea338c8 0x10e9ad000 + 551112
29 org.python.python 0x000000010ea304d4 PyEval_EvalFrameEx + 13079
30 org.python.python 0x000000010ea2d093 PyEval_EvalCodeEx + 1641
31 org.python.python 0x000000010ea338c8 0x10e9ad000 + 551112
32 org.python.python 0x000000010ea304d4 PyEval_EvalFrameEx + 13079
33 org.python.python 0x000000010ea33864 0x10e9ad000 + 551012
34 org.python.python 0x000000010ea304d4 PyEval_EvalFrameEx + 13079
35 org.python.python 0x000000010ea2d093 PyEval_EvalCodeEx + 1641
36 org.python.python 0x000000010ea338c8 0x10e9ad000 + 551112
37 org.python.python 0x000000010ea304d4 PyEval_EvalFrameEx + 13079
38 org.python.python 0x000000010ea2d093 PyEval_EvalCodeEx + 1641
39 org.python.python 0x000000010ea338c8 0x10e9ad000 + 551112
40 org.python.python 0x000000010ea304d4 PyEval_EvalFrameEx + 13079
41 org.python.python 0x000000010ea2d093 PyEval_EvalCodeEx + 1641
42 org.python.python 0x000000010e9d4796 0x10e9ad000 + 161686
43 org.python.python 0x000000010e9b6f72 PyObject_Call + 101
44 org.python.python 0x000000010ea31395 PyEval_EvalFrameEx + 16856
45 org.python.python 0x000000010ea2d093 PyEval_EvalCodeEx + 1641
46 org.python.python 0x000000010e9d4796 0x10e9ad000 + 161686
47 org.python.python 0x000000010e9b6f72 PyObject_Call + 101
48 org.python.python 0x000000010e9c19a7 0x10e9ad000 + 84391
49 org.python.python 0x000000010e9b6f72 PyObject_Call + 101
50 org.python.python 0x000000010e9fbcad 0x10e9ad000 + 322733
51 org.python.python 0x000000010e9b6f72 PyObject_Call + 101
52 org.python.python 0x000000010ea30df5 PyEval_EvalFrameEx + 15416
53 org.python.python 0x000000010ea2d093 PyEval_EvalCodeEx + 1641
54 org.python.python 0x000000010e9d4796 0x10e9ad000 + 161686
55 org.python.python 0x000000010e9b6f72 PyObject_Call + 101
56 org.python.python 0x000000010ea31395 PyEval_EvalFrameEx + 16856
57 org.python.python 0x000000010ea2d093 PyEval_EvalCodeEx + 1641
58 org.python.python 0x000000010e9d4796 0x10e9ad000 + 161686
59 org.python.python 0x000000010e9b6f72 PyObject_Call + 101
60 org.python.python 0x000000010e9c19a7 0x10e9ad000 + 84391
61 org.python.python 0x000000010e9b6f72 PyObject_Call + 101
62 org.python.python 0x000000010e9fbcad 0x10e9ad000 + 322733
63 org.python.python 0x000000010e9b6f72 PyObject_Call + 101
64 org.python.python 0x000000010ea30df5 PyEval_EvalFrameEx + 15416
65 org.python.python 0x000000010ea2d093 PyEval_EvalCodeEx + 1641
66 org.python.python 0x000000010e9d4796 0x10e9ad000 + 161686
67 org.python.python 0x000000010e9b6f72 PyObject_Call + 101
68 org.python.python 0x000000010ea31395 PyEval_EvalFrameEx + 16856
69 org.python.python 0x000000010ea2d093 PyEval_EvalCodeEx + 1641
70 org.python.python 0x000000010e9d4796 0x10e9ad000 + 161686
71 org.python.python 0x000000010e9b6f72 PyObject_Call + 101
72 org.python.python 0x000000010e9c19a7 0x10e9ad000 + 84391
73 org.python.python 0x000000010e9b6f72 PyObject_Call + 101
74 org.python.python 0x000000010e9fbcad 0x10e9ad000 + 322733
75 org.python.python 0x000000010e9b6f72 PyObject_Call + 101
76 org.python.python 0x000000010ea30df5 PyEval_EvalFrameEx + 15416
77 org.python.python 0x000000010ea33864 0x10e9ad000 + 551012
78 org.python.python 0x000000010ea304d4 PyEval_EvalFrameEx + 13079
79 org.python.python 0x000000010ea33864 0x10e9ad000 + 551012
80 org.python.python 0x000000010ea304d4 PyEval_EvalFrameEx + 13079
81 org.python.python 0x000000010ea2d093 PyEval_EvalCodeEx + 1641
82 org.python.python 0x000000010e9d4796 0x10e9ad000 + 161686
83 org.python.python 0x000000010e9b6f72 PyObject_Call + 101
84 org.python.python 0x000000010e9c19a7 0x10e9ad000 + 84391
85 org.python.python 0x000000010e9b6f72 PyObject_Call + 101
86 org.python.python 0x000000010e9fc6ce 0x10e9ad000 + 325326
87 org.python.python 0x000000010e9f8184 0x10e9ad000 + 307588
88 org.python.python 0x000000010e9b6f72 PyObject_Call + 101
89 org.python.python 0x000000010ea30df5 PyEval_EvalFrameEx + 15416
90 org.python.python 0x000000010ea2d093 PyEval_EvalCodeEx + 1641
91 org.python.python 0x000000010ea2ca24 PyEval_EvalCode + 54
92 org.python.python 0x000000010ea4bc2c 0x10e9ad000 + 650284
93 org.python.python 0x000000010ea4bcd3 PyRun_FileExFlags + 137
94 org.python.python 0x000000010ea4b821
PyRun_SimpleFileExFlags + 718
95 org.python.python 0x000000010ea5c363 Py_Main + 2995
96 libdyld.dylib 0x00007fff97e915fd start + 1

Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x0000000000000000 rcx:
0x000000010f24c3f8 rdx: 0x0000000000000000
rdi: 0x0000000000000000 rsi: 0x000000010f098a9a rbp:
0x00007fff512542d0 rsp: 0x00007fff512542c0
r8: 0x0000000000000005 r9: 0x47b2eccb84fd23a6 r10:
0x0000000000000065 r11: 0x00000000009532b2
r12: 0x0000000000000000 r13: 0x000000010f3da7e8 r14:
0x000000000000022f r15: 0x0000000000000001
rip: 0x000000010e9e5470 rfl: 0x0000000000010246 cr2: 0x0000000000000008

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

Binary Images:
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0x7fff918b1000 - 0x7fff918d5fff libxpc.dylib (300.1.17)
<4554927A-9467-365C-91F1-5A116989DD7F> /usr/lib/system/libxpc.dylib
0x7fff918e0000 - 0x7fff91ac5ff7 com.apple.CoreFoundation (6.9
- 855.11) <E22C6A1F-8996-349C-905E-96C3BBE07C2F>
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
0x7fff91bac000 - 0x7fff91bdbfd2 libsystem_m.dylib (3047.16)
<B7F0E2E4-2777-33FC-A787-D6430B630D54>
/usr/lib/system/libsystem_m.dylib
0x7fff91bdc000 - 0x7fff91bddfff libunc.dylib (28)
<62682455-1862-36FE-8A04-7A6B91256438> /usr/lib/system/libunc.dylib
0x7fff91cb9000 - 0x7fff91d98fff libcrypto.0.9.8.dylib (50)
<B95B9DBA-39D3-3EEF-AF43-44608B28894E> /usr/lib/libcrypto.0.9.8.dylib
0x7fff92002000 - 0x7fff9201dff7 libsystem_malloc.dylib
(23.1.10) <FFE5C472-B23A-318A-85BF-77CDE61900D1>
/usr/lib/system/libsystem_malloc.dylib
0x7fff92b85000 - 0x7fff92ba1ff7 libsystem_kernel.dylib
(2422.1.72) <D14913DB-47F1-3591-8DAF-D4B4EF5F8818>
/usr/lib/system/libsystem_kernel.dylib
0x7fff939ba000 - 0x7fff939e1ff7 libsystem_network.dylib
(241.3) <8B1E1F1D-A5CC-3BAE-8B1E-ABC84337A364>
/usr/lib/system/libsystem_network.dylib
0x7fff93a1e000 - 0x7fff93a23ff7 libunwind.dylib (35.3)
<78DCC358-2FC1-302E-B395-0155B47CB547> /usr/lib/system/libunwind.dylib
0x7fff93c30000 - 0x7fff93c34fff libsystem_stats.dylib
(93.1.26) <B9E26A9E-FBBC-3938-B8B7-6CF7CA8C99AD>
/usr/lib/system/libsystem_stats.dylib
0x7fff93cde000 - 0x7fff93cdfff7
libDiagnosticMessagesClient.dylib (100)
<4CDB0F7B-C0AF-3424-BC39-495696F0DB1E>
/usr/lib/libDiagnosticMessagesClient.dylib
0x7fff9447e000 - 0x7fff9448efff libbsm.0.dylib (33)
<2CAC00A2-1352-302A-88FA-C567D4D69179> /usr/lib/libbsm.0.dylib
0x7fff944bf000 - 0x7fff944c0ff7 libsystem_sandbox.dylib
(278.10) <A47E7E11-3C76-318E-B67D-98972B86F094>
/usr/lib/system/libsystem_sandbox.dylib
0x7fff95fb7000 - 0x7fff95ff9ff7 libauto.dylib (185.5)
<F45C36E8-B606-3886-B5B1-B6745E757CA8> /usr/lib/libauto.dylib
0x7fff960bd000 - 0x7fff960beffb libremovefile.dylib (33)
<3543F917-928E-3DB2-A2F4-7AB73B4970EF>
/usr/lib/system/libremovefile.dylib
0x7fff97e7e000 - 0x7fff97e85fff libcompiler_rt.dylib (35)
<4CD916B2-1B17-362A-B403-EF24A1DAC141>
/usr/lib/system/libcompiler_rt.dylib
0x7fff97e86000 - 0x7fff97e8dff3 libcopyfile.dylib (103)
<5A881779-D0D6-3029-B371-E3021C2DDA5E>
/usr/lib/system/libcopyfile.dylib
0x7fff97e8e000 - 0x7fff97e91ff7 libdyld.dylib (239.3)
<62F4D752-4089-31A8-8B73-B95A68893B3C> /usr/lib/system/libdyld.dylib
0x7fff9825f000 - 0x7fff98260ff7 libsystem_blocks.dylib (63)
<FB856CD1-2AEA-3907-8E9B-1E54B6827F82>
/usr/lib/system/libsystem_blocks.dylib
0x7fff982e6000 - 0x7fff9830fff7 libc++abi.dylib (48)
<8C16158F-CBF8-3BD7-BEF4-022704B2A326> /usr/lib/libc++abi.dylib
0x7fff98578000 - 0x7fff98601ff7 libsystem_c.dylib (997.1.1)
<61833FAA-7281-3FF9-937F-686B6F20427C>
/usr/lib/system/libsystem_c.dylib
0x7fff988fe000 - 0x7fff98aabf27 libobjc.A.dylib (551.1)
<AD7FD984-271E-30F4-A361-6B20319EC73B> /usr/lib/libobjc.A.dylib
0x7fff98aac000 - 0x7fff98abdff7 libsystem_asl.dylib (217.1.4)
<655FB343-52CF-3E2F-B14D-BEBF5AAEF94D>
/usr/lib/system/libsystem_asl.dylib
0x7fff98acb000 - 0x7fff98acdff3 libsystem_configuration.dylib
(596.12) <C4F633D9-94C8-35D9-BB2D-84C5122533C7>
/usr/lib/system/libsystem_configuration.dylib
0x7fff9951f000 - 0x7fff99525ff7 libsystem_platform.dylib
(24.1.4) <331BA4A5-55CE-3B95-99EB-44E0C89D7FB8>
/usr/lib/system/libsystem_platform.dylib
0x7fff9955d000 - 0x7fff995affff libc++.1.dylib (120)
<4F68DFC5-2077-39A8-A449-CAC5FDEE7BDE> /usr/lib/libc++.1.dylib
0x7fff995b0000 - 0x7fff995cafff libdispatch.dylib (339.1.9)
<46878A5B-4248-3057-962C-6D4A235EEF31>
/usr/lib/system/libdispatch.dylib
0x7fff995f8000 - 0x7fff99600fff libsystem_dnssd.dylib
(522.1.11) <270DCF6C-502D-389A-AA9F-DE4624A36FF7>
/usr/lib/system/libsystem_dnssd.dylib

External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by all processes on this machine:
task_for_pid: 1774273
thread_create: 1
thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=78.1M resident=11.8M(15%)
swapped_out_or_unallocated=66.2M(85%)
Writable regions: Total=60.7M written=18.2M(30%) resident=21.4M(35%)
swapped_out=0K(0%) unallocated=39.3M(65%)

REGION TYPE VIRTUAL
=========== =======
Kernel Alloc Once 4K
MALLOC 52.2M
MALLOC (admin) 16K
STACK GUARD 56.0M
Stack 8192K
VM_ALLOCATE 12K
__DATA 1844K
__LINKEDIT 65.8M
__TEXT 12.3M
__UNICODE 544K
shared memory 4K
=========== =======
TOTAL 196.7M

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