Mutalyzer py.test在python魔术错误中失败
Mutalyzer py.test在python魔术错误中失败
提问于 2015-12-31 04:43:32
我正试图按照变性剂2.0.14指令使用Anaconda Python 2.7在Centos 6.7上安装这些。
我的安装很好，但是当我尝试运行py.test套件时，会遇到一系列的失败。
我怀疑操作系统的libmagic版本和python2.7包python-magic之间存在版本冲突。
如果有人能解释这里发生了什么，或者更好地建议解决这个问题，我会非常感兴趣的。
我的魔术装备：
$ rpm -qa | grep 'file-'
file-libs-5.04-21.el6.x86_64
file-5.04-21.el6.x86_64
file-devel-5.04-21.el6.x86_64相应的Python包：
$ source activate py27
discarding /opt/anaconda2/bin from PATH
prepending /opt/anaconda2/envs/py27/bin to PATH
(py27) $ pip list | grep magic
Magic-file-extensions (0.2, /home/chris.guest/temp/mutalyzer/src/magic-file-extensions)
python-magic (0.4.10)py.test的开头如下：
# py.test
======================================================= test session starts =======================================================
platform linux2 -- Python 2.7.11, pytest-2.8.2, py-1.4.30, pluggy-0.3.1
rootdir: /home/chris.guest/temp/mutalyzer, inifile:
collected 610 items / 3 errors
tests/test_backtranslator.py ......
tests/test_base.py .
tests/test_crossmap.py .......................
tests/test_grammar.py ........................................................................................
tests/test_mapping.py ..............................
tests/test_migrations.py .
tests/test_mutator.py ................................................................................................................................................................
tests/test_ncbi.py ............................................................................................................
tests/test_parsers_genbank.py ..........最后犯了很多错误。许多测试由于undefined symbol: magic_list而失败
_________________________________________ ERROR at setup of test_batch_unicode[sqlite://] _________________________________________
@pytest.fixture
def website():
> return create_app().test_client()
tests/test_website.py:29:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
mutalyzer/website/__init__.py:35: in create_app
from mutalyzer.website.views import website
mutalyzer/website/views.py:26: in <module>
from mutalyzer import (announce, backtranslator, File, Retriever, Scheduler,
mutalyzer/File.py:23: in <module>
import magic # open(), MAGIC_MIME, MAGIC_NONE
src/magic-file-extensions/magic.py:94: in <module>
_list = _libraries['magic'].magic_list
/opt/anaconda2/envs/py27/lib/python2.7/ctypes/__init__.py:378: in __getattr__
func = self.__getitem__(name)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <CDLL 'libmagic.so.1', handle 160cc50 at 7f23b97340d0>, name_or_ordinal = 'magic_list'
def __getitem__(self, name_or_ordinal):
> func = self._FuncPtr((name_or_ordinal, self))
E AttributeError: /usr/lib64/libmagic.so.1: undefined symbol: magic_list
/opt/anaconda2/envs/py27/lib/python2.7/ctypes/__init__.py:383: AttributeError
______________________________________ ERROR at setup of test_batch_unicode_email[sqlite://] ______________________________________
@pytest.fixture
def website():
> return create_app().test_client()
tests/test_website.py:29:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
mutalyzer/website/__init__.py:35: in create_app
from mutalyzer.website.views import website
mutalyzer/website/views.py:26: in <module>
from mutalyzer import (announce, backtranslator, File, Retriever, Scheduler,
mutalyzer/File.py:23: in <module>
import magic # open(), MAGIC_MIME, MAGIC_NONE
src/magic-file-extensions/magic.py:94: in <module>
_list = _libraries['magic'].magic_list
/opt/anaconda2/envs/py27/lib/python2.7/ctypes/__init__.py:378: in __getattr__
func = self.__getitem__(name)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <CDLL 'libmagic.so.1', handle 160cc50 at 7f23b984ef50>, name_or_ordinal = 'magic_list'
def __getitem__(self, name_or_ordinal):
> func = self._FuncPtr((name_or_ordinal, self))
E AttributeError: /usr/lib64/libmagic.so.1: undefined symbol: magic_list
/opt/anaconda2/envs/py27/lib/python2.7/ctypes/__init__.py:383: AttributeError
============================================== 548 passed, 65 error in 41.42 seconds ==============================================
(py27)[root@localhost mutalyzer]# 回答 2
Stack Overflow用户
回答已采纳
发布于 2016-01-11 04:39:29
与CentOS6.7一起打包的magiclib版本缺少magic_list函数。
我能够将这个补丁安装到src/magic-file-extensions/magic.py上，这样py.test就可以正常运行了。
$ diff -u src/magic-file-extensions/magic.old.py src/magic-file-extensions/magic.py
--- src/magic-file-extensions/magic.old.py 2015-12-31 14:04:50.769635453 +1100
+++ src/magic-file-extensions/magic.py 2016-01-11 15:17:49.987270845 +1100
@@ -91,9 +91,13 @@
_check.restype = c_int
_check.argtypes = [magic_t, c_char_p]
-_list = _libraries['magic'].magic_list
-_list.restype = c_int
-_list.argtypes = [magic_t, c_char_p]
+try:
+ _list = _libraries['magic'].magic_list
+ _list.restype = c_int
+ _list.argtypes = [magic_t, c_char_p]
+except AttributeError, e:
+ _list = None
+
_errno = _libraries['magic'].magic_errno
_errno.restype = c_int虽然直接的AttributeError是用这个补丁处理的，但是如果调用src/magic-file-extensions/magic.py中的Magic.list方法，它仍然会失败。这不是一个直接的问题，因为它似乎不是在mutalyzer代码库中调用的。
Stack Overflow用户
发布于 2015-12-31 14:14:55
我们有一个早期的报告说，一个用户试图在CentOS 6上安装Mutalyzer，而他们也遇到了Lib魔术的麻烦。我不认为这是解决了，除了他们切换到CentOS 7。
不幸的是，我们的资源非常有限，Debian是我们自己使用的唯一操作系统，这是我们能够实际支持的全部。当然，我们很乐意接受补丁或文档更新:)
谢谢你使用Mutalyzer！
页面原文内容由Stack Overflow提供。腾讯云小微IT领域专用引擎提供翻译支持
原文链接：
https://stackoverflow.com/questions/34541129
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