Mageia上的Biopython构建错误

Question

我正在尝试安装bioppython 1.61。我以root身份在bash终端中登录。我正在使用Mageia 2.0，并且我已经更新了操作系统上的所有软件包/程序(使用urpmi update -a)。

我提取源代码，然后运行python setup.py build，它有两个错误:

FAIL: test_protein_16130152 (test_SeqIO_online.EntrezTests)
Bio.Entrez.efetch(protein, 16130152, ...)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_SeqIO_online.py", line 77, in <lambda>
    method = lambda x : x.simple(d, f, e, l, c)
  File "test_SeqIO_online.py", line 65, in simple
    self.assertEqual(seguid(record.seq), checksum)
AssertionError: 'NT/aFiTXyD/7KixizZ9sq2FcniU' != 'fCjcjMFeGIrilHAn6h+yju267lg'
======================================================================
ERROR: test_doctests (test_Tutorial.TutorialTestCase)
Run tutorial doctests.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Tutorial.py", line 152, in test_doctests
ValueError: 4 Tutorial doctests failed: test_from_line_05671, test_from_line_06030, test_from_line_06190, test_from_line_06479

然后我运行python setup.py install，但它也失败了。我用(urpmi install lib64python-devel)和gcc更新了我的python，但它已经是最新的了。

这是我从python setup.py install得到的错误:

[root@localhost biopython-1.61]# python setup.py install
running install
running build
running build_py
warning: build_py_biopython: byte-compiling is disabled, skipping.
running build_ext
building 'Bio.Cluster.cluster' extension
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -I/usr/include/ncursesw -DNDEBUG -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -g -fPIC -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c Bio/Cluster/clustermodule.c -o build/temp.linux-x86_64-2.7/Bio/Cluster/clustermodule.o
Bio/Cluster/clustermodule.c:2:31: fatal error: numpy/arrayobject.h: No such file or directory
compilation terminated.
error: command 'gcc' failed with exit status 1

Answer 1

修复了bioppython本身的单元测试失败。

编译器错误提示您缺少NumPy头文件，通常包含在操作系统包管理器中的一个单独的包中，名为NumPy -dev或NumPy -devel。