I'm trying to install Biopython 1.61. I'm logged in as root in a bash terminal. I'm using Mageia 2.0, and I've updated all the packages/programs on the OS (with urpmi update -a).
I extracted the source, then ran python setup.py build, which had two errors:
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
Then I ran python setup.py install, but it failed, too. I updated my python with (urpmi install lib64python-devel) and my gcc, but it was already up to date.
This is the error I get from python setup.py install:
[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
The unit test failures have been fixed in Biopython itself.
The compiler error suggests you are missing the NumPy header files, often included in the OS package manager in a separate package called something like numpy-dev or numpy-devel.