pip安装biom错误-找不到格式为'numpy/arrayobject.h‘的文件

Question

我无法使用pip install biom-format安装biom格式。这是我得到的错误。

N85566:~ smitra$ pip install biom-format
Collecting biom-format
  Using cached biom-format-2.1.5.tar.gz
Requirement already satisfied (use --upgrade to upgrade): click in /usr/local/lib/python2.7/site-packages (from biom-format)
Requirement already satisfied (use --upgrade to upgrade): numpy>=1.3.0 in /Library/Python/2.7/site-packages (from biom-format)
Requirement already satisfied (use --upgrade to upgrade): future>=0.14.3 in /usr/local/lib/python2.7/site-packages (from biom-format)
Collecting scipy>=0.13.0 (from biom-format)
  Using cached scipy-0.17.0-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting pyqi (from biom-format)
Building wheels for collected packages: biom-format
  Running setup.py bdist_wheel for biom-format ... error
  Complete output from command /usr/local/opt/python/bin/python2.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/w0/sg297rxj3738tghvhq3fhr5c0000gp/T/pip-build-TljllL/biom-format/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" bdist_wheel -d /var/folders/w0/sg297rxj3738tghvhq3fhr5c0000gp/T/tmpmTturCpip-wheel- --python-tag cp27:
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.macosx-10.10-x86_64-2.7
  creating build/lib.macosx-10.10-x86_64-2.7/biom
  copying biom/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/biom
  copying biom/err.py -> build/lib.macosx-10.10-x86_64-2.7/biom
  copying biom/exception.py -> build/lib.macosx-10.10-x86_64-2.7/biom
  copying biom/parse.py -> build/lib.macosx-10.10-x86_64-2.7/biom
  copying biom/table.py -> build/lib.macosx-10.10-x86_64-2.7/biom
  copying biom/util.py -> build/lib.macosx-10.10-x86_64-2.7/biom
  creating build/lib.macosx-10.10-x86_64-2.7/tests
  copying tests/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/tests
  copying tests/test_err.py -> build/lib.macosx-10.10-x86_64-2.7/tests
  copying tests/test_parse.py -> build/lib.macosx-10.10-x86_64-2.7/tests
  copying tests/test_table.py -> build/lib.macosx-10.10-x86_64-2.7/tests
  copying tests/test_util.py -> build/lib.macosx-10.10-x86_64-2.7/tests
  creating build/lib.macosx-10.10-x86_64-2.7/biom/cli
  copying biom/cli/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/biom/cli
  copying biom/cli/installation_informer.py -> build/lib.macosx-10.10-x86_64-2.7/biom/cli
  copying biom/cli/metadata_adder.py -> build/lib.macosx-10.10-x86_64-2.7/biom/cli
  copying biom/cli/table_converter.py -> build/lib.macosx-10.10-x86_64-2.7/biom/cli
  copying biom/cli/table_head.py -> build/lib.macosx-10.10-x86_64-2.7/biom/cli
  copying biom/cli/table_normalizer.py -> build/lib.macosx-10.10-x86_64-2.7/biom/cli
  copying biom/cli/table_subsetter.py -> build/lib.macosx-10.10-x86_64-2.7/biom/cli
  copying biom/cli/table_summarizer.py -> build/lib.macosx-10.10-x86_64-2.7/biom/cli
  copying biom/cli/table_validator.py -> build/lib.macosx-10.10-x86_64-2.7/biom/cli
  copying biom/cli/uc_processor.py -> build/lib.macosx-10.10-x86_64-2.7/biom/cli
  copying biom/cli/util.py -> build/lib.macosx-10.10-x86_64-2.7/biom/cli
  creating build/lib.macosx-10.10-x86_64-2.7/tests/test_cli
  copying tests/test_cli/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/tests/test_cli
  copying tests/test_cli/test_add_metadata.py -> build/lib.macosx-10.10-x86_64-2.7/tests/test_cli
  copying tests/test_cli/test_show_install_info.py -> build/lib.macosx-10.10-x86_64-2.7/tests/test_cli
  copying tests/test_cli/test_subset_table.py -> build/lib.macosx-10.10-x86_64-2.7/tests/test_cli
  copying tests/test_cli/test_summarize_table.py -> build/lib.macosx-10.10-x86_64-2.7/tests/test_cli
  copying tests/test_cli/test_table_converter.py -> build/lib.macosx-10.10-x86_64-2.7/tests/test_cli
  copying tests/test_cli/test_table_normalizer.py -> build/lib.macosx-10.10-x86_64-2.7/tests/test_cli
  copying tests/test_cli/test_uc_processor.py -> build/lib.macosx-10.10-x86_64-2.7/tests/test_cli
  copying tests/test_cli/test_validate_table.py -> build/lib.macosx-10.10-x86_64-2.7/tests/test_cli
  running egg_info
  writing requirements to biom_format.egg-info/requires.txt
  writing biom_format.egg-info/PKG-INFO
  writing top-level names to biom_format.egg-info/top_level.txt
  writing dependency_links to biom_format.egg-info/dependency_links.txt
  writing entry points to biom_format.egg-info/entry_points.txt
  warning: manifest_maker: standard file '-c' not found

  reading manifest file 'biom_format.egg-info/SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  no previously-included directories found matching 'docs/_build'
  warning: no previously-included files matching '*.pyc' found anywhere in distribution
  warning: no previously-included files matching '*.pyo' found anywhere in distribution
  warning: no previously-included files matching '.git' found anywhere in distribution
  writing manifest file 'biom_format.egg-info/SOURCES.txt'
  copying biom/_filter.c -> build/lib.macosx-10.10-x86_64-2.7/biom
  copying biom/_filter.pyx -> build/lib.macosx-10.10-x86_64-2.7/biom
  copying biom/_subsample.c -> build/lib.macosx-10.10-x86_64-2.7/biom
  copying biom/_subsample.pyx -> build/lib.macosx-10.10-x86_64-2.7/biom
  copying biom/_transform.c -> build/lib.macosx-10.10-x86_64-2.7/biom
  copying biom/_transform.pyx -> build/lib.macosx-10.10-x86_64-2.7/biom
  running build_ext
  building 'biom._filter' extension
  creating build/temp.macosx-10.10-x86_64-2.7
  creating build/temp.macosx-10.10-x86_64-2.7/biom
  clang -fno-strict-aliasing -fno-common -dynamic -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch x86_64 -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c biom/_filter.c -o build/temp.macosx-10.10-x86_64-2.7/biom/_filter.o
  biom/_filter.c:258:10: fatal error: 'numpy/arrayobject.h' file not found
  #include "numpy/arrayobject.h"
           ^
  1 error generated.
  error: command 'clang' failed with exit status 1

  ----------------------------------------
  Failed building wheel for biom-format
  Running setup.py clean for biom-format
Failed to build biom-format
Installing collected packages: scipy, pyqi, biom-format
  Found existing installation: scipy 0.12.0
    Uninstalling scipy-0.12.0:
Exception:
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site-packages/pip/basecommand.py", line 209, in main
    status = self.run(options, args)
  File "/usr/local/lib/python2.7/site-packages/pip/commands/install.py", line 317, in run
    prefix=options.prefix_path,
  File "/usr/local/lib/python2.7/site-packages/pip/req/req_set.py", line 726, in install
    requirement.uninstall(auto_confirm=True)
  File "/usr/local/lib/python2.7/site-packages/pip/req/req_install.py", line 746, in uninstall
    paths_to_remove.remove(auto_confirm)
  File "/usr/local/lib/python2.7/site-packages/pip/req/req_uninstall.py", line 115, in remove
    renames(path, new_path)
  File "/usr/local/lib/python2.7/site-packages/pip/utils/__init__.py", line 267, in renames
    shutil.move(old, new)
  File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 300, in move
    rmtree(src)
  File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 252, in rmtree
    onerror(os.remove, fullname, sys.exc_info())
  File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 250, in rmtree
    os.remove(fullname)
OSError: [Errno 13] Permission denied: '/Library/Python/2.7/site-packages/scipy-0.12.0-py2.7.egg-info/dependency_links.txt'
N85566:~ smitra$ 

还有一件事，我试着更新============，它似乎仍然显示了worked..but的早期版本。这就是我所做的。

=========

N85566:~ smitra$ pip install numpy --upgrade
Collecting numpy
  Downloading numpy-1.11.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (3.9MB)
    100% |████████████████████████████████| 3.9MB 347kB/s 
Installing collected packages: numpy
  Found existing installation: numpy 1.7.1
    Uninstalling numpy-1.7.1:
Exception:
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site-packages/pip/basecommand.py", line 209, in main
    status = self.run(options, args)
  File "/usr/local/lib/python2.7/site-packages/pip/commands/install.py", line 317, in run
    prefix=options.prefix_path,
  File "/usr/local/lib/python2.7/site-packages/pip/req/req_set.py", line 726, in install
    requirement.uninstall(auto_confirm=True)
  File "/usr/local/lib/python2.7/site-packages/pip/req/req_install.py", line 746, in uninstall
    paths_to_remove.remove(auto_confirm)
  File "/usr/local/lib/python2.7/site-packages/pip/req/req_uninstall.py", line 115, in remove
    renames(path, new_path)
  File "/usr/local/lib/python2.7/site-packages/pip/utils/__init__.py", line 267, in renames
    shutil.move(old, new)
  File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 300, in move
    rmtree(src)
  File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 252, in rmtree
    onerror(os.remove, fullname, sys.exc_info())
  File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 250, in rmtree
    os.remove(fullname)
OSError: [Errno 13] Permission denied: '/Library/Python/2.7/site-packages/numpy-1.7.1-py2.7.egg-info/dependency_links.txt'
N85566:~ smitra$ 
N85566:~ smitra$ python -c "import numpy; print numpy.version.version"
1.7.1
N85566:~ smitra$ 

==========路径的任何问题可能是？？

请帮助我解决此问题。谢谢，米特拉

Answer 1

我也有同样的问题。

尝试执行以下命令：

sudo pip install -Iv https://pypi.python.org/packages/source/b/biom-format/biom-format-1.3.0.tar.gz#md5=bd35f9b7e1c7daf244fe2dffb2777606

希望能对您有所帮助。

阿德里安