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I followed the installation instructions as provided by the developers and installed biopython as follows: python3.5 -m pip install biopython I get the following errors (see below my message), and I think the main problem of all issues is that Python modules cannot be opened. I reinstalled Python completely, I tried to download the modules separate but nothing helped.

Does perhaps anyone has a solution?

Full output:

$ python3.5 -m pip install biopython
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_posixsubprocess.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_posixsubprocess.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_posixsubprocess.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_posixsubprocess.gcda:Cannot open
Collecting biopython
  Downloading https://files.pythonhosted.org/packages/59/8f/454d961e821d5f600eb59885dc32aa39e3f226357f5d18a839d7ae088722/biopython-1.76-cp35-cp35m-manylinux1_x86_64.whl (2.3MB)
    100% |████████████████████████████████| 2.3MB 836kB/s 
Collecting numpy (from biopython)
  Downloading https://files.pythonhosted.org/packages/ff/18/c0b937e2f84095ae230196899e56d1d7d76c8e8424fb235ed7e5bb6d68af/numpy-1.18.2-cp35-cp35m-manylinux1_x86_64.whl (20.0MB)
    100% |████████████████████████████████| 20.0MB 101kB/s 
Installing collected packages: numpy, biopython
Exception:
Traceback (most recent call last):
  File "/usr/local/lib/python3.5/site-packages/pip/basecommand.py", line 215, in main
    status = self.run(options, args)
  File "/usr/local/lib/python3.5/site-packages/pip/commands/install.py", line 342, in run
    prefix=options.prefix_path,
  File "/usr/local/lib/python3.5/site-packages/pip/req/req_set.py", line 784, in install
    **kwargs
  File "/usr/local/lib/python3.5/site-packages/pip/req/req_install.py", line 851, in install
    self.move_wheel_files(self.source_dir, root=root, prefix=prefix)
  File "/usr/local/lib/python3.5/site-packages/pip/req/req_install.py", line 1064, in move_wheel_files
    isolated=self.isolated,
  File "/usr/local/lib/python3.5/site-packages/pip/wheel.py", line 345, in move_wheel_files
    clobber(source, lib_dir, True)
  File "/usr/local/lib/python3.5/site-packages/pip/wheel.py", line 316, in clobber
    ensure_dir(destdir)
  File "/usr/local/lib/python3.5/site-packages/pip/utils/__init__.py", line 83, in ensure_dir
    os.makedirs(path)
  File "/usr/local/lib/python3.5/os.py", line 241, in makedirs
    mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: '/usr/local/lib/python3.5/site-packages/numpy'
You are using pip version 9.0.1, however version 20.0.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/unicodedata.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/fcntlmodule.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_elementtree.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_csv.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/arraymodule.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_multiprocessing/semaphore.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_multiprocessing/multiprocessing.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/termios.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/expat/xmltok.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/expat/xmlrole.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/expat/xmlparse.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/pyexpat.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_pickle.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_bisectmodule.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_json.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_posixsubprocess.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/grpmodule.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_lzmamodule.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_bz2module.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/zlibmodule.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_ctypes/libffi/src/x86/ffi64.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_ctypes/libffi/src/closures.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_ctypes/libffi/src/prep_cif.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_ctypes/cfield.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_ctypes/stgdict.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_ctypes/callproc.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_ctypes/callbacks.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_ctypes/_ctypes.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_randommodule.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_hashopenssl.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_datetimemodule.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/binascii.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_ssl.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/selectmodule.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_math.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/mathmodule.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/socketmodule.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_struct.gcda:Cannot open
profiling:/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/build/temp.linux-x86_64-3.5/media/biosys5/bigDisk/Users/Programs/Python-3.5.9/Modules/_heapqmodule.gcda:Cannot open
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2 Answers 2

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1

The Permission Denied error has probably occurred because your user does not have write permissions in the python installation folder.

pip install biopython --user

OR

sudo pip install biopython should do the trick. Hope this helps!

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2 Comments

Thanks, this helped also. The strange thing is that whenever I run python3.5, it prints the list of modules that cannot be opened. What does this mean, and how can I get rid of this?
This seems to be due to the use of a python version with optimisations and profiling. Check this answer and this one. --disable-profiling seems to work.
1

To solve Permission denied problem, try to run pip install with --user flag:

$ python3.5 -m pip install --user biopython
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2 Comments

Thanks Artem, it did solve some of the errors. But it is strange because on one hand I get the output: 'Successfully installed biopython-1.76 numpy-1.18.2' But still the extensive lists of cannot open modules is still there. Does anyone know what this means?
It seems that you use Python version compiled with optimizations and profiling, see stackoverflow.com/a/59824965/13134272. Try to re-install Python (maybe via pyenv or conda) or just leave these warnings as-is, unless they don't break the functionality.

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