The "make" step of installation is failing for me. I am running on a mac with 10.13.6 High Sierra, running python "Python 2.7.13 :: Anaconda 2.1.0 (x86_64)".
I followed these installation instructions:
git clone git://github.com/glennhickey/progressiveCactus.git
cd progressiveCactus
git pull
git submodule update --init
make
Here's the output:
cd submodules && make all
rm -f /Users/irwin/Documents/Biology/git/progressiveCactus/submodules/../environment
python2.7 /Users/irwin/Documents/Biology/git/progressiveCactus/submodules/virtualenv/virtualenv.py /Users/irwin/Documents/Biology/git/progressiveCactus/python
New python executable in /Users/irwin/Documents/Biology/git/progressiveCactus/python/bin/python2.7
Not overwriting existing python script /Users/irwin/Documents/Biology/git/progressiveCactus/python/bin/python (you must use /Users/irwin/Documents/Biology/git/progressiveCactus/python/bin/python2.7)
Installing setuptools, pip, wheel...
Complete output from command /Users/irwin/Documen...python/bin/python2.7 - setuptools pip wheel:
Traceback (most recent call last):
File "", line 4, in
File "//anaconda/lib/python2.7/tempfile.py", line 32, in
import io as _io
File "//anaconda/lib/python2.7/io.py", line 51, in
import _io
ImportError: dlopen(/Users/irwin/Documents/Biology/git/progressiveCactus/python/lib/python2.7/lib-dynload/_io.so, 2): Symbol not found: __PyCodecInfo_GetIncrementalDecoder
Referenced from: /Users/irwin/Documents/Biology/git/progressiveCactus/python/lib/python2.7/lib-dynload/_io.so
Expected in: flat namespace
in /Users/irwin/Documents/Biology/git/progressiveCactus/python/lib/python2.7/lib-dynload/_io.so
...Installing setuptools, pip, wheel...done.
Traceback (most recent call last):
File "/Users/irwin/Documents/Biology/git/progressiveCactus/submodules/virtualenv/virtualenv.py", line 2331, in
main()
File "/Users/irwin/Documents/Biology/git/progressiveCactus/submodules/virtualenv/virtualenv.py", line 712, in main
symlink=options.symlink)
File "/Users/irwin/Documents/Biology/git/progressiveCactus/submodules/virtualenv/virtualenv.py", line 943, in create_environment
download=download,
File "/Users/irwin/Documents/Biology/git/progressiveCactus/submodules/virtualenv/virtualenv.py", line 900, in install_wheel
call_subprocess(cmd, show_stdout=False, extra_env=env, stdin=SCRIPT)
File "/Users/irwin/Documents/Biology/git/progressiveCactus/submodules/virtualenv/virtualenv.py", line 796, in call_subprocess
% (cmd_desc, proc.returncode))
OSError: Command /Users/irwin/Documen...python/bin/python2.7 - setuptools pip wheel failed with error code 1
make[1]: [virtPyRule] Error 1
make: [all] Error 2
The "make" step of installation is failing for me. I am running on a mac with 10.13.6 High Sierra, running python "Python 2.7.13 :: Anaconda 2.1.0 (x86_64)".
I followed these installation instructions: git clone git://github.com/glennhickey/progressiveCactus.git cd progressiveCactus git pull git submodule update --init make
Here's the output: cd submodules && make all rm -f /Users/irwin/Documents/Biology/git/progressiveCactus/submodules/../environment python2.7 /Users/irwin/Documents/Biology/git/progressiveCactus/submodules/virtualenv/virtualenv.py /Users/irwin/Documents/Biology/git/progressiveCactus/python New python executable in /Users/irwin/Documents/Biology/git/progressiveCactus/python/bin/python2.7 Not overwriting existing python script /Users/irwin/Documents/Biology/git/progressiveCactus/python/bin/python (you must use /Users/irwin/Documents/Biology/git/progressiveCactus/python/bin/python2.7) Installing setuptools, pip, wheel... Complete output from command /Users/irwin/Documen...python/bin/python2.7 - setuptools pip wheel: Traceback (most recent call last): File "", line 4, in
File "//anaconda/lib/python2.7/tempfile.py", line 32, in
import io as _io
File "//anaconda/lib/python2.7/io.py", line 51, in
import _io
ImportError: dlopen(/Users/irwin/Documents/Biology/git/progressiveCactus/python/lib/python2.7/lib-dynload/_io.so, 2): Symbol not found: __PyCodecInfo_GetIncrementalDecoder
Referenced from: /Users/irwin/Documents/Biology/git/progressiveCactus/python/lib/python2.7/lib-dynload/_io.so
Expected in: flat namespace
in /Users/irwin/Documents/Biology/git/progressiveCactus/python/lib/python2.7/lib-dynload/_io.so
...Installing setuptools, pip, wheel...done. Traceback (most recent call last): File "/Users/irwin/Documents/Biology/git/progressiveCactus/submodules/virtualenv/virtualenv.py", line 2331, in
main()
File "/Users/irwin/Documents/Biology/git/progressiveCactus/submodules/virtualenv/virtualenv.py", line 712, in main
symlink=options.symlink)
File "/Users/irwin/Documents/Biology/git/progressiveCactus/submodules/virtualenv/virtualenv.py", line 943, in create_environment
download=download,
File "/Users/irwin/Documents/Biology/git/progressiveCactus/submodules/virtualenv/virtualenv.py", line 900, in install_wheel
call_subprocess(cmd, show_stdout=False, extra_env=env, stdin=SCRIPT)
File "/Users/irwin/Documents/Biology/git/progressiveCactus/submodules/virtualenv/virtualenv.py", line 796, in call_subprocess
% (cmd_desc, proc.returncode))
OSError: Command /Users/irwin/Documen...python/bin/python2.7 - setuptools pip wheel failed with error code 1
make[1]: [virtPyRule] Error 1
make: [all] Error 2
This sounds similar to the problem described here: https://stackoverflow.com/questions/34386527/symbol-not-found-pycodecinfo-getincrementaldecoder This suggests the problem is related to a python 2.7.10 module importing a module from a later version.