CLIPper install problem
Nick Webster
^
clipper/src/peaksmodule.cc:468:36: error: use of undeclared identifier 'PyInt_FromLong'; did you mean 'PyLong_FromLong'?
PyList_SetItem(retWiggle, i, PyInt_FromLong(wiggle[i]));
^~~~~~~~~~~~~~
PyLong_FromLong
/Users/nicholaswebster/anaconda2/envs/py3/include/python3.5m/longobject.h:18:24: note: 'PyLong_FromLong' declared here
PyAPI_FUNC(PyObject *) PyLong_FromLong(long);
^
clipper/src/peaksmodule.cc:471:38: error: use of undeclared identifier 'PyInt_FromLong'; did you mean 'PyLong_FromLong'?
PyList_SetItem(retPos_counts, i, PyInt_FromLong(pos_counts[i]));
^~~~~~~~~~~~~~
PyLong_FromLong
/Users/nicholaswebster/anaconda2/envs/py3/include/python3.5m/longobject.h:18:24: note: 'PyLong_FromLong' declared here
PyAPI_FUNC(PyObject *) PyLong_FromLong(long);
^
clipper/src/peaksmodule.cc:455:21: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long')
[-Wsign-compare]
for (int i = 0; i < lengths.size(); i++) {
~ ^ ~~~~~~~~~~~~~~
clipper/src/peaksmodule.cc:464:21: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long')
[-Wsign-compare]
for (int i = 0; i < wiggle.size(); i++) {
~ ^ ~~~~~~~~~~~~~
clipper/src/peaksmodule.cc:498:12: warning: duplicate 'extern' declaration specifier [-Wduplicate-decl-specifier]
extern "C" PyMODINIT_FUNC initpeaks(void)
^
/Users/nicholaswebster/anaconda2/envs/py3/include/python3.5m/pyport.h:784:39: note: expanded from macro 'PyMODINIT_FUNC'
# define PyMODINIT_FUNC extern "C" PyObject*
^
clipper/src/peaksmodule.cc:501:3: error: use of undeclared identifier 'Py_InitModule'
Py_InitModule("peaks", peaks_methods);
^
10 warnings and 18 errors generated.
error: command '/usr/bin/clang' failed with exit status 1
Any thoughts?
Nick Webster
Nick
Nick Webster
Gabriel Pratt
Further complications. I installed in python 2.7 environment. Everything seemed to be going fine until RuntimeError: Scikit-learn requires python3.5 or later. So if Scikit-learn is required by clipper then clipper cannot be run in python2.x.
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code4DNA
On Thursday, January 23, 2020 at 3:48:54 PM UTC-6, Gabriel Pratt wrote:
I know Python2 has been EOLed, but Clipper doesn't currently support Python3.We may upgrade in the future, but thats up to the current maintainers, or anyone who feels like making an open source contribution to the tool.Gabriel Pratt
On Thu, Jan 23, 2020 at 1:30 PM 'Nick Webster' via CLIPper-discuss <clipper...@googlegroups.com> wrote:
Further complications. I installed in python 2.7 environment. Everything seemed to be going fine until RuntimeError: Scikit-learn requires python3.5 or later. So if Scikit-learn is required by clipper then clipper cannot be run in python2.x.--
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Nick Webster
Using /Users/nicholaswebster/anaconda2/lib/python2.7/site-packages
Searching for kiwisolver==1.1.0
Best match: kiwisolver 1.1.0
Adding kiwisolver 1.1.0 to easy-install.pth file
Using /Users/nicholaswebster/anaconda2/lib/python2.7/site-packages
Finished processing dependencies for clipper==0.2.0
webster-imac:clipper nicholaswebster$ cd ..
Then when I ran clipper -h i got
RuntimeError: Python is not installed as a framework. The Mac OS X backend will not be able to function correctly if Python is not installed as a framework. See the Python documentation for more information on installing Python as a framework on Mac OS X. Please either reinstall Python as a framework, or try one of the other backends. If you are using (Ana)Conda please install python.app and replace the use of 'python' with 'pythonw'. See 'Working with Matplotlib on OSX' in the Matplotlib FAQ for more information.
So I used conda install to reinstall matplotlib as I read that conda install prevents the framework problems with pip
Now when I run clipper -h I get a different error:
Traceback (most recent call last):
File "/Users/nicholaswebster/anaconda2/bin/clipper", line 11, in <module>
load_entry_point('clipper==0.2.0', 'console_scripts', 'clipper')()
File "/Users/nicholaswebster/anaconda2/lib/python2.7/site-packages/pkg_resources/__init__.py", line 489, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/Users/nicholaswebster/anaconda2/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2852, in load_entry_point
return ep.load()
File "/Users/nicholaswebster/anaconda2/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2443, in load
return self.resolve()
File "/Users/nicholaswebster/anaconda2/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2449, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
File "/Users/nicholaswebster/anaconda2/lib/python2.7/site-packages/clipper-0.2.0-py2.7-macosx-10.7-x86_64.egg/clipper/src/peakfinder.py", line 17, in <module>
from clipper.src.call_peak import call_peaks, poissonP
File "/Users/nicholaswebster/anaconda2/lib/python2.7/site-packages/clipper-0.2.0-py2.7-macosx-10.7-x86_64.egg/clipper/src/call_peak.py", line 694, in <module>
class MyGMM(mixture.GMM):
AttributeError: 'module' object has no attribute 'GMM'
Any thoughts? Thanks
code4DNA
pip install scikit-learn==0.18.2