installation of hiclib

Issue #23 new
Xianfeng Li
created an issue

Dear all,

I am interested in analysis of Hi-C data sets. And I download your powerful library from https://bitbucket.org/mirnylab/hiclib. When I filter Hi-C data set after mapping, I caught some bugs as fellows.


Please compile binarySearch!!! It is in the main folder of the library ............. File "/panfs/home/sun/wujinyu/loopy/lib/python2.7/site-packages/hiclib-0.0.0-py2.7.egg/hiclib/fragmentHiC.py", line 386, in setattr raise TypeError: exceptions must be old-style classes or derived from BaseException, not NoneType


Then, I tried to compile binarySearch. And some error appeared.


cd ~/lxf/soft/mirnylab-hiclib-460c3fbc0f72/binarySearch

make


cython --cplus fastBinSearch.pyx g++ -g -Ofast -fpic -c -std=c++11 -O2 mycode.cpp -o mycode.o -fopenmp cc1plus: error: invalid option argument ‘-Ofast’ cc1plus: error: unrecognized command line option "-std=c++11" make: *** [all] Error 1


Comments (2)

  1. Ilya Flyamer

    I'm not a hiclib developer so I can't help you with the compilation, but everything should work without the binarySearch as well using np.searchsorted, albeit slower. So the error you are getting is not related to this.

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