fatal error: 'numpy/arrayobject.h' file not found

[kesteph]

Hello
I installed the most recent version of nucleoatac and am now receiving the following error. It seems that the program is looking for "numpy/arrayobject.h". I'm not too familiar with Python. Can you advise?

I am using Python 2.7.10 with the following dependencies installed:
Cython==0.26
pysam==0.11.2.2
numpy==1.13.1
scipy==0.19.1
matplotlib==2.0.2

thank you
Kim

Lucy:nucleoATAC kims$ nucleoatac run --bed macs2.Cpeaks.bed --bam ATACMC.bam --fasta /Users/kims/ReferenceGenomes/rn6.fa --out ATACMC.NucleoATAC --cores 8
Command run: /usr/local/bin/nucleoatac run --bed macs2.Cpeaks.bed --bam ATACMC.bam --fasta /Users/kims/ReferenceGenomes/rn6.fa --out ATACMC.NucleoATAC --cores 8
nucleoatac version 0.3.4
start run at: 2017-07-30 15:40
/Users/kims/.pyxbld/temp.macosx-10.12-x86_64-2.7/pyrex/pyatac/fragments.c:435:10: fatal error: 'numpy/arrayobject.h' file not found
#include "numpy/arrayobject.h"
^
1 error generated.
Traceback (most recent call last):
File "/usr/local/bin/nucleoatac", line 33, in
nucleoatac_main(args)
File "/usr/local/lib/python2.7/site-packages/nucleoatac/cli.py", line 50, in nucleoatac_main
from nucleoatac.run_occ import run_occ
File "/usr/local/lib/python2.7/site-packages/nucleoatac/run_occ.py", line 19, in
from nucleoatac.Occupancy import FragmentMixDistribution, OccupancyParameters, OccChunk
File "/usr/local/lib/python2.7/site-packages/nucleoatac/Occupancy.py", line 12, in
from pyatac.fragmentsizes import FragmentSizes
File "/usr/local/lib/python2.7/site-packages/pyatac/fragmentsizes.py", line 10, in
from pyatac.fragments import getAllFragmentSizes, getFragmentSizesFromChunkList
File "/usr/local/lib/python2.7/site-packages/pyximport/pyximport.py", line 445, in load_module
language_level=self.language_level)
File "/usr/local/lib/python2.7/site-packages/pyximport/pyximport.py", line 234, in load_module
exec("raise exc, None, tb", {'exc': exc, 'tb': tb})
File "/usr/local/lib/python2.7/site-packages/pyximport/pyximport.py", line 216, in load_module
inplace=build_inplace, language_level=language_level)
File "/usr/local/lib/python2.7/site-packages/pyximport/pyximport.py", line 192, in build_module
reload_support=pyxargs.reload_support)
File "/usr/local/lib/python2.7/site-packages/pyximport/pyxbuild.py", line 102, in pyx_to_dll
dist.run_commands()
File "/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/usr/local/lib/python2.7/site-packages/Cython/Distutils/old_build_ext.py", line 185, in run
_build_ext.build_ext.run(self)
File "/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/command/build_ext.py", line 340, in run
self.build_extensions()
File "/usr/local/lib/python2.7/site-packages/Cython/Distutils/old_build_ext.py", line 193, in build_extensions
self.build_extension(ext)
File "/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/command/build_ext.py", line 499, in build_extension
depends=ext.depends)
File "/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/ccompiler.py", line 574, in compile
self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
File "/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/unixccompiler.py", line 124, in _compile
raise CompileError, msg
ImportError: Building module pyatac.fragments failed: ["CompileError: command 'clang' failed with exit status 1\n"]

[AliciaSchep]

this is on a mac? also, to clarify, had you previously run earlier version of nucleoatac without issue but now see this error with most recent error, or is this the first version you have tried?

[kesteph]

Hi Alicia Yes, I am trying to run this on macOS 10.12.6. I have used previous versions without difficulty, but this is the first installation of NucleoATAC on this machine. thank you On Jul 30, 2017, at 23:58, Alicia Schep <[email protected]<mailto:[email protected]>> wrote: this is on a mac? also, to clarify, had you previously run earlier version of nucleoatac without issue but now see this error with most recent error, or is this the first version you have tried? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#64 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/ANrO9EVGyMT56pzMqzuYLxnF3EDy2mSkks5sTVDfgaJpZM4Onuyy>.

[sarawernig]

Has this issue been resolved? I have exactly the same problem installing on macOS 10.14.3.

[kesteph]

No I never received a response, but I was able to install it on another system running Linux. On Feb 28, 2019, at 11:19, Fluorine <[email protected]<mailto:[email protected]>> wrote: Has this issue been resolved? I have exactly the same problem installing on macOS 10.14.3. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#64 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/ANrO9HlyCDfnRYxfleWklYnOSpU1hOm5ks5vSAGdgaJpZM4Onuyy>.

[sarawernig]

I solved it by installing it via conda. For some reason, this works on MacOS.

conda install -c bioconda nucleoatac