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 GitHubhttps://github.com/GreenleafLab/NucleoATAC/issues/64#issuecomment-318961546, or mute the threadhttps://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 GitHubhttps://github.com/GreenleafLab/NucleoATAC/issues/64#issuecomment-468335638, or mute the threadhttps://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