error installing moose via brew

[angiechamberland]

I keep getting the following error when trying to install via "brew install moose":

CMake Error at cmake_modules/FindNumPy.cmake:64 (message):
NumPy import failure:

Traceback (most recent call last):

File "<string>", line 1, in <module>

ImportError: No module named numpy

Call Stack (most recent call first):
pymoose/CMakeLists.txt:31 (find_package)

-- Configuring incomplete, errors occurred!

But have confirmed I already have numpy installed.

[dilawar]

I could reproduce this error with python3.7 on Majavae. These formulae needs updating since numpy has dropped support for python2.

Meanwhile, you can try this:

$ python3 -m pip install pymoose --user --pre

this will install the wheel of nightly release. Remove the --pre if you want version 3.1.4 .

[angiechamberland]

Thanks for the quick response! Tried it out and still gives me the same error I've been getting using pip:

"Angies-MacBook-Pro:~ angiechamberland$ python3 -m pip install pymoose --user --pre
Collecting pymoose
Using cached pymoose-3.2.0.dev20200128-py3-none-any.whl (5.5 MB)
Requirement already satisfied: numpy in ./anaconda3/lib/python3.7/site-packages (from pymoose) (1.15.4)
Installing collected packages: pymoose
Successfully installed pymoose-3.2.0.dev20200128
Angies-MacBook-Pro:~ angiechamberland$ python
Python 3.7.1 (default, Dec 14 2018, 13:28:58)
[Clang 4.0.1 (tags/RELEASE_401/final)] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.

import moose
Traceback (most recent call last):
File "", line 1, in
File "/Users/angiechamberland/.local/lib/python3.7/site-packages/moose/init.py", line 10, in
from moose._moose import *
ImportError: dlopen(/Users/angiechamberland/.local/lib/python3.7/site-packages/moose/_moose.so, 2): no suitable image found. Did find:
/Users/angiechamberland/.local/lib/python3.7/site-packages/moose/_moose.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x03
/Users/angiechamberland/.local/lib/python3.7/site-packages/moose/_moose.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x03
"

[dilawar]

This looks like a packaging bug. Ideally, anaconda should not install the Linux wheel on OSX. I've to dig a little to resolve this. Meanwhile, you can try the following: - Set up a virtual environment using homebrew's python. $ /usr/local/bin/python3.7 -m venv ~/PY37 # setup isolated venv at ~/PY37 $ source ~/PY37/bin/activate # activate venv $ pip install pymoose --pre # install moose in virtualenv $ python -c 'import moose' # test importing moose - Or, use docker. There is an image on dockerhub. $ docker run -it bhallalab/moose best, Dilawar

…

On Wed, Jan 29, 2020 at 5:27 PM angiechamberland ***@***.***> wrote: Thanks for the quick response! Tried it out and still gives me the same error I've been getting using pip: "Angies-MacBook-Pro:~ angiechamberland$ python3 -m pip install pymoose --user --pre Collecting pymoose Using cached pymoose-3.2.0.dev20200128-py3-none-any.whl (5.5 MB) Requirement already satisfied: numpy in ./anaconda3/lib/python3.7/site-packages (from pymoose) (1.15.4) Installing collected packages: pymoose Successfully installed pymoose-3.2.0.dev20200128 Angies-MacBook-Pro:~ angiechamberland$ python Python 3.7.1 (default, Dec 14 2018, 13:28:58) [Clang 4.0.1 (tags/RELEASE_401/final)] :: Anaconda, Inc. on darwin Type "help", "copyright", "credits" or "license" for more information. import moose Traceback (most recent call last): File "", line 1, in File "/Users/angiechamberland/.local/lib/python3.7/site-packages/moose/ *init*.py", line 10, in from moose._moose import * ImportError: dlopen(/Users/angiechamberland/.local/lib/python3.7/site-packages/moose/_moose.so, 2): no suitable image found. Did find: /Users/angiechamberland/.local/lib/python3.7/site-packages/moose/_moose.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x03 /Users/angiechamberland/.local/lib/python3.7/site-packages/moose/_moose.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x03 " — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1?email_source=notifications&email_token=AAG2VQLUY5E76PUA3URHR2LRAFVKNA5CNFSM4KM5T7CKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEKG56XY#issuecomment-579723103>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAG2VQM7TL6EUENKU3KDOJ3RAFVKNANCNFSM4KM5T7CA> .

-- Dilawar NCBS Bangalore

[angiechamberland]

Thanks.

the virtual environment script gives me this:

-bash: /usr/local/bin/python3.7: No such file or directory

and docker script gives me:

/usr/bin/xterm: Xt error: Can't open display:
/usr/bin/xterm: DISPLAY is not set

[dilawar]

@angiechamberland Sorry, I should have tested these commands beforehand. It seems that either our wheels for OSX are broken or pip is pulling linux wheel on OSX.

Sorry again for the docker image. The right command is the following.

$ docker run -ti --rm -e DISPLAY=:0 -v /tmp/.X11-unix:/tmp/.X11-unix bhallalab/moose:latest

I'll update this issue when I fix the wheel and brew install scripts.

[dilawar]

UPDATE Above docker command works on Linux host. I can't figure out how to run it in a OSX host. There are some pointers here if you want to try: https://sourabhbajaj.com/blog/2017/02/07/gui-applications-docker-mac/

[dilawar]

I have created a test homebrew tap that should work now.

In terminal, I did the following.

$ brew untap bhallalab/moose
$ brew tap dilawar/moose
$ brew install --HEAD moose-nightly
$ python3 -c 'import moose; print(moose.version())'
3.2.0-9e0b0d1ad

The official release will be after BhallaLab/moose-core#383 and BhallaLab/moose-core#382 are merged.

[angiechamberland]

Everything seemed to work right up until trying to import moose. still getting this response:

Traceback (most recent call last):
File "", line 1, in
File "/Users/angiechamberland/.local/lib/python3.7/site-packages/moose/init.py", line 5, in
from moose.moose import *
File "/Users/angiechamberland/.local/lib/python3.7/site-packages/moose/moose.py", line 21, in
from moose._moose import *
ImportError: dlopen(/Users/angiechamberland/.local/lib/python3.7/site-packages/moose/_moose.so, 2): no suitable image found. Did find:
/Users/angiechamberland/.local/lib/python3.7/site-packages/moose/_moose.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00
/Users/angiechamberland/.local/lib/python3.7/site-packages/moose/_moose.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00

[angiechamberland]

Also, thanks for all your help and assistance on this.

[dilawar]

Uninstall all instances of moose installed previously either using PIP or manually. $ pip uninstall pymoose $ rm -rf Users/angiechamberland/.local/lib/python3.7/site-packages/moose/ ⁣Get BlueMail for Android ​

…

On 1 Feb 2020, 04:37, at 04:37, angiechamberland ***@***.***> wrote: Everything seemed to work right up until trying to import moose. still getting this response: Traceback (most recent call last): File "<string>", line 1, in <module> File "/Users/angiechamberland/.local/lib/python3.7/site-packages/moose/__init__.py", line 5, in <module> from moose.moose import * File "/Users/angiechamberland/.local/lib/python3.7/site-packages/moose/moose.py", line 21, in <module> from moose._moose import * ImportError: dlopen(/Users/angiechamberland/.local/lib/python3.7/site-packages/moose/_moose.so, 2): no suitable image found. Did find: /Users/angiechamberland/.local/lib/python3.7/site-packages/moose/_moose.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 /Users/angiechamberland/.local/lib/python3.7/site-packages/moose/_moose.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 -- You are receiving this because you commented. Reply to this email directly or view it on GitHub: #1 (comment)

[angiechamberland]

Awesome, thanks. That made some progress.

Moose seems to install, but once in moose, the commands don't seem to work:

Angies-MacBook-Pro:~ angiechamberland$ python3 -c 'import moose; print(moose.version())' 3.2.0-9e0b0d1ad
Traceback (most recent call last):
File "", line 1, in
AttributeError: module 'moose' has no attribute 'version'
Angies-MacBook-Pro:~ angiechamberland$ python
Python 3.7.1 (default, Dec 14 2018, 13:28:58)
[Clang 4.0.1 (tags/RELEASE_401/final)] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.

import moose
moose.le
Traceback (most recent call last):
File "", line 1, in
AttributeError: module 'moose' has no attribute 'le'
moose.le()
Traceback (most recent call last):
File "", line 1, in
AttributeError: module 'moose' has no attribute 'le'
dir(moose)
['doc', 'file', 'loader', 'name', 'package', 'path', 'spec']

any ideas?

[dilawar]

Yes. It's my fault :-( !

I promise next update will resolve it. It is getting embarrassing now; can't blame unfamiliarity with OSX anymore :-/. I am almost there.

[angiechamberland]

No problem - I keep assuming I'm doing something wrong, I appreciate how quickly you've been responding.
Is there a workaround for now or do you know how long it'll take to resolve? We're using this for a class I'm taking, so just want to make whatever alternate arrangements necessary if needed. Thanks again!