Cryosparc can not install: No module named numpy.distutils.core

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#1

Hello,
When attempting to perform the basic install I get the following:

The cryoSPARC System master installation will host a database,
web application, and command layer for cryoSPARC, but will not
perform processing jobs.

Please read and confirm the above settings. The cryoSPARC database
will be stored at the database directory which is relative to the
root directory, unless provided as an absolute path.
You can change the database directory now by passing the --dbapth
parameter to this installer, or later via the command line.

Are the above settings correct?

  1. Yes
  2. No
    #? 1
    Continuing.

Setting up hard-coded config.sh environment variables


Installing all dependencies.

Checking dependencies…
Dependencies for python have changed - reinstalling…

Installing anaconda python…

PREFIX=/home/hellion/cryosparcv2/cryosparc2_master/deps/anaconda
installing: python-2.7.14-h1571d57_29 …
Python 2.7.14 :: Anaconda, Inc.
installing: ca-certificates-2017.08.26-h1d4fec5_0 …
installing: conda-env-2.6.0-h36134e3_1 …
installing: libgcc-ng-7.2.0-h7cc24e2_2 …
installing: libstdcxx-ng-7.2.0-h7a57d05_2 …
installing: libffi-3.2.1-hd88cf55_4 …
installing: ncurses-6.0-h9df7e31_2 …
installing: openssl-1.0.2n-hb7f436b_0 …
installing: tk-8.6.7-hc745277_3 …
installing: yaml-0.1.7-had09818_2 …
installing: zlib-1.2.11-ha838bed_2 …
installing: libedit-3.1-heed3624_0 …
installing: readline-7.0-ha6073c6_4 …
installing: sqlite-3.20.1-hb898158_2 …
installing: asn1crypto-0.23.0-py27h7b0c810_0 …
installing: certifi-2017.11.5-py27h71e7faf_0 …
installing: chardet-3.0.4-py27hfa10054_1 …
installing: enum34-1.1.6-py27h99a27e9_1 …
installing: idna-2.6-py27h5722d68_1 …
installing: ipaddress-1.0.18-py27h337fd85_0 …
installing: pycosat-0.6.3-py27ha4109ae_0 …
installing: pycparser-2.18-py27hefa08c5_1 …
installing: pysocks-1.6.7-py27he2db6d2_1 …
installing: ruamel_yaml-0.11.14-py27h672d447_2 …
installing: six-1.11.0-py27h5f960f1_1 …
installing: cffi-1.11.2-py27ha7929c6_0 …
installing: setuptools-36.5.0-py27h68b189e_0 …
installing: cryptography-2.1.4-py27h6697b16_0 …
installing: wheel-0.30.0-py27h2bc6bb2_1 …
installing: pip-9.0.1-py27ha730c48_4 …
installing: pyopenssl-17.5.0-py27hcee3be0_0 …
installing: urllib3-1.22-py27ha55213b_0 …
installing: requests-2.18.4-py27hc5b0589_1 …
installing: conda-4.3.31-py27_0 …
installation finished.

Done.
anaconda python installation successful.

Preparing to install all conda packages…


Done.
conda packages installation successful.

Preparing to install all pip packages…

Processing ./deps_bundle/python/python_packages/pip_packages/Flask-JSONRPC-0.3.1.tar.gz
Processing ./deps_bundle/python/python_packages/pip_packages/Flask-PyMongo-0.5.1.tar.gz
Processing ./deps_bundle/python/python_packages/pip_packages/libtiff-0.4.2.tar.gz
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File “”, line 1, in
File “/tmp/pip-P1TnNX-build/setup.py”, line 77, in
from numpy.distutils.core import setup, Extension
ImportError: No module named numpy.distutils.core

----------------------------------------

Command “python setup.py egg_info” failed with error code 1 in /tmp/pip-P1TnNX-build/
You are using pip version 9.0.1, however version 19.0.3 is available.
You should consider upgrading via the ‘pip install --upgrade pip’ command.

Done.
pip packages installation successful.

Main dependency installation completed. Continuing…

Completed.
Currently checking hash for mongodb
Dependencies for mongodb have changed - reinstalling…

mongodb 3.4.10 installation successful.

Completed.
Completed dependency check.

************ CRYOSPARC MASTER INSTALLATION COMPLETE **************

CryoSPARC System master has now been installed.
Add bin directory to your ~/.bashrc ?

  1. Yes
  2. No
    #? 1

The following lines were appended to your ~/.bashrc:
export PATH=/home/hellion/cryosparcv2/cryosparc2_master/bin:$PATH

************ CRYOSPARC SYSTEM: STANDALONE INSTALLER **************

The installer will now download, install and connect the worker
package on this machine. The worker package will allow cryoSPARC
to run compute jobs.


Starting cryoSPARC…

Starting cryoSPARC System master process…
/home/hellion/cryosparcv2/cryosparc2_master/bin/cryosparcm: line 380: supervisorctl: command not found

any solutions ?Thank you in advance


#2

Hi @biolifei,

Can you try force reinstalling your instance? Also, you’re not running this installer as root, correct?


#3

Thanks for your reply, I extracted and installed it again as root, now it works well.


#4

Hi @biolifei,

I’m glad the “forced reinstall” worked well, but I don’t recommend installing cryoSPARC as root. Not only does it introduce permission errors while running specific jobs, it can introduce security holes that our team at Structura cannot support. To be on the safe side, I’d recommend turning off cryoSPARC (cryosparcm stop), then deleting both cryosparc2_master and cryosparc2_worker directories (you can leave your database as-is). Then reinstall cryoSPARC with a regular user account as you would normally.


#5

I have the same issue. you cannot re-install cryosparc as normal user. it stops with this error code

CryoSPARC current version v2.5.0
update starting on Fri Mar 22 16:38:17 EDT 2019
No version specified - updating to latest version.
=============================
Forcing update to version v2.5.0…
=============================
/home/behrouzi/cryosparc2/cryosparc2_master/bin/cryosparcm: line 444: supervisorctl: command not found

However I can install as root and see

Successfully installed Flask-JSONRPC-0.3.1 Flask-PyMongo-0.5.1 libtiff-0.4.2

where it used to break before.
I’ve only had this issue with the current version 2.5. Did not see it on previous installs.

Thanks.