ERROR when installing pygrappa in a singularity image

[mckib2]

ERROR when installing pygrappa in a singularity image

[zaccharieramzi]

I managed to get access to the logs by installing everything but pygrappa and then in the container, trying to install pygrappa. The error is as follows:

2020-07-01T18:08:57,312 Exception information:
2020-07-01T18:08:57,312 Traceback (most recent call last):
2020-07-01T18:08:57,312   File "/usr/local/lib/python3.6/dist-packages/pip/_internal/req/req_install.py", line 841, in install
2020-07-01T18:08:57,312     req_description=str(self.req),
2020-07-01T18:08:57,312   File "/usr/local/lib/python3.6/dist-packages/pip/_internal/operations/install/legacy.py", line 86, in install
2020-07-01T18:08:57,312     raise LegacyInstallFailure
2020-07-01T18:08:57,312 pip._internal.operations.install.legacy.LegacyInstallFailure
2020-07-01T18:08:57,312 
2020-07-01T18:08:57,312 During handling of the above exception, another exception occurred:
2020-07-01T18:08:57,312 
2020-07-01T18:08:57,312 Traceback (most recent call last):
2020-07-01T18:08:57,312   File "/usr/local/lib/python3.6/dist-packages/pip/_internal/cli/base_command.py", line 188, in _main
2020-07-01T18:08:57,312     status = self.run(options, args)
2020-07-01T18:08:57,312   File "/usr/local/lib/python3.6/dist-packages/pip/_internal/cli/req_command.py", line 185, in wrapper
2020-07-01T18:08:57,312     return func(self, options, args)
2020-07-01T18:08:57,312   File "/usr/local/lib/python3.6/dist-packages/pip/_internal/commands/install.py", line 407, in run
2020-07-01T18:08:57,312     use_user_site=options.use_user_site,
2020-07-01T18:08:57,312   File "/usr/local/lib/python3.6/dist-packages/pip/_internal/req/__init__.py", line 71, in install_given_reqs
2020-07-01T18:08:57,312     **kwargs
2020-07-01T18:08:57,312   File "/usr/local/lib/python3.6/dist-packages/pip/_internal/req/req_install.py", line 845, in install
2020-07-01T18:08:57,312     six.reraise(*exc.parent)
2020-07-01T18:08:57,312   File "/usr/local/lib/python3.6/dist-packages/pip/_vendor/six.py", line 703, in reraise
2020-07-01T18:08:57,312     raise value
2020-07-01T18:08:57,312   File "/usr/local/lib/python3.6/dist-packages/pip/_internal/operations/install/legacy.py", line 76, in install
2020-07-01T18:08:57,312     cwd=unpacked_source_directory,
2020-07-01T18:08:57,312   File "/usr/local/lib/python3.6/dist-packages/pip/_internal/utils/subprocess.py", line 274, in runner
2020-07-01T18:08:57,312     spinner=spinner,
2020-07-01T18:08:57,312   File "/usr/local/lib/python3.6/dist-packages/pip/_internal/utils/subprocess.py", line 241, in call_subprocess
2020-07-01T18:08:57,312     raise InstallationError(exc_msg)
2020-07-01T18:08:57,312 pip._internal.exceptions.InstallationError: Command errored out with exit status 1: /usr/bin/python3.6 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-frxa9xn1/pygrappa/setup.py'"'"'; __file__='"'"'/tmp/pip-install-frxa9xn1/pygrappa/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-k9cnozx8/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.6/pygrappa Check the logs for full command output.

[mckib2]

I have not seen this error before, but I can take a look at it later today.

[remmaria]

I have not seen this error before, but I can take a look at it later today.

I had the same issue here. I would really appreciate that! =)))

[mckib2]

Bootstrap: docker
From: ubuntu:16.04

Is there a reason you're using Ubuntu 16 instead of 18 or 20 (16 will lose support next year, so no rush to upgrade, just curious)? I'm just starting to take a look at this. I can recreate your issue.

[mckib2]

As a work around, this recipe based on Ubuntu 18 appears to install without a hitch:

Bootstrap: docker
From: ubuntu:18.04


%help
    Singularity container for GRAPPA.

%post
  apt update -y
  apt-get install -y python3-pip
  pip3 install numpy
  pip3 install pygrappa

[mckib2]

@zaccharieramzi and @remmaria The following adjustments to the singularity recipe are working for me:

Bootstrap: docker
From: ubuntu:16.04


%help
    Singularity container for GRAPPA.

%post
  apt update -y
  apt install software-properties-common curl build-essential -y
  apt update -y
  add-apt-repository ppa:deadsnakes/ppa -y
  apt update -y
  apt install -y python3.6 python3.6-dev
  curl https://bootstrap.pypa.io/get-pip.py | python3.6
  python3.6 -m pip install numpy
  python3.6 -m pip install pygrappa

I believe the fix is to install the build-essential package along with the software-properties-common package. This will get you everything you need to build the C/C++ extensions required for pygrappa. The other small differences are probably inconsequential, just me experimenting with things. Let me know if it does not work for you

[zaccharieramzi]

@mckib2 thanks your fixes worked for me.