numpy-1.14.2 build error

[nick-youngblut]

I'm trying to create a conda package for nanopack. I'm runing conda skeleton pypi nanopack --recursive and getting the following error:

# many lines of output...
Applying patch: '/tmp/tmpw692xrc4conda_skeleton_numpy-1.14.2.zip/pypi-distutils.patch'
patching file core.py
Hunk #1 succeeded at 167 with fuzz 2 (offset 1 line).
Running from numpy source directory.

Note: if you need reliable uninstall behavior, then install
with pip instead of using `setup.py install`:

  - `pip install .`       (from a git repo or downloaded source
                           release)
  - `pip install numpy`   (last NumPy release on PyPi)

Traceback (most recent call last):
  File "setup.py", line 394, in <module>
    setup_package()
  File "setup.py", line 386, in setup_package
    setup(**metadata)
  File "/tmp/tmpw692xrc4conda_skeleton_numpy-1.14.2.zip/numpy-1.14.2/numpy/distutils/core.py", line 130, in setup
    if dist.help or not _command_line_ok():
AttributeError: 'NoneType' object has no attribute 'help'
$PYTHONPATH = /tmp/tmpw692xrc4conda_skeleton_numpy-1.14.2.zip/numpy-1.14.2

Leaving build/test directories:
  Work:  /ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/skeleton_1522480590389/work
  Test:  /ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/skeleton_1522480590389/test_tmp
Leaving build/test environments:
  Test: source activate  /ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/skeleton_1522480590389/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac
  Build:    source activate  /ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/skeleton_1522480590389/_build_env

Error: command failed: /ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/skeleton_1522480590389/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/python setup.py install

Is there anything that I can do about the AttributeError: 'NoneType' object has no attribute 'help'?

$ conda info

     active environment : R_pkg_build
    active env location : /ebio/abt3_projects/software/dev/miniconda3_dev/envs/R_pkg_build
            shell level : 1
       user config file : /ebio/abt3/nyoungblut/.condarc
 populated config files : /ebio/abt3_projects/software/dev/miniconda3_dev/.condarc
                          /ebio/abt3/nyoungblut/.condarc
          conda version : 4.5.0
    conda-build version : 3.7.2
         python version : 3.6.4.final.0
       base environment : /ebio/abt3_projects/software/dev/miniconda3_dev  (writable)
           channel URLs : https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/linux-64
                          https://repo.anaconda.com/pkgs/pro/noarch
                          https://conda.anaconda.org/r/linux-64
                          https://conda.anaconda.org/r/noarch
                          https://conda.anaconda.org/qiime2/linux-64
                          https://conda.anaconda.org/qiime2/noarch
          package cache : /ebio/abt3_projects/software/dev/miniconda3_dev/pkgs
                          /ebio/abt3/nyoungblut/.conda/pkgs
       envs directories : /ebio/abt3_projects/software/dev/miniconda3_dev/envs
                          /ebio/abt3/nyoungblut/.conda/envs
               platform : linux-64
             user-agent : conda/4.5.0 requests/2.18.4 CPython/3.6.4 Linux/4.4.67 ubuntu/16.04 glibc/2.23
                UID:GID : 6354:350
             netrc file : None
           offline mode : False

[msarahan]

--recursive is finding that it needs to build numpy somehow. You should really never build numpy. It looks like nanomath is the one responsible:

Preparing transaction: ...working... done
Executing transaction: ...working... done
Applying patch: '/var/folders/94/cb44zrcj06n_vj5zgxvjpb0h0000gp/T/tmp4xyhtdw2conda_skeleton_nanomath-0.21.0.tar.gz/pypi-distutils.patch'
patching file core.py
Hunk #1 succeeded at 168 with fuzz 2 (offset 1 line).
Warning, the following versions were found for numpy

I don't understand why it's recursing into building numpy, and that's a bug, but unfortunately not a very high priority one. I advise you to ctrl-c it to prevent it from trying to build numpy, and take the recipes you have already obtained. If you need others, re-attempt the recursive build down below nanomath in the chain.

[rodgomesc]

same error for me in numpy-1.14.3

[msarahan]

@rodgomesc if you are trying to build numpy itself, you need a different recipe. You absolutely will not succeed with the skeleton generator for numpy. It is a much more complicated beast.

[msarahan]

You should make a compiler paçkage that points to your android SDK, then use the recipe that we already have for numpy. Installing to android/$ARCH is kind of an antipattern with conda. Any single env should be self-consistent in the programs and libraries it has installed (with the exception of compiler packages that target foreign architectures.

More in the docs at https://conda.io/docs/user-guide/tasks/build-packages/compiler-tools.html

and example recipe at https://github.com/AnacondaRecipes/aggregate/tree/master/ctng-compilers-activation-feedstock/recipe

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