Tensorflow install breaks (likely due to numpy)

[mortonjt]

Issue: Tensorflow seems to be breaking across multiple versions.

I'm trying to install tensorflow with another package, qiime2. That install procedure is as follows

wget -q https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py35-osx-conda.yml
conda env create -q -n q2-dev --file qiime2-latest-py35-osx-conda.yml
source activate q2-dev
conda install tensorflow=1.5 -c conda-forge

Environment (conda list):

$ conda list
# packages in environment at /Users/mortonjt/miniconda3/envs/q2-dev:
#
# Name                    Version                   Build  Channel
absl-py                   0.5.0                      py_0    conda-forge
appnope                   0.1.0                    py35_0    conda-forge
arb-bio-tools             6.0.6                         4    bioconda
asn1crypto                0.24.0                   py35_3    conda-forge
backcall                  0.1.0                      py_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.weakref         1.0.post1                py35_0    conda-forge
bibtexparser              1.0.1                      py_1    conda-forge
bioconductor-biobase      2.38.0           r341h219a75b_1    bioconda
bioconductor-biocgenerics 0.24.0                   r341_1    bioconda
bioconductor-biocparallel 1.12.0           r341h219a75b_1    bioconda
bioconductor-biostrings   2.46.0                 r3.4.1_0    bioconda
bioconductor-dada2        1.6.0                  r3.4.1_0    bioconda
bioconductor-delayedarray 0.4.1                  r3.4.1_0    bioconda
bioconductor-genomeinfodb 1.14.0                 r3.4.1_0    bioconda
bioconductor-genomeinfodbdata 1.0.0                  r3.4.1_1    bioconda
bioconductor-genomicalignments 1.14.1                 r3.4.1_0    bioconda
bioconductor-genomicranges 1.30.3                 r3.4.1_0    bioconda
bioconductor-iranges      2.12.0                 r3.4.1_0    bioconda
bioconductor-rsamtools    1.30.0                 r3.4.1_0    bioconda
bioconductor-s4vectors    0.16.0                 r3.4.1_0    bioconda
bioconductor-shortread    1.36.0                 r3.4.1_0    bioconda
bioconductor-summarizedexperiment 1.8.0                  r3.4.1_0    bioconda
bioconductor-xvector      0.18.0                 r3.4.1_0    bioconda
bioconductor-zlibbioc     1.24.0                 r3.4.1_0    bioconda
biom-format               2.1.7            py35h7eb728f_0    conda-forge
blas                      1.0                         mkl  
blast                     2.6.0               boost1.64_2    bioconda
bleach                    1.5.0                    py35_0    conda-forge
bokeh                     0.13.0                   py35_0    conda-forge
boost                     1.67.0           py35h3e44d54_0    conda-forge
boost-cpp                 1.67.0               h3a22d5f_0    conda-forge
bz2file                   0.98                       py_0    conda-forge
bzip2                     1.0.6                         1    conda-forge
ca-certificates           2018.10.15           ha4d7672_0    conda-forge
cachecontrol              0.12.5                     py_0    conda-forge
cairo                     1.14.12              he6fea26_5    conda-forge
certifi                   2018.8.24                py35_1  
cffi                      1.11.5           py35h5e8e0c9_1    conda-forge
chardet                   3.0.4                    py35_3    conda-forge
click                     7.0                        py_0    conda-forge
cryptography              2.3.1            py35hdffb7b8_0    conda-forge
cryptography-vectors      2.3.1                    py35_0    conda-forge
curl                      7.62.0               h74213dd_0    conda-forge
cutadapt                  1.18                     py35_0    bioconda
cycler                    0.10.0                     py_1    conda-forge
cython                    0.28.5           py35hfc679d8_0    conda-forge
deblur                    1.1.0                    py35_0    bioconda
decorator                 4.3.0                      py_0    conda-forge
emperor                   1.0.0beta18              py35_1    conda-forge
entrypoints               0.2.3                    py35_2    conda-forge
fastcluster               1.1.25           py35hf8a1672_0    conda-forge
fasttree                  2.1.10                        0    bioconda
fontconfig                2.13.1               hce039c3_0    conda-forge
fragment-insertion        4.3.5                    py35_0    biocore
freetype                  2.9.1                h6debe1e_4    conda-forge
future                    0.16.0                   py35_2    conda-forge
gettext                   0.19.8.1             h1f1d5ed_1    conda-forge
glib                      2.55.0               h464dc38_2    conda-forge
gneiss                    0.4.4                      py_0    bioconda
graphite2                 1.3.12               h7d4d677_1    conda-forge
gsl                       2.1                           2    conda-forge
h5py                      2.7.0               np112py35_0    conda-forge
harfbuzz                  1.9.0                h08d66d9_0    conda-forge
hdf5                      1.8.17                       11    conda-forge
hdmedians                 0.13             py35h7eb728f_1    conda-forge
html5lib                  0.9999999                py35_0    conda-forge
icu                       58.2                 hfc679d8_0    conda-forge
idna                      2.7                      py35_2    conda-forge
ijson                     2.3                      py35_0    qiime2
intel-openmp              2019.0                      118  
ipykernel                 5.1.0              pyh24bf2e0_0    conda-forge
ipython                   7.0.1            py35h24bf2e0_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.4.2                      py_0    conda-forge
iqtree                    1.6.8                he941832_0    bioconda
java-jdk                  8.0.92                        1    bioconda
jedi                      0.12.1                   py35_0    conda-forge
jinja2                    2.10                       py_1    conda-forge
jpeg                      9c                   h470a237_1    conda-forge
jsonschema                2.6.0                    py35_2    conda-forge
jupyter_client            5.2.3                      py_1    conda-forge
jupyter_core              4.4.0                      py_0    conda-forge
kiwisolver                1.0.1            py35h2d50403_2    conda-forge
krb5                      1.16.2               hbb41f41_0    conda-forge
libarbdb                  6.0.6                         4    bioconda
libcurl                   7.62.0               hbdb9355_0    conda-forge
libcxx                    7.0.0                h2d50403_2    conda-forge
libedit                   3.1.20170329                  0    conda-forge
libffi                    3.2.1                hfc679d8_5    conda-forge
libgcc                    4.8.5               hdbeacc1_10    conda-forge
libgfortran               3.0.1                h93005f0_2  
libiconv                  1.15                 h470a237_3    conda-forge
libpng                    1.6.34               ha92aebf_2    conda-forge
libprotobuf               3.6.0                hd28b015_0    conda-forge
libsodium                 1.0.16               h470a237_1    conda-forge
libssh2                   1.8.0                h5b517e9_2    conda-forge
libtiff                   4.0.9                he6b73bb_2    conda-forge
libxml2                   2.9.8                h422b904_5    conda-forge
llvm-meta                 7.0.0                         0    conda-forge
lockfile                  0.12.2                     py_1    conda-forge
mafft                     7.310                         1    bioconda
markdown                  2.6.11                     py_0    conda-forge
markupsafe                1.0              py35h470a237_1    conda-forge
matplotlib                2.2.3            py35h0e0179f_0    conda-forge
mistune                   0.8.3            py35h470a237_2    conda-forge
mkl                       2019.0                      118  
msgpack-python            0.5.6            py35h2d50403_3    conda-forge
natsort                   5.4.0                      py_0    conda-forge
nbconvert                 5.3.1                      py_1    conda-forge
nbformat                  4.4.0                      py_1    conda-forge
ncurses                   5.9                          10    conda-forge
nose                      1.3.7                    py35_2    conda-forge
notebook                  5.7.0                    py35_0    conda-forge
numpy                     1.12.1           py35h655160a_1  
openjdk                   8.0.152              h393ad39_1  
openmp                    7.0.0                h2d50403_0    conda-forge
openssl                   1.0.2p               h1de35cc_0  
packaging                 18.0                       py_0    conda-forge
pandas                    0.22.0                   py35_1    conda-forge
pandoc                    2.3.1                         0    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
pango                     1.40.14              he752989_2    conda-forge
parso                     0.3.1                      py_0    conda-forge
patsy                     0.5.1                      py_0    conda-forge
pcre                      8.39                          0    conda-forge
pexpect                   4.6.0                    py35_0    conda-forge
pickleshare               0.7.5                    py35_0    conda-forge
pigz                      2.3.4                         0    conda-forge
pip                       18.0                  py35_1001    conda-forge
pixman                    0.34.0               h470a237_3    conda-forge
prometheus_client         0.4.2                      py_0    conda-forge
prompt_toolkit            2.0.7                      py_0    conda-forge
protobuf                  3.6.0            py35hfc679d8_0    conda-forge
psutil                    5.4.7            py35h470a237_1    conda-forge
ptyprocess                0.6.0                 py35_1000    conda-forge
pycparser                 2.19                       py_0    conda-forge
pygments                  2.2.0                      py_1    conda-forge
pyopenssl                 18.0.0                   py35_0    conda-forge
pyparsing                 2.3.0                      py_0    conda-forge
pysocks                   1.6.8                    py35_2    conda-forge
python                    3.5.5                         1    conda-forge
python-dateutil           2.7.5                      py_0    conda-forge
pytz                      2018.7                     py_0    conda-forge
pyyaml                    3.13             py35h470a237_1    conda-forge
pyzmq                     17.1.2           py35hae99301_0    conda-forge
q2-alignment              2018.11.0                py35_0    qiime2-staging/label/r2018.11
q2-composition            2018.11.0                py35_0    qiime2-staging/label/r2018.11
q2-cutadapt               2018.11.0                py35_0    qiime2-staging/label/r2018.11
q2-dada2                  2018.11.0                py35_0    qiime2-staging/label/r2018.11
q2-deblur                 2018.11.0                py35_0    qiime2-staging/label/r2018.11
q2-demux                  2018.11.0                py35_0    qiime2-staging/label/r2018.11
q2-diversity              2018.11.0                py35_0    qiime2-staging/label/r2018.11
q2-emperor                2018.11.0                py35_0    qiime2-staging/label/r2018.11
q2-feature-classifier     2018.11.0                py35_0    qiime2-staging/label/r2018.11
q2-feature-table          2018.11.0                py35_0    qiime2-staging/label/r2018.11
q2-fragment-insertion     2018.11.0                py35_0    qiime2-staging/label/r2018.11
q2-gneiss                 2018.11.0                py35_0    qiime2-staging/label/r2018.11
q2-longitudinal           2018.11.0                py35_0    qiime2-staging/label/r2018.11
q2-metadata               2018.11.0                py35_0    qiime2-staging/label/r2018.11
q2-phylogeny              2018.11.0                py35_0    qiime2-staging/label/r2018.11
q2-quality-control        2018.11.0                py35_0    qiime2-staging/label/r2018.11
q2-quality-filter         2018.11.0                py35_0    qiime2-staging/label/r2018.11
q2-sample-classifier      2018.11.0                py35_0    qiime2-staging/label/r2018.11
q2-taxa                   2018.11.0                py35_0    qiime2-staging/label/r2018.11
q2-types                  2018.11.0                py35_0    qiime2-staging/label/r2018.11
q2-vsearch                2018.11.0                py35_0    qiime2-staging/label/r2018.11
q2cli                     2018.11.0                py35_0    qiime2-staging/label/r2018.11
q2templates               2018.11.0                py35_0    qiime2-staging/label/r2018.11
qiime2                    2018.11.0                py35_0    qiime2-staging/label/r2018.11
r-assertthat              0.2.0            r341h6115d3f_1    conda-forge
r-base                    3.4.1                         4    conda-forge
r-bh                      1.66.0_1              r341_1001    conda-forge
r-bitops                  1.0_6            r341hc070d10_2    conda-forge
r-cli                     1.0.0            r341h6115d3f_1    conda-forge
r-colorspace              1.3_2            r341hc070d10_2    conda-forge
r-crayon                  1.3.4            r341h6115d3f_1    conda-forge
r-data.table              1.11.4           r341hc070d10_2    conda-forge
r-digest                  0.6.18           r341hc070d10_0    conda-forge
r-fansi                   0.3.0            r341hc070d10_0    conda-forge
r-formatr                 1.5              r341h6115d3f_1    conda-forge
r-futile.logger           1.4.3            r341h6115d3f_1    conda-forge
r-futile.options          1.0.1            r341h6115d3f_0    conda-forge
r-ggplot2                 3.1.0            r341h6115d3f_0    conda-forge
r-glue                    1.3.0            r341h470a237_2    conda-forge
r-gtable                  0.2.0            r341h6115d3f_1    conda-forge
r-hwriter                 1.3.2            r341h6115d3f_1    conda-forge
r-labeling                0.3              r341h6115d3f_1    conda-forge
r-lambda.r                1.2.3            r341h6115d3f_0    conda-forge
r-lattice                 0.20_35          r341hc070d10_0    conda-forge
r-latticeextra            0.6_28           r341h6115d3f_1    conda-forge
r-lazyeval                0.2.1            r341hc070d10_2    conda-forge
r-magrittr                1.5              r341h6115d3f_1    conda-forge
r-mass                    7.3_50           r341hc070d10_2    conda-forge
r-matrix                  1.2_14           r341hc070d10_2    conda-forge
r-matrixstats             0.54.0           r341hc070d10_0    conda-forge
r-mgcv                    1.8_24           r341hc070d10_2    conda-forge
r-munsell                 0.5.0            r341h6115d3f_1    conda-forge
r-nlme                    3.1_137          r341h364d78e_0    conda-forge
r-pillar                  1.3.0            r341h6115d3f_0    conda-forge
r-plyr                    1.8.4            r341h9d2a408_2    conda-forge
r-r6                      2.2.2            r341h6115d3f_1    conda-forge
r-rcolorbrewer            1.1_2            r341h6115d3f_1    conda-forge
r-rcpp                    1.0.0            r341h9d2a408_0    conda-forge
r-rcppparallel            4.4.1            r341h9d2a408_0    conda-forge
r-rcurl                   1.95_4.11        r341hc070d10_3    conda-forge
r-reshape2                1.4.3            r341h9d2a408_2    conda-forge
r-rlang                   0.3.0.1          r341h470a237_0    conda-forge
r-scales                  1.0.0            r341h9d2a408_1    conda-forge
r-snow                    0.4_3            r341h6115d3f_0    conda-forge
r-stringi                 1.2.4            r341h9d2a408_1    conda-forge
r-stringr                 1.3.1            r341h6115d3f_1    conda-forge
r-tibble                  1.4.2            r341hc070d10_2    conda-forge
r-utf8                    1.1.4            r341hc070d10_0    conda-forge
r-viridislite             0.3.0            r341h6115d3f_1    conda-forge
r-withr                   2.1.2            r341h6115d3f_0    conda-forge
raxml                     8.2.12               h470a237_0    bioconda
readline                  7.0                           0    conda-forge
requests                  2.19.1                   py35_1    conda-forge
scikit-bio                0.5.4                    py35_0    conda-forge
scikit-learn              0.19.1           py35h2b554eb_0  
scipy                     0.19.1           py35hf362045_3  
seaborn                   0.9.0                      py_0    conda-forge
send2trash                1.5.0                      py_0    conda-forge
setuptools                40.4.3                   py35_0    conda-forge
simplegeneric             0.8.1                      py_1    conda-forge
sina                      1.4.0                h4ef8376_0    bioconda
six                       1.11.0                   py35_1  
sortmerna                 2.0                  he941832_3    bioconda
sqlite                    3.20.1                        2    conda-forge
statsmodels               0.9.0                    py35_0    conda-forge
tbb                       2019.2               h2d50403_0    conda-forge
tensorboard               1.5.1                    py35_1    conda-forge
tensorflow                1.5.1                    py35_0    conda-forge
terminado                 0.8.1                    py35_1    conda-forge
testpath                  0.3.1                    py35_1    conda-forge
tk                        8.6.9                ha92aebf_0    conda-forge
tornado                   5.1.1            py35h470a237_0    conda-forge
traitlets                 4.3.2                    py35_0    conda-forge
tzlocal                   1.3                      py35_0    qiime2
unifrac                   0.9.2            py35h1806a49_1    biocore
urllib3                   1.23                     py35_1    conda-forge
vsearch                   2.7.0                         1    bioconda
wcwidth                   0.1.7                      py_1    conda-forge
webencodings              0.5.1                      py_1    conda-forge
werkzeug                  0.14.1                     py_0    conda-forge
wget                      1.19.5               hf30b1f0_0  
wheel                     0.32.0                py35_1000    conda-forge
widgetsnbextension        3.4.2                    py35_0    conda-forge
xopen                     0.3.5                      py_0    bioconda
xz                        5.2.4                h470a237_1    conda-forge
yaml                      0.1.7                h470a237_1    conda-forge
zeromq                    4.2.5                hfc679d8_6    conda-forge
zlib                      1.2.11               h470a237_3    conda-forge

Details about conda and system ( conda info ):

$ conda info
     active environment : q2-dev
    active env location : /Users/mortonjt/miniconda3/envs/q2-dev
            shell level : 1
       user config file : /Users/mortonjt/.condarc
 populated config files : 
          conda version : 4.5.11
    conda-build version : not installed
         python version : 3.7.0.final.0
       base environment : /Users/mortonjt/miniconda3  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/osx-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/osx-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : /Users/mortonjt/miniconda3/pkgs
                          /Users/mortonjt/.conda/pkgs
       envs directories : /Users/mortonjt/miniconda3/envs
                          /Users/mortonjt/.conda/envs
               platform : osx-64
             user-agent : conda/4.5.11 requests/2.19.1 CPython/3.7.0 Darwin/15.6.0 OSX/10.11.6
                UID:GID : 501:20
             netrc file : None
           offline mode : False

I'm trying to conda install tensorflow=1.5 and get the following error when importing in python

python -c "import tensorflow"
RuntimeError: module compiled against API version 0xb but this version of numpy is 0xa
ImportError: numpy.core.multiarray failed to import
ImportError: numpy.core.umath failed to import
ImportError: numpy.core.umath failed to import
2018-11-17 22:23:17.984293: F tensorflow/python/lib/core/bfloat16.cc:664] Check failed: PyBfloat16_Type.tp_base != nullptr 
Abort trap: 6

Has anyone else noticed these sorts of errors? Not entirely sure why this is the case, especially since numpy=1.12 should be compatible.

I then tried to see if I could install tensorflow by itself, and still had issues.

conda create -n tf-test tensorflow -c conda-forge
source activate tf-test
python -c "import tensorflow"

Traceback (most recent call last):
  File "/Users/mortonjt/miniconda3/envs/tf-test/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
    from tensorflow.python.pywrap_tensorflow_internal import *
  File "/Users/mortonjt/miniconda3/envs/tf-test/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
    _pywrap_tensorflow_internal = swig_import_helper()
  File "/Users/mortonjt/miniconda3/envs/tf-test/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
    _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
  File "/Users/mortonjt/miniconda3/envs/tf-test/lib/python3.6/imp.py", line 243, in load_module
    return load_dynamic(name, filename, file)
  File "/Users/mortonjt/miniconda3/envs/tf-test/lib/python3.6/imp.py", line 343, in load_dynamic
    return _load(spec)
ImportError: dlopen(/Users/mortonjt/miniconda3/envs/tf-test/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _SecKeyCopyExternalRepresentation
  Referenced from: /Users/mortonjt/miniconda3/envs/tf-test/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so (which was built for Mac OS X 10.12)
  Expected in: /System/Library/Frameworks/Security.framework/Versions/A/Security
 in /Users/mortonjt/miniconda3/envs/tf-test/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/mortonjt/miniconda3/envs/tf-test/lib/python3.6/site-packages/tensorflow/__init__.py", line 22, in <module>
    from tensorflow.python import pywrap_tensorflow  # pylint: disable=unused-import
  File "/Users/mortonjt/miniconda3/envs/tf-test/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 49, in <module>
    from tensorflow.python import pywrap_tensorflow
  File "/Users/mortonjt/miniconda3/envs/tf-test/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 74, in <module>
    raise ImportError(msg)
ImportError: Traceback (most recent call last):
  File "/Users/mortonjt/miniconda3/envs/tf-test/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
    from tensorflow.python.pywrap_tensorflow_internal import *
  File "/Users/mortonjt/miniconda3/envs/tf-test/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
    _pywrap_tensorflow_internal = swig_import_helper()
  File "/Users/mortonjt/miniconda3/envs/tf-test/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
    _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
  File "/Users/mortonjt/miniconda3/envs/tf-test/lib/python3.6/imp.py", line 243, in load_module
    return load_dynamic(name, filename, file)
  File "/Users/mortonjt/miniconda3/envs/tf-test/lib/python3.6/imp.py", line 343, in load_dynamic
    return _load(spec)
ImportError: dlopen(/Users/mortonjt/miniconda3/envs/tf-test/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _SecKeyCopyExternalRepresentation
  Referenced from: /Users/mortonjt/miniconda3/envs/tf-test/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so (which was built for Mac OS X 10.12)
  Expected in: /System/Library/Frameworks/Security.framework/Versions/A/Security
 in /Users/mortonjt/miniconda3/envs/tf-test/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so


Failed to load the native TensorFlow runtime.

See https://www.tensorflow.org/install/install_sources#common_installation_problems

for some common reasons and solutions.  Include the entire stack trace
above this error message when asking for help.

Below are the environment details for the 2nd attempt

Environment (conda list):

$ conda list
# packages in environment at /Users/mortonjt/miniconda3/envs/tf-test:
#
# Name                    Version                   Build  Channel
absl-py                   0.6.1                 py36_1000    conda-forge
astor                     0.7.1                      py_0    conda-forge
blas                      1.0                         mkl  
bzip2                     1.0.6                         1    conda-forge
c-ares                    1.15.0               h470a237_1    conda-forge
ca-certificates           2018.10.15           ha4d7672_0    conda-forge
certifi                   2018.10.15            py36_1000    conda-forge
gast                      0.2.0                      py_0    conda-forge
grpcio                    1.16.0           py36hd60e7a3_0    conda-forge
intel-openmp              2019.0                      118  
libffi                    3.2.1                hfc679d8_5    conda-forge
libgfortran               3.0.1                h93005f0_2  
libprotobuf               3.6.1                hd28b015_0    conda-forge
markdown                  2.6.11                     py_0    conda-forge
mkl                       2019.0                      118  
mkl_fft                   1.0.6                    py36_0    conda-forge
mkl_random                1.0.2                    py36_0    conda-forge
ncurses                   6.1                  hfc679d8_1    conda-forge
numpy                     1.15.4           py36h6a91979_0  
numpy-base                1.15.4           py36h8a80b8c_0  
openssl                   1.0.2p               h470a237_1    conda-forge
pip                       18.1                  py36_1000    conda-forge
protobuf                  3.6.1            py36hfc679d8_1    conda-forge
python                    3.6.6                h5001a0f_0    conda-forge
readline                  7.0                  haf1bffa_1    conda-forge
setuptools                40.6.2                   py36_0    conda-forge
six                       1.11.0                py36_1001    conda-forge
sqlite                    3.25.3               hb1c47c0_0    conda-forge
tensorboard               1.10.0                   py36_0    conda-forge
tensorflow                1.10.0                   py36_0    conda-forge
termcolor                 1.1.0                      py_2    conda-forge
tk                        8.6.9                ha92aebf_0    conda-forge
werkzeug                  0.14.1                     py_0    conda-forge
wheel                     0.32.2                   py36_0    conda-forge
xz                        5.2.4                h470a237_1    conda-forge
zlib                      1.2.11               h470a237_3    conda-forge

Details about conda and system ( conda info ):

$ conda info
     active environment : tf-test
    active env location : /Users/mortonjt/miniconda3/envs/tf-test
            shell level : 1
       user config file : /Users/mortonjt/.condarc
 populated config files : 
          conda version : 4.5.11
    conda-build version : not installed
         python version : 3.7.0.final.0
       base environment : /Users/mortonjt/miniconda3  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/osx-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/osx-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : /Users/mortonjt/miniconda3/pkgs
                          /Users/mortonjt/.conda/pkgs
       envs directories : /Users/mortonjt/miniconda3/envs
                          /Users/mortonjt/.conda/envs
               platform : osx-64
             user-agent : conda/4.5.11 requests/2.19.1 CPython/3.7.0 Darwin/15.6.0 OSX/10.11.6
                UID:GID : 501:20
             netrc file : None
           offline mode : False

Any insights will be greatly appreciated! And this resource is extremely useful, particularly for tools that heavily rely on the conda build!

[jjhelmus]

Can you upgrade the numpy package in the first environment to 1.13 or newer? There were some issues with the Tensorflow 1.5.1 wheels requiring a newer NumPy version than the requirements expressed, cf tensorflow/tensorflow#16488, which were copied into the conda package. Upgrading NumPy usually fixes the issue.

The later issue I believe is caused by the minimum version of macOS being 10.12 for Tensorflow 1.10.0.

[mortonjt]

Makes sense. Thanks!

At the moment, qiime2 is fixed at numpy=1.12 -- but we are currently in discussion about bumping up the numpy version there.

That being said, I was still having issues with the standalone TF installation with conda-forge (even without specifying the numpy version or other qiime2 dependencies).
The anaconda version seems to be working though via

conda create -n tf-test2 tensorflow -c anaconda
source activate tf-test2
python -c "import tensorflow as tf; print(tf.__version__)" 
'1.12.0'

[jjhelmus]

The anaconda package (but please use defaults not anaconda) is built from source and will work with macOS 10.11 and above. The conda-forge package is a repackage of the wheels provided by Google, which appear to support macOS 10.12 and above. Building Tensorflow from source, see #6, could solve this problem but is quite challenging.

[hmaarrfk]

I believe this has been addressed in recent versions.

i would suggest adding a tensorflow pinning >=2.6. should help with these builds.

[h-vetinari]

Yeah, this is an ancient issue, let's close it (but please feel free to open a new one if there are any remaining problems!)