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conda-forge / tensorflow-feedstock

A conda-smithy repository for tensorflow.
BSD 3-Clause "New" or "Revised" License
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Tensorflow install breaks (likely due to numpy) #64

Closed mortonjt closed 2 years ago

mortonjt commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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 commented 2 years ago

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 commented 2 years ago

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!)