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conda-forge / cython-blis-feedstock

A conda-smithy repository for cython-blis.
BSD 3-Clause "New" or "Revised" License
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All conda-forge packages are failing to install in fresh install of Anaconda #4

Closed mhworth closed 5 years ago

mhworth commented 5 years ago

Issue: All conda-forge packages are failing to install in fresh install of Anaconda

We have been using a docker-based build and deploy system with Anaconda+conda-forge at it's core for about two years now with no hiccups. Yesterday (after no changes from our side), all of our builds started failing, saying that packages were missing. Now I can't install anything that comes from conda-forge.

This only seems to happen on a fresh installation--I can install things in my environments that were already initialized before, just when I'm starting from scratch it doesn't work.

Nothing at all has changed in our dockerfiles, so I'm not sure what happened. Here is a simple dockerfile that can replicate my issue:

FROM centos:7
RUN yum install -y wget
RUN wget -qO- "https://repo.anaconda.com/archive/Anaconda3-2019.07-Linux-x86_64.sh" -O /tmp/anaconda.sh && \
    chmod +x /tmp/anaconda.sh &&  mkdir -p /usr/local &&  /tmp/anaconda.sh -b -p /usr/local/anaconda
ENV PATH="/usr/local/anaconda/bin:${PATH}"
RUN conda install -y conda-build conda-verify anaconda-client python=3.7.3
RUN conda install -y -c conda-forge spacy=2.1.6

Running docker build -t test . with that Dockerfile yields the following:

Step 8/8 : RUN conda install -y -c conda-forge spacy=2.1.6
 ---> Running in b75a55270a84
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with current_repodata.json, will retry with next repodata source.
Initial quick solve with frozen env failed.  Unfreezing env and trying again.
Solving environment: ...working... failed with current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed
Initial quick solve with frozen env failed.  Unfreezing env and trying again.
Solving environment: ...working... failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Package murmurhash conflicts for:
spacy=2.1.6 -> murmurhash[version='>=0.28.0,<1.1.0']
Package jsonschema conflicts for:
spacy=2.1.6 -> jsonschema[version='>=2.6.0,<3.0.0']
Package pip conflicts for:
python=3.7.3 -> pip
Package numpy conflicts for:
spacy=2.1.6 -> numpy[version='>=1.15.4,<2.0a0']
Package ncurses conflicts for:
python=3.7.3 -> ncurses[version='>=6.1,<6.2.0a0|>=6.1,<7.0a0']
Package zlib conflicts for:
python=3.7.3 -> zlib[version='>=1.2.11,<1.3.0a0']
Package bzip2 conflicts for:
python=3.7.3 -> bzip2[version='>=1.0.6,<2.0a0']
Package libffi conflicts for:
python=3.7.3 -> libffi[version='>=3.2.1,<3.3.0a0|>=3.2.1,<4.0a0']
Package srsly conflicts for:
spacy=2.1.6 -> srsly[version='>=0.0.5,<1.1.0']
Package sqlite conflicts for:
python=3.7.3 -> sqlite[version='>=3.26.0,<4.0a0|>=3.27.2,<4.0a0|>=3.28.0,<4.0a0']
Package requests conflicts for:
spacy=2.1.6 -> requests[version='>=2.13.0,<3.0.0']
Package readline conflicts for:
python=3.7.3 -> readline[version='>=7.0,<8.0a0|>=8.0,<9.0a0']
Package libgcc-ng conflicts for:
python=3.7.3 -> libgcc-ng[version='>=7.3.0']
spacy=2.1.6 -> libgcc-ng[version='>=7.3.0']
Package thinc conflicts for:
spacy=2.1.6 -> thinc[version='>=7.0.4,<7.1.0']
Package tk conflicts for:
python=3.7.3 -> tk[version='>=8.6.8,<8.7.0a0|>=8.6.9,<8.7.0a0']
Package wasabi conflicts for:
spacy=2.1.6 -> wasabi[version='>=0.0.12,<1.1.0']
Package plac conflicts for:
spacy=2.1.6 -> plac[version='<1.0.0,>=0.9.6']
Package cymem conflicts for:
spacy=2.1.6 -> cymem[version='>=2.0.2,<2.1.0']
Package xz conflicts for:
python=3.7.3 -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.4,<6.0a0']
Package libstdcxx-ng conflicts for:
spacy=2.1.6 -> libstdcxx-ng[version='>=7.3.0']
python=3.7.3 -> libstdcxx-ng[version='>=7.3.0']
Package cython-blis conflicts for:
spacy=2.1.6 -> cython-blis[version='>=0.2.2,<0.3.0']
Package openssl conflicts for:
python=3.7.3 -> openssl[version='>=1.1.1a,<1.1.2a|>=1.1.1b,<1.1.2a']
Package preshed conflicts for:
spacy=2.1.6 -> preshed[version='>=2.0.1,<2.1.0']
Package pathlib conflicts for:
spacy=2.1.6 -> pathlib[version='>=1.0.0,<2.0.0']

This is the actual output from our build (python incompatibilities seems to be a commonality):

  - alembic=1.0.8 -> python
  - ansible=2.7.5 -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
  - antlr-python-runtime=4.7.1 -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
  - arrow-cpp=0.13.0 -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
  - arrow=0.12.1 -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
  - beaker=1.10.0 -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0']
  - beautifulsoup4=4.7.1 -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
  - bjoern=2.2.2 -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
  - boltons=18.0.1 -> python
  - boto3=1.9.134 -> python
  - click=7.0 -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
  - cryptography -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
  - elasticsearch=7.0.0 -> python
  - eventlet=0.23.0 -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
  - flask-bcrypt=0.7.1 -> python[version='2.7.*|3.4.*|3.5.*']
  - flask-cache=0.13.1 -> python[version='2.7.*|3.4.*|3.5.*|3.6.*']
  - flask-jwt-extended=3.13.1 -> python
  - flask-restful=0.3.6 -> python[version='2.7.*|3.5.*|3.6.*']
  - flask-restplus=0.11.0 -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
  - flask-sqlalchemy=2.3.2 -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
  - flask-user=1.0.1.4 -> python
  - flask=0.12.4 -> python
  - fs=2.4.4 -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
  - gevent -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']

Perhaps something all of the sudden doesn't like python 3.7.3, despite it having worked for months. Maybe something changed in the build process?

Any idea what's happened all of the sudden? Our entire company has ground to a halt over this one, so I'm happy to help however I can to resolve this.


Environment (conda list):

``` $ conda list _anaconda_depends 2019.03 py37_0 _ipyw_jlab_nb_ext_conf 0.1.0 py37_0 _libgcc_mutex 0.1 main alabaster 0.7.12 py37_0 anaconda custom py37_1 anaconda-client 1.7.2 py37_0 anaconda-navigator 1.9.7 py37_0 anaconda-project 0.8.3 py_0 asn1crypto 0.24.0 py37_0 astroid 2.2.5 py37_0 astropy 3.2.1 py37h7b6447c_0 atomicwrites 1.3.0 py37_1 attrs 19.1.0 py37_1 babel 2.7.0 py_0 backcall 0.1.0 py37_0 backports 1.0 py_2 backports.functools_lru_cache 1.5 py_2 backports.os 0.1.1 py37_0 backports.shutil_get_terminal_size 1.0.0 py37_2 backports.tempfile 1.0 py_1 backports.weakref 1.0.post1 py_1 beautifulsoup4 4.7.1 py37_1 bitarray 0.9.3 py37h7b6447c_0 bkcharts 0.2 py37_0 blas 1.0 mkl bleach 3.1.0 py37_0 blosc 1.16.3 hd408876_0 bokeh 1.2.0 py37_0 boto 2.49.0 py37_0 bottleneck 1.2.1 py37h035aef0_1 bzip2 1.0.8 h7b6447c_0 ca-certificates 2019.5.15 0 cairo 1.14.12 h8948797_3 certifi 2019.6.16 py37_1 cffi 1.12.3 py37h2e261b9_0 chardet 3.0.4 py37_1 click 7.0 py37_0 cloudpickle 1.2.1 py_0 clyent 1.2.2 py37_1 colorama 0.4.1 py37_0 conda 4.7.10 py37_0 conda-build 3.18.9 py37_0 conda-env 2.6.0 1 conda-package-handling 1.3.11 py37_0 conda-verify 3.4.2 py_1 contextlib2 0.5.5 py37_0 cryptography 2.7 py37h1ba5d50_0 curl 7.65.2 hbc83047_0 cycler 0.10.0 py37_0 cython 0.29.12 py37he6710b0_0 cytoolz 0.10.0 py37h7b6447c_0 dask 2.1.0 py_0 dask-core 2.1.0 py_0 dbus 1.13.6 h746ee38_0 decorator 4.4.0 py37_1 defusedxml 0.6.0 py_0 distributed 2.1.0 py_0 docutils 0.14 py37_0 entrypoints 0.3 py37_0 et_xmlfile 1.0.1 py37_0 expat 2.2.6 he6710b0_0 fastcache 1.1.0 py37h7b6447c_0 filelock 3.0.12 py_0 flask 1.1.1 py_0 fontconfig 2.13.0 h9420a91_0 freetype 2.9.1 h8a8886c_1 fribidi 1.0.5 h7b6447c_0 future 0.17.1 py37_0 get_terminal_size 1.0.0 haa9412d_0 gevent 1.4.0 py37h7b6447c_0 glib 2.56.2 hd408876_0 glob2 0.7 py_0 gmp 6.1.2 h6c8ec71_1 gmpy2 2.0.8 py37h10f8cd9_2 graphite2 1.3.13 h23475e2_0 greenlet 0.4.15 py37h7b6447c_0 gst-plugins-base 1.14.0 hbbd80ab_1 gstreamer 1.14.0 hb453b48_1 h5py 2.9.0 py37h7918eee_0 harfbuzz 1.8.8 hffaf4a1_0 hdf5 1.10.4 hb1b8bf9_0 heapdict 1.0.0 py37_2 html5lib 1.0.1 py37_0 icu 58.2 h9c2bf20_1 idna 2.8 py37_0 imageio 2.5.0 py37_0 imagesize 1.1.0 py37_0 importlib_metadata 0.17 py37_1 intel-openmp 2019.4 243 ipykernel 5.1.1 py37h39e3cac_0 ipython 7.6.1 py37h39e3cac_0 ipython_genutils 0.2.0 py37_0 ipywidgets 7.5.0 py_0 isort 4.3.21 py37_0 itsdangerous 1.1.0 py37_0 jbig 2.1 hdba287a_0 jdcal 1.4.1 py_0 jedi 0.13.3 py37_0 jeepney 0.4 py37_0 jinja2 2.10.1 py37_0 joblib 0.13.2 py37_0 jpeg 9b h024ee3a_2 json5 0.8.4 py_0 jsonschema 3.0.1 py37_0 jupyter 1.0.0 py37_7 jupyter_client 5.3.1 py_0 jupyter_console 6.0.0 py37_0 jupyter_core 4.5.0 py_0 jupyterlab 1.0.2 py37hf63ae98_0 jupyterlab_server 1.0.0 py_0 keyring 18.0.0 py37_0 kiwisolver 1.1.0 py37he6710b0_0 krb5 1.16.1 h173b8e3_7 lazy-object-proxy 1.4.1 py37h7b6447c_0 libarchive 3.3.3 h5d8350f_5 libcurl 7.65.2 h20c2e04_0 libedit 3.1.20181209 hc058e9b_0 libffi 3.2.1 hd88cf55_4 libgcc-ng 9.1.0 hdf63c60_0 libgfortran-ng 7.3.0 hdf63c60_0 liblief 0.9.0 h7725739_2 libpng 1.6.37 hbc83047_0 libsodium 1.0.16 h1bed415_0 libssh2 1.8.2 h1ba5d50_0 libstdcxx-ng 9.1.0 hdf63c60_0 libtiff 4.0.10 h2733197_2 libtool 2.4.6 h7b6447c_5 libuuid 1.0.3 h1bed415_2 libxcb 1.13 h1bed415_1 libxml2 2.9.9 hea5a465_1 libxslt 1.1.33 h7d1a2b0_0 llvmlite 0.29.0 py37hd408876_0 locket 0.2.0 py37_1 lxml 4.3.4 py37hefd8a0e_0 lz4-c 1.8.1.2 h14c3975_0 lzo 2.10 h49e0be7_2 markupsafe 1.1.1 py37h7b6447c_0 matplotlib 3.1.0 py37h5429711_0 mccabe 0.6.1 py37_1 mistune 0.8.4 py37h7b6447c_0 mkl 2019.4 243 mkl-service 2.0.2 py37h7b6447c_0 mkl_fft 1.0.12 py37ha843d7b_0 mkl_random 1.0.2 py37hd81dba3_0 mock 3.0.5 py37_0 more-itertools 7.0.0 py37_0 mpc 1.1.0 h10f8cd9_1 mpfr 4.0.1 hdf1c602_3 mpmath 1.1.0 py37_0 msgpack-python 0.6.1 py37hfd86e86_1 multipledispatch 0.6.0 py37_0 navigator-updater 0.2.1 py37_0 nbconvert 5.5.0 py_0 nbformat 4.4.0 py37_0 ncurses 6.1 he6710b0_1 networkx 2.3 py_0 nltk 3.4.4 py37_0 nose 1.3.7 py37_2 notebook 6.0.0 py37_0 numba 0.44.1 py37h962f231_0 numexpr 2.6.9 py37h9e4a6bb_0 numpy 1.16.4 py37h7e9f1db_0 numpy-base 1.16.4 py37hde5b4d6_0 numpydoc 0.9.1 py_0 olefile 0.46 py37_0 openpyxl 2.6.2 py_0 openssl 1.1.1c h7b6447c_1 packaging 19.0 py37_0 pandas 0.24.2 py37he6710b0_0 pandoc 2.2.3.2 0 pandocfilters 1.4.2 py37_1 pango 1.42.4 h049681c_0 parso 0.5.0 py_0 partd 1.0.0 py_0 patchelf 0.9 he6710b0_3 path.py 12.0.1 py_0 pathlib2 2.3.4 py37_0 patsy 0.5.1 py37_0 pcre 8.43 he6710b0_0 pep8 1.7.1 py37_0 pexpect 4.7.0 py37_0 pickleshare 0.7.5 py37_0 pillow 6.1.0 py37h34e0f95_0 pip 19.0.3 py37_0 pixman 0.38.0 h7b6447c_0 pkginfo 1.5.0.1 py37_0 pluggy 0.12.0 py_0 ply 3.11 py37_0 prometheus_client 0.7.1 py_0 prompt_toolkit 2.0.9 py37_0 psutil 5.6.3 py37h7b6447c_0 ptyprocess 0.6.0 py37_0 py 1.8.0 py37_0 py-lief 0.9.0 py37h7725739_2 pycodestyle 2.5.0 py37_0 pycosat 0.6.3 py37h14c3975_0 pycparser 2.19 py37_0 pycrypto 2.6.1 py37h14c3975_9 pycurl 7.43.0.3 py37h1ba5d50_0 pyflakes 2.1.1 py37_0 pygments 2.4.2 py_0 pylint 2.3.1 py37_0 pyodbc 4.0.26 py37he6710b0_0 pyopenssl 19.0.0 py37_0 pyparsing 2.4.0 py_0 pyqt 5.9.2 py37h05f1152_2 pyrsistent 0.14.11 py37h7b6447c_0 pysocks 1.7.0 py37_0 pytables 3.5.2 py37h71ec239_1 pytest 5.0.1 py37_0 pytest-arraydiff 0.3 py37h39e3cac_0 pytest-astropy 0.5.0 py37_0 pytest-doctestplus 0.3.0 py37_0 pytest-openfiles 0.3.2 py37_0 pytest-remotedata 0.3.1 py37_0 python 3.7.3 h0371630_0 python-dateutil 2.8.0 py37_0 python-libarchive-c 2.8 py37_11 pytz 2019.1 py_0 pywavelets 1.0.3 py37hdd07704_1 pyyaml 5.1.1 py37h7b6447c_0 pyzmq 18.0.0 py37he6710b0_0 qt 5.9.7 h5867ecd_1 qtawesome 0.5.7 py37_1 qtconsole 4.5.1 py_0 qtpy 1.8.0 py_0 readline 7.0 h7b6447c_5 requests 2.22.0 py37_0 rope 0.14.0 py_0 ruamel_yaml 0.15.46 py37h14c3975_0 scikit-image 0.15.0 py37he6710b0_0 scikit-learn 0.21.2 py37hd81dba3_0 scipy 1.3.0 py37h7c811a0_0 seaborn 0.9.0 py37_0 secretstorage 3.1.1 py37_0 send2trash 1.5.0 py37_0 setuptools 41.0.1 py37_0 simplegeneric 0.8.1 py37_2 singledispatch 3.4.0.3 py37_0 sip 4.19.8 py37hf484d3e_0 six 1.12.0 py37_0 snappy 1.1.7 hbae5bb6_3 snowballstemmer 1.9.0 py_0 sortedcollections 1.1.2 py37_0 sortedcontainers 2.1.0 py37_0 soupsieve 1.8 py37_0 sphinx 2.1.2 py_0 sphinxcontrib 1.0 py37_1 sphinxcontrib-applehelp 1.0.1 py_0 sphinxcontrib-devhelp 1.0.1 py_0 sphinxcontrib-htmlhelp 1.0.2 py_0 sphinxcontrib-jsmath 1.0.1 py_0 sphinxcontrib-qthelp 1.0.2 py_0 sphinxcontrib-serializinghtml 1.1.3 py_0 sphinxcontrib-websupport 1.1.2 py_0 spyder 3.3.6 py37_0 spyder-kernels 0.5.1 py37_0 sqlalchemy 1.3.5 py37h7b6447c_0 sqlite 3.29.0 h7b6447c_0 statsmodels 0.10.0 py37hdd07704_0 sympy 1.4 py37_0 tblib 1.4.0 py_0 terminado 0.8.2 py37_0 testpath 0.4.2 py37_0 tk 8.6.8 hbc83047_0 toolz 0.10.0 py_0 tornado 6.0.3 py37h7b6447c_0 tqdm 4.32.1 py_0 traitlets 4.3.2 py37_0 unicodecsv 0.14.1 py37_0 unixodbc 2.3.7 h14c3975_0 urllib3 1.24.2 py37_0 wcwidth 0.1.7 py37_0 webencodings 0.5.1 py37_1 werkzeug 0.15.4 py_0 wheel 0.33.4 py37_0 widgetsnbextension 3.5.0 py37_0 wrapt 1.11.2 py37h7b6447c_0 wurlitzer 1.0.2 py37_0 xlrd 1.2.0 py37_0 xlsxwriter 1.1.8 py_0 xlwt 1.3.0 py37_0 xz 5.2.4 h14c3975_4 yaml 0.1.7 had09818_2 zeromq 4.3.1 he6710b0_3 zict 1.0.0 py_0 zipp 0.5.1 py_0 zlib 1.2.11 h7b6447c_3 zstd 1.3.7 h0b5b093_0 ```


Details about conda and system ( conda info ):

``` $ conda info ```
isuruf commented 5 years ago

We removed blis due to a license violation. See https://github.com/conda-forge/cython-blis-feedstock/issues/2. Tried fixing it in https://github.com/conda-forge/cython-blis-feedstock/pull/3, but ran into a different issue.

CCorrado commented 5 years ago

+1 on this, our builds started failing this AM since spaCy depends on the cython-blis package. Will keep an eye on #3!

isuruf commented 5 years ago

Help in fixing the failures in #3 will resolve this issue