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Conda env create fails using environment.yml file. #9480

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soerendip opened this issue May 29, 2018 · 12 comments

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@soerendip
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commented May 29, 2018

I exported an environment using conda env export > environment.yml.
I installed miniconda3 on a different system, updated conda, installed pip.
Then conda env create -f environment.yml -n py3

Actual Behavior

It gives me this error message:

Solving environment: failed
ResolvePackageNotFound:
  - brewer2mpl==1.4=py36_0
  - ggplot==0.9.4=py36_0

Expected Behavior

The environment should be installed with the same packages indicated in the yml file. All necessary information, such as channels, should be provided by the yml file. And it should give a warning about packages from locally installed sources. I noted that e.g. the packages pyqsar from my source system is not available on the target system. Though conda did not raise a warning.

Steps to Reproduce

TARGET SYSTEM
     active environment : None
       user config file : /home/swacker/.condarc
 populated config files :
          conda version : 4.5.4
    conda-build version : not installed
         python version : 3.6.5.final.0
       base environment : /home/swacker/miniconda3  (writable)
           channel URLs : 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
          package cache : /home/swacker/miniconda3/pkgs
                          /home/swacker/.conda/pkgs
       envs directories : /home/swacker/miniconda3/envs
                          /home/swacker/.conda/envs
               platform : linux-64
             user-agent : conda/4.5.4 requests/2.18.4 CPython/3.6.5 Linux/3.10.0-693.17.1.el7.x86_64 centos/7 glibc/2.17
                UID:GID : 16608087:16608087
             netrc file : None
           offline mode : False

# packages in environment at /home/swacker/miniconda3:
#
# Name                    Version                   Build  Channel
asn1crypto                0.24.0                   py36_0    defaults
ca-certificates           2018.03.07                    0    defaults
certifi                   2018.4.16                py36_0    defaults
cffi                      1.11.5           py36h9745a5d_0    defaults
chardet                   3.0.4            py36h0f667ec_1    defaults
conda                     4.5.4                    py36_0    defaults
conda-env                 2.6.0                h36134e3_1    defaults
cryptography              2.2.2            py36h14c3975_0    defaults
idna                      2.6              py36h82fb2a8_1    defaults
libedit                   3.1                  heed3624_0    defaults
libffi                    3.2.1                hd88cf55_4    defaults
libgcc-ng                 7.2.0                hdf63c60_3    defaults
libstdcxx-ng              7.2.0                hdf63c60_3    defaults
ncurses                   6.0                  h9df7e31_2    defaults
openssl                   1.0.2o               h20670df_0    defaults
pip                       9.0.3                    py36_0    defaults
pycosat                   0.6.3            py36h0a5515d_0    defaults
pycparser                 2.18             py36hf9f622e_1    defaults
pyopenssl                 17.5.0           py36h20ba746_0    defaults
pysocks                   1.6.8                    py36_0    defaults
python                    3.6.5                hc3d631a_0    defaults
readline                  7.0                  ha6073c6_4    defaults
requests                  2.18.4           py36he2e5f8d_1    defaults
ruamel_yaml               0.15.35          py36h14c3975_1    defaults
setuptools                39.0.1                   py36_0    defaults
six                       1.11.0           py36h372c433_1    defaults
sqlite                    3.23.1               he433501_0    defaults
tk                        8.6.7                hc745277_3    defaults
urllib3                   1.22             py36hbe7ace6_0    defaults
wheel                     0.31.0                   py36_0    defaults
xz                        5.2.3                h55aa19d_2    defaults
yaml                      0.1.7                had09818_2    defaults
zlib                      1.2.11               ha838bed_2    defaults
environment.yml
cat environment.yml
name: py3
channels:
- conda-forge
- bioconda
- bokeh
- defaults
dependencies:
- p7zip=15.09=3
- brewer2mpl=1.4=py36_0
- ggplot=0.9.4=py36_0
- jupyter_dashboards=0.7.0=py36_0
- _tflow_180_select=1.0=gpu
- absl-py=0.2.1=py36_0
- asn1crypto=0.24.0=py36_0
- astor=0.6.2=py36_0
- backcall=0.1.0=py36_0
- backports=1.0=py36hfa02d7e_1
- backports.weakref=1.0.post1=py36h39d5b32_0
- blas=1.0=mkl
- bleach=1.5.0=py36_0
- blosc=1.14.3=hdbcaa40_0
- bokeh=0.12.16=py36_0
- bzip2=1.0.6=h14c3975_5
- ca-certificates=2018.03.07=0
- certifi=2018.4.16=py36_0
- cffi=1.11.5=py36h9745a5d_0
- chardet=3.0.4=py36h0f667ec_1
- click=6.7=py36h5253387_0
- cloudpickle=0.5.3=py36_0
- colorcet=1.0.0=py36_0
- cryptography=2.2.2=py36h14c3975_0
- cudatoolkit=9.0=h13b8566_0
- cudnn=7.1.2=cuda9.0_0
- cupti=9.0.176=0
- cycler=0.10.0=py36h93f1223_0
- cython=0.28.2=py36h14c3975_0
- cytoolz=0.9.0.1=py36h14c3975_0
- dask=0.17.5=py36_0
- dask-core=0.17.5=py36_0
- datashader=0.6.5=py36_0
- datashape=0.5.4=py36h3ad6b5c_0
- dbus=1.13.2=h714fa37_1
- decorator=4.3.0=py36_0
- distributed=1.21.8=py36_0
- entrypoints=0.2.3=py36h1aec115_2
- expat=2.2.5=he0dffb1_0
- fontconfig=2.12.6=h49f89f6_0
- freetype=2.8=hab7d2ae_1
- gast=0.2.0=py36_0
- glib=2.56.1=h000015b_0
- gmp=6.1.2=h6c8ec71_1
- grpcio=1.11.0=py36hf484d3e_0
- gst-plugins-base=1.14.0=hbbd80ab_1
- gstreamer=1.14.0=hb453b48_1
- h5py=2.7.1=py36h3585f63_0
- hdf5=1.10.1=h9caa474_1
- heapdict=1.0.0=py36_2
- html5lib=0.9999999=py36_0
- icu=58.2=h9c2bf20_1
- idna=2.6=py36h82fb2a8_1
- imageio=2.3.0=py36_0
- inflection=0.3.1=py36_0
- intel-openmp=2018.0.0=8
- ipykernel=4.8.2=py36_0
- ipython=6.4.0=py36_0
- ipython_genutils=0.2.0=py36hb52b0d5_0
- ipywidgets=7.2.1=py36_0
- jedi=0.12.0=py36_1
- jinja2=2.10=py36ha16c418_0
- jpeg=9b=h024ee3a_2
- jsonschema=2.6.0=py36h006f8b5_0
- jupyter=1.0.0=py36_4
- jupyter_client=5.2.3=py36_0
- jupyter_console=5.2.0=py36he59e554_1
- jupyter_core=4.4.0=py36h7c827e3_0
- jupyterlab=0.32.1=py36_0
- jupyterlab_launcher=0.10.5=py36_0
- keras=2.1.5=py36_0
- kiwisolver=1.0.1=py36h764f252_0
- libedit=3.1.20170329=h6b74fdf_2
- libffi=3.2.1=hd88cf55_4
- libgcc-ng=7.2.0=hdf63c60_3
- libgfortran-ng=7.2.0=hdf63c60_3
- libpng=1.6.34=hb9fc6fc_0
- libprotobuf=3.5.2=h6f1eeef_0
- libsodium=1.0.16=h1bed415_0
- libstdcxx-ng=7.2.0=hdf63c60_3
- libtiff=4.0.9=he85c1e1_1
- libxcb=1.13=h1bed415_1
- libxml2=2.9.8=h26e45fe_1
- llvmlite=0.23.1=py36hdbcaa40_0
- locket=0.2.0=py36h787c0ad_1
- lzo=2.10=h49e0be7_2
- markdown=2.6.11=py36_0
- markupsafe=1.0=py36hd9260cd_1
- matplotlib=2.2.2=py36h0e671d2_1
- mistune=0.8.3=py36h14c3975_1
- mkl=2018.0.2=1
- mkl_fft=1.0.1=py36h3010b51_0
- mkl_random=1.0.1=py36h629b387_0
- mock=2.0.0=py36h3c5bf6c_0
- more-itertools=4.1.0=py36_0
- msgpack-python=0.5.6=py36h6bb024c_0
- multipledispatch=0.5.0=py36_0
- nbconvert=5.3.1=py36hb41ffb7_0
- nbformat=4.4.0=py36h31c9010_0
- ncurses=6.1=hf484d3e_0
- networkx=2.1=py36_0
- nose=1.3.7=py36hcdf7029_2
- notebook=5.5.0=py36_0
- numba=0.38.0=py36h637b7d7_0
- numexpr=2.6.5=py36h7bf3b9c_0
- numpy=1.14.3=py36hcd700cb_1
- numpy-base=1.14.3=py36h9be14a7_1
- olefile=0.45.1=py36_0
- openssl=1.0.2o=h20670df_0
- packaging=17.1=py36_0
- pandas=0.23.0=py36h637b7d7_0
- pandoc=1.19.2.1=hea2e7c5_1
- pandocfilters=1.4.2=py36ha6701b7_1
- param=1.6.1=py36_0
- parso=0.2.0=py36_0
- partd=0.3.8=py36h36fd896_0
- patsy=0.5.0=py36_0
- pbr=4.0.3=py36_0
- pcre=8.42=h439df22_0
- pexpect=4.5.0=py36_0
- pickleshare=0.7.4=py36h63277f8_0
- pillow=5.1.0=py36h3deb7b8_0
- pip=10.0.1=py36_0
- plotly=2.6.0=py36_0
- prompt_toolkit=1.0.15=py36h17d85b1_0
- protobuf=3.5.2=py36hf484d3e_0
- psutil=5.4.5=py36h14c3975_0
- ptyprocess=0.5.2=py36h69acd42_0
- pycparser=2.18=py36hf9f622e_1
- pygments=2.2.0=py36h0d3125c_0
- pyopenssl=18.0.0=py36_0
- pyparsing=2.2.0=py36hee85983_1
- pyqt=5.9.2=py36h751905a_0
- pysocks=1.6.8=py36_0
- pytables=3.4.3=py36h02b9ad4_0
- python=3.6.5=hc3d631a_2
- python-dateutil=2.7.3=py36_0
- pytz=2018.4=py36_0
- pywavelets=0.5.2=py36he602eb0_0
- pyyaml=3.12=py36hafb9ca4_1
- pyzmq=17.0.0=py36h14c3975_0
- qt=5.9.5=h7e424d6_0
- qtconsole=4.3.1=py36h8f73b5b_0
- quandl=3.3.0=py36_0
- readline=7.0=ha6073c6_4
- requests=2.18.4=py36he2e5f8d_1
- scikit-image=0.13.1=py36h14c3975_1
- scikit-learn=0.19.1=py36h7aa7ec6_0
- scipy=1.1.0=py36hfc37229_0
- seaborn=0.8.1=py36hfad7ec4_0
- send2trash=1.5.0=py36_0
- setuptools=39.1.0=py36_0
- simplegeneric=0.8.1=py36_2
- sip=4.19.8=py36hf484d3e_0
- six=1.11.0=py36h372c433_1
- snappy=1.1.7=hbae5bb6_3
- sortedcontainers=1.5.10=py36_0
- sqlalchemy=1.2.7=py36h6b74fdf_0
- sqlite=3.23.1=he433501_0
- statsmodels=0.9.0=py36h3010b51_0
- tblib=1.3.2=py36h34cf8b6_0
- tensorboard=1.8.0=py36hf484d3e_0
- tensorflow=1.8.0=hb11d968_0
- tensorflow-base=1.8.0=py36hc1a7637_0
- tensorflow-tensorboard=1.5.1=py36hf484d3e_1
- termcolor=1.1.0=py36_1
- terminado=0.8.1=py36_1
- testpath=0.3.1=py36h8cadb63_0
- tk=8.6.7=hc745277_3
- toolz=0.9.0=py36_0
- tornado=5.0.2=py36_0
- tqdm=4.23.3=py36_0
- traitlets=4.3.2=py36h674d592_0
- urllib3=1.22=py36hbe7ace6_0
- wcwidth=0.1.7=py36hdf4376a_0
- werkzeug=0.14.1=py36_0
- wheel=0.31.1=py36_0
- widgetsnbextension=3.2.1=py36_0
- xarray=0.10.4=py36_0
- xz=5.2.4=h14c3975_4
- yaml=0.1.7=had09818_2
- zeromq=4.2.5=h439df22_0
- zict=0.1.3=py36h3a3bf81_0
- zlib=1.2.11=ha838bed_2
- pip:
  - args==0.1.0
  - chembl-webresource-client==0.9.31
  - clint==0.5.1
  - dill==0.2.7.1
  - easydict==1.7
  - enum34==1.1.6
  - floyd-cli==0.10.31
  - gevent==1.3.1
  - gevent-openssl==1.2
  - greenlet==0.4.13
  - grequests==0.2.0
  - holoviews (/mnt/c/Users/soere/workspace/holoviews)==1.10.4.post10+g8711663
  - ipython-genutils==0.2.0
  - jupyter-client==5.2.3
  - jupyter-console==5.2.0
  - jupyter-core==4.4.0
  - jupyter-dashboards==0.7.0
  - jupyterlab-launcher==0.10.5
  - lightgbm==2.0.11
  - lxml==4.2.1
  - marshmallow==2.15.0
  - mkl-fft==1.0.0
  - mkl-random==1.0.1
  - molvs==0.1.1
  - mytoolbox==0+untagged.3.gde0cad4
  - oauthlib==2.0.6
  - pathlib2==2.3.0
  - prompt-toolkit==1.0.15
  - pyqsar-ML-publication==1.ge51d073.dirty
  - pyteomics==3.4.2
  - raven==6.5.0
  - requests-cache==0.4.13
  - requests-oauthlib==0.8.0
  - requests-toolbelt==0.8.0
  - tables==3.4.3
  - tabulate==0.8.2
  - tweepy==3.5.0
  - unittest2py3k==0.5.1
  - unittest2six==0.0.0
  - versioneer==0.18
  - xgboost==0.7.post3
prefix: /home/swacker/miniconda3/envs/py3
@SKalt

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commented Jun 5, 2018

Seems like those packages don't exist at that combination of version and build on the channels searched by your target system. I found broadening my search by eliminating build info helped. The command I used was conda env export --no-builds > environment.yml.

@soerendip

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commented Jun 6, 2018

Ok, I will try that. Though, I don't understand why the packages should not be available, since I also installed them at the source system.

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commented Jun 11, 2018

The error changed a bit.

conda env create -f environment.yml -n py3
Solving environment: failed

ResolvePackageNotFound:
  - brewer2mpl==1.4=py36_0
@SKalt

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commented Jun 11, 2018

That was my experience as well: fixed around half the unresolved dependencies. FWIW, my eventual fix was installing the stubborn ones via pip.

@mahboobmm

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commented Oct 10, 2018

Any updates on this? Going through the same issue.

@vv111y

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commented Oct 20, 2018

same here

@chauek

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commented Oct 26, 2018

@MrCurl

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commented Dec 4, 2018

Had that issue and solved it by first conda update --all on the host sytem, then conda export --no-builds > env.yml and regular installation via conda env create -f env.yml on the remote machine.

Guess for me the problem was that the base env conda on remote had packages installed that were not working with the older packages on the host system.

@6Hhcy

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commented Apr 8, 2019

Does anyone here know why we have any Python packages in the top section "dependencies". It seems like it only causes problems. Why not put them all under "pip"

@TejasAvinashShetty

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commented May 5, 2019

I think there is a small error in https://github.com/ContinuumIO/anaconda-issues/issues/9480#issuecomment-444117929 namely that

conda export --no-builds > env.yml

should instead be written as

conda env export --no-builds > env.yml

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commented May 5, 2019

One could also try adding a conda channel if the said packages are not present in the default channels. E.g. qutip package appears in conda-forge channel. One can add the channel by typing the following command.
conda config --append channels conda-forge Off course one needs to replace the name conda-forge by the appropriate channel name.

@TejasAvinashShetty

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commented May 5, 2019

I think it also helps to remove any packages which would not be necessary to prevent conflicts. One thing that we must try is by removing the version numbers associated with the packages in the .yml file.

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