Conda: Cannot pass environment.yml file to conda create
I'm submitting a bug report for a Win7 64bit 3.6 install. This appears to be a reoccurring issue (#2124, #2800, etc.).
Current Behavior
My environment was all messed up, so I removed it (renname anaconda3 anaconda3.bak) and am trying to use the yaml file (conda to reinstall it. Here is what happens:
C:\Users\212>conda` install --name root --file environment.yml
CondaValueError: could not parse 'name: root' in: environment.yml
C:\Users\212>conda install --name root --file environment.yml -v
Traceback (most recent call last):
File "C:\Users\212\AppData\Local\Continuum\Anaconda3\lib\site-packages\conda\exceptions.py", line 772, in __call__
return func(*args, **kwargs)
File "C:\Users\212\AppData\Local\Continuum\Anaconda3\lib\site-packages\conda\cli\main.py", line 78, in _main
exit_code = do_call(args, p)
File "C:\Users\212\AppData\Local\Continuum\Anaconda3\lib\site-packages\conda\cli\conda_argparse.py", line 77, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "C:\Users\212\AppData\Local\Continuum\Anaconda3\lib\site-packages\conda\cli\main_install.py", line 11, in execute
install(args, parser, 'install')
File "C:\Users\212\AppData\Local\Continuum\Anaconda3\lib\site-packages\conda\cli\install.py", line 182, in install
specs.extend(common.specs_from_url(fpath, json=context.json))
File "C:\Users\212\AppData\Local\Continuum\Anaconda3\lib\site-packages\conda\cli\common.py", line 139, in specs_from_url
(line, url))
conda.exceptions.CondaValueError: could not parse 'name: root' in: environment.yml
The environment.yml file
name: root
channels:
- conda-forge
- defaults
dependencies:
- altair=1.2.1=py_0
- beakerx=0.12.0=py36_1
- curl=7.55.1=vc14_0
- hdf5=1.10.1=vc14_1
- jupyter_contrib_core=0.3.3=py36_0
- jupyter_nbextensions_configurator=0.2.8=py36_0
- krb5=1.14.2=vc14_0
- libiconv=1.14=vc14_4
- libssh2=1.8.0=vc14_2
- libxml2=2.9.5=vc14_1
- libxslt=1.1.32=vc14_0
- lzo=2.10=vc14_0
- maven=3.5.0=0
- plac=0.9.6=py36_0
- termcolor=1.1.0=py36_1
- ujson=1.35=py36_0
- vega=0.4.4=py36_1
- _ipyw_jlab_nb_ext_conf=0.1.0=py36he6757f0_0
- alabaster=0.7.10=py36hcd07829_0
- anaconda-client=1.6.6=py36ha174c20_0
- anaconda=custom=py36h363777c_0
- anaconda-navigator=1.6.11=py36h25c516c_0
- anaconda-project=0.8.2=py36hfad2e28_0
- asn1crypto=0.24.0=py36_0
- astroid=1.5.3=py36h9d85297_0
- astropy=2.0.3=py36hfa6e2cd_0
- attrs=17.3.0=py36hc87868e_0
- babel=2.5.0=py36h35444c1_0
- backports=1.0=py36h81696a8_1
- backports.shutil_get_terminal_size=1.0.0=py36h79ab834_2
- beautifulsoup4=4.6.0=py36hd4cc5e8_1
- bitarray=0.8.1=py36h6af124b_0
- bkcharts=0.2=py36h7e685f7_0
- blaze=0.11.3=py36h8a29ca5_0
- bleach=2.1.2=py36_0
- bokeh=0.12.13=py36h047fa9f_0
- boto=2.48.0=py36h1a776d2_1
- bottleneck=1.2.1=py36hd119dfa_0
- bzip2=1.0.6=haa5b126_2
- ca-certificates=2017.08.26=h94faf87_0
- cachecontrol=0.12.3=py36hfe50d7b_0
- certifi=2018.1.18=py36_0
- cffi=1.11.4=py36hfa6e2cd_0
- chardet=3.0.4=py36h420ce6e_1
- click=6.7=py36hec8c647_0
- cloudpickle=0.5.2=py36h6b1d831_0
- clyent=1.2.2=py36hb10d595_1
- colorama=0.3.9=py36h029ae33_0
- colorcet=0.9.1=py36_0
- comtypes=1.1.2=py36heb9b3d1_0
- conda=4.4.8=py36_0
- conda-build=3.4.0=py36_0
- conda-env=2.6.0=h36134e3_1
- conda-verify=2.0.0=py36h065de53_0
- console_shortcut=0.1.1=h6bb2dd7_3
- contextlib2=0.5.5=py36he5d52c0_0
- coverage=4.4.2=py36hd32d05b_0
- cryptography=2.1.4=py36he1d7878_0
- cycler=0.10.0=py36h009560c_0
- cymem=1.31.2=py36h51d26f2_0
- cython=0.27.3=py36h22f4c84_0
- cytoolz=0.8.2=py36h547e66e_0
- dask=0.16.1=py36_0
- dask-core=0.16.1=py36_0
- datashader=0.6.2=py36h5177652_0
- datashape=0.5.4=py36h5770b85_0
- decorator=4.2.1=py36_0
- dill=0.2.7.1=py36hf552773_0
- distlib=0.2.5=py36h51371be_0
- distributed=1.20.2=py36_0
- docutils=0.14=py36h6012d8f_0
- entrypoints=0.2.3=py36hfd66bb0_2
- et_xmlfile=1.0.1=py36h3d2d736_0
- fastcache=1.0.2=py36hffdae1b_0
- filelock=2.0.13=py36h20000bf_0
- flask=0.12.2=py36h98b5e8f_0
- flask-cors=3.0.3=py36h8a3855d_0
- freetype=2.8=h51f8f2c_1
- ftfy=4.4.3=py36hb6b3982_0
- get_terminal_size=1.0.0=h38e98db_0
- gevent=1.2.2=py36h342a76c_0
- glob2=0.6=py36hdf76b57_0
- graphviz=2.38.0=4
- greenlet=0.4.12=py36ha00ad21_0
- h5py=2.7.1=py36he54a1c3_0
- heapdict=1.0.0=py36h21fa5f4_0
- holoviews=1.9.2=py36_0
- html5lib=1.0.1=py36h047fa9f_0
- hypothesis=3.38.5=py36h987501d_0
- icc_rt=2017.0.4=h97af966_0
- icu=58.2=ha66f8fd_1
- idna=2.6=py36h148d497_1
- imageio=2.2.0=py36had6c2d2_0
- imagesize=0.7.1=py36he29f638_0
- intel-openmp=2018.0.0=hd92c6cd_8
- ipykernel=4.8.0=py36_0
- ipython=6.2.1=py36h9cf0123_1
- ipython_genutils=0.2.0=py36h3c5d0ee_0
- ipywidgets=7.1.1=py36_0
- isort=4.2.15=py36h6198cc5_0
- itsdangerous=0.24=py36hb6c5a24_1
- jdcal=1.3=py36h64a5255_0
- jedi=0.11.1=py36_0
- jinja2=2.10=py36h292fed1_0
- jpeg=9b=hb83a4c4_2
- jsonschema=2.6.0=py36h7636477_0
- jupyter=1.0.0=py36h422fd7e_2
- jupyter_client=5.2.2=py36_0
- jupyter_console=5.2.0=py36h6d89b47_1
- jupyter_core=4.4.0=py36h56e9d50_0
- jupyterlab=0.30.6=py36h047fa9f_0
- jupyterlab_launcher=0.6.0=py36_0
- lazy-object-proxy=1.3.1=py36hd1c21d2_0
- libpng=1.6.34=h79bbb47_0
- libtiff=4.0.9=h0f13578_0
- llvmlite=0.21.0=py36he0b0552_0
- locket=0.2.0=py36hfed976d_1
- lockfile=0.12.2=py36h0468280_0
- lxml=4.1.1=py36he0adb16_0
- markupsafe=1.0=py36h0e26971_1
- matplotlib=2.1.2=py36h016c42a_0
- mccabe=0.6.1=py36hb41005a_1
- menuinst=1.4.10=py36h42196fb_0
- mistune=0.8.3=py36_0
- mkl=2018.0.1=h2108138_4
- mkl-service=1.1.2=py36h57e144c_4
- mpmath=1.0.0=py36hacc8adf_2
- msgpack-numpy=0.4.1=py36h93564ae_0
- msgpack-python=0.5.1=py36he980bc4_0
- multipledispatch=0.4.9=py36he44c36e_0
- murmurhash=0.26.4=py36h2b517bc_0
- navigator-updater=0.1.0=py36h8a7b86b_0
- nbconvert=5.3.1=py36h8dc0fde_0
- nbformat=4.4.0=py36h3a5bc1b_0
- networkx=2.1=py36_0
- nltk=3.2.5=py36h76d52bb_0
- nose=1.3.7=py36h1c3779e_2
- notebook=5.3.1=py36_2
- numba=0.36.2=np113py36h0128aa7_0
- numexpr=2.6.4=py36h30784b8_0
- numpy=1.13.3=py36h4a99626_2
- numpydoc=0.7.0=py36ha25429e_0
- odo=0.5.1=py36h7560279_0
- olefile=0.45.1=py36_0
- openjdk=8.0.121=1
- openpyxl=2.4.9=py36h6c6577a_0
- openssl=1.0.2n=h74b6da3_0
- packaging=16.8=py36ha0986f6_1
- pandas=0.20.3=py36hce827b7_2
- pandoc=1.19.2.1=hb2460c7_1
- pandocfilters=1.4.2=py36h3ef6317_1
- param=1.5.1=py36_0
- parso=0.1.1=py36hae3edee_0
- partd=0.3.8=py36hc8e763b_0
- path.py=10.5=py36h2b94a8f_0
- pathlib=1.0.1=py36_0
- pathlib2=2.3.0=py36h7bfb78b_0
- patsy=0.4.1=py36h42cefec_0
- pep8=1.7.0=py36h0f3d67a_0
- pickleshare=0.7.4=py36h9de030f_0
- pillow=5.0.0=py36h0738816_0
- pip=9.0.1=py36h226ae91_4
- pkginfo=1.4.1=py36hb0f9cfa_1
- pluggy=0.6.0=py36hc7daf1e_0
- ply=3.10=py36h1211beb_0
- preshed=1.0.0=py36h065ec1e_0
- progress=1.3=py36hbeca8d3_0
- prompt_toolkit=1.0.15=py36h60b8f86_0
- psutil=5.4.3=py36hfa6e2cd_0
- py=1.5.2=py36hbcfbabc_0
- pycodestyle=2.3.1=py36h7cc55cd_0
- pycosat=0.6.3=py36h413d8a4_0
- pycparser=2.18=py36hd053e01_1
- pycrypto=2.6.1=py36he68e6e2_1
- pycurl=7.43.0=py36h086bf4c_3
- pyflakes=1.6.0=py36h0b975d6_0
- pygments=2.2.0=py36hb010967_0
- pylint=1.7.4=py36ha4e6ded_0
- pympler=0.5=py36h863af32_0
- pyodbc=4.0.21=py36h82c9817_0
- pyopenssl=17.5.0=py36h5b7d817_0
- pyparsing=2.2.0=py36h785a196_1
- pyqt=5.6.0=py36hb5ed885_5
- pyreadline=2.1=py36h094d952_1
- pysocks=1.6.7=py36h698d350_1
- pytables=3.4.2=py36h71138e3_2
- pytest=3.3.0=py36hf3522a2_0
- python=3.6.4=h6538335_1
- python-dateutil=2.6.1=py36h509ddcb_1
- pytz=2017.3=py36h1d3fa6b_0
- pywavelets=0.5.2=py36hc649158_0
- pywin32=222=py36hfa6e2cd_0
- pyyaml=3.12=py36h1d1928f_1
- pyzmq=16.0.3=py36he714bf5_0
- qt=5.6.2=vc14h6f8c307_12
- qtawesome=0.4.4=py36h5aa48f6_0
- qtconsole=4.3.1=py36h99a29a9_0
- qtpy=1.3.1=py36hb8717c5_0
- regex=2017.11.09=py36ha090894_0
- requests=2.18.4=py36h4371aae_1
- rope=0.10.7=py36had63a69_0
- ruamel_yaml=0.15.35=py36hfa6e2cd_1
- scikit-image=0.13.0=py36h6dffa3f_1
- scikit-learn=0.19.1=py36h53aea1b_0
- scipy=1.0.0=py36h1260518_0
- seaborn=0.8.1=py36h9b69545_0
- send2trash=1.4.2=py36_0
- setuptools=38.4.0=py36_0
- simplegeneric=0.8.1=py36heab741f_0
- singledispatch=3.4.0.3=py36h17d0c80_0
- sip=4.18.1=py36h9c25514_2
- six=1.11.0=py36h4db2310_1
- snowballstemmer=1.2.1=py36h763602f_0
- sortedcollections=0.5.3=py36hbefa0ab_0
- sortedcontainers=1.5.9=py36_0
- spacy=1.9.0=py36_vc14hffcad6b_1
- sphinx=1.6.3=py36h9bb690b_0
- sphinxcontrib=1.0=py36hbbac3d2_1
- sphinxcontrib-websupport=1.0.1=py36hb5e5916_1
- spyder=3.2.5=py36_0
- sqlalchemy=1.1.13=py36h5948d12_0
- sqlite=3.22.0=h9d3ae62_0
- statsmodels=0.8.0=py36h6189b4c_0
- sympy=1.1.1=py36h96708e0_0
- tblib=1.3.2=py36h30f5020_0
- testpath=0.3.1=py36h2698cfe_0
- thinc=6.5.2=py36_vc14he7005f8_0
- tk=8.6.7=hcb92d03_3
- toolz=0.9.0=py36_0
- tornado=4.5.3=py36_0
- tqdm=4.19.4=py36h02a35f0_0
- traitlets=4.3.2=py36h096827d_0
- typing=3.6.2=py36hb035bda_0
- unicodecsv=0.14.1=py36h6450c06_0
- urllib3=1.22=py36h276f60a_0
- vc=14=h0510ff6_3
- vs2015_runtime=14.0.25123=3
- wcwidth=0.1.7=py36h3d5aa90_0
- webencodings=0.5.1=py36h67c50ae_1
- werkzeug=0.14.1=py36_0
- wheel=0.30.0=py36h6c3ec14_1
- widgetsnbextension=3.1.0=py36_0
- win_inet_pton=1.0.1=py36he67d7fd_1
- win_unicode_console=0.5=py36hcdbd4b5_0
- wincertstore=0.2=py36h7fe50ca_0
- wrapt=1.10.11=py36he5f5981_0
- xarray=0.10.0=py36hbbb8305_0
- xlrd=1.1.0=py36h1cb58dc_1
- xlsxwriter=1.0.2=py36hf723b7d_0
- xlwings=0.11.4=py36hd3cf94d_0
- xlwt=1.3.0=py36h1a4751e_0
- yaml=0.1.7=hc54c509_2
- zict=0.1.3=py36h2d8e73e_0
- zlib=1.2.11=h8395fce_2
- zope=1.0=py36_0
- zope.interface=4.4.3=py36h56cab3c_0
- pip:
- amqp==2.2.2
- args==0.1.0
- autopep8==1.3.2
- billiard==3.5.0.3
- boto3==1.5.22
- botocore==1.8.36
- celery==4.1.0
- clint==0.5.1
- dateparser==0.6.0
- deap==1.0.2
- expynent==1.0.0
- flake8==3.5.0
- flashtext==2.6
- floyd-cli==0.10.31
- humanize==0.5.1
- jmespath==0.9.3
- jupyter-pip==0.3.1
- kombu==4.1.0
- marshmallow==2.15.0
- maya==0.3.3
- mimesis==1.0.5
- objgraph==3.3.0
- pandas-profiling==1.4.1
- pendulum==1.4.0
- pew==1.1.2
- pipenv==9.0.3
- psycopg2==2.7.3.1
- pydot==1.2.4
- pytzdata==2018.3
- pywinauto==0.6.4
- pywinpty==0.5.1
- raven==6.5.0
- requests-toolbelt==0.8.0
- s3transfer==0.1.12
- stopit==1.1.1
- tables==3.4.2
- tabulate==0.8.2
- terminado==0.8.1
- tk-tools==0.4.5
- tpot==0.9.0
- tzlocal==1.5.1
- update-checker==0.16
- vine==1.1.4
- virtualenv==15.1.0
- virtualenv-clone==0.2.6
- wxpython==4.0.0b2
- xdot==0.9
- yapf==0.18.0
prefix: C:\Users\212\AppData\Local\Continuum\anaconda3
Steps to Reproduce
activate root
conda env export > environment.yml
conda install --name root --file environment.yml
Expected Behavior
" to quickly reproduce your environment, with all of its packages and versions, give them a copy of your environment.yml file." -- https://conda.io/docs/user-guide/tasks/manage-environments.html#sharing-an-environment
Environment Information
conda info active environment : None
user config file : C:\Users\212563417\.condarc
populated config files : C:\Users\212563417\.condarc
conda version : 4.4.8
conda-build version : 3.0.27
python version : 3.6.3.final.0
base environment : C:\Users\212563417\AppData\Local\Continuum\Anaconda3 (writable)
channel URLs : https://repo.continuum.io/pkgs/main/win-64
https://repo.continuum.io/pkgs/main/noarch
https://repo.continuum.io/pkgs/free/win-64
https://repo.continuum.io/pkgs/free/noarch
https://repo.continuum.io/pkgs/r/win-64
https://repo.continuum.io/pkgs/r/noarch
https://repo.continuum.io/pkgs/pro/win-64
https://repo.continuum.io/pkgs/pro/noarch
https://repo.continuum.io/pkgs/msys2/win-64
https://repo.continuum.io/pkgs/msys2/noarch
package cache : C:\Users\212563417\AppData\Local\Continuum\Anaconda3\pkgs
C:\Users\212563417\AppData\Local\conda\conda\pkgs
envs directories : C:\Users\212563417\AppData\Local\Continuum\Anaconda3\envs
C:\Users\212563417\AppData\Local\conda\conda\envs
C:\Users\212563417\.conda\envs
platform : win-64
user-agent : conda/4.4.8 requests/2.18.4 CPython/3.6.3 Windows/7 Windows/6.1.7601
administrator : False
netrc file : None
offline mode : False
conda config --show-sourcesC:\Users\212>conda config --show-sources
==> C:\Users\212\.condarc <==
ssl_verify: False
proxy_servers:
http: gateway.zscalertwo.net:18000
https: gateway.zscalertwo.net:18000
channels:
- defaults
show_channel_urls: True
conda list --show-channel-urls
C:\Users\212563417>conda list --show-channel-urls
# packages in environment at C:\Users\212563417\AppData\Local\Continuum\Anaconda3:
#
# Name Version Build Channel
_ipyw_jlab_nb_ext_conf 0.1.0 py36he6757f0_0 defaults
alabaster 0.7.10 py36hcd07829_0 defaults
anaconda custom py36h363777c_0 defaults
anaconda-client 1.6.5 py36hd36550c_0 defaults
anaconda-navigator 1.6.9 py36hc720852_0 defaults
anaconda-project 0.8.0 py36h8b3bf89_0 defaults
asn1crypto 0.22.0 py36h8e79faa_1 defaults
astroid 1.5.3 py36h9d85297_0 defaults
astropy 2.0.2 py36h06391c4_4 defaults
babel 2.5.0 py36h35444c1_0 defaults
backports 1.0 py36h81696a8_1 defaults
backports.shutil_get_terminal_size 1.0.0 py36h79ab834_2 defaults
beautifulsoup4 4.6.0 py36hd4cc5e8_1 defaults
bitarray 0.8.1 py36h6af124b_0 defaults
bkcharts 0.2 py36h7e685f7_0 defaults
blaze 0.11.3 py36h8a29ca5_0 defaults
bleach 2.0.0 py36h0a7e3d6_0 defaults
bokeh 0.12.10 py36h0be3b39_0 defaults
boto 2.48.0 py36h1a776d2_1 defaults
bottleneck 1.2.1 py36hd119dfa_0 defaults
bzip2 1.0.6 vc14hdec8e7a_1 [vc14] defaults
ca-certificates 2017.08.26 h94faf87_0 defaults
cachecontrol 0.12.3 py36hfe50d7b_0 defaults
certifi 2017.7.27.1 py36h043bc9e_0 defaults
cffi 1.10.0 py36hae3d1b5_1 defaults
chardet 3.0.4 py36h420ce6e_1 defaults
click 6.7 py36hec8c647_0 defaults
cloudpickle 0.4.0 py36h639d8dc_0 defaults
clyent 1.2.2 py36hb10d595_1 defaults
colorama 0.3.9 py36h029ae33_0 defaults
comtypes 1.1.2 py36heb9b3d1_0 defaults
conda 4.4.8 py36_0 defaults
conda-build 3.0.27 py36h309a530_0 defaults
conda-env 2.6.0 h36134e3_1 defaults
conda-verify 2.0.0 py36h065de53_0 defaults
console_shortcut 0.1.1 h6bb2dd7_3 defaults
contextlib2 0.5.5 py36he5d52c0_0 defaults
cryptography 2.0.3 py36h123decb_1 defaults
curl 7.55.1 vc14hdaba4a4_3 [vc14] defaults
cycler 0.10.0 py36h009560c_0 defaults
cython 0.26.1 py36h18049ac_0 defaults
cytoolz 0.8.2 py36h547e66e_0 defaults
dask 0.15.3 py36h396fcb9_0 defaults
dask-core 0.15.3 py36hd651449_0 defaults
datashape 0.5.4 py36h5770b85_0 defaults
decorator 4.1.2 py36he63a57b_0 defaults
distlib 0.2.5 py36h51371be_0 defaults
distributed 1.19.1 py36h8504682_0 defaults
docutils 0.14 py36h6012d8f_0 defaults
entrypoints 0.2.3 py36hfd66bb0_2 defaults
et_xmlfile 1.0.1 py36h3d2d736_0 defaults
fastcache 1.0.2 py36hffdae1b_0 defaults
filelock 2.0.12 py36hd7ddd41_0 defaults
flask 0.12.2 py36h98b5e8f_0 defaults
flask-cors 3.0.3 py36h8a3855d_0 defaults
freetype 2.8 vc14h17c9bdf_0 [vc14] defaults
get_terminal_size 1.0.0 h38e98db_0 defaults
gevent 1.2.2 py36h342a76c_0 defaults
glob2 0.5 py36h11cc1bd_1 defaults
greenlet 0.4.12 py36ha00ad21_0 defaults
h5py 2.7.0 py36hfbe0a52_1 defaults
hdf5 1.10.1 vc14hb361328_0 [vc14] defaults
heapdict 1.0.0 py36h21fa5f4_0 defaults
html5lib 0.999999999 py36ha09b1f3_0 defaults
icc_rt 2017.0.4 h97af966_0 defaults
icu 58.2 vc14hc45fdbb_0 [vc14] defaults
idna 2.6 py36h148d497_1 defaults
imageio 2.2.0 py36had6c2d2_0 defaults
imagesize 0.7.1 py36he29f638_0 defaults
intel-openmp 2018.0.0 hcd89f80_7 defaults
ipykernel 4.6.1 py36hbb77b34_0 defaults
ipython 6.1.0 py36h236ecc8_1 defaults
ipython_genutils 0.2.0 py36h3c5d0ee_0 defaults
ipywidgets 7.0.0 py36h2e74ada_0 defaults
isort 4.2.15 py36h6198cc5_0 defaults
itsdangerous 0.24 py36hb6c5a24_1 defaults
jdcal 1.3 py36h64a5255_0 defaults
jedi 0.10.2 py36hed927a0_0 defaults
jinja2 2.9.6 py36h10aa3a0_1 defaults
jpeg 9b vc14h4d7706e_1 [vc14] defaults
jsonschema 2.6.0 py36h7636477_0 defaults
jupyter 1.0.0 py36h422fd7e_2 defaults
jupyter_client 5.1.0 py36h9902a9a_0 defaults
jupyter_console 5.2.0 py36h6d89b47_1 defaults
jupyter_core 4.3.0 py36h511e818_0 defaults
jupyterlab 0.27.0 py36h34cc53b_2 defaults
jupyterlab_launcher 0.4.0 py36h22c3ccf_0 defaults
lazy-object-proxy 1.3.1 py36hd1c21d2_0 defaults
libiconv 1.15 vc14h29686d3_5 [vc14] defaults
libpng 1.6.32 vc14h5163883_3 [vc14] defaults
libssh2 1.8.0 vc14hcf584a9_2 [vc14] defaults
libtiff 4.0.8 vc14h04e2a1e_10 [vc14] defaults
libxml2 2.9.4 vc14h8fd0f11_5 [vc14] defaults
libxslt 1.1.29 vc14hf85b8d4_5 [vc14] defaults
llvmlite 0.20.0 py36_0 defaults
locket 0.2.0 py36hfed976d_1 defaults
lockfile 0.12.2 py36h0468280_0 defaults
lxml 4.1.0 py36h0dcd83c_0 defaults
lzo 2.10 vc14h0a64fa6_1 [vc14] defaults
markupsafe 1.0 py36h0e26971_1 defaults
matplotlib 2.1.0 py36h11b4b9c_0 defaults
mccabe 0.6.1 py36hb41005a_1 defaults
menuinst 1.4.10 py36h42196fb_0 defaults
mistune 0.7.4 py36h4874169_0 defaults
mkl 2018.0.0 h36b65af_4 defaults
mkl-service 1.1.2 py36h57e144c_4 defaults
mpmath 0.19 py36he326802_2 defaults
msgpack-python 0.4.8 py36h58b1e9d_0 defaults
multipledispatch 0.4.9 py36he44c36e_0 defaults
navigator-updater 0.1.0 py36h8a7b86b_0 defaults
nbconvert 5.3.1 py36h8dc0fde_0 defaults
nbformat 4.4.0 py36h3a5bc1b_0 defaults
networkx 2.0 py36hff991e3_0 defaults
nltk 3.2.4 py36hd0e0a39_0 defaults
nose 1.3.7 py36h1c3779e_2 defaults
notebook 5.0.0 py36hd9fbf6f_2 defaults
numba 0.35.0 np113py36_10 defaults
numexpr 2.6.2 py36h7ca04dc_1 defaults
numpy 1.13.3 py36ha320f96_0 defaults
numpydoc 0.7.0 py36ha25429e_0 defaults
odo 0.5.1 py36h7560279_0 defaults
olefile 0.44 py36h0a7bdd2_0 defaults
openpyxl 2.4.8 py36hf3b77f6_1 defaults
openssl 1.0.2l vc14hcac20b0_2 [vc14] defaults
packaging 16.8 py36ha0986f6_1 defaults
pandas 0.20.3 py36hce827b7_2 defaults
pandoc 1.19.2.1 hb2460c7_1 defaults
pandocfilters 1.4.2 py36h3ef6317_1 defaults
partd 0.3.8 py36hc8e763b_0 defaults
path.py 10.3.1 py36h3dd8b46_0 defaults
pathlib2 2.3.0 py36h7bfb78b_0 defaults
patsy 0.4.1 py36h42cefec_0 defaults
pep8 1.7.0 py36h0f3d67a_0 defaults
pickleshare 0.7.4 py36h9de030f_0 defaults
pillow 4.2.1 py36hdb25ab2_0 defaults
pip 9.0.1 py36hadba87b_3 defaults
pkginfo 1.4.1 py36hb0f9cfa_1 defaults
ply 3.10 py36h1211beb_0 defaults
progress 1.3 py36hbeca8d3_0 defaults
prompt_toolkit 1.0.15 py36h60b8f86_0 defaults
psutil 5.4.0 py36h4e662fb_0 defaults
py 1.4.34 py36ha4aca3a_1 defaults
pycodestyle 2.3.1 py36h7cc55cd_0 defaults
pycosat 0.6.3 py36h413d8a4_0 defaults
pycparser 2.18 py36hd053e01_1 defaults
pycrypto 2.6.1 py36he68e6e2_1 defaults
pycurl 7.43.0 py36h086bf4c_3 defaults
pyflakes 1.6.0 py36h0b975d6_0 defaults
pygments 2.2.0 py36hb010967_0 defaults
pylint 1.7.4 py36ha4e6ded_0 defaults
pyodbc 4.0.17 py36h0006bc2_0 defaults
pyopenssl 17.2.0 py36h15ca2fc_0 defaults
pyparsing 2.2.0 py36h785a196_1 defaults
pyqt 5.6.0 py36hb5ed885_5 defaults
pysocks 1.6.7 py36h698d350_1 defaults
pytables 3.4.2 py36h71138e3_2 defaults
pytest 3.2.1 py36h753b05e_1 defaults
python 3.6.3 h9e2ca53_1 defaults
python-dateutil 2.6.1 py36h509ddcb_1 defaults
pytz 2017.2 py36h05d413f_1 defaults
pywavelets 0.5.2 py36hc649158_0 defaults
pywin32 221 py36h9c10281_0 defaults
pyyaml 3.12 py36h1d1928f_1 defaults
pyzmq 16.0.2 py36h38c27d9_2 defaults
qt 5.6.2 vc14h6f8c307_12 [vc14] defaults
qtawesome 0.4.4 py36h5aa48f6_0 defaults
qtconsole 4.3.1 py36h99a29a9_0 defaults
qtpy 1.3.1 py36hb8717c5_0 defaults
requests 2.18.4 py36h4371aae_1 defaults
rope 0.10.5 py36hcaf5641_0 defaults
ruamel_yaml 0.11.14 py36h9b16331_2 defaults
scikit-image 0.13.0 py36h6dffa3f_1 defaults
scikit-learn 0.19.1 py36h53aea1b_0 defaults
scipy 0.19.1 py36h7565378_3 defaults
seaborn 0.8.0 py36h62cb67c_0 defaults
setuptools 36.5.0 py36h65f9e6e_0 defaults
simplegeneric 0.8.1 py36heab741f_0 defaults
singledispatch 3.4.0.3 py36h17d0c80_0 defaults
sip 4.18.1 py36h9c25514_2 defaults
six 1.11.0 py36h4db2310_1 defaults
snowballstemmer 1.2.1 py36h763602f_0 defaults
sortedcollections 0.5.3 py36hbefa0ab_0 defaults
sortedcontainers 1.5.7 py36ha90ac20_0 defaults
sphinx 1.6.3 py36h9bb690b_0 defaults
sphinxcontrib 1.0 py36hbbac3d2_1 defaults
sphinxcontrib-websupport 1.0.1 py36hb5e5916_1 defaults
spyder 3.2.4 py36h8845eaa_0 defaults
sqlalchemy 1.1.13 py36h5948d12_0 defaults
sqlite 3.20.1 vc14h7ce8c62_1 [vc14] defaults
statsmodels 0.8.0 py36h6189b4c_0 defaults
sympy 1.1.1 py36h96708e0_0 defaults
tblib 1.3.2 py36h30f5020_0 defaults
testpath 0.3.1 py36h2698cfe_0 defaults
tk 8.6.7 vc14hb68737d_1 [vc14] defaults
toolz 0.8.2 py36he152a52_0 defaults
tornado 4.5.2 py36h57f6048_0 defaults
traitlets 4.3.2 py36h096827d_0 defaults
typing 3.6.2 py36hb035bda_0 defaults
unicodecsv 0.14.1 py36h6450c06_0 defaults
urllib3 1.22 py36h276f60a_0 defaults
vc 14 h2379b0c_2 defaults
vs2015_runtime 14.0.25123 hd4c4e62_2 defaults
wcwidth 0.1.7 py36h3d5aa90_0 defaults
webencodings 0.5.1 py36h67c50ae_1 defaults
werkzeug 0.12.2 py36h866a736_0 defaults
wheel 0.29.0 py36h6ce6cde_1 defaults
widgetsnbextension 3.0.2 py36h364476f_1 defaults
win_inet_pton 1.0.1 py36he67d7fd_1 defaults
win_unicode_console 0.5 py36hcdbd4b5_0 defaults
wincertstore 0.2 py36h7fe50ca_0 defaults
wrapt 1.10.11 py36he5f5981_0 defaults
xlrd 1.1.0 py36h1cb58dc_1 defaults
xlsxwriter 1.0.2 py36hf723b7d_0 defaults
xlwings 0.11.4 py36hd3cf94d_0 defaults
xlwt 1.3.0 py36h1a4751e_0 defaults
yaml 0.1.7 vc14hb31d195_1 [vc14] defaults
zict 0.1.3 py36h2d8e73e_0 defaults
zlib 1.2.11 vc14h1cdd9ab_1 [vc14] defaults
gnomic
All 3 comments
Hello, I have a similar issue.
I'm trying to update an existing env and I get this
CondaValueError: could not parse '- anaconda' in: environment.yml
although I used the same file than before adding a line or two in the dependencies.
Using conda 4.4.10 on ubuntu 7.10
conda list --show-channel-urls
asn1crypto 0.23.0 py36h4639342_0 defaults
ca-certificates 2017.08.26 h1d4fec5_0 defaults
certifi 2018.1.18 py36_0 defaults
cffi 1.11.2 py36h2825082_0 defaults
chardet 3.0.4 py36h0f667ec_1 defaults
conda 4.4.10 py36_0 defaults
conda-env 2.6.0 h36134e3_1 defaults
cryptography 2.1.4 py36hd09be54_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 h7cc24e2_2 defaults
libstdcxx-ng 7.2.0 h7a57d05_2 defaults
ncurses 6.0 h9df7e31_2 defaults
numpy 1.14.0 <pip>
openssl 1.0.2n hb7f436b_0 defaults
pandas 0.22.0 <pip>
pip 9.0.1 py36h6c6f9ce_4 defaults
pycosat 0.6.3 py36h0a5515d_0 defaults
pycparser 2.18 py36hf9f622e_1 defaults
pyopenssl 17.5.0 py36h20ba746_0 defaults
pysocks 1.6.7 py36hd97a5b1_1 defaults
python 3.6.3 h6c0c0dc_5 defaults
python-dateutil 2.6.1 <pip>
pytz 2017.3 <pip>
readline 7.0 ha6073c6_4 defaults
requests 2.18.4 py36he2e5f8d_1 defaults
ruamel_yaml 0.11.14 py36ha2fb22d_2 defaults
setuptools 36.5.0 py36he42e2e1_0 defaults
six 1.11.0 py36h372c433_1 defaults
sqlite 3.20.1 hb898158_2 defaults
tk 8.6.7 hc745277_3 defaults
urllib3 1.22 py36hbe7ace6_0 defaults
wheel 0.30.0 py36hfd4bba0_1 defaults
xz 5.2.3 h55aa19d_2 defaults
yaml 0.1.7 had09818_2 defaults
zlib 1.2.11 ha838bed_2 defaults
conda info
active environment : None
shell level : 0
user config file : /home/patrick/.condarc
populated config files :
conda version : 4.4.10
conda-build version : not installed
python version : 3.6.3.final.0
base environment : /home/patrick/miniconda3 (writable)
channel URLs : https://repo.continuum.io/pkgs/main/linux-64
https://repo.continuum.io/pkgs/main/noarch
https://repo.continuum.io/pkgs/free/linux-64
https://repo.continuum.io/pkgs/free/noarch
https://repo.continuum.io/pkgs/r/linux-64
https://repo.continuum.io/pkgs/r/noarch
https://repo.continuum.io/pkgs/pro/linux-64
https://repo.continuum.io/pkgs/pro/noarch
package cache : /home/patrick/miniconda3/pkgs
/home/patrick/.conda/pkgs
envs directories : /home/patrick/miniconda3/envs
/home/patrick/.conda/envs
platform : linux-64
user-agent : conda/4.4.10 requests/2.18.4 CPython/3.6.3 Linux/4.4.0-104-generic ubuntu/14.04 glibc/2.19
UID:GID : 1000:1000
netrc file : None
offline mode : False
environment.yaml
channels:
- anaconda
- conda-forge
- bioconda
dependencies:
- cairo
- picard=2.14.1.0
- graphviz
- python
- snakemake=4.6.0
- r=3.4.1
- r-ggplot2
- pytz
- pandas
- trimmomatic
- STAR
- fastqc
- multiqc
- samtools
- r-ggpubr
- readline=6.2
Hoohm
on 14 Feb 2018
Ok, my bad, used:
conda update env --file environment.yaml --name dropSeqPipe
instead of
conda env update --file environment.yaml --name dropSeqPipe
Hoohm
on 14 Feb 2018
environment.yml doesn't work with conda install --file. You need to use conda env commands with environment.yml.
kalefranz
on 14 Feb 2018
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environment.ymldoesn't work withconda install --file. You need to useconda envcommands withenvironment.yml.