New conflict from environment.yml with conda 4.1.11

[Skipper Seabold]

Hi,

I have an environment.yml file that hasn't changed in months. 

I'm using the defaults channel.

I use latest conda (newly using 4.1.11 in this case) installed via the latest miniconda boostrap script to build this environment. As of the last time I tried to do this, I get

```

# conda env create -f environment.yml

Fetching package metadata .........

Solving package specifications: ....

Error: The following specifications were found to be in conflict:

  - beautifulsoup4 4.4.1*

  - notebook 4.1.0*

Use "conda info <package>" to see the dependencies for each package.

```

As far as I can see these packages don't depend on each other. Any ideas?

[Dharhas Pothina]

So when this happened to me recently with gdal and pytables. The latest gdal was pinned to hdf5>1.17 and the latest version of pytables was was pinned to hdf5==1.17

conda info <package> will list dependencies and you can work out which one is the culprit.

- dharhas

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[Skipper Seabold]

Thanks. I'm not sure how to figure this out / how this happened (again) given I haven't changed anything and I don't have any fuzzy dependencies.

Does this mean a new build got submitted with new dependencies? Was there a change in the dependency resolver?

Does the notebook have a dependency on beautiful soup? That seems odd to me. Doing a 

conda info notebook=4.1.0

I see a few dependencies, but there are no versions listed for these dependencies so I don't know how to check for changes if one of these libraries has a dependency on bs4.

[Skipper Seabold]

Just doing a conda info on all of the dependencies listed, I still don't see beautifulsoup and it doesn't have any dependencies. I also have all of these dependencies listed and pinned as well AFAICT. Hmm.

[Ben Zaitlen]

Is it possible to publish the environment.yml file ?

--Ben

To view this discussion on the web visit https://groups.google.com/a/continuum.io/d/msgid/conda/CAKF%3DDjvTykNhOnLOTfmhHOW7i%3D9%3DGG8BPq0S2phpAp8wa4qXxw%40mail.gmail.com.

[Skipper Seabold]

Sure.

http://pastebin.com/yFCZBmhG

[Ben Zaitlen]

I pulled out the the conda bit into something I could `conda --debug install --file ./conda.list` and got the following:

root@head:~# conda --debug install --file ./conda.list
DEBUG:conda.config:Could not import binstar
DEBUG:conda.fetch:channel_urls=OrderedDict([('https://repo.continuum.io/pkgs/free/linux-64/', ('defaults', 1)), ('https://repo.continuum.io/pkgs/free/noarch/', ('defaults', 1)), ('https://repo.continuum.io/pkgs/pro/linux-64/', ('defaults', 1)), ('https://repo.continuum.io/pkgs/pro/noarch/', ('defaults', 1)), ('https://conda.anaconda.org/anaconda-adam/linux-64/', ('anaconda-adam', 2)), ('https://conda.anaconda.org/anaconda-adam/noarch/', ('anaconda-adam', 2))])
Fetching package metadata ...INFO:stdoutlog:Fetching package metadata ...
DEBUG:requests.packages.urllib3.util.retry:Converted retries value: 3 -> Retry(total=3, connect=None, read=None, redirect=None)
INFO:requests.packages.urllib3.connectionpool:Starting new HTTPS connection (1): repo.continuum.io
DEBUG:requests.packages.urllib3.connectionpool:"GET /pkgs/free/linux-64/repodata.json.bz2 HTTP/1.1" 304 0
.DEBUG:dotupdate:fetching repodata: args ('https://repo.continuum.io/pkgs/free/linux-64/',) kwargs {'session': <conda.connection.CondaSession object at 0x7f0ab257a610>, 'use_cache': False}
DEBUG:requests.packages.urllib3.connectionpool:"GET /pkgs/free/noarch/repodata.json.bz2 HTTP/1.1" 304 0
.DEBUG:dotupdate:fetching repodata: args ('https://repo.continuum.io/pkgs/free/noarch/',) kwargs {'session': <conda.connection.CondaSession object at 0x7f0ab257a610>, 'use_cache': False}
DEBUG:requests.packages.urllib3.connectionpool:"GET /pkgs/pro/linux-64/repodata.json.bz2 HTTP/1.1" 304 0
.DEBUG:dotupdate:fetching repodata: args ('https://repo.continuum.io/pkgs/pro/linux-64/',) kwargs {'session': <conda.connection.CondaSession object at 0x7f0ab257a610>, 'use_cache': False}
DEBUG:requests.packages.urllib3.connectionpool:"GET /pkgs/pro/noarch/repodata.json.bz2 HTTP/1.1" 304 0
.DEBUG:dotupdate:fetching repodata: args ('https://repo.continuum.io/pkgs/pro/noarch/',) kwargs {'session': <conda.connection.CondaSession object at 0x7f0ab257a610>, 'use_cache': False}
INFO:stdoutlog:
DEBUG:conda.plan:H0 specs=['beautifulsoup4 4.4.1', 'cairo 1.12.18', 'coverage 4.0', 'cycler 0.9.0', 'cython 0.23.4', 'decorator 4.0.6', 'docutils 0.12', 'fontconfig 2.11.1', 'freetype 2.5.5', 'glib 2.43.0', 'ipykernel 4.2.2', 'ipython 4.0.2', 'ipython_genutils 0.1.0', 'ipywidgets 4.1.1', 'jbig 2.1', 'jinja2 2.8', 'jpeg 8d', 'jsonschema 2.4.0', 'jupyter 1.0.0', 'jupyter_client 4.1.1', 'jupyter_console 4.0.3', 'jupyter_core 4.0.6', 'libffi 3.0.13', 'libgcc 4.8.5', 'libgfortran 1.0', 'libpng 1.6.17', 'libsodium 1.0.3', 'libtiff 4.0.6', 'libxml2 2.9.2', 'markupsafe 0.23', 'matplotlib 1.5.1', 'mistune 0.7.1', 'nbconvert 4.1.0', 'nbformat 4.0.1', 'ncurses 5.9', 'nltk 3.1', 'nomkl', 'nose 1.3.7', 'notebook 4.1.0', 'numexpr 2.4.6', 'numpy 1.10.2', 'openblas 0.2.14', 'openssl 1.0.2e', 'pandas 0.17.1', 'path.py 8.1.2', 'patsy 0.4.0', 'pcre 8.31', 'pexpect 3.3', 'pickleshare 0.5', 'pip 7.1.2', 'pixman 0.32.6', 'psycopg2 2.6.1', 'ptyprocess 0.5', 'pycosat 0.6.1', 'pycrypto 2.6.1', 'pygments 2.0.2', 'pyparsing 2.0.3', 'pyqt 4.11.4', 'python 3.5.1', 'python-dateutil 2.4.2', 'pytz 2015.7', 'pyyaml 3.11', 'pyzmq 15.2.0', 'qt 4.8.7', 'qtconsole 4.1.1', 'readline 6.2', 'requests 2.9.1', 'scikit-learn 0.17', 'scipy 0.17.0', 'seaborn 0.6.0', 'setuptools 19.2', 'simplegeneric 0.8.1', 'sip 4.16.9', 'six 1.10.0', 'sqlite 3.9.2', 'statsmodels 0.6.1', 'terminado 0.5', 'tk 8.5.18', 'tornado 4.3', 'traitlets 4.0.0', 'wheel 0.26.0', 'xz 5.0.5', 'yaml 0.1.6', 'zeromq 4.1.3', 'zlib 1.2.8']
DEBUG:conda.plan:H1 python
DEBUG:conda.plan:H2 lua False
DEBUG:conda.plan:H2A lua
DEBUG:conda.plan:HF specs=['beautifulsoup4 4.4.1', 'cairo 1.12.18', 'coverage 4.0', 'cycler 0.9.0', 'cython 0.23.4', 'decorator 4.0.6', 'docutils 0.12', 'fontconfig 2.11.1', 'freetype 2.5.5', 'glib 2.43.0', 'ipykernel 4.2.2', 'ipython 4.0.2', 'ipython_genutils 0.1.0', 'ipywidgets 4.1.1', 'jbig 2.1', 'jinja2 2.8', 'jpeg 8d', 'jsonschema 2.4.0', 'jupyter 1.0.0', 'jupyter_client 4.1.1', 'jupyter_console 4.0.3', 'jupyter_core 4.0.6', 'libffi 3.0.13', 'libgcc 4.8.5', 'libgfortran 1.0', 'libpng 1.6.17', 'libsodium 1.0.3', 'libtiff 4.0.6', 'libxml2 2.9.2', 'markupsafe 0.23', 'matplotlib 1.5.1', 'mistune 0.7.1', 'nbconvert 4.1.0', 'nbformat 4.0.1', 'ncurses 5.9', 'nltk 3.1', 'nomkl', 'nose 1.3.7', 'notebook 4.1.0', 'numexpr 2.4.6', 'numpy 1.10.2', 'openblas 0.2.14', 'openssl 1.0.2e', 'pandas 0.17.1', 'path.py 8.1.2', 'patsy 0.4.0', 'pcre 8.31', 'pexpect 3.3', 'pickleshare 0.5', 'pip 7.1.2', 'pixman 0.32.6', 'psycopg2 2.6.1', 'ptyprocess 0.5', 'pycosat 0.6.1', 'pycrypto 2.6.1', 'pygments 2.0.2', 'pyparsing 2.0.3', 'pyqt 4.11.4', 'python 3.5.1', 'python-dateutil 2.4.2', 'pytz 2015.7', 'pyyaml 3.11', 'pyzmq 15.2.0', 'qt 4.8.7', 'qtconsole 4.1.1', 'readline 6.2', 'requests 2.9.1', 'scikit-learn 0.17', 'scipy 0.17.0', 'seaborn 0.6.0', 'setuptools 19.2', 'simplegeneric 0.8.1', 'sip 4.16.9', 'six 1.10.0', 'sqlite 3.9.2', 'statsmodels 0.6.1', 'terminado 0.5', 'tk 8.5.18', 'tornado 4.3', 'traitlets 4.0.0', 'wheel 0.26.0', 'xz 5.0.5', 'yaml 0.1.6', 'zeromq 4.1.3', 'zlib 1.2.8']
DEBUG:conda.plan:Pinned specs=[]
DEBUG:conda.resolve:Checking satisfiability of current install
DEBUG:conda.resolve:Checking if the current environment is consistent
Solving package specifications: INFO:stdoutlog:Solving package specifications:
.DEBUG:dotupdate:Solving for [MatchSpec('beautifulsoup4 4.4.1'), MatchSpec('cairo 1.12.18'), MatchSpec('coverage 4.0'), MatchSpec('cycler 0.9.0'), MatchSpec('cython 0.23.4'), MatchSpec('decorator 4.0.6'), MatchSpec('docutils 0.12'), MatchSpec('fontconfig 2.11.1'), MatchSpec('freetype 2.5.5'), MatchSpec('glib 2.43.0'), MatchSpec('ipykernel 4.2.2'), MatchSpec('ipython 4.0.2'), MatchSpec('ipython_genutils 0.1.0'), MatchSpec('ipywidgets 4.1.1'), MatchSpec('jbig 2.1'), MatchSpec('jinja2 2.8'), MatchSpec('jpeg 8d'), MatchSpec('jsonschema 2.4.0'), MatchSpec('jupyter 1.0.0'), MatchSpec('jupyter_client 4.1.1'), MatchSpec('jupyter_console 4.0.3'), MatchSpec('jupyter_core 4.0.6'), MatchSpec('libffi 3.0.13'), MatchSpec('libgcc 4.8.5'), MatchSpec('libgfortran 1.0'), MatchSpec('libpng 1.6.17'), MatchSpec('libsodium 1.0.3'), MatchSpec('libtiff 4.0.6'), MatchSpec('libxml2 2.9.2'), MatchSpec('markupsafe 0.23'), MatchSpec('matplotlib 1.5.1'), MatchSpec('mistune 0.7.1'), MatchSpec('nbconvert 4.1.0'), MatchSpec('nbformat 4.0.1'), MatchSpec('ncurses 5.9'), MatchSpec('nltk 3.1'), MatchSpec('nomkl'), MatchSpec('nose 1.3.7'), MatchSpec('notebook 4.1.0'), MatchSpec('numexpr 2.4.6'), MatchSpec('numpy 1.10.2'), MatchSpec('openblas 0.2.14'), MatchSpec('openssl 1.0.2e'), MatchSpec('pandas 0.17.1'), MatchSpec('path.py 8.1.2'), MatchSpec('patsy 0.4.0'), MatchSpec('pcre 8.31'), MatchSpec('pexpect 3.3'), MatchSpec('pickleshare 0.5'), MatchSpec('pip 7.1.2'), MatchSpec('pixman 0.32.6'), MatchSpec('psycopg2 2.6.1'), MatchSpec('ptyprocess 0.5'), MatchSpec('pycosat 0.6.1'), MatchSpec('pycrypto 2.6.1'), MatchSpec('pygments 2.0.2'), MatchSpec('pyparsing 2.0.3'), MatchSpec('pyqt 4.11.4'), MatchSpec('python 3.5.1'), MatchSpec('python-dateutil 2.4.2'), MatchSpec('pytz 2015.7'), MatchSpec('pyyaml 3.11'), MatchSpec('pyzmq 15.2.0'), MatchSpec('qt 4.8.7'), MatchSpec('qtconsole 4.1.1'), MatchSpec('readline 6.2'), MatchSpec('requests 2.9.1'), MatchSpec('scikit-learn 0.17'), MatchSpec('scipy 0.17.0'), MatchSpec('seaborn 0.6.0'), MatchSpec('setuptools 19.2'), MatchSpec('simplegeneric 0.8.1'), MatchSpec('sip 4.16.9'), MatchSpec('six 1.10.0'), MatchSpec('sqlite 3.9.2'), MatchSpec('statsmodels 0.6.1'), MatchSpec('terminado 0.5'), MatchSpec('tk 8.5.18'), MatchSpec('tornado 4.3'), MatchSpec('traitlets 4.0.0'), MatchSpec('wheel 0.26.0'), MatchSpec('xz 5.0.5'), MatchSpec('yaml 0.1.6'), MatchSpec('zeromq 4.1.3'), MatchSpec('zlib 1.2.8')]
DEBUG:conda.resolve:Retrieving packages for: [MatchSpec('beautifulsoup4 4.4.1'), MatchSpec('cairo 1.12.18'), MatchSpec('coverage 4.0'), MatchSpec('cycler 0.9.0'), MatchSpec('cython 0.23.4'), MatchSpec('decorator 4.0.6'), MatchSpec('docutils 0.12'), MatchSpec('fontconfig 2.11.1'), MatchSpec('freetype 2.5.5'), MatchSpec('glib 2.43.0'), MatchSpec('ipykernel 4.2.2'), MatchSpec('ipython 4.0.2'), MatchSpec('ipython_genutils 0.1.0'), MatchSpec('ipywidgets 4.1.1'), MatchSpec('jbig 2.1'), MatchSpec('jinja2 2.8'), MatchSpec('jpeg 8d'), MatchSpec('jsonschema 2.4.0'), MatchSpec('jupyter 1.0.0'), MatchSpec('jupyter_client 4.1.1'), MatchSpec('jupyter_console 4.0.3'), MatchSpec('jupyter_core 4.0.6'), MatchSpec('libffi 3.0.13'), MatchSpec('libgcc 4.8.5'), MatchSpec('libgfortran 1.0'), MatchSpec('libpng 1.6.17'), MatchSpec('libsodium 1.0.3'), MatchSpec('libtiff 4.0.6'), MatchSpec('libxml2 2.9.2'), MatchSpec('markupsafe 0.23'), MatchSpec('matplotlib 1.5.1'), MatchSpec('mistune 0.7.1'), MatchSpec('nbconvert 4.1.0'), MatchSpec('nbformat 4.0.1'), MatchSpec('ncurses 5.9'), MatchSpec('nltk 3.1'), MatchSpec('nomkl'), MatchSpec('nose 1.3.7'), MatchSpec('notebook 4.1.0'), MatchSpec('numexpr 2.4.6'), MatchSpec('numpy 1.10.2'), MatchSpec('openblas 0.2.14'), MatchSpec('openssl 1.0.2e'), MatchSpec('pandas 0.17.1'), MatchSpec('path.py 8.1.2'), MatchSpec('patsy 0.4.0'), MatchSpec('pcre 8.31'), MatchSpec('pexpect 3.3'), MatchSpec('pickleshare 0.5'), MatchSpec('pip 7.1.2'), MatchSpec('pixman 0.32.6'), MatchSpec('psycopg2 2.6.1'), MatchSpec('ptyprocess 0.5'), MatchSpec('pycosat 0.6.1'), MatchSpec('pycrypto 2.6.1'), MatchSpec('pygments 2.0.2'), MatchSpec('pyparsing 2.0.3'), MatchSpec('pyqt 4.11.4'), MatchSpec('python 3.5.1'), MatchSpec('python-dateutil 2.4.2'), MatchSpec('pytz 2015.7'), MatchSpec('pyyaml 3.11'), MatchSpec('pyzmq 15.2.0'), MatchSpec('qt 4.8.7'), MatchSpec('qtconsole 4.1.1'), MatchSpec('readline 6.2'), MatchSpec('requests 2.9.1'), MatchSpec('scikit-learn 0.17'), MatchSpec('scipy 0.17.0'), MatchSpec('seaborn 0.6.0'), MatchSpec('setuptools 19.2'), MatchSpec('simplegeneric 0.8.1'), MatchSpec('sip 4.16.9'), MatchSpec('six 1.10.0'), MatchSpec('sqlite 3.9.2'), MatchSpec('statsmodels 0.6.1'), MatchSpec('terminado 0.5'), MatchSpec('tk 8.5.18'), MatchSpec('tornado 4.3'), MatchSpec('traitlets 4.0.0'), MatchSpec('wheel 0.26.0'), MatchSpec('xz 5.0.5'), MatchSpec('yaml 0.1.6'), MatchSpec('zeromq 4.1.3'), MatchSpec('zlib 1.2.8')]
DEBUG:conda.resolve:beautifulsoup4: pruned from 9 -> 3
DEBUG:conda.resolve:python: pruned from 77 -> 52
DEBUG:conda.resolve:pip: pruned from 95 -> 53
DEBUG:conda.resolve:cairo: pruned from 10 -> 7
DEBUG:conda.resolve:libpng: pruned from 5 -> 4
DEBUG:conda.resolve:coverage: pruned from 17 -> 3
DEBUG:conda.resolve:cycler: pruned from 6 -> 3
DEBUG:conda.resolve:six: pruned from 37 -> 18
DEBUG:conda.resolve:cython: pruned from 79 -> 3
DEBUG:conda.resolve:decorator: pruned from 25 -> 3
DEBUG:conda.resolve:docutils: pruned from 19 -> 6
DEBUG:conda.resolve:freetype: pruned from 6 -> 5
DEBUG:conda.resolve:freetype: pruned from 5 -> 2
DEBUG:conda.resolve:libpng: pruned from 4 -> 2
DEBUG:conda.resolve:ipykernel: pruned from 18 -> 3
DEBUG:conda.resolve:ipython: pruned from 89 -> 30
DEBUG:conda.resolve:pexpect: pruned from 8 -> 6
DEBUG:conda.resolve:pyzmq: pruned from 70 -> 43
DEBUG:conda.resolve:ipython: pruned from 30 -> 3
DEBUG:conda.resolve:pexpect: pruned from 6 -> 3
DEBUG:conda.resolve:ipywidgets: pruned from 15 -> 3
DEBUG:conda.resolve:notebook: pruned from 28 -> 9
DEBUG:conda.resolve:jsonschema: pruned from 8 -> 6
DEBUG:conda.resolve:tornado: pruned from 63 -> 35
DEBUG:conda.resolve:mistune: pruned from 26 -> 16
DEBUG:conda.resolve:pygments: pruned from 25 -> 17
DEBUG:conda.resolve:jinja2: pruned from 29 -> 15
DEBUG:conda.resolve:terminado: pruned from 10 -> 9
DEBUG:conda.resolve:ptyprocess: pruned from 10 -> 8
DEBUG:conda.resolve:anaconda-client: pruned from 35 -> 28
DEBUG:conda.resolve:pyyaml: pruned from 16 -> 10
DEBUG:conda.resolve:clyent: pruned from 32 -> 24
DEBUG:conda.resolve:pytz: pruned from 64 -> 40
DEBUG:conda.resolve:setuptools: pruned from 194 -> 118
DEBUG:conda.resolve:python-dateutil: pruned from 21 -> 17
DEBUG:conda.resolve:requests: pruned from 89 -> 49
DEBUG:conda.resolve:jinja2: pruned from 15 -> 6
DEBUG:conda.resolve:markupsafe: pruned from 12 -> 8
DEBUG:conda.resolve:jsonschema: pruned from 6 -> 3
DEBUG:conda.resolve:pyqt: pruned from 28 -> 22
DEBUG:conda.resolve:sip: pruned from 15 -> 11
DEBUG:conda.resolve:qt: pruned from 10 -> 9
DEBUG:conda.resolve:jupyter_client: pruned from 15 -> 3
DEBUG:conda.resolve:jupyter_console: pruned from 19 -> 3
DEBUG:conda.resolve:jupyter_core: pruned from 16 -> 3
DEBUG:conda.resolve:libffi: pruned from 2 -> 1
DEBUG:conda.resolve:libgcc: pruned from 3 -> 1
DEBUG:conda.resolve:libgfortran: pruned from 3 -> 1
DEBUG:conda.resolve:libpng: pruned from 2 -> 1
DEBUG:conda.resolve:libsodium: pruned from 3 -> 1
DEBUG:conda.resolve:libtiff: pruned from 5 -> 3
DEBUG:conda.resolve:libxml2: pruned from 2 -> 1
DEBUG:conda.resolve:markupsafe: pruned from 8 -> 6
DEBUG:conda.resolve:matplotlib: pruned from 102 -> 6
DEBUG:conda.resolve:numpy: pruned from 222 -> 42
DEBUG:conda.resolve:pyparsing: pruned from 18 -> 12
DEBUG:conda.resolve:mistune: pruned from 16 -> 3
DEBUG:conda.resolve:nbconvert: pruned from 9 -> 3
DEBUG:conda.resolve:nbformat: pruned from 9 -> 3
DEBUG:conda.resolve:nltk: pruned from 57 -> 3
DEBUG:conda.resolve:nose: pruned from 37 -> 6
DEBUG:conda.resolve:notebook: pruned from 9 -> 0
...INFO:stderrlog:...
INFO:stdoutlog:

The following specifications were found to be in conflict:
  - beautifulsoup4 4.4.1

  - notebook 4.1.0

Use "conda info <package>" to see the dependencies for each package.

Maybe one of the conda devs can comment of the dependency solution here 

[Ben Zaitlen]

After a bit more playing i think the following is causing a problem:

```

conda --debug install notebook=4.1.0 beautifulsoup4=4.4.1 jupyter=1.0.0

```

[Skipper Seabold]

I was unable to replicate with that. Now the same environment file works on my machine and in my CI container. Mysterious.