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Miniconda2 conda does not select python3 dependencies [UnsatisfiableError] #4492

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mvdbeek opened this issue Feb 1, 2017 · 1 comment

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commented Feb 1, 2017

If I try to create an environment for a python3 dependency,
conda won't add the correct python version.

(.venv) mvandenb@u934-bdd-4-89-6580:~/src/tag_reads$ conda --version
conda 4.3.8
(.venv) mvandenb@u934-bdd-4-89-6580:~/src/tag_reads$ python --version
Python 2.7.13 :: Continuum Analytics, Inc.
(.venv) mvandenb@u934-bdd-4-89-6580:~/src/tag_reads$ conda create -n unicycler unicycler
Fetching package metadata ...............
Solving package specifications: .


UnsatisfiableError: The following specifications were found to be in conflict:
  - python 2.7*
  - unicycler -> python 3.4*
Use "conda info <package>" to see the dependencies for each package.


(.venv) mvandenb@u934-bdd-4-89-6580:~/src/tag_reads$ conda info unicycler
Fetching package metadata ...............

unicycler 0.2.0 py35_0
----------------------
file name   : unicycler-0.2.0-py35_0.tar.bz2
name        : unicycler
version     : 0.2.0
build string: py35_0
build number: 0
channel     : bioconda
size        : 1019 KB
arch        : x86_64
has_prefix  : True
license     : GPL-3.0
md5         : a80ad24c6d599dca78e6cc2e3e5bc0e7
platform    : darwin
requires    : ()
subdir      : osx-64
url         : https://conda.anaconda.org/bioconda/osx-64/unicycler-0.2.0-py35_0.tar.bz2
dependencies:
    blast
    bowtie2
    freebayes
    java-jdk
    libgcc
    pilon
    python 3.5*
    samtools >=1.0
    spades >=3.6.2

unicycler 0.2.0 py34_0
----------------------
file name   : unicycler-0.2.0-py34_0.tar.bz2
name        : unicycler
version     : 0.2.0
build string: py34_0
build number: 0
channel     : bioconda
size        : 1020 KB
arch        : x86_64
has_prefix  : True
license     : GPL-3.0
md5         : 61f74983ac807b8495418697c21bc353
platform    : darwin
requires    : ()
subdir      : osx-64
url         : https://conda.anaconda.org/bioconda/osx-64/unicycler-0.2.0-py34_0.tar.bz2
dependencies:
    blast
    bowtie2
    freebayes
    java-jdk
    libgcc
    pilon
    python 3.4*
    samtools >=1.0
    spades >=3.6.2

unicycler 0.3.0b py34_0
-----------------------
file name   : unicycler-0.3.0b-py34_0.tar.bz2
name        : unicycler
version     : 0.3.0b
build string: py34_0
build number: 0
channel     : bioconda
size        : 1017 KB
arch        : x86_64
has_prefix  : True
license     : GPL-3.0
md5         : 9cf80e015c78d22e2c7d77af3a953eda
platform    : darwin
requires    : ()
subdir      : osx-64
url         : https://conda.anaconda.org/bioconda/osx-64/unicycler-0.3.0b-py34_0.tar.bz2
dependencies:
    blast
    bowtie2
    freebayes
    java-jdk
    libgcc
    pilon
    python 3.4*
    samtools >=1.0
    spades >=3.6.2

unicycler 0.3.0b py35_0
-----------------------
file name   : unicycler-0.3.0b-py35_0.tar.bz2
name        : unicycler
version     : 0.3.0b
build string: py35_0
build number: 0
channel     : bioconda
size        : 1017 KB
arch        : x86_64
has_prefix  : True
license     : GPL-3.0
md5         : 800504a989a23942f8fa4139585573d4
platform    : darwin
requires    : ()
subdir      : osx-64
url         : https://conda.anaconda.org/bioconda/osx-64/unicycler-0.3.0b-py35_0.tar.bz2
dependencies:
    blast
    bowtie2
    freebayes
    java-jdk
    libgcc
    pilon
    python 3.5*
    samtools >=1.0
    spades >=3.6.2

Either specifying unicycler=0.2.0=py35_0 or including python3 in the environment resolves the issue, but it does look like a bug to me.
Of note, there is no problem with miniconda3 for dependencies that need python2.

@mvdbeek mvdbeek changed the title Miniconda2 conda does not select python3 dependencies Miniconda2 conda does not select python3 dependencies [UnsatisfiableError Feb 1, 2017

@mvdbeek mvdbeek changed the title Miniconda2 conda does not select python3 dependencies [UnsatisfiableError Miniconda2 conda does not select python3 dependencies [UnsatisfiableError] Feb 1, 2017

@kalefranz

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commented May 4, 2017

This is by design. Up through conda 4.3, conda will hold onto the python major-minor version that's in the root environment when creating new environments that contain python packages. If you want a version of python that's different from your root environment, you'll need to specify it. So in your case

conda create -n unicycler unicycler python=3

should work.

@kalefranz kalefranz closed this May 4, 2017

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