Issue
I'm trying to get a program called BEAST on my local Ubuntu using Anaconda but get this message:
Package libgcc-ng conflicts for:
beast2 -> beagle-lib -> libgcc-ng[version='>=4.9|>=7.3.0|>=7.2.0']
python=3.7 -> libgcc-ng[version='>=7.2.0|>=7.3.0']
I thought I had Anaconda to be rid of package conflicts
What does this conflict mean?
Seems like two programs are prioritizing a package version differently, so what? Can't these two programs continue with their lives with different priorities?
And by the way: how would I solve this?
Edit:
conda create -n test python=3.7 beast2
gives me this:
UnsatisfiableError: The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versions
Package libffi conflicts for:
python=3.7 -> libffi[version='>=3.2.1,<3.3a0|>=3.3,<3.4.0a0']
beast2 -> gettext[version='>=0.19.8.1,<1.0a0'] -> libffi[version='>=3.2.1,<3.3a0']
Solution
TLDR
conda create -n beast -c conda-forge -c bioconda python=3.7 beast2
Longer version
By telling conda that it can visit conda-forge, it has some extra options to resolve the dependency conflicts. However, that doesn't really explain why this happens:
$ conda create -n beast python=3.7 libgcc-ng=7.3 libstdcxx-ng=7.3
$ activate beast
$ conda install -c bioconda beast2
Package libstdcxx-ng conflicts for:
python=3.7 -> libstdcxx-ng[version='>=7.2.0|>=7.3.0']
beast2 -> beagle-lib -> libstdcxx-ng[version='>=7.3.0|>=7.5.0']
It isn't clear why these dependencies aren't satisfied, since we already installed libstdcxx-ng version 7.3.
Alternative
If you instead use mamba to make the environment, you get slightly more helpful feedback:
$ conda install mamba
$ mamba create -n beast-mamba python=3.7 beast2
...
Problem: nothing provides requested beast2
...
$ mamba create -n beast-mamba -c bioconda python=3.7 beast2
...
Encountered problems while solving.
Problem: nothing provides openjdk 8.0* zulu8* needed by beast2-2.4.5-0
...
$ mamba create -n beast-mamba -c bioconda -c conda-forge python=3.7 beast2
...
Success
Answered By - FiddleStix Answer Checked By - Dawn Plyler (WPSolving Volunteer)