Fix conda / Bioconda install conflicts and solver failures

TL;DR

For "Solving environment: failed with initial frozen solve. Retrying with flexible solve.": press CTRL-C to abort. hanging for a long time → the classic solver is struggling (class B), or a real conflict it will eventually report (class A). Your installed version is: 2.35 attached to a __glibc complaint → the system glibc is too old for the requested builds (class A, system-level).

Solving environment: failed with initial frozen solve. Retrying with flexible solve.
...
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.

When to use

You are seeing this: The three signatures: ` UnsatisfiableError: The following specifications were found to be incompatible with each other: → a genuine version conflict (class A). ` Solving environment: failed with initial frozen solve. Use this skill when you run into "Fix conda / Bioconda install conflicts and solver failures".

When not to use

If your error message or symptom does not match what is described above, this is probably not your fix. Search for your exact error text instead of forcing this one to fit.

Use this when conda install or conda create with Bioconda packages fails with UnsatisfiableError, hangs on Solving environment, or reports Found conflicts!. These errors look alike but have four distinct causes with different fixes. Classify from the exact error text FIRST, the fix for a genuine version conflict is the opposite of the fix for a slow solver.

0. Read the error text, not just "it failed"

The three signatures:

UnsatisfiableError: The following specifications were found to be incompatible with each other:

→ a genuine version conflict (class A).

Solving environment: failed with initial frozen solve. Retrying with flexible solve.
...
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.

hanging for a long time → the classic solver is struggling (class B), or a real conflict it will eventually report (class A).

Your installed version is: 2.35

attached to a __glibc complaint → the system glibc is too old for the requested builds (class A, system-level).

1. Class A, genuine version conflict (UnsatisfiableError)

The solver is telling the truth: the requested combination cannot exist. Common triggers seen on Biostars:

• Installing into an existing environment (especially base). The existing packages pin half the dependency tree. Almost every "conda error" thread is fixed the same way, install into a fresh environment:

  conda create -n sratools -c conda-forge -c bioconda sra-tools
  conda activate sratools

• Over-pinned versions. samtools=1.9 on a new conda-forge stack fails because the old recipe's libgcc-ng/libstdcxx-ng/zlib pins collide with what modern python pulls in. Unless you have a hard reason for the old version, drop the pin and let the solver pick; then pin the resolved versions (conda list --export) for reproducibility.

• Python version drift. Bioconda currently builds for Python 3.10 3.13; old recipes expecting older Pythons conflict with the current stack. If you must have an old package, create the env with an old python explicitly (conda create -n old -c conda-forge -c bioconda python=3.9 [pkg]) instead of fighting the default.

• System glibc too old. Errors naming __glibc (e.g. recipe needs >=2.17 and the system reports something older) cannot be solved by channel juggling, you need a newer OS image or a container.

Do not "fix" class A by adding more channels or --force; that hides the conflict until runtime.

2. Class B, solver hangs or crawls (no UnsatisfiableError yet)

The classic conda solver is slow on Bioconda's large dependency graph. Check the solver first:

conda --version

• conda 23.10 or newer: the libmamba solver is already the default. If solving still hangs, it's probably a genuine conflict (class A), let it finish or Ctrl-C and read the report.

• conda older than 23.10: install the faster solver and make it default:

  conda update -n base conda
  conda install -n base conda-libmamba-solver
  conda config --set solver libmamba

or use it for one command only:

  conda install -c conda-forge -c bioconda [pkg] --solver=libmamba

• Alternative: mamba / micromamba are drop-in replacements that use the same libsolv-based solver and the same channels:

  mamba create -n tools -c conda-forge -c bioconda samtools bcftools

3. Class C, wrong channel order / priority

Bioconda's documented setup (bioconda.github.io), order matters because conda config --add prepends, so add in this exact sequence to end up with conda-forge at highest priority:

conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

Resulting priority (highest first): conda-forge, bioconda. Rationale from the docs: Bioconda heavily depends on conda-forge, so conda-forge must win for general-purpose libraries; strict priority "avoids cryptic errors" by respecting that order during solving instead of mixing channels per package.

Diagnose: conda config --show channels, if bioconda outranks conda-forge, or channel_priority is flexible/disabled, fix it with the three commands above.

Without touching .condarc, pass the same policy per command (note: on the command line, -c flags are read in decreasing priority order, the reverse of conda config):

conda create -n myenv -c conda-forge -c bioconda --strict-channel-priority samtools bwa

4. Class D, environment YAML won't resolve

For conda env create -f env.yml conflicts:

1. Check the channels: list in the YAML, it must list conda-forge before bioconda (same priority rule as class C).

2. Loosen or drop version pins on the tools (samtools, rsubread); over-pinning transitive deps (libgcc-ng=...) is the usual culprit remove them first, re-add only what still resolves.

3. Solve with mamba (mamba env create -f env.yml); its error messages name the conflicting chain more precisely than conda's.

Quick decision tree

1. UnsatisfiableError → fresh env, drop pins, check python/glibc (class A).

2. Hangs at Solving environment / Found conflicts! → conda ≥23.10? yes: wait for the real report; no: libmamba solver (class B).

3. Worked before, fails now on a new machine → conda config --show channels; fix order to conda-forge > bioconda + strict priority (class C).

4. YAML create fails → channel order in YAML, unpin tools, solve with mamba (class D).
5. Never install bioinformatics tools into base; never "fix" a conflict with --force.

Variants

Other phrasings of the same problem that show up in reports:

UnsatisfiableError: The following specifications were found to be incompatible with each other:

UnsatisfiableError: The following specifications were found to be incompatible with each other: