Could not build wheels for megalodon

[vzupan3]

Hi!
when using pip install megalodon command I get this error: "Failed to build megalodon
ERROR: Could not build wheels for megalodon, which is required to install pyproject.toml-based projects"

Any suggestions would be appreciated. Guppy version is 6.5.7+ca6d6af, minimap2 version 2.24-r1122.

[Jordi0102]

I have the same problem

[thekugelmeister]

I too am experiencing this installation error. Here are some (possibly) relevant details:

• I am installing megalodon on an AWS instance
• I am installing a pinned version, with the command sudo pip install megalodon==2.3.4
• I successfully installed megalodon on an instance with the exact same configuration last Monday, using the exact same series of commands

Based on this, is it possible one of the dependencies has updated in the last week, in a way that circumvents pinning the version of megalodon?

Here is a file containing the pip installation log dump for building the wheel:
megalodon_install_error_log.txt

Taking a brief look at the output, the piece that jumps out to me is the following:

      Error compiling Cython file:
      ------------------------------------------------------------
      ...
          if mod_weights is not None:
              mods_scores = np.empty(
                  (runval.shape[0], len(can_alphabet) + sum(can_nmods)),
                  dtype=np.float32)
              mods_scores[0] = 0
              mods_scores[1:] = mod_weights[rl_cumsum[1:-1] - 1]
                                           ^
      ------------------------------------------------------------

      megalodon/_decode.pyx:790:37: Compiler crash in AnalyseExpressionsTransform

[thekugelmeister]

I did some digging into the error, and may have found a root cause. It looks as if the upgrade from cython v3.0.3 to v3.0.4 caused this same error for multiple other projects. See cython/cython#5771 as a reference.

I attempted to downgrade cython to previous versions, but unfortunately did not have any success installing megalodon after doing so.