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Is spectra correct dependency? #12

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mfansler opened this issue Aug 31, 2021 · 0 comments · Fixed by #13
Closed

Is spectra correct dependency? #12

mfansler opened this issue Aug 31, 2021 · 0 comments · Fixed by #13

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@mfansler
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I was surprised today to find that one of my R environments also has Python installed. Using Mamba's repoquery tool to track down why python got pulled in, I found:

(bioc_3_12) host:dir usr$ mamba repoquery whoneeds -t python

Executing the query python

python[3.9.2]
  ├─ numpy[1.20.2]
  │  └─ colormath[3.0.0]
  │     └─ spectra[0.0.11]
  │        └─ r-rspectra[0.16_0]     # <- this package is the culprit!
  │           └─ r-uwot[0.1.10]
  ├─ networkx[2.5]
  │  └─ colormath already visited
  ├─ certifi[2021.5.30]
  │  └─ setuptools[49.6.0]
  │     ├─ networkx already visited
  │     └─ pip[21.0.1]
  ├─ python_abi[3.9]
  │  ├─ numpy already visited
  │  ├─ certifi already visited
  │  └─ setuptools already visited
  ├─ colormath already visited
  ├─ spectra already visited
  ├─ decorator[4.4.2]
  │  └─ networkx already visited
  ├─ wheel[0.36.2]
  │  └─ pip already visited
  ├─ pip already visited
  └─ setuptools already visited

which implicates this package. I really don't think this is correct.

The conda-forge::spectra package corresponds to this Python package. Whereas the RSpectra package is developed by maintainer of the C++ Spectra library, which would correspond to the spectralib feedstock.

I'm not sure any spectra (or spectralib) at all is needed as a dependency, since the C++ code is directly included in the R package and gets compiled there. That is, despite the author calling it a "wrapper" for Spectra, it simply bundles parts of Spectra into an R package and runs on the RcppEigen implementation (which is already a dependency). At least, that's how it looks to me.

@conda-forge/help-r I'll submit a PR to address this, but I hope someone can double-check my reasoning here. Thanks!

@mfansler mfansler mentioned this issue Sep 1, 2021
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