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Update cramino to 0.15.0 #51900

Merged
merged 3 commits into from
Nov 4, 2024
Merged

Update cramino to 0.15.0 #51900

merged 3 commits into from
Nov 4, 2024

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Update cramino: 0.14.50.15.0

install with bioconda Conda

Info Link or Description
Recipe recipes/cramino (click to view/edit other files)
Summary A tool for very fast quality assessment of long read cram/bam files.
Home https://github.com/wdecoster/cramino
Releases https://github.com/wdecoster/cramino/tags
Author @wdecoster

This pull request was automatically generated (see docs).

@BiocondaBot BiocondaBot added autobump Automatic Version Update new version labels Nov 4, 2024
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coderabbitai bot commented Nov 4, 2024

📝 Walkthrough
📝 Walkthrough

Walkthrough

The pull request introduces updates to the meta.yaml file for the cramino package. The version number has been changed from "0.14.5" to "0.15.0". Alongside this version increment, the source URL has been updated to reflect the new version, changing from v0.14.5 to v0.15.0. Additionally, the SHA256 checksum for the source archive has been modified to ensure integrity, with the previous checksum d3b31ab76808ca76171e2539cfe30e66fe24cbd4af4ff9a941c282a0bc438032 being replaced by 731d4232e8a5503f704825b04e8ff081294381a1324fec3e59771ca773c68465. New build requirements have been added, including {{ compiler('rust') }} and {{ compiler('cxx') }}, while the existing requirement for rust has been specified as >=1.60. No other alterations to the structure or content of the meta.yaml file have been made.

Possibly related PRs

  • Update panacus recipe to add cmake and c++ dependency #50982: This PR updates the meta.yaml file for the panacus package by adding the C++ compiler as a build requirement, which is similar to the addition of {{ compiler('cxx') }} in the cramino package's meta.yaml.
  • Update pyhmmer to 0.10.15 #51257: This PR updates the pyhmmer package's version and SHA256 checksum, similar to the version and checksum updates in the cramino package's meta.yaml.
  • Update nanomotif to 0.4.15 #51429: This PR updates the nanomotif package's version and SHA256 checksum, reflecting similar changes made in the cramino package's meta.yaml.
  • Update biobb_cmip to 5.0.0 #51455: This PR updates the biobb_cmip package's version and SHA256 checksum, akin to the version and checksum modifications in the cramino package's meta.yaml.
  • [biobb_cp2k] update 5.0.0 #51528: This PR updates the biobb_cp2k package's version and SHA256 checksum, paralleling the changes made in the cramino package's meta.yaml.
  • Rebuild biobb_cp2k #51531: This PR also updates the version and SHA256 checksum in the meta.yaml file for the biobb_cp2k package, which is relevant to the changes in the cramino package's meta.yaml.
  • Update crabs to 1.0.4 #51645: This PR updates the crabs package's version and SHA256 checksum, similar to the updates in the cramino package's meta.yaml.
  • Update crabs to 1.0.5 #51677: This PR updates the crabs package's version and SHA256 checksum, reflecting similar changes made in the cramino package's meta.yaml.
  • Update crabs to 1.0.6 #51694: This PR updates the crabs package's version and SHA256 checksum, akin to the version and checksum updates in the cramino package's meta.yaml.
  • Update pbmm2 to 1.16.0 #51791: This PR updates the pbmm2 package's version and SHA256 checksum, similar to the updates in the cramino package's meta.yaml.

Suggested reviewers

  • armintoepfer

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@wdecoster
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Error:

10:26:41 BIOCONDA INFO (OUT)   thread 'main' panicked at /opt/conda/conda-bld/cramino_1730715642110/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/bindgen-0.69.5/lib.rs:622:31:
10:26:41 BIOCONDA INFO (OUT)   Unable to find libclang: "couldn't find any valid shared libraries matching: ['libclang.so', 'libclang-*.so', 'libclang.so.*', 'libclang-*.so.*'], set the `LIBCLANG_PATH` environment variable to a path where one of these files can be found (invalid: [])"

trying something I saw on twitter
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Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (1)
recipes/cramino/meta.yaml (1)

Line range hint 17-25: Add clang/llvm dependency to fix build error

The build is failing due to missing libclang, which is required by bindgen. This needs to be addressed by adding clang/llvm to the build requirements.

Apply this diff to fix the build error:

  requirements:
    build:
      - {{ compiler('c') }}
      - {{ compiler('rust') }}
      - {{ compiler('cxx') }}
+     - clangdev
+     - llvmdev
      - rust >=1.60
      - cmake
      - make
      - openssl

This should resolve the error:

thread 'main' panicked at [...] Unable to find libclang [...]
📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 6e66917 and d9f93d6.

📒 Files selected for processing (1)
  • recipes/cramino/meta.yaml (2 hunks)
🧰 Additional context used
🪛 yamllint
recipes/cramino/meta.yaml

[error] 1-1: syntax error: found character '%' that cannot start any token

(syntax)

🔇 Additional comments (3)
recipes/cramino/meta.yaml (3)

Line range hint 1-5: LGTM: Version update looks correct

The version bump from 0.14.5 to 0.15.0 is properly reflected in the package metadata.

🧰 Tools
🪛 yamllint

[error] 1-1: syntax error: found character '%' that cannot start any token

(syntax)


Line range hint 7-11: LGTM: Build configuration is appropriate

Build number reset to 0 is correct for a version bump, and the run exports configuration is properly maintained.

🧰 Tools
🪛 yamllint

[error] 1-1: syntax error: found character '%' that cannot start any token

(syntax)


13-15: Verify the source archive checksum

The source URL and checksum have been updated for the new version.

the rabbit told me
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Actionable comments posted: 1

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between d9f93d6 and fa039e5.

📒 Files selected for processing (1)
  • recipes/cramino/meta.yaml (2 hunks)
🧰 Additional context used
🪛 yamllint
recipes/cramino/meta.yaml

[error] 1-1: syntax error: found character '%' that cannot start any token

(syntax)

🔇 Additional comments (3)
recipes/cramino/meta.yaml (3)

1-1: LGTM: Version update matches PR objective.

The version bump to 0.15.0 aligns with the PR's purpose.

🧰 Tools
🪛 yamllint

[error] 1-1: syntax error: found character '%' that cannot start any token

(syntax)


15-15: LGTM: SHA256 checksum updated.

The new SHA256 checksum has been properly updated for the 0.15.0 release tarball.


20-24: Verify rust compiler compatibility.

The requirement rust >=1.60 seems appropriate, but let's verify it's sufficient for the new version's build dependencies.

Comment on lines +20 to +23
- {{ compiler('rust') }}
- {{ compiler('cxx') }}
- clangdev
- llvmdev
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⚠️ Potential issue

Address the libclang dependency issue.

The build error reported in the PR comments indicates missing libclang libraries. While you've added clangdev and llvmdev as build requirements, there might be additional configuration needed.

Consider these solutions:

  1. Add LIBCLANG_PATH to build environment:
  build:
    number: 0
    skip: true  # [osx]
+   script_env:
+     - LIBCLANG_PATH=$PREFIX/lib
  1. Alternatively, ensure proper linking by adding:
  build:
    number: 0
    skip: true  # [osx]
+   missing_dso_whitelist:
+     - "$RPATH/libclang.so.*"

Committable suggestion skipped: line range outside the PR's diff.

@wdecoster wdecoster added the please review & merge set to ask for merge label Nov 4, 2024
@martin-g martin-g merged commit f15d991 into master Nov 4, 2024
6 checks passed
@martin-g martin-g deleted the bump/cramino branch November 4, 2024 13:50
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3 participants