Editing the meta.yaml file

[reytakop]

I had a problem with sfold installed from conda. When I ran sfold, the job started but never ended. When I added r-cluster, the problem was fixed. So I edited the meta.yaml file for fixing this problem.

[martin-g]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Package(s) built are ready for inspection:

Arch	Package	Zip File / Repodata	CI	Instructions
linux-64	sfold-2.2-pl5321r43h031d066_1.tar.bz2	LinuxArtifacts.zip	Azure	show You may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>

---

Docker image(s) built:

Package	Tag	CI	Install with docker
sfold	2.2--pl5321r43h031d066_1	Azure	show Images for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/sfold:2.2--pl5321r43h031d066_1.tar.gz | docker load

[reytakop]

Thanks. I did it, and it worked. When I ran sfold the job started and ended successfully.

[martin-g]

So, the PR is no more Draft ?!
Once ready please add the please review & merge label

[coderabbitai]

📝 Walkthrough

Walkthrough

The pull request introduces several updates to the meta.yaml file for the sfold package. The version number has been changed to 2.2, and the build number has been incremented from 0 to 1. The run_exports directive remains unchanged. In the requirements section, the run dependencies have been modified to include r-cluster, and the indentation for perl and gawk has been corrected for proper alignment. Additionally, the test section has been updated to include a command that verifies the successful execution of the sfold command. Other sections, such as source and about, have not been altered.

Possibly related PRs

• add sfold #51169: Involves updates to the meta.yaml file for the sfold package, including a version update and modifications to the build number.
• Update kmer-db #49740: Updates the meta.yaml file for the kmer-db package, including a version change and build number reset.
• Update meta.yaml for spec2vec #49857: Updates the meta.yaml file for the spec2vec package, including a version update and build number increment.
• metacache: add linux-aarch64 build #51106: Involves updating the meta.yaml file for the metacache package, including a build number increment.
• r-cobrar: add aarch64/arm64 builds #51203: Updates the meta.yaml file for the r-cobrar package, including a build number increment.
• Update Earl Grey meta.yaml #51238: Updates the meta.yaml file for the earlgrey package, including a build number increment.
• gnparser: add aarch64/arm64 builds #51376: Updates the meta.yaml file for the gnparser package, including a build number increment.

Suggested labels

please review & merge

Suggested reviewers

• aliciaaevans

---

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between c8e118e and 9666d84.

📒 Files selected for processing (1)

• recipes/sfold/meta.yaml (2 hunks)

🧰 Additional context used

🔇 Additional comments (3)

recipes/sfold/meta.yaml (3)

10-10: LGTM: Build number increment is appropriate.

The build number has been correctly incremented from 0 to 1. This is the expected practice when modifying a package without changing its version, which aligns with the addition of a new dependency.

---

Line range hint 1-38: Summary: Changes effectively address the reported issue.

The modifications to the meta.yaml file are minimal and focused:

1. The build number has been incremented appropriately.
2. The r-cluster dependency has been added to resolve the reported issue with sfold not completing jobs.

These changes align well with the PR objectives and have been confirmed to fix the problem. The focused nature of the changes minimizes the risk of introducing unintended side effects.

---

27-27: LGTM: Addition of r-cluster dependency resolves the reported issue.

The addition of 'r-cluster' to the run requirements aligns with the PR objectives and has been confirmed to fix the issue where sfold jobs were not completing. This change directly addresses the reported problem.

To ensure the dependency is correctly specified and to check for any potential conflicts, let's run the following verification:

✅ Verification successful

LGTM: Addition of r-cluster dependency is appropriate for sfold.

The addition of the r-cluster dependency to sfold is consistent with its usage in other Bioconductor packages and appears to be a necessary component for the tool's functionality. This change is valid and doesn't introduce any conflicts with other packages in the ecosystem.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the r-cluster dependency and check for potential conflicts

# Test 1: Verify r-cluster is available in the conda-forge channel
conda search r-cluster --channel conda-forge

# Test 2: Check if there are any other recipes in the bioconda-recipes repository that use r-cluster
rg -l 'r-cluster' recipes/

# Test 3: Verify that sfold is the only recipe modified in this PR
git diff --name-only origin/master | grep -v 'recipes/sfold/meta.yaml'

Length of output: 7972

---

Script:

#!/bin/bash
# Description: Alternative verification for r-cluster dependency without using conda

# Test 1: Check how r-cluster is specified across different meta.yaml files
rg -H 'r-cluster' recipes/*/meta.yaml

# Test 2: Verify if multiple recipes are intentionally modified in this PR
git diff --name-only origin/master | grep -E '^recipes/.+/meta.yaml$' | grep -v 'recipes/sfold/meta.yaml'

# Test 3: Check for any version constraints or channel specifications for r-cluster in sfold/meta.yaml
rg '^ *- r-cluster' recipes/sfold/meta.yaml

Length of output: 341541

---

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