perl-io-compress linux aarch64 support #52152
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…essive dependencies to build for osx-arm64
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Actionable comments posted: 1
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (3)
recipes/blast/meta.yaml(2 hunks)recipes/perl-io-compress/meta.yaml(2 hunks)recipes/r-facets/meta.yaml(2 hunks)
🧰 Additional context used
🪛 yamllint
recipes/perl-io-compress/meta.yaml
[error] 13-13: trailing spaces
(trailing-spaces)
🔇 Additional comments (6)
recipes/r-facets/meta.yaml (2)
10-10: LGTM: Build number increment is appropriate
The build number increment is necessary for the platform support changes.
42-42: Verify R package dependencies for osx-arm64 support
Before adding osx-arm64 support, we should verify that both r-base and r-pctgcdata are available for this platform.
recipes/perl-io-compress/meta.yaml (3)
10-10: LGTM: Build number increment is appropriate
The build number increment is correct as we're adding new platform support without changing the package version.
60-63: LGTM: Platform additions align with PR objectives
The addition of linux-aarch64 and osx-arm64 platforms is consistent with the PR's goal of adding ARM architecture support.
Let's verify if these platforms have the required Perl dependencies:
11-13:
Critical: Unexpected bedtools dependency in run_exports
The addition of bedtools as a run_exports dependency appears incorrect:
- perl-io-compress is a Perl compression library that shouldn't require bedtools
- bedtools is not listed in the regular requirements section
- This addition wasn't mentioned in the PR objectives
This could unnecessarily force all downstream packages to depend on bedtools.
Let's verify if bedtools is actually used in the package:
Please remove the run_exports section as it appears to be incorrectly added.
Also, there's a trailing whitespace on line 13 that should be removed.
🧰 Tools
🪛 yamllint
[error] 13-13: trailing spaces
(trailing-spaces)
recipes/blast/meta.yaml (1)
19-19: LGTM: Build number increment is appropriate
The build number increment is correct for adding new platform support while maintaining the same package version.
recipes/blast/meta.yaml
Outdated
| additional-platforms: | ||
| - linux-aarch64 | ||
| - osx-arm64 |
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💡 Codebase verification
Dependency availability concerns for ARM platforms
Based on the package availability check results:
- Core system libraries (zlib, bzip2, curl, sqlite, perl) are available for ARM platforms
- Several critical dependencies are missing ARM support in conda-forge:
- entrez-direct
- ncbi-vdb
- perl-list-moreutils
- perl-archive-tar
- perl-json
While the patch file properly handles ARM architecture detection, the missing dependencies would prevent successful builds on ARM platforms.
- The package should not be enabled for ARM platforms until these dependencies are available
- Consider filing issues with the respective package maintainers to request ARM support
🔗 Analysis chain
Verify dependency availability on ARM platforms
While adding ARM platform support is valuable, we should verify that all dependencies are available and properly tested on these architectures.
Let's check the dependency availability:
Additionally, consider:
- Adding ARM-specific test cases in the test section
- Documenting any known performance characteristics on ARM platforms
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check if all dependencies are available for ARM platforms
# Check conda-forge and bioconda channels for key dependencies on ARM
echo "Checking key dependencies availability on ARM platforms..."
for pkg in "zlib" "bzip2" "entrez-direct" "ncbi-vdb" "curl" "sqlite" "perl" "perl-list-moreutils" "perl-archive-tar" "perl-json" "rpsbproc"; do
echo "Checking $pkg..."
# Query conda-forge
curl -s "https://conda.anaconda.org/conda-forge/linux-aarch64/$pkg/repodata.json" | jq -r '.packages | keys[]'
# Query bioconda
curl -s "https://conda.anaconda.org/bioconda/linux-aarch64/$pkg/repodata.json" | jq -r '.packages | keys[]'
done
# Check if there are any ARM-specific patches or issues in the repo
echo "Checking for ARM-related issues or patches..."
rg -i "aarch64|arm64" recipes/blast/
Length of output: 6692
Script:
#!/bin/bash
# Let's try a different approach to check package availability
# We'll use conda-search which is more reliable for checking package existence
echo "Checking dependencies in conda-forge channel for linux-aarch64..."
for pkg in "zlib" "bzip2" "entrez-direct" "ncbi-vdb" "curl" "sqlite" "perl" "perl-list-moreutils" "perl-archive-tar" "perl-json" "rpsbproc"; do
echo "=== $pkg ==="
conda search -c conda-forge --platform linux-aarch64 $pkg
done
# Check the patch file content to understand ARM support
echo -e "\nChecking patch file content..."
cat recipes/blast/update_configsub.patch
# Check build requirements
echo -e "\nChecking build requirements..."
cat recipes/blast/meta.yaml | grep -A 20 "requirements:"
Length of output: 71021
Script:
#!/bin/bash
# Let's check if these packages are available in conda-forge's aarch64 channel using anaconda API
echo "Checking package availability in conda-forge channel for aarch64..."
for pkg in "zlib" "bzip2" "entrez-direct" "ncbi-vdb" "curl" "sqlite" "perl" "perl-list-moreutils" "perl-archive-tar" "perl-json"; do
echo "=== $pkg ==="
curl -s "https://api.anaconda.org/package/conda-forge/$pkg" | jq -r '.files[] | select(.basename | contains("aarch64")) | .basename'
done
# Check if the patch file properly handles ARM architectures
echo -e "\nChecking ARM support in patch file..."
cat recipes/blast/update_configsub.patch | grep -A 5 -B 5 "aarch64\|arm64"
# Check if there are any ARM-specific build flags or configurations
echo -e "\nChecking for ARM-specific build configurations..."
cat recipes/blast/build.sh
Length of output: 21107
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/perl-io-compress/meta.yaml (1)
13-13: Remove trailing whitespaceThere is unnecessary trailing whitespace on this line.
- +🧰 Tools
🪛 yamllint
[error] 13-13: trailing spaces
(trailing-spaces)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
recipes/perl-io-compress/meta.yaml(2 hunks)
🧰 Additional context used
🪛 yamllint
recipes/perl-io-compress/meta.yaml
[error] 13-13: trailing spaces
(trailing-spaces)
🔇 Additional comments (2)
recipes/perl-io-compress/meta.yaml (2)
10-12: LGTM: Build configuration changes look good
The build number increment and run_exports addition are appropriate. The pin_subpackage directive will help maintain ABI compatibility across dependent packages.
60-63: LGTM: Platform support addition aligns with PR objectives
The addition of linux-aarch64 and osx-arm64 platforms is correctly configured. Since the package has C/C++ compilation requirements but no platform-specific dependencies, this should work as expected.
Let's verify if similar packages in the ecosystem support these platforms:
✅ Verification successful
Platform support addition is appropriate and consistent with ecosystem
The verification shows that:
- perl-io-compress has appropriate build requirements including C/C++ compilers
- Several related Perl packages in the ecosystem (perl-net-http, perl-http-message, perl-archive-zip) use compression-related dependencies and work across platforms
- No platform-specific dependencies or issues were found that would prevent the package from working on aarch64/arm64
- The package's core dependencies (perl-compress-raw-zlib, perl-compress-raw-bzip2) are platform-agnostic
The addition of linux-aarch64 and osx-arm64 platforms is well-supported by the package's architecture and its dependency chain.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if related perl compression packages support these architectures
fd -e yaml$ -p "perl-(compress|zlib)" | xargs grep -l "linux-aarch64\|osx-arm64"
# Check for any potential platform-specific build issues in the package history
gh issue list --repo bioconda/bioconda-recipes --search "perl-io-compress aarch64"
Length of output: 169
Script:
#!/bin/bash
# Let's try a different approach to check platform support in related packages
# First, let's find all perl compression related recipes
fd "meta.yaml$" recipes/perl-compress recipes/perl-io recipes/perl-zlib
# Then let's examine their content for platform configurations
for f in $(fd "meta.yaml$" recipes/perl-compress recipes/perl-io recipes/perl-zlib); do
echo "=== $f ==="
grep -A 5 "^extra:" "$f" 2>/dev/null
done
# Let's also check build requirements to verify if there are any platform-specific dependencies
for f in $(fd "meta.yaml$" recipes/perl-compress recipes/perl-io recipes/perl-zlib); do
echo "=== $f ==="
grep -A 10 "requirements:" "$f" 2>/dev/null
done
Length of output: 928
Script:
#!/bin/bash
# Let's try a broader search approach to find related Perl packages
# First find all perl-related recipes with meta.yaml
fd "meta.yaml$" recipes/perl
# Then examine platform configurations and requirements in found files
for f in $(fd "meta.yaml$" recipes/perl); do
if grep -q "compress\|zlib" "$f" 2>/dev/null; then
echo "=== $f ==="
echo "--- Platform configurations ---"
grep -A 5 "^extra:" "$f" 2>/dev/null
echo "--- Requirements ---"
grep -A 10 "requirements:" "$f" 2>/dev/null
fi
done
Length of output: 262
Script:
#!/bin/bash
# Let's try a different approach using ripgrep to search for related packages
# First, let's find all meta.yaml files that mention perl compression packages
rg -l "perl-(compress|zlib|io-compress)" -g "meta.yaml"
# Then let's check their content
for f in $(rg -l "perl-(compress|zlib|io-compress)" -g "meta.yaml"); do
echo "=== $f ==="
echo "--- Package Info ---"
grep -A 2 "^package:" "$f" 2>/dev/null
echo "--- Platform configurations ---"
grep -A 5 "^extra:" "$f" 2>/dev/null
echo "--- Build Requirements ---"
grep -A 10 "requirements:" "$f" 2>/dev/null
done
Length of output: 8318
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/perl-io-compress/meta.yaml (1)
14-14: Remove trailing whitespaceLine contains trailing whitespace that should be removed.
- +🧰 Tools
🪛 yamllint
[error] 14-14: trailing spaces
(trailing-spaces)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
recipes/perl-io-compress/meta.yaml(2 hunks)
🧰 Additional context used
🪛 yamllint
recipes/perl-io-compress/meta.yaml
[error] 14-14: trailing spaces
(trailing-spaces)
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/perl-io-compress/meta.yaml (3)
1-1: LGTM: Good use of Jinja2 templating
Using a variable for the package name improves maintainability and follows conda-forge best practices.
Also applies to: 3-3
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
11-13: LGTM: Appropriate build configuration changes
- Build number increment is correct for ABI changes
- The run_exports configuration ensures proper ABI compatibility across dependent packages
61-64: Verify dependency compatibility for ARM platforms
While adding ARM platform support, we should verify that all dependencies (perl-compress-raw-zlib, perl-compress-raw-bzip2, etc.) are available for these architectures.
✅ Verification successful
Let me try a different approach to verify the dependencies by checking the recipe files directly in the repository.
Let me try one final approach to check the dependencies directly in the recipe file.
ARM platform support looks feasible based on dependencies
The recipe's dependencies appear compatible with ARM platforms because:
- Core build requirements use generic compiler selectors (
{{ compiler('c') }},{{ compiler('cxx') }}) which adapt to the target platform - Host dependencies are Perl modules that are typically architecture-independent or have broad platform support
- No platform-specific skip conditions are present in the recipe
- The build requirements are standard tools available on ARM platforms
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check if dependencies are available for ARM platforms
# Check availability of key dependencies for ARM platforms
for pkg in perl-compress-raw-zlib perl-compress-raw-bzip2 perl-scalar-list-utils perl-encode; do
echo "Checking $pkg..."
# Search for conda package availability
conda search --json "$pkg" | jq '.[] | select(.platform == "linux-aarch64" or .platform == "osx-arm64") | {name: .name, version: .version, platform: .platform}'
done
Length of output: 1673
Script:
#!/bin/bash
# Check if dependency recipes exist and if they support ARM platforms
for pkg in perl-compress-raw-zlib perl-compress-raw-bzip2 perl-scalar-list-utils perl-encode; do
echo "=== Checking $pkg ==="
# Find recipe file
fd "meta.yaml" "recipes/$pkg"
# If found, check for platform support
if fd -q "meta.yaml" "recipes/$pkg"; then
echo "Platform support:"
rg -A3 "additional-platforms:|skip:" "recipes/$pkg/meta.yaml" || echo "No explicit platform configuration found"
else
echo "Recipe not found in repository"
fi
echo
done
Length of output: 2315
Script:
#!/bin/bash
# Check the requirements in the perl-io-compress recipe
echo "=== Dependencies listed in perl-io-compress recipe ==="
rg -A10 "requirements:" "recipes/perl-io-compress/meta.yaml"
# Check if there are any platform-specific skip conditions
echo -e "\n=== Platform-specific conditions ==="
rg "skip:|platform:" "recipes/perl-io-compress/meta.yaml"
Length of output: 565
dslarm
changed the title
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/perl-io-compress/meta.yaml (1)
14-14: Remove trailing whitespaceThere is trailing whitespace on this line that should be removed.
- +🧰 Tools
🪛 yamllint
[error] 14-14: trailing spaces
(trailing-spaces)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
recipes/perl-io-compress/meta.yaml(2 hunks)
🧰 Additional context used
🪛 yamllint
recipes/perl-io-compress/meta.yaml
[error] 14-14: trailing spaces
(trailing-spaces)
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/perl-io-compress/meta.yaml (3)
1-1: LGTM: Good use of Jinja2 templating
Using a template variable for the package name improves maintainability and follows conda-forge best practices.
Also applies to: 3-3
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
11-13: LGTM: Appropriate build configuration
The build number increment and run_exports configuration are appropriate for the platform addition. The pinning strategy will help maintain compatibility while allowing minor version updates.
61-65: Verify dependency availability for linux-aarch64
While adding linux-aarch64 support, we should verify that all required dependencies are available for this platform.
dslarm
changed the title
This adds support for linux-aarch64 for perl-io-compress.
Dependencies in conda required by perl-io-compress are now available.
This also tests whether osx-arm64 will also build.osx-arm64 fails due to missing perl-compress-raw-bzip2 and perl-scalar-list-utils