adding RDEVAL #52070
adding RDEVAL #52070
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📝 Walkthrough📝 WalkthroughWalkthroughThis pull request introduces a new shell script Possibly related PRs
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/rdeval/meta.yaml (1)
8-10: Consider using .tar.gz instead of .zipFor Unix/Linux packages, it's more conventional to use .tar.gz archives. GitHub provides both formats, and .tar.gz is generally preferred in the Linux ecosystem.
- url: https://github.com/vgl-hub/{{ name }}/archive/refs/tags/v{{ version }}.zip + url: https://github.com/vgl-hub/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz sha256: # Update this checksum for the .tar.gz file
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recipes/rdeval/meta.yaml(1 hunks)
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🪛 yamllint
recipes/rdeval/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/rdeval/meta.yaml (4)
12-15: Verify runtime dependencies
The recipe only specifies build requirements. Please verify if there are any runtime dependencies needed.
#!/bin/bash
# Check source code for potential library dependencies
rg -g '*.cpp' -g '*.h' '#include\s*<' --no-filename | sort -u
# Check if there's a requirements.txt or similar
fd -g '*requirement*.txt' -g 'CMakeLists.txt' -g 'Makefile'26-31: Verify license file and Bioconda compatibility
Please ensure:
- The LICENSE file exists in the source repository
- The summary indicates biological relevance as required by Bioconda guidelines
#!/bin/bash
# Check if LICENSE file exists in the repository
curl -s -I https://raw.githubusercontent.com/vgl-hub/rdeval/main/LICENSE
# Look for biological terms in source code to verify relevance
rg -g '*.cpp' -g '*.h' -g '*.md' -i 'genom|dna|rna|seq|bio|allele|variant'17-20: Verify the need for run_exports
The run_exports section suggests this package provides a library that other packages might depend on. Please verify if this is necessary, as it appears to be primarily a command-line tool based on the test section.
✅ Verification successful
Remove unnecessary run_exports
The run_exports section is not required as the package does not build shared libraries or provide header files for other packages.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if the package builds any shared libraries
fd -g '*.so' -g '*.dylib' -g '*.dll'
# Check if there are any header files that might be used by other packages
fd -g '*.h' -g '*.hpp'
Length of output: 9627
1-6: Verify package version compatibility
The version 0.0.2 suggests this is an early development release. Please ensure this version is stable enough for distribution via Bioconda.
✅ Verification successful
Package version verified
The version 0.0.2 is the latest release with no open bug issues, ensuring its stability for distribution via Bioconda.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if this is the latest version
curl -s https://api.github.com/repos/vgl-hub/rdeval/releases/latest | jq -r '.tag_name'
# Check if there are any open issues related to version 0.0.2
gh api graphql -f query='
{
repository(owner: "vgl-hub", name: "rdeval") {
issues(first: 5, states: OPEN, filterBy: {labels: ["bug"]}) {
nodes {
title
body
labels(first: 5) {
nodes {
name
}
}
}
}
}
}'
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recipes/rdeval/meta.yaml
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| test: | ||
| commands: | ||
| - ${PREFIX}/bin/genodsp --help |
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💡 Codebase verification
Naming inconsistency between binary and package
The binary name genodsp in recipes/rdeval/meta.yaml differs from the package name rdeval. Please verify if this is intentional and update for consistency if necessary.
🔗 Analysis chain
Enhance test coverage and clarify binary name
Two concerns:
- The test only verifies that the help command works. Consider adding more comprehensive tests.
- The binary name
genodspdiffers from the package namerdeval. Please clarify if this is intentional.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check source code for available command-line options
rg -g '*.cpp' -g '*.h' 'add_option|getopt' -A 5
# Look for test files in the source repository
fd -g '*test*'
Length of output: 9627
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (3)
recipes/rdeval/meta.yaml (3)
1-6: Consider version pinning strategy for early development packageGiven that this is an early development version (0.0.2), consider implementing strict version pinning in downstream dependencies to avoid potential breaking changes.
🧰 Tools
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[error] 1-1: syntax error: found character '%' that cannot start any token
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8-10: Consider using .tar.gz instead of .zipThe .tar.gz format is more commonly used in Unix environments and typically provides better compression. Consider updating the URL from:
https://github.com/vgl-hub/rdeval/archive/refs/tags/v0.0.2.zipto:
https://github.com/vgl-hub/rdeval/archive/refs/tags/v0.0.2.tar.gz
28-28: Enhance package summary descriptionThe current summary is quite general. Consider providing more specific details about:
- What types of read analysis it performs
- What kind of read manipulations are supported
- Its primary use cases in bioinformatics
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recipes/rdeval/build.sh(1 hunks)recipes/rdeval/meta.yaml(1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- recipes/rdeval/build.sh
🧰 Additional context used
🪛 yamllint
recipes/rdeval/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (2)
recipes/rdeval/meta.yaml (2)
12-15:
Add runtime dependencies section
The recipe only specifies build dependencies. For a C++ project, you might need to specify runtime dependencies (e.g., libstdc++, system libraries). Consider adding a run: section under requirements:.
Let's check the source code for potential runtime dependencies:
#!/bin/bash
# Look for library dependencies in source files
rg -g '*.cpp' -g '*.h' '#include\s+<' -A 1
# Check for linking flags in build files
fd -g 'Makefile*' -x cat {} \; | rg -i 'LDFLAGS|LIBS'1-31: Verify Bioconda-specific requirements
Please ensure the recipe complies with Bioconda guidelines:
- The package is directly related to biological sciences (confirmed by read analysis functionality)
- The recipe follows the required format
- Dependencies should preferably come from conda-forge or bioconda channels
Let's check for similar packages and channel preferences:
✅ Verification successful
Bioconda-specific requirements verified
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check for similar packages in bioconda
curl -s https://conda.anaconda.org/bioconda/noarch/repodata.json | jq '.packages | keys[] | select(contains("read") or contains("eval"))'
# Verify if dependencies are available in conda-forge
curl -s https://conda.anaconda.org/conda-forge/noarch/repodata.json | jq '.packages | keys[] | select(. == "make")'
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🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
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Actionable comments posted: 2
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📒 Files selected for processing (2)
recipes/rdeval/build.sh(1 hunks)recipes/rdeval/meta.yaml(1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- recipes/rdeval/build.sh
🧰 Additional context used
🪛 yamllint
recipes/rdeval/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
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🔇 Additional comments (5)
recipes/rdeval/meta.yaml (5)
18-21: LGTM! Good use of run_exports
The build configuration correctly uses pin_subpackage to maintain ABI compatibility across updates.
23-25: Enhance test coverage and verify binary name
-
The test section only verifies the help command. Consider adding more comprehensive tests:
- Version check
- Basic functionality test
- Input/output verification
-
Previous review mentioned a binary named
genodsp, but test usesrdeval. Please verify the correct binary name.
#!/bin/bash
# Search for binary name references in build scripts
rg -g 'build.sh' -g 'CMakeLists.txt' -g 'Makefile' 'bin/[^/]*$|install.*bin' -A 2
# Look for test files in upstream repository
gh api repos/vgl-hub/rdeval/contents --jq '.[] | select(.name | contains("test"))'1-6: Consider version number implications
The version 0.0.2 suggests this package is in early development. Please ensure this version matches the upstream release version. Also, consider adding a note in the package description if this is a beta/development version.
#!/bin/bash
# Verify if the version matches the latest release
gh api repos/vgl-hub/rdeval/releases/latest --jq .tag_name🧰 Tools
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[error] 1-1: syntax error: found character '%' that cannot start any token
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1-32: Verify Bioconda requirements compliance
According to the PR objectives, new recipes not directly related to biological sciences should be submitted to conda-forge instead. Please:
- Clarify how this tool is specifically used in biological sciences
- Consider whether conda-forge would be more appropriate if the tool is general-purpose
#!/bin/bash
# Search for bioinformatics-related terms in documentation
gh api repos/vgl-hub/rdeval/contents/README.md --jq '.content' | base64 -d | rg -i 'bio|genom|seq|dna|rna|fastq|sam|bam'
# Check if already exists in conda-forge
curl -s https://api.anaconda.org/package/conda-forge/rdeval🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
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8-10: Verify source package integrity
The source URL points to a release with submodules. Let's verify:
- The URL is accessible
- The SHA256 checksum matches
- The package contains all necessary submodules
recipes/rdeval/meta.yaml
Outdated
| requirements: | ||
| build: | ||
| - {{ compiler('cxx') }} | ||
| - make | ||
| - zlib |
There was a problem hiding this comment.
Add runtime dependencies section
The recipe is missing a run section under requirements. Since you're using zlib during build, it's likely needed at runtime too.
Add the following section:
requirements:
build:
- {{ compiler('cxx') }}
- make
- zlib
+ host:
+ - zlib
+ run:
+ - zlib📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| requirements: | |
| build: | |
| - {{ compiler('cxx') }} | |
| - make | |
| - zlib | |
| requirements: | |
| build: | |
| - {{ compiler('cxx') }} | |
| - make | |
| host: | |
| - zlib | |
| run: | |
| - zlib |
recipes/rdeval/meta.yaml
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| about: | ||
| home: https://github.com/vgl-hub/{{ name }} | ||
| summary: A general purpose, multithreaded read analysis and manipulation tool. | ||
| license: MIT | ||
| license_file: LICENSE | ||
| license_url: https://github.com/vgl-hub/{{ name }}/blob/main/LICENSE |
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💡 Codebase verification
LICENSE file verified and README requires a detailed Description section
- The LICENSE file exists and is compliant with the MIT License.
- README.md lacks a detailed Description section as recommended.
🔗 Analysis chain
Verify license file and update summary
- Please verify that the LICENSE file exists in the source package.
- Consider expanding the summary to mention:
- The specific types of read analysis it supports
- Its relevance to bioinformatics (since this is for Bioconda)
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Verify license file existence and content
gh api repos/vgl-hub/rdeval/contents/LICENSE --jq '.content' | base64 -d
# Check if there's a more detailed description in README
gh api repos/vgl-hub/rdeval/contents/README.md --jq '.content' | base64 -d | grep -A 5 "^#.*Description"
Length of output: 298
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#!/bin/bash
# Verify license file existence and content without using base64
gh api repos/vgl-hub/rdeval/contents/LICENSE --raw
# Check if there's a more detailed description in README
gh api repos/vgl-hub/rdeval/contents/README.md --raw | grep -A 5 "^#.*Description"
Length of output: 2865
Script:
#!/bin/bash
# Verify license file existence and content using jq to decode base64
gh api repos/vgl-hub/rdeval/contents/LICENSE --jq '.content | @base64d'
# Check if there's a more detailed description in README using jq to decode and grep for keywords
gh api repos/vgl-hub/rdeval/contents/README.md --jq '.content | @base64d' | grep -A 5 "^#.*Description"
Length of output: 1244
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
recipes/rdeval/meta.yaml (2)
20-23: Review dependency pinning strategyThe current pinning strategy (
max_pin="x.x") allows updates only to patch versions. For a pre-1.0 version, this might be too restrictive as breaking changes are expected.Consider using
max_pin="x"until version 1.0 is released.run_exports: - - {{ pin_subpackage(name|lower, max_pin="x.x") }} + - {{ pin_subpackage(name|lower, max_pin="x") }}
29-34: Enhance package summary for Bioconda contextThe current summary is brief. For Bioconda packages, it's helpful to include:
- Specific bioinformatics use cases
- Types of reads supported
- Key features relevant to biological analysis
- summary: A general purpose, multithreaded read analysis and manipulation tool. + summary: A general purpose, multithreaded NGS read analysis and manipulation tool supporting various sequencing formats and providing quality assessment, filtering, and transformation capabilities.
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📒 Files selected for processing (2)
recipes/rdeval/build.sh(1 hunks)recipes/rdeval/meta.yaml(1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- recipes/rdeval/build.sh
🧰 Additional context used
🪛 yamllint
recipes/rdeval/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/rdeval/meta.yaml (3)
25-27: 🛠️ Refactor suggestion
Enhance test coverage
The current test only verifies that the help command works. Consider adding:
- Basic functionality tests
- Version command test
- Input/output verification
commands:
- ${PREFIX}/bin/rdeval --help
+ - ${PREFIX}/bin/rdeval --version
+ - ${PREFIX}/bin/rdeval 2>&1 | grep "input file required"Note: A previous review raised concerns about binary name inconsistency between genodsp and rdeval. Please confirm if this has been resolved.
8-10: Verify submodule stability and versioning
The source includes submodules (-with_submodules.zip). Please ensure:
- All submodules are properly versioned
- No security vulnerabilities exist in the submodules
1-6: Verify version stability for production use
Given that this is version 0.0.2, which suggests early development, please verify:
- API stability
- Presence of breaking changes
- Production readiness
✅ Verification successful
Version stability verified
No breaking changes detected in commit history.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check for version history and stability
gh api repos/vgl-hub/rdeval/releases --jq '.[].name'
# Look for breaking changes in commit history
gh api repos/vgl-hub/rdeval/commits --jq '.[] | select(.commit.message | contains("BREAKING CHANGE") or contains("breaking change"))'
Length of output: 1739
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#!/bin/bash
# Fetch release names
gh api repos/vgl-hub/rdeval/releases --jq '.[].name'
# Search commit messages for breaking changes
gh api repos/vgl-hub/rdeval/commits --jq '.[] | select(.commit.message | test("(?i)breaking change")) | .commit.message'
Length of output: 205
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🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (1)
recipes/rdeval/meta.yaml (1)
29-34: Enhance package summary for Bioconda usersThe current summary is quite brief. Since this is a Bioconda package, consider expanding it to include:
- Specific types of read analysis supported
- Relevance to bioinformatics workflows
- Key features that distinguish it from similar tools
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recipes/rdeval/meta.yaml(1 hunks)recipes/rdeval/quote.patch(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/rdeval/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
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🔇 Additional comments (6)
recipes/rdeval/quote.patch (2)
21-22: LGTM: Appropriate header inclusion style
The change from "zlib.h" to <zlib.h> is correct as it properly indicates zlib as a system library rather than a local header.
1-25: Verify zlib dependency configuration
Since this patch modifies zlib linking and includes, we should verify the proper configuration in meta.yaml.
✅ Verification successful
Zlib dependency correctly configured
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check if zlib is properly configured in meta.yaml and verify no hardcoded paths
# are present in other build files
# Check meta.yaml for zlib dependency
echo "Checking meta.yaml for zlib configuration..."
rg "zlib" recipes/rdeval/meta.yaml
# Look for any other hardcoded library paths that might need fixing
echo "Checking for other hardcoded library paths..."
rg -g "Makefile*" -g "*.mk" "/usr/lib"
Length of output: 284
recipes/rdeval/meta.yaml (4)
20-23: LGTM!
The build configuration follows best practices with proper version pinning.
14-18: Verify build dependencies completeness
Let's check the source code to ensure all necessary build dependencies are included.
#!/bin/bash
# Check for additional dependencies in build files
gh api repos/vgl-hub/rdeval/contents/Makefile --raw | grep -i 'LIBS\|LDFLAGS'
# Look for include statements that might indicate missing dependencies
rg -g '*.cpp' -g '*.hpp' -g '*.h' '^[[:space:]]*#include'1-6: Verify latest version availability
The package version is set to 0.0.2, which seems to be an early release. Let's verify if this is the latest version.
✅ Verification successful
Package version is up-to-date
The package version in meta.yaml is set to 0.0.2, which matches the latest release.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check latest release version
gh api repos/vgl-hub/rdeval/releases/latest --jq '.tag_name'
# List all releases to see version history
gh api repos/vgl-hub/rdeval/releases --jq '.[].tag_name'
Length of output: 140
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🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
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8-12: Verify patch file and source URL
Please ensure:
- The purpose of
quote.patchis documented - The source URL is accessible and the checksum matches
recipes/rdeval/quote.patch
Outdated
| LIBS = -lz | ||
| +-L/usr/lib/x86_64-linux-gnu -lz |
There was a problem hiding this comment.
Remove hard-coded library path and fix duplicate linker flags
The current changes introduce two issues:
- Hard-coding
/usr/lib/x86_64-linux-gnupath breaks cross-platform compatibility and violates Conda's build practices - The
-lzflag is duplicated
Apply this fix to maintain portability and clean up duplicates:
LDFLAGS := -pthread
-LIBS = -lz
--L/usr/lib/x86_64-linux-gnu -lz
+LIBS = -lzInstead of hard-coding the library path, rely on Conda's build environment variables and the proper dependency specification in meta.yaml.
📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| LIBS = -lz | |
| +-L/usr/lib/x86_64-linux-gnu -lz | |
| LDFLAGS := -pthread | |
| LIBS = -lz |
recipes/rdeval/meta.yaml
Outdated
| test: | ||
| commands: | ||
| - ${PREFIX}/bin/rdeval --help |
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🛠️ Refactor suggestion
Enhance test coverage
The current test only verifies that the help command works. Consider adding more comprehensive tests:
- Test basic functionality with sample input
- Verify output format
- Test error handling
Would you like assistance in generating additional test commands based on the tool's functionality?
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/rdeval/meta.yaml (1)
31-36: Enhance package summaryWhile the current summary is concise, consider expanding it to better describe:
- The specific types of read analysis supported
- The key features that differentiate it from similar tools
- The target audience or use cases
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📒 Files selected for processing (3)
recipes/rdeval/libs.patch(1 hunks)recipes/rdeval/meta.yaml(1 hunks)recipes/rdeval/zlib.patch(1 hunks)
✅ Files skipped from review due to trivial changes (2)
- recipes/rdeval/libs.patch
- recipes/rdeval/zlib.patch
🧰 Additional context used
🪛 yamllint
recipes/rdeval/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/rdeval/meta.yaml (3)
22-25: LGTM! Build configuration follows best practices
The build configuration correctly:
- Starts with build number 0
- Uses pin_subpackage for version compatibility
11-14: Review patch file naming and necessity
The patch file foo.patch has a non-descriptive name that doesn't indicate its purpose. Additionally:
- Verify if all three patches are necessary
- Ensure each patch follows the principle of minimal changes
- Consider more descriptive names that reflect the patch's purpose
#!/bin/bash
# Check patch contents
for patch in zlib.patch libs.patch foo.patch; do
echo "=== Contents of $patch ==="
if [ -f "recipes/rdeval/$patch" ]; then
cat "recipes/rdeval/$patch"
else
echo "Patch file not found"
fi
done1-6: Consider version stability implications
The version 0.0.2 indicates an early development release. Please ensure:
- The API is stable enough for distribution
- Breaking changes are documented
- A roadmap exists for reaching a stable 1.0.0 release
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/rdeval/foo.patch (1)
12-12: Consider adding ABI stability flagsGiven Bioconda's emphasis on API/ABI stability, consider adding appropriate compile flags to ensure ABI compatibility:
-CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS) +CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS) -fvisibility=hidden -D_GLIBCXX_USE_CXX11_ABI=0This change helps maintain ABI compatibility across different gcc versions and ensures symbols are properly hidden by default.
📜 Review details
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Review profile: CHILL
📒 Files selected for processing (3)
-
recipes/rdeval/build.sh(1 hunks) -
recipes/rdeval/foo.patch(1 hunks) -
recipes/rdeval/meta.yaml(1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- recipes/rdeval/build.sh
🧰 Additional context used
🪛 yamllint
recipes/rdeval/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (8)
recipes/rdeval/foo.patch (3)
17-18: LGTM: Linker flags are properly configured
The addition of -L${PREFIX}/lib to LDFLAGS is correct and follows Conda packaging best practices while preserving the required -pthread flag.
25-27:
Remove $(LIBS) from object file compilation
The addition of $(LIBS) to the object file compilation command is incorrect. Library linking should only occur during the final linking stage, not during object file compilation. This change could cause unnecessary dependencies and potential build issues.
Apply this change:
- $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@ $(LIBS)
+ $(CXX) $(CXXFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@Additionally, ensure the final linking command includes both
#!/bin/bash
# Search for the linking rule in the Makefile
rg -A 5 '\.o.*:.*' recipes/rdeval/8-9:
Fix the circular CXX variable reference
The line CXX ?= ${CXX} creates a circular reference. In a Conda build environment, this could lead to undefined behavior if CXX isn't pre-defined.
Apply this change:
-CXX ?= ${CXX}
+CXX ?= g++Let's verify if this is a common pattern in other Bioconda recipes:
recipes/rdeval/meta.yaml (5)
16-20: LGTM!
The build settings are well-configured with appropriate version pinning for ABI compatibility.
21-27: LGTM with previous suggestions!
The build and host requirements are correctly specified. Please address the previous review comment about adding runtime dependencies.
28-30: LGTM with previous suggestions!
The basic test is in place. Please address the previous review comment about enhancing test coverage.
1-6: Verify API stability for early version
The package version (0.0.2) suggests an early development stage. Please ensure the API is stable enough for distribution, or consider adding a note in the package description about potential API changes.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
8-14: Consider submitting patches upstream
The recipe includes three patch files (zlib.patch, libs.patch, foo.patch). While patches are acceptable for temporary fixes, consider:
- Submitting these changes upstream to reduce maintenance burden
- Documenting the purpose of each patch in the recipe
✅ Verification successful
Consider submitting patches upstream
The recipe includes three patch files (zlib.patch, libs.patch, foo.patch). Patches are currently necessary based on the codebase. Consider submitting these changes upstream to reduce maintenance burden and ensure long-term support. Additionally, document the purpose of each patch within the recipe.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if patches are still necessary
for patch in zlib.patch libs.patch foo.patch; do
echo "=== $patch ==="
if [ -f "recipes/rdeval/$patch" ]; then
cat "recipes/rdeval/$patch"
else
echo "Patch file not found"
fi
done
Length of output: 2945
recipes/rdeval/meta.yaml
Outdated
| about: | ||
| home: https://github.com/vgl-hub/{{ name }} | ||
| summary: A general purpose, multithreaded read analysis and manipulation tool. | ||
| license: MIT | ||
| license_family: MIT | ||
| license_file: LICENSE | ||
| license_url: https://github.com/vgl-hub/{{ name }}/blob/main/LICENSE | ||
| dev_url: https://github.com/vgl-hub/{{ name }} |
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🛠️ Refactor suggestion
Enhance summary for Bioconda context
While the license information is complete, the summary should better explain:
- The tool's specific role in bioinformatics
- The types of read analysis it performs
- Key features that make it relevant for biological data analysis
This helps users understand why the package belongs in Bioconda rather than conda-forge.
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/rdeval/meta.yaml (1)
15-19: Consider relaxing version pinning for development versionsFor packages in early development (0.0.x), strict version pinning might be too restrictive. Consider using a more relaxed pin like
x.x.xuntil the API stabilizes.run_exports: - - {{ pin_subpackage(name|lower, max_pin="x.x") }} + - {{ pin_subpackage(name|lower, max_pin="x.x.x") }}
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recipes/rdeval/foo.patch(1 hunks)recipes/rdeval/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/rdeval/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (9)
recipes/rdeval/foo.patch (4)
6-6: LGTM! Proper compiler configuration.
The change from hardcoded g++ to ${CXX} is correct and follows Conda build best practices, allowing the build system to control the compiler choice.
Also applies to: 8-8
7-7: LGTM! Proper include path configuration.
Adding ${PREFIX}/include is correct for Conda builds, ensuring the compiler can find headers installed by dependencies.
Also applies to: 9-9
28-29:
Critical: Remove $(LIBS) from object file compilation
The -c flag indicates this command is for compilation only (generating object files), but $(LIBS) is being incorrectly added. Library linking should only occur during the final linking step, not during object file compilation.
Apply this fix:
- $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@ $(LIBS)
+ $(CXX) $(CXXFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@Additionally, ensure there's a proper linking step in the Makefile that uses both $(LDFLAGS) and $(LIBS).
#!/bin/bash
# Check if there's a proper linking step in the Makefile
rg "^\s*\$\(CXX\).*\$\(LDFLAGS\).*\$\(LIBS\)" recipes/rdeval/Makefile17-20: Verify zlib dependency handling in meta.yaml
The linker configuration looks correct, but ensure that:
- zlib is properly listed as a dependency in meta.yaml
- The package uses run_exports for zlib to handle ABI compatibility
✅ Verification successful
zlib dependency is correctly specified and handled via run_exports
🏁 Scripts executed
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# Check if zlib is properly declared as a dependency
rg -A 5 "zlib" recipes/rdeval/meta.yaml
# Check if run_exports is used
rg "run_exports" recipes/rdeval/meta.yaml
Length of output: 250
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#!/bin/bash
# Check if zlib is listed under requirements in meta.yaml
rg -A 10 "^requirements:" recipes/rdeval/meta.yaml | rg "zlib"
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rg "run_exports" recipes/rdeval/meta.yaml
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rg -A 10 "run_exports:" recipes/rdeval/meta.yaml
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rg "zlib" recipes/rdeval/meta.yaml
Length of output: 269
recipes/rdeval/meta.yaml (5)
1-6: LGTM: Package declaration follows Conda conventions
The package name and version are correctly defined using Jinja2 templating.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
20-26: LGTM: Build and host requirements are properly specified
The separation between build and host requirements is correct.
31-39: LGTM: Metadata section is complete
All required metadata fields are present with proper URLs.
27-30: Verify binary name consistency
The test command uses rdeval while past reviews mentioned genodsp. Let's verify the correct binary name.
#!/bin/bash
# Check source code for the actual binary name
rg -g 'Makefile*' 'BINARY.*=' -A 28-13: Verify patch files and their purposes
The source configuration includes two patch files, but their purposes need clarification.
✅ Verification successful
Re-run the patch verification script with corrected syntax
Re-run the patch verification script with corrected syntax
Patch files are present and correctly referenced
🏁 Scripts executed
The following scripts were executed for the analysis:
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for patch in zlib.patch foo.patch; do
echo "=== Checking $patch ==="
if [ -f "recipes/rdeval/$patch" ]; then
echo "File exists"
head -n 10 "recipes/rdeval/$patch"
else
echo "File missing"
fi
done
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for patch in zlib.patch foo.patch; do
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for patch in zlib.patch foo.patch; do
echo "=== Checking $patch ==="
if [ -f "recipes/rdeval/$patch" ]; then
echo "File exists"
head -n 10 "recipes/rdeval/$patch"
else
echo "File missing"
fi
done
Length of output: 952
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (2)
recipes/rdeval/gfalibs.patch (1)
26-26: Remove redundant INCLUDE_DIR flag.The
$(INCLUDE_DIR)is already included in$(CXXFLAGS)(see line 12), making its inclusion here redundant.- $(CXX) $(CXXFLAGS) $(INCLUDE_DIR) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@ -lz + $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@ -lzAlso applies to: 27-27
recipes/rdeval/meta.yaml (1)
11-14: Use descriptive names for patch filesThe patch names 'foo.patch' and 'gfalibs.patch' are not descriptive. Consider renaming them to reflect their purpose, such as:
foo.patch→build-config.patchor similargfalibs.patch→library-paths.patchor similarThis helps maintainers understand the purpose of each patch without having to examine their contents.
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📒 Files selected for processing (2)
recipes/rdeval/gfalibs.patch(1 hunks)recipes/rdeval/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/rdeval/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/rdeval/gfalibs.patch (3)
6-6: LGTM! Good practice using environment variable for compiler.
The change from hardcoded g++ to $(CXX) allows for proper compiler selection in the Conda build environment.
Also applies to: 8-8
17-17: LGTM! Correct library path configuration.
Adding -L${PREFIX}/lib to LDFLAGS is the proper way to locate libraries in the Conda environment.
Also applies to: 18-18
26-26: Verify zlib dependency.
The addition of -lz indicates a dependency on zlib. Ensure this dependency is properly declared in the recipe's meta.yaml.
#!/bin/bash
# Description: Check if zlib is declared as a dependency in meta.yaml
# Look for zlib in meta.yaml
echo "Checking meta.yaml for zlib dependency..."
rg -i "zlib" "recipes/rdeval/meta.yaml"
# Check if there are any other files requiring zlib
echo "Checking for other zlib usage..."
rg -l "zlib\.h" "recipes/rdeval"Also applies to: 27-27
recipes/rdeval/meta.yaml (1)
41-44: Verify ARM platform compatibility
The recipe includes support for ARM architectures (linux-aarch64 and osx-arm64). Please verify:
- Has the tool been tested on these platforms?
- Are there any platform-specific build requirements or configurations needed?
#!/bin/bash
# Check for platform-specific code or configurations
rg -g 'Makefile*' -g '*.cpp' -g '*.h' 'aarch64|arm64|__arm__|__aarch64__'
# Look for CI configurations that might test ARM platforms
fd -g '.travis.yml' -g '.github/workflows/*.yml' -g 'azure-pipelines.yml'| +++ b/gfalibs/Makefile | ||
| @@ -1,5 +1,5 @@ | ||
| -CXX = g++ | ||
| -INCLUDE_DIR = -I./include |
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💡 Codebase verification
parallel-hashmap dependency not declared in meta.yaml.
The addition of parallel-hashmap include path suggests a dependency, but it's not declared in recipes/rdeval/meta.yaml. Please declare parallel-hashmap as a dependency.
🔗 Analysis chain
Verify parallel-hashmap dependency.
The addition of parallel-hashmap include path suggests a dependency. Ensure this dependency is properly declared in the recipe's meta.yaml.
Also applies to: 9-9
🏁 Scripts executed
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Script:
#!/bin/bash
# Description: Check if parallel-hashmap is declared as a dependency in meta.yaml
# Look for parallel-hashmap in meta.yaml
echo "Checking meta.yaml for parallel-hashmap dependency..."
rg -i "parallel-hashmap" "recipes/rdeval/meta.yaml"
# Check if parallel-hashmap headers exist in the include directory
echo "Checking for parallel-hashmap headers..."
fd -t f . "recipes/rdeval" -E "*.h" | rg -i "parallel-hashmap"
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#!/bin/bash
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echo "Checking meta.yaml for parallel-hashmap dependency..."
rg -i "parallel-hashmap" "recipes/rdeval/meta.yaml"
# Check if parallel-hashmap headers exist in the include directory
echo "Checking for parallel-hashmap headers..."
rg -i "parallel-hashmap\.h" "recipes/rdeval/include/"
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# Description: Search the entire repository for any references to parallel-hashmap.
echo "Searching for 'parallel-hashmap' in the entire codebase..."
rg -i "parallel-hashmap"
Length of output: 2649
| commands: | ||
| - rdeval --help |
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💡 Codebase verification
Binary rdeval not found in the codebase
The test command references rdeval, but no such binary exists. Please verify the correct binary name and update the test configuration accordingly.
🔗 Analysis chain
Verify binary name and enhance test coverage
The test command uses rdeval while a past review noted a different binary name genodsp. Please clarify:
- Which is the correct binary name?
- Are both binaries provided by this package?
Additionally, consider adding tests with sample data to verify core functionality.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check source code for binary names
rg -g 'Makefile*' -g '*.cpp' 'rdeval|genodsp'
# Look for example data files that could be used in tests
fd -g '*.fa' -g '*.fasta' -g '*.fastq'
Length of output: 448
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#!/bin/bash
# Check source code for binary names
rg -g 'Makefile*' -g '*.cpp' -g '*.h' 'rdeval|genodsp'
# Look for example data files that could be used in tests
fd -e fa -e fasta -e fastq
Length of output: 915
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Actionable comments posted: 4
🧹 Outside diff range and nitpick comments (1)
recipes/rdeval/foo.patch (1)
1-38: Consider enhancing Makefile robustness for conda buildsThe Makefile could benefit from several improvements to make it more robust in the conda build environment:
- Add proper dependency tracking using
.dfiles- Make paths more configurable using conda build variables
- Separate build configuration into a config file that can be easily modified by conda scripts
Would you like me to provide an example of a more robust Makefile structure suitable for conda builds?
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📒 Files selected for processing (3)
recipes/rdeval/foo.patch(1 hunks)recipes/rdeval/gfalibs.patch(1 hunks)recipes/rdeval/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/rdeval/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (10)
recipes/rdeval/gfalibs.patch (4)
6-6: LGTM! Good improvement in compiler configuration.
Using $(CXX) instead of hardcoded g++ properly respects the build environment's compiler settings, which is essential for conda builds.
Also applies to: 8-8
7-7:
Declare parallel-hashmap as a dependency.
While adding the include path for parallel-hashmap is correct, the dependency itself needs to be declared in meta.yaml.
Let's verify if the dependency has been added:
#!/bin/bash
# Description: Check if parallel-hashmap is declared in meta.yaml
echo "Checking meta.yaml for parallel-hashmap dependency..."
rg -i "parallel-hashmap" "recipes/rdeval/meta.yaml"Also applies to: 9-9
17-17: Verify pthread build requirement.
The addition of -pthread flag is correct, but ensure that the corresponding build requirement is declared in meta.yaml if needed.
Let's check the build requirements:
#!/bin/bash
# Description: Check if pthread is properly handled in meta.yaml
echo "Checking meta.yaml for pthread handling..."
rg -i "pthread|thread" "recipes/rdeval/meta.yaml"Also applies to: 18-18
26-26: 🛠️ Refactor suggestion
Refactor compilation command and verify dependencies.
Several issues need to be addressed:
- $(INCLUDE_DIR) is redundant as it's already included in CXXFLAGS
- -lz and -lpthread should be moved to LDFLAGS
- Ensure zlib is declared as a dependency in meta.yaml
Apply this diff to improve the Makefile:
-LDFLAGS := -L${PREFIX}/lib -pthread
+LDFLAGS := -L${PREFIX}/lib -pthread -lz
%.o: $(SOURCE)/%.cpp $(INCLUDE)/%.h
- $(CXX) $(CXXFLAGS) $(INCLUDE_DIR) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@ -lz -lpthread
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@Let's verify the zlib dependency:
Also applies to: 27-27
recipes/rdeval/meta.yaml (6)
1-7: LGTM!
The package metadata is well-structured and follows Conda packaging conventions.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
16-20: Verify pinning strategy
The run_exports section uses max_pin="x.x", which means dependencies will be compatible up to patch version changes. Given this is version 0.0.2, consider if this is the appropriate pinning strategy for pre-1.0 software.
Consider using max_pin="x.x.x" for pre-1.0 versions to ensure stricter compatibility, as even minor version changes might introduce breaking changes.
29-32: Enhance test coverage and verify binary name
- The test coverage is minimal. Consider adding tests that:
- Process sample input files
- Verify output format
- Test error handling
- Previous reviews noted a binary name inconsistency between
rdevalandgenodsp. Please clarify which is correct.
#!/bin/bash
# Description: Verify binary name in source code
# Check Makefile and source files for binary names
rg -g 'Makefile*' -g '*.cpp' -g '*.h' 'rdeval|genodsp'
# Check for example data that could be used in tests
fd -e fa -e fasta -e fastq33-41: Enhance package description for Bioconda context
The current summary is too brief. Since this is a Bioconda package, please:
- Expand the summary to describe specific bioinformatics applications
- Detail the types of read analysis it performs
- List key features relevant to biological data analysis
42-45: Verify platform compatibility
Please confirm that the package has been tested on the additional platforms:
- linux-aarch64
- osx-arm64
Consider:
- Are there any platform-specific dependencies?
- Have the patches been tested on all platforms?
21-28:
Add missing runtime dependencies
The recipe is missing runtime dependencies. Since you're using zlib and pthread-stubs during build, they're likely needed at runtime too.
Apply this diff:
requirements:
build:
- {{ compiler('cxx') }}
- make
host:
- pthread-stubs
- zlib
+ run:
+ - pthread-stubs
+ - zlib| source: | ||
| url: https://github.com/vgl-hub/{{ name }}/releases/download/v{{ version }}/{{ name }}.v{{ version }}-with_submodules.zip | ||
| sha256: 56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d | ||
| patches: | ||
| - zlib.patch | ||
| - foo.patch | ||
| - gfalibs.patch | ||
|
|
There was a problem hiding this comment.
💡 Codebase verification
Patch files have not been submitted upstream
The patches zlib.patch, foo.patch, and gfalibs.patch have not been submitted upstream. Please verify their necessity and consider submitting them to the upstream repository to ensure maintainability.
🔗 Analysis chain
Verify patch files and their necessity
Three patch files are specified:
- zlib.patch
- foo.patch
- gfalibs.patch
Please provide:
- A brief description of each patch's purpose in the recipe
- Confirmation that these patches have been submitted upstream
Further verify upstream submission of patch files
Please run the following script to check if the patches have been submitted upstream via pull requests or commits:
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check patch contents and related upstream issues
# Check patch contents
for patch in zlib.patch foo.patch gfalibs.patch; do
echo "=== Contents of $patch ==="
if [ -f "recipes/rdeval/$patch" ]; then
cat "recipes/rdeval/$patch"
fi
done
# Check for related upstream issues
gh api repos/vgl-hub/rdeval/issues --jq '.[] | select(.title | contains("patch") or contains("build") or contains("zlib") or contains("gfalibs")) | {title: .title, url: .html_url}'
Length of output: 4190
Script:
#!/bin/bash
# Description: Check if patches have been submitted upstream via pull requests or commits
echo "=== Checking Pull Requests for patch submissions ==="
gh pr list --repo vgl-hub/rdeval --json title,url --jq '.[] | select(.title | test("zlib.patch|foo.patch|gfalibs.patch")) | {title: .title, url: .url}'
echo "=== Checking Commit Messages for patch references ==="
gh api repos/vgl-hub/rdeval/commits --paginate --jq '.[] | select(.commit.message | test("zlib.patch|foo.patch|gfalibs.patch")) | {message: .commit.message, url: .html_url}'
Length of output: 561
| head: $(BINS) gfalibs | $(BUILD) | ||
| - $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(BUILD)/$(TARGET) $(BINDIR)/* $(GFALIBS_DIR)/*.o $(LIBS) | ||
| + $(CXX) $(CXXFLAGS) $(INCLUDE_DIR) $(LDFLAGS) -o $(BUILD)/$(TARGET) $(BINDIR)/* $(GFALIBS_DIR)/*.o $(LIBS) |
There was a problem hiding this comment.
Fix compilation and linking command issues
There are several issues with the compilation commands:
- Include paths (
$(INCLUDE_DIR)) aren't needed during linking - Libraries (
$(LIBS)) shouldn't be specified during object file compilation
Apply these fixes:
- $(CXX) $(CXXFLAGS) $(INCLUDE_DIR) $(LDFLAGS) -o $(BUILD)/$(TARGET) $(BINDIR)/* $(GFALIBS_DIR)/*.o $(LIBS)
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(BUILD)/$(TARGET) $(BINDIR)/* $(GFALIBS_DIR)/*.o $(LIBS)
- $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@ $(LIBS)
+ $(CXX) $(CXXFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@Also applies to: 33-35
| -LDFLAGS := -pthread | ||
| -LIBS = -lz | ||
| +LDFLAGS := -pthread -L${PREFIX}/lib | ||
| +LIBS := -lz -lpthread |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Fix duplicate pthread linking and variable assignment
There are two issues in the linker configuration:
-pthreadappears both inLDFLAGSandLIBS, which is redundant- Using
:=forLIBSmight override important conda build environment variables
Apply this fix:
-LDFLAGS := -pthread -L${PREFIX}/lib
-LIBS := -lz -lpthread
+LDFLAGS = -L${PREFIX}/lib
+LIBS = -lz -pthread📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| -LDFLAGS := -pthread | |
| -LIBS = -lz | |
| +LDFLAGS := -pthread -L${PREFIX}/lib | |
| +LIBS := -lz -lpthread | |
| LDFLAGS = -L${PREFIX}/lib | |
| LIBS = -lz -pthread |
| -CXX ?= g++ | ||
| -INCLUDE_DIR = -I./include -I./gfalibs/include | ||
| +CXX ?= ${CXX} | ||
| +INCLUDE_DIR = -I${PREFIX}/include -I./include -I./gfalibs/include |
There was a problem hiding this comment.
💡 Codebase verification
🛠️ Refactor suggestion
Verify the existence and necessity of the ./gfalibs/include directory
The ./gfalibs/include directory was not found, which may lead to build issues. Please ensure that this path is correct and that the necessary directories are present in the repository.
🔗 Analysis chain
Review include paths for conda build environment compatibility
While using ${CXX} and adding ${PREFIX}/include aligns with conda build practices, the relative paths ./include and ./gfalibs/include might cause issues in the conda build environment where the source directory structure could differ.
Consider using absolute paths or environment variables for all include paths:
-INCLUDE_DIR = -I${PREFIX}/include -I./include -I./gfalibs/include
+INCLUDE_DIR = -I${PREFIX}/include -I${SRC_DIR}/include -I${SRC_DIR}/gfalibs/include🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if the include directories exist in the expected locations
echo "Checking for include directories..."
fd -t d "include$"
fd -t d "gfalibs"
Length of output: 119
adding RDEVAL
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
General instructions
@BiocondaBot please add labelcommand.@bioconda/corein a comment.Instructions for avoiding API, ABI, and CLI breakage issues
Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify
run_exports(see here for the rationale and comprehensive explanation).Add a
run_exportssection like this:with
...being one of:{{ pin_subpackage("myrecipe", max_pin="x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin="x.x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin=None) }}while replacing
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