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Build bindash on osx #51661

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merged 1 commit into from
Oct 25, 2024
Merged

Build bindash on osx #51661

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20 changes: 19 additions & 1 deletion recipes/bindash/build.sh
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Original file line number Diff line number Diff line change
@@ -1,7 +1,25 @@
#!/bin/bash

export INCLUDES="-I${PREFIX}/include"
export LIBPATH="-L${PREFIX}/lib"
export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"

mkdir release && pushd release
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⚠️ Potential issue

Add error handling for directory operations.

The pushd command should handle potential failures to prevent silent build errors.

Apply this diff to add error handling:

-mkdir release && pushd release
+mkdir release || exit 1
+pushd release || exit 1
📝 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.

Suggested change
mkdir release && pushd release
mkdir release || exit 1
pushd release || exit 1
🧰 Tools
🪛 Shellcheck

[warning] 7-7: Use 'pushd ... || exit' or 'pushd ... || return' in case pushd fails.

(SC2164)

cmake -DCMAKE_BUILD_TYPE=Release ..

if [[ `uname` == "Darwin" ]]; then
export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
else
export CONFIG_ARGS=""
fi

cmake -S .. -B . -DCMAKE_BUILD_TYPE=Release \
-DCMAKE_INSTALL_PREFIX="${PREFIX}" \
-DCMAKE_CXX_COMPILER="${CXX}" \
-DCMAKE_CXX_FLAGS="${CXXFLAGS} -O3 -std=c++14 -I${PREFIX}/include" \
"${CONFIG_ARGS}"

make VERBOSE=1 -j ${CPU_COUNT}

install -d $PREFIX/bin
install bindash $PREFIX/bin
popd
12 changes: 6 additions & 6 deletions recipes/bindash/meta.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,8 +10,7 @@ source:
sha256: 6e4bf36fd04195ed0738ea8bf835eca1e400b5ce6eef3902bdf0673955d15166

build:
skip: True # [osx]
number: 2
number: 3
run_exports:
- {{ pin_subpackage('bindash', max_pin="x") }}

Expand All @@ -25,7 +24,6 @@ requirements:
- libgomp # [linux]
- llvm-openmp # [osx]
run:
- zlib
- libgomp # [linux]
- llvm-openmp # [osx]

Expand All @@ -34,16 +32,18 @@ test:
- bindash --help 2>&1 | grep sketch

about:
home: https://github.com/zhaoxiaofei/bindash
license: Apache-2.0
home: "https://github.com/zhaoxiaofei/bindash"
license: "Apache-2.0"
Comment on lines +35 to +36
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💡 Codebase verification

Update documentation URLs to point to the original repository

The verification shows that jianshu93/bindash is a fork of zhaoxiaofei/bindash (the original repository). For consistency and long-term maintainability, all URLs should point to the original repository since:

  • zhaoxiaofei/bindash is the parent repository
  • jianshu93/bindash is marked as a fork
  • The README exists in both repositories

Please update the doc_url to point to the original repository: "https://github.com/zhaoxiaofei/bindash/blob/v2.3/README.md"

🔗 Analysis chain

Verify repository relationships and documentation links

The URLs point to different repositories:

  • home/dev_url: "zhaoxiaofei/bindash"
  • doc_url: "jianshu93/bindash"

This could lead to documentation inconsistencies or broken links if the repositories get out of sync.

Also applies to: 40-41

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify repository relationships and README existence

# Check if both repositories exist and their relationship
gh repo view zhaoxiaofei/bindash --json parent,isFork,defaultBranchRef
gh repo view jianshu93/bindash --json parent,isFork,defaultBranchRef

# Verify README existence at the specified version
gh api repos/jianshu93/bindash/contents/README.md?ref=v2.3 --jq '.sha'

Length of output: 506

license_family: APACHE
license_file: LICENSE
summary: "Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop."
dev_url: https://github.com/zhaoxiaofei/bindash
dev_url: "https://github.com/zhaoxiaofei/bindash"
doc_url: "https://github.com/jianshu93/bindash/blob/v{{ version }}/README.md"

extra:
additional-platforms:
- linux-aarch64
- osx-arm64
identifiers:
- doi:10.1093/bioinformatics/bty651
- doi:10.1101/2024.03.13.584875
Expand Down