adding RDEVAL #52070
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| #!/usr/bin/env bash | ||
|
|
||
| set -o errexit | ||
| set -o nounset | ||
| set -o xtrace | ||
|
|
||
| cd "$SRC_DIR" | ||
|
|
||
| export CXXFLAGS="$CXXFLAGS -O3 -I$PREFIX/include" | ||
| export LDFLAGS="$LDFLAGS -L$PREFIX/lib" | ||
|
|
||
| make -j"${CPU_COUNT}" CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}" | ||
| install -v -m 0755 build/bin/rdeval "$PREFIX/bin/rdeval" |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| @@ -0,0 +1,38 @@ | ||||||||||||||
| diff --git a/Makefile b/Makefile | ||||||||||||||
| index 5823f28..6d448f3 100644 | ||||||||||||||
| --- a/Makefile | ||||||||||||||
| +++ b/Makefile | ||||||||||||||
| @@ -1,5 +1,5 @@ | ||||||||||||||
| -CXX ?= g++ | ||||||||||||||
| -INCLUDE_DIR = -I./include -I./gfalibs/include | ||||||||||||||
| +CXX ?= ${CXX} | ||||||||||||||
| +INCLUDE_DIR = -I${PREFIX}/include -I./include -I./gfalibs/include | ||||||||||||||
| WARNINGS = -Wall -Wextra | ||||||||||||||
|
|
||||||||||||||
| CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS) | ||||||||||||||
| @@ -12,8 +12,8 @@ SOURCE = src | ||||||||||||||
| INCLUDE = include | ||||||||||||||
| BINDIR := $(BUILD)/.o | ||||||||||||||
|
|
||||||||||||||
| -LDFLAGS := -pthread | ||||||||||||||
| -LIBS = -lz | ||||||||||||||
| +LDFLAGS := -pthread -L${PREFIX}/lib | ||||||||||||||
| +LIBS := -lz -lpthread | ||||||||||||||
|
Comment on lines
+17
to
+20
There was a problem hiding this comment. 🛠️ Refactor suggestion Fix duplicate pthread linking and variable assignment There are two issues in the linker configuration:
Apply this fix: -LDFLAGS := -pthread -L${PREFIX}/lib
-LIBS := -lz -lpthread
+LDFLAGS = -L${PREFIX}/lib
+LIBS = -lz -pthread📝 Committable suggestion
Suggested change
|
||||||||||||||
|
|
||||||||||||||
| OBJS := main input reads | ||||||||||||||
| BINS := $(addprefix $(BINDIR)/, $(OBJS)) | ||||||||||||||
| @@ -22,12 +22,12 @@ BINS := $(addprefix $(BINDIR)/, $(OBJS)) | ||||||||||||||
| GFALIBS_DIR := $(CURDIR)/gfalibs | ||||||||||||||
|
|
||||||||||||||
| 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) | ||||||||||||||
|
Comment on lines
+27
to
+29
There was a problem hiding this comment. Fix compilation and linking command issues There are several issues with the compilation commands:
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 |
||||||||||||||
|
|
||||||||||||||
| all: head validate regenerate | ||||||||||||||
|
|
||||||||||||||
| $(BINDIR)%: $(SOURCE)/%.cpp $(INCLUDE)/%.h | $(BINDIR) | ||||||||||||||
| - $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@ | ||||||||||||||
| + $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@ $(LIBS) | ||||||||||||||
|
|
||||||||||||||
| .PHONY: gfalibs | ||||||||||||||
| gfalibs: | ||||||||||||||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| diff --git a/gfalibs/Makefile b/gfalibs/Makefile | ||
| index de9ab9b..90a703c 100644 | ||
| --- a/gfalibs/Makefile | ||
| +++ b/gfalibs/Makefile | ||
| @@ -1,5 +1,5 @@ | ||
| -CXX = g++ | ||
| -INCLUDE_DIR = -I./include | ||
|
There was a problem hiding this comment. 💡 Codebase verification parallel-hashmap dependency not declared in meta.yaml. The addition of 🔗 Analysis chainVerify parallel-hashmap dependency. The addition of Also applies to: 9-9 🏁 Scripts executedThe following scripts were executed for the analysis: 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"
Length of output: 387 Script: #!/bin/bash
# Description: Verify if parallel-hashmap is declared as a dependency in meta.yaml and check for its headers.
# 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..."
rg -i "parallel-hashmap\.h" "recipes/rdeval/include/"
Length of output: 375 Script: #!/bin/bash
# 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 |
||
| +CXX = $(CXX) | ||
| +INCLUDE_DIR = -I${PREFIX}/include -I./include -I./include/parallel-hashmap | ||
| WARNINGS = -Wall -Wextra | ||
|
|
||
| CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS) | ||
| @@ -8,7 +8,7 @@ TARGET = gfalibs | ||
| BUILD = build/bin | ||
| SOURCE = src | ||
| INCLUDE = include | ||
| -LDFLAGS := | ||
| +LDFLAGS := -L${PREFIX}/lib -pthread | ||
|
|
||
| SOURCES = $(addsuffix .o, input-filters input-gfa input-agp gfa gfa-lines log stream-obj uid-generator struct output memory) | ||
|
|
||
| @@ -16,7 +16,7 @@ all: $(SOURCES) | ||
| @ | ||
|
|
||
| %.o: $(SOURCE)/%.cpp $(INCLUDE)/%.h | ||
| - $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@ | ||
| + $(CXX) $(CXXFLAGS) $(INCLUDE_DIR) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@ -lz -lpthread | ||
|
|
||
| clean: | ||
| $(RM) *.o | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| {% set name = "rdeval" %} | ||
| {% set version = "0.0.2" %} | ||
|
|
||
| package: | ||
| name: {{ name|lower }} | ||
| version: {{ version }} | ||
|
|
||
| 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 | ||
|
|
||
|
Comment on lines
+8
to
+15
There was a problem hiding this comment. 💡 Codebase verification Patch files have not been submitted upstream The patches 🔗 Analysis chainVerify patch files and their necessity Three patch files are specified:
Please provide:
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 executedThe 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 |
||
| build: | ||
| number: 0 | ||
| run_exports: | ||
| - {{ pin_subpackage(name|lower, max_pin="x.x") }} | ||
|
|
||
| requirements: | ||
| build: | ||
| - {{ compiler('cxx') }} | ||
| - make | ||
| host: | ||
| - pthread-stubs | ||
| - zlib | ||
|
|
||
| test: | ||
| commands: | ||
| - rdeval --help | ||
|
Comment on lines
+30
to
+31
There was a problem hiding this comment. 💡 Codebase verification Binary The test command references 🔗 Analysis chainVerify binary name and enhance test coverage The test command uses
Additionally, consider adding tests with sample data to verify core functionality. 🏁 Scripts executedThe 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 Script: #!/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 |
||
|
|
||
| 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 | ||
| dev_url: https://github.com/vgl-hub/{{ name }} | ||
| doc_url: https://github.com/vgl-hub/rdeval/blob/v{{ version }}/README.md | ||
|
|
||
| extra: | ||
| additional-platforms: | ||
| - linux-aarch64 | ||
| - osx-arm64 | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,52 @@ | ||
| diff --git a/gfalibs/include/output.h b/gfalibs/include/output.h | ||
| index aabbec0..20f0dc1 100644 | ||
| --- a/gfalibs/include/output.h | ||
| +++ b/gfalibs/include/output.h | ||
| @@ -12,7 +12,7 @@ | ||
| #include "gfa-lines.h" | ||
| #include "gfa.h" | ||
|
|
||
| -#include "zlib.h" | ||
| +#include <zlib.h> | ||
| #include "zstream/zstream_common.hpp" | ||
| #include "zstream/ozstream.hpp" | ||
| #include "zstream/ozstream_impl.hpp" | ||
| diff --git a/gfalibs/include/stream-obj.h b/gfalibs/include/stream-obj.h | ||
| index 1faa4df..8e28bf6 100644 | ||
| --- a/gfalibs/include/stream-obj.h | ||
| +++ b/gfalibs/include/stream-obj.h | ||
| @@ -2,7 +2,7 @@ | ||
| #define STREAM_OBJ_H | ||
|
|
||
| #include <fstream> | ||
| -#include "zlib.h" | ||
| +#include <zlib.h> | ||
|
|
||
| class membuf : public std::streambuf { | ||
|
|
||
| diff --git a/gfalibs/src/stream-obj.cpp b/gfalibs/src/stream-obj.cpp | ||
| index e9694ee..c6eca26 100644 | ||
| --- a/gfalibs/src/stream-obj.cpp | ||
| +++ b/gfalibs/src/stream-obj.cpp | ||
| @@ -5,7 +5,7 @@ | ||
|
|
||
| #include "bed.h" | ||
| #include "struct.h" | ||
| -#include "zlib.h" | ||
| +#include <zlib.h> | ||
| #include "global.h" | ||
| #include "log.h" | ||
| #include "threadpool.h" | ||
| diff --git a/src/reads.cpp b/src/reads.cpp | ||
| index 866f49b..ac714cf 100644 | ||
| --- a/src/reads.cpp | ||
| +++ b/src/reads.cpp | ||
| @@ -14,7 +14,7 @@ | ||
| #include "functions.h" // global functions | ||
| #include "stream-obj.h" | ||
|
|
||
| -#include "zlib.h" | ||
| +#include <zlib.h> | ||
| #include "zstream/zstream_common.hpp" | ||
| #include "zstream/ozstream.hpp" | ||
| #include "zstream/ozstream_impl.hpp" |
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
💡 Codebase verification
🛠️ Refactor suggestion
Verify the existence and necessity of the
./gfalibs/includedirectoryThe
./gfalibs/includedirectory 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}/includealigns with conda build practices, the relative paths./includeand./gfalibs/includemight 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:
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
Length of output: 119