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nicolaasuninicolaasuni
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fix: handle paths containing spaces in Makefiles
1 parent 1cec84e commit b24bacc

19 files changed

Lines changed: 591 additions & 74 deletions

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‎.github/FUNDING.yml‎

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This file was deleted.

‎.github/workflows/check.yml‎

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@@ -20,7 +20,7 @@ jobs:
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runs-on: ubuntu-latest
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steps:
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- name: checkout repository
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uses: actions/checkout@v6
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uses: actions/checkout@v7
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- name: install dependencies
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run: sudo apt install -y lcov astyle
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- name: set RELEASE number
@@ -37,7 +37,7 @@ jobs:
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runs-on: ubuntu-latest
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steps:
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- name: checkout repository
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uses: actions/checkout@v6
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uses: actions/checkout@v7
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- name: setup go build environment
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uses: actions/setup-go@v6
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with:
@@ -52,7 +52,7 @@ jobs:
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runs-on: ubuntu-latest
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steps:
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- name: checkout repository
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uses: actions/checkout@v6
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uses: actions/checkout@v7
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- name: setup node build environment
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uses: actions/setup-node@v6
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with:
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runs-on: ubuntu-latest
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steps:
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- name: checkout repository
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uses: actions/checkout@v6
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uses: actions/checkout@v7
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- name: setup python build environment
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uses: actions/setup-python@v6
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with:
@@ -86,7 +86,7 @@ jobs:
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runs-on: ubuntu-latest
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steps:
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- name: checkout repository
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uses: actions/checkout@v6
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uses: actions/checkout@v7
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- name: setup python build environment
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uses: actions/setup-python@v6
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with:
@@ -104,7 +104,7 @@ jobs:
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runs-on: ubuntu-latest
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steps:
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- name: checkout repository
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uses: actions/checkout@v6
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uses: actions/checkout@v7
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- name: setup R build environment
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uses: r-lib/actions/setup-r@v2
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- name: Install dependencies

‎.github/workflows/codeql.yml‎

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@@ -60,7 +60,7 @@ jobs:
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# your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
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steps:
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- name: Checkout repository
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uses: actions/checkout@v6
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uses: actions/checkout@v7
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# Initializes the CodeQL tools for scanning.
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- name: Initialize CodeQL

‎.github/workflows/dependency-review.yml‎

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@@ -15,6 +15,6 @@ jobs:
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runs-on: ubuntu-latest
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steps:
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- name: 'Checkout Repository'
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uses: actions/checkout@v6
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uses: actions/checkout@v7
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- name: 'Dependency Review'
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uses: actions/dependency-review-action@v4

‎Makefile‎

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Original file line numberDiff line numberDiff line change
@@ -29,10 +29,10 @@ VERSION=$(shell cat VERSION)
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RELEASE=$(shell cat RELEASE)
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# Current directory
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CURRENTDIR=$(dir $(realpath $(firstword $(MAKEFILE_LIST))))
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CURRENTDIR=$(CURDIR)/
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# Target directory
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TARGETDIR=$(CURRENTDIR)target
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TARGETDIR=target
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# Docker command
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ifeq ($(DOCKER),)
@@ -97,16 +97,16 @@ clean:
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## Build everything inside a Docker container
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.PHONY: dbuild
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dbuild: dockerdev
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@mkdir -p $(TARGETDIR)
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@rm -rf $(TARGETDIR)/*
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@echo 0 > $(TARGETDIR)/make.exit
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CVSPATH=$(CVSPATH) VENDOR=$(LCVENDOR) PROJECT=$(PROJECT) MAKETARGET='$(MAKETARGET)' $(CURRENTDIR)dockerbuild.sh
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@mkdir -p "$(TARGETDIR)"
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@rm -rf "$(TARGETDIR)/"*
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@echo 0 > "$(TARGETDIR)/make.exit"
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CVSPATH=$(CVSPATH) VENDOR=$(LCVENDOR) PROJECT=$(PROJECT) MAKETARGET='$(MAKETARGET)' "$(CURRENTDIR)dockerbuild.sh"
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@exit `cat $(TARGETDIR)/make.exit`
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## Build a base development Docker image
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.PHONY: dockerdev
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dockerdev:
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$(DOCKER) build --pull --tag ${LCVENDOR}/dev_${PROJECT} --file ./resources/docker/Dockerfile.dev ./resources/docker/
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$(DOCKER) build --pull --tag "${LCVENDOR}/dev_${PROJECT}" --file ./resources/docker/Dockerfile.dev ./resources/docker/
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## Publish Documentation in GitHub (requires writing permissions)
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.PHONY: pubdocs

‎VERSION‎

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Original file line numberDiff line numberDiff line change
@@ -1 +1 @@
1-
5.7.29
1+
5.7.30

‎c/Makefile‎

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Original file line numberDiff line numberDiff line change
@@ -26,7 +26,7 @@ VERSION=$(shell cat ../VERSION)
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RELEASE=$(shell cat ../RELEASE)
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# Current directory
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CURRENTDIR=$(dir $(realpath $(firstword $(MAKEFILE_LIST))))
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CURRENTDIR=$(CURDIR)/
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# Name of RPM or DEB package
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PKGNAME=${VENDOR}-${PROJECT}-headers
@@ -158,26 +158,27 @@ clean:
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## Install this application
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.PHONY: install
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install: uninstall
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mkdir -p $(PATHINSTLIB)
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cp src/variantkey/*.h $(PATHINSTLIB)
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find $(PATHINSTLIB) -type f -exec chmod 644 {} \;
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mkdir -p $(PATHINSTDOC)
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cp -f ../LICENSE $(PATHINSTDOC)
166-
cp -f ../README.md $(PATHINSTDOC)
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cp -f ../VERSION $(PATHINSTDOC)
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cp -f ../RELEASE $(PATHINSTDOC)
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chmod -R 644 $(PATHINSTDOC)*
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mkdir -p "$(PATHINSTLIB)"
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cp src/variantkey/*.h "$(PATHINSTLIB)"
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find "$(PATHINSTLIB)" -type f -exec chmod 644 {} \;
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mkdir -p "$(PATHINSTDOC)"
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cp -f ../LICENSE "$(PATHINSTDOC)"
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cp -f ../README.md "$(PATHINSTDOC)"
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cp -f ../VERSION "$(PATHINSTDOC)"
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cp -f ../RELEASE "$(PATHINSTDOC)"
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chmod -R 644 "$(PATHINSTDOC)"*
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## Remove all installed files (excluding configuration files)
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.PHONY: uninstall
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uninstall:
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rm -rf $(PATHINSTLIB)
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rm -rf $(PATHINSTDOC)
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rm -rf "$(PATHINSTLIB)"
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rm -rf "$(PATHINSTDOC)"
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## Build the RPM package for RedHat-like Linux distributions
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.PHONY: rpm
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rpm:
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rm -rf $(PATHRPMPKG)
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@test $(words $(CURDIR)) -eq 1 || { echo "ERROR: rpmbuild does not support spaces in the project path: $(CURDIR)"; exit 1; }
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rm -rf "$(PATHRPMPKG)"
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rpmbuild \
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--define "_topdir $(PATHRPMPKG)" \
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--define "_vendor $(VENDOR)" \
@@ -194,18 +195,18 @@ rpm:
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## Build the DEB package for Debian-like Linux distributions
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.PHONY: deb
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deb:
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rm -rf $(PATHDEBPKG)
198-
make install DESTDIR=$(PATHDEBPKG)/$(PKGNAME)-$(VERSION)
199-
rm -f $(PATHDEBPKG)/$(PKGNAME)-$(VERSION)/$(DOCPATH)LICENSE
200-
tar -zcvf $(PATHDEBPKG)/$(PKGNAME)_$(VERSION).orig.tar.gz -C $(PATHDEBPKG)/ $(PKGNAME)-$(VERSION)
201-
cp -rf ./resources/debian $(PATHDEBPKG)/$(PKGNAME)-$(VERSION)/debian
202-
find $(PATHDEBPKG)/$(PKGNAME)-$(VERSION)/debian/ -type f -exec sed $(SEDINPLACE) "s/~#DATE#~/`date -R`/" {} \;
203-
find $(PATHDEBPKG)/$(PKGNAME)-$(VERSION)/debian/ -type f -exec sed $(SEDINPLACE) "s/~#PKGNAME#~/$(PKGNAME)/" {} \;
204-
find $(PATHDEBPKG)/$(PKGNAME)-$(VERSION)/debian/ -type f -exec sed $(SEDINPLACE) "s/~#VERSION#~/$(VERSION)/" {} \;
205-
find $(PATHDEBPKG)/$(PKGNAME)-$(VERSION)/debian/ -type f -exec sed $(SEDINPLACE) "s/~#RELEASE#~/$(RELEASE)/" {} \;
206-
echo $(LIBPATH) > $(PATHDEBPKG)/$(PKGNAME)-$(VERSION)/debian/$(PKGNAME).dirs
207-
echo "$(LIBPATH)* $(LIBPATH)" > $(PATHDEBPKG)/$(PKGNAME)-$(VERSION)/debian/install
208-
echo $(DOCPATH) >> $(PATHDEBPKG)/$(PKGNAME)-$(VERSION)/debian/$(PKGNAME).dirs
209-
echo "$(DOCPATH)* $(DOCPATH)" >> $(PATHDEBPKG)/$(PKGNAME)-$(VERSION)/debian/install
210-
echo "new-package-should-close-itp-bug" >> $(PATHDEBPKG)/$(PKGNAME)-$(VERSION)/debian/$(PKGNAME).lintian-overrides
211-
cd $(PATHDEBPKG)/$(PKGNAME)-$(VERSION) && debuild -us -uc
198+
rm -rf "$(PATHDEBPKG)"
199+
make install DESTDIR="$(PATHDEBPKG)/$(PKGNAME)-$(VERSION)"
200+
rm -f "$(PATHDEBPKG)/$(PKGNAME)-$(VERSION)/$(DOCPATH)LICENSE"
201+
tar -zcvf "$(PATHDEBPKG)/$(PKGNAME)_$(VERSION).orig.tar.gz" -C "$(PATHDEBPKG)/" "$(PKGNAME)-$(VERSION)"
202+
cp -rf ./resources/debian "$(PATHDEBPKG)/$(PKGNAME)-$(VERSION)/debian"
203+
find "$(PATHDEBPKG)/$(PKGNAME)-$(VERSION)/debian/" -type f -exec sed $(SEDINPLACE) "s/~#DATE#~/`date -R`/" {} \;
204+
find "$(PATHDEBPKG)/$(PKGNAME)-$(VERSION)/debian/" -type f -exec sed $(SEDINPLACE) "s/~#PKGNAME#~/$(PKGNAME)/" {} \;
205+
find "$(PATHDEBPKG)/$(PKGNAME)-$(VERSION)/debian/" -type f -exec sed $(SEDINPLACE) "s/~#VERSION#~/$(VERSION)/" {} \;
206+
find "$(PATHDEBPKG)/$(PKGNAME)-$(VERSION)/debian/" -type f -exec sed $(SEDINPLACE) "s/~#RELEASE#~/$(RELEASE)/" {} \;
207+
echo "$(LIBPATH)" > "$(PATHDEBPKG)/$(PKGNAME)-$(VERSION)/debian/$(PKGNAME).dirs"
208+
echo "$(LIBPATH)* $(LIBPATH)" > "$(PATHDEBPKG)/$(PKGNAME)-$(VERSION)/debian/install"
209+
echo "$(DOCPATH)" >> "$(PATHDEBPKG)/$(PKGNAME)-$(VERSION)/debian/$(PKGNAME).dirs"
210+
echo "$(DOCPATH)* $(DOCPATH)" >> "$(PATHDEBPKG)/$(PKGNAME)-$(VERSION)/debian/install"
211+
echo "new-package-should-close-itp-bug" >> "$(PATHDEBPKG)/$(PKGNAME)-$(VERSION)/debian/$(PKGNAME).lintian-overrides"
212+
cd "$(PATHDEBPKG)/$(PKGNAME)-$(VERSION)" && debuild -us -uc

‎c/doc/Doxyfile‎

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Original file line numberDiff line numberDiff line change
@@ -32,7 +32,7 @@ PROJECT_NAME = "VariantKey"
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# This could be handy for archiving the generated documentation or
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# if some version control system is used.
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35-
PROJECT_NUMBER = 5.7.29
35+
PROJECT_NUMBER = 5.7.30
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# Using the PROJECT_BRIEF tag one can provide an optional one line description
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# for a project that appears at the top of each page and should give viewer

‎c/resources/rpm/rpm.spec‎

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Original file line numberDiff line numberDiff line change
@@ -28,8 +28,8 @@ ESID, a reversible numerical encoding schema for genetic string identifiers.
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#(cd %{_current_directory} && make build)
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%install
31-
rm -rf $RPM_BUILD_ROOT
32-
(cd %{_current_directory} && make install DESTDIR=$RPM_BUILD_ROOT)
31+
rm -rf "$RPM_BUILD_ROOT"
32+
(cd "%{_current_directory}" && make install DESTDIR="$RPM_BUILD_ROOT")
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#%clean
3535
#rm -rf $RPM_BUILD_ROOT

‎c/test/rsidvar_bench/CMakeLists.txt‎

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@@ -9,3 +9,6 @@ include_directories(${CMAKE_CURRENT_BINARY_DIR} ${PROJECT_BINARY_DIR}/src/varian
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file(COPY DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
1010
add_executable(rsidvar_bench rsidvar_bench.c)
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target_link_libraries(rsidvar_bench variantkey)
12+
13+
add_executable(vk_csv_lookup_bench vk_csv_lookup_bench.c)
14+
target_link_libraries(vk_csv_lookup_bench variantkey)

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