Bwa-mem2: fix compilation issue (#380725)
This commit is contained in:
Gaétan Lepage
@@ -0,0 +1,42 @@
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diff --git a/Makefile b/Makefile
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index 359585f..13ec279 100644
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--- a/Makefile
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+++ b/Makefile
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@@ -49,7 +49,6 @@ OBJS= src/fastmap.o src/bwtindex.o src/utils.o src/memcpy_bwamem.o src/kthread.
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src/FMI_search.o src/read_index_ele.o src/bwamem_pair.o src/kswv.o src/bwa.o \
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src/bwamem_extra.o src/kopen.o
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BWA_LIB= libbwa.a
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-SAFE_STR_LIB= ext/safestringlib/libsafestring.a
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ifeq ($(arch),sse41)
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ifeq ($(CXX), icpc)
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@@ -101,16 +100,6 @@ CXXFLAGS+= -g -O3 -fpermissive $(ARCH_FLAGS) #-Wall ##-xSSE2
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all:$(EXE)
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multi:
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- rm -f src/*.o $(BWA_LIB); cd ext/safestringlib/ && $(MAKE) clean;
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- $(MAKE) arch=sse41 EXE=bwa-mem2.sse41 CXX=$(CXX) all
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- rm -f src/*.o $(BWA_LIB); cd ext/safestringlib/ && $(MAKE) clean;
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- $(MAKE) arch=sse42 EXE=bwa-mem2.sse42 CXX=$(CXX) all
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- rm -f src/*.o $(BWA_LIB); cd ext/safestringlib/ && $(MAKE) clean;
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- $(MAKE) arch=avx EXE=bwa-mem2.avx CXX=$(CXX) all
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- rm -f src/*.o $(BWA_LIB); cd ext/safestringlib/ && $(MAKE) clean;
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- $(MAKE) arch=avx2 EXE=bwa-mem2.avx2 CXX=$(CXX) all
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- rm -f src/*.o $(BWA_LIB); cd ext/safestringlib/ && $(MAKE) clean;
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- $(MAKE) arch=avx512 EXE=bwa-mem2.avx512bw CXX=$(CXX) all
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$(CXX) -Wall -O3 src/runsimd.cpp -Iext/safestringlib/include -Lext/safestringlib/ -lsafestring $(STATIC_GCC) -o bwa-mem2
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@@ -120,12 +109,8 @@ $(EXE):$(BWA_LIB) $(SAFE_STR_LIB) src/main.o
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$(BWA_LIB):$(OBJS)
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ar rcs $(BWA_LIB) $(OBJS)
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-$(SAFE_STR_LIB):
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- cd ext/safestringlib/ && $(MAKE) clean && $(MAKE) CC=$(CC) directories libsafestring.a
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-
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clean:
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rm -fr src/*.o $(BWA_LIB) $(EXE) bwa-mem2.sse41 bwa-mem2.sse42 bwa-mem2.avx bwa-mem2.avx2 bwa-mem2.avx512bw
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- cd ext/safestringlib/ && $(MAKE) clean
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depend:
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(LC_ALL=C; export LC_ALL; makedepend -Y -- $(CXXFLAGS) $(CPPFLAGS) -I. -- src/*.cpp)
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@@ -2,6 +2,7 @@
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lib,
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stdenv,
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fetchFromGitHub,
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safestringlib,
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zlib,
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}:
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@@ -13,21 +14,11 @@ stdenv.mkDerivation (finalAttrs: {
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owner = "bwa-mem2";
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repo = "bwa-mem2";
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rev = "cf4306a47dac35e7e79a9e75398a35f33900cfd0";
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fetchSubmodules = true;
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hash = "sha256-1AYSn7nBrDwbX7oSrdEoa1d3t6xzwKnA0S87Y/XeXJg=";
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hash = "sha256-hY8nLRFWt0GAElhDIcYdUX6cJrzOE3NlYRQr0tC3on4=";
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};
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buildInputs = [ zlib ];
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# see https://github.com/bwa-mem2/bwa-mem2/issues/93
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postPatch = lib.optionalString stdenv.hostPlatform.isDarwin ''
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sed -i 's/memset_s/memset8_s/g' ext/safestringlib/include/safe_mem_lib.h
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sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/memset16_s.c
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sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/memset32_s.c
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sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/memset_s.c
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sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/wmemset_s.c
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'';
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buildFlags = [
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(
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if stdenv.hostPlatform.sse4_2Support then
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@@ -43,14 +34,45 @@ stdenv.mkDerivation (finalAttrs: {
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)
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];
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env = lib.optionalAttrs stdenv.hostPlatform.isDarwin {
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NIX_CFLAGS_COMPILE = toString [
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patches = [
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./no-submodule.patch
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];
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# Also, patch the tests
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postPatch =
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# Force path to static link, otherwise, it fails at runtime to
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# find the shared library
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''
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substituteInPlace Makefile \
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--replace-fail "-Iext/safestringlib/include" "-I${safestringlib}/include" \
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--replace-fail "-Lext/safestringlib" "-L${safestringlib}/lib"
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''
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# Make test compile by changing the compiler and path to library
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# Remove xeonbsw test that fails to compile due to missing _rdsc
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# also, not portable
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+ ''
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substituteInPlace test/Makefile \
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--replace-fail "icpc" "g++" \
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--replace-fail "../ext/safestringlib/libsafestring.a" \
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"${safestringlib}/lib/libsafestring.a" \
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--replace-fail \
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"fmi_test smem2_test bwt_seed_strategy_test sa2ref_test xeonbsw" \
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"fmi_test smem2_test bwt_seed_strategy_test sa2ref_test"
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'';
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env.NIX_CFLAGS_COMPILE = toString (
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lib.optionals stdenv.hostPlatform.isDarwin [
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"-Wno-error=register"
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"-Wno-error=implicit-function-declaration"
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];
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};
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]
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);
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nativeBuildInputs = [
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safestringlib
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];
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enableParallelBuilding = true;
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installPhase = ''
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runHook preInstall
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@@ -67,6 +89,6 @@ stdenv.mkDerivation (finalAttrs: {
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homepage = "https://github.com/bwa-mem2/bwa-mem2/";
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changelog = "https://github.com/bwa-mem2/bwa-mem2/blob/${finalAttrs.src.rev}/NEWS.md";
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platforms = platforms.x86_64;
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maintainers = with maintainers; [ alxsimon ];
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maintainers = with maintainers; [ apraga ];
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};
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})
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@@ -0,0 +1,78 @@
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{
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lib,
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stdenv,
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cmake,
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fetchFromGitHub,
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fetchpatch,
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}:
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stdenv.mkDerivation {
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pname = "safestringlib";
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# Latest release is 1.2.0 and has compilation issues
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version = "1.2.0-unstable-2024-10-21";
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src = fetchFromGitHub {
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owner = "intel";
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repo = "safestringlib";
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rev = "e99c03cfafdce5311c4dbf1fd3f916ccc6e300be";
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hash = "sha256-d+6YDtMtdaS2eW0eIfuwzdQRiExsoexL3fKj7C2zENM=";
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};
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outputs = [
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"out"
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];
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nativeBuildInputs = [ cmake ];
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cmakeFlags = [
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(lib.cmakeBool "BUILD_UNITTESTS" true)
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];
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patches = [
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# https://github.com/intel/safestringlib/issues/74
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(fetchpatch {
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name = "darwin-fix";
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url = "https://github.com/intel/safestringlib/pull/75/commits/3ff9c6234be7dd4ee1dd5cdc2ccbb2c7541adfec.patch";
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hash = "sha256-4HS7XyKPQSmKczaMCi1s6NxgTNzRZXTds2CXBTbpuAM=";
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})
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];
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# see https://github.com/bwa-mem2/bwa-mem2/issues/93
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# Skip wmemset too
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postPatch = lib.optionalString stdenv.hostPlatform.isDarwin ''
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sed -i 's/memset_s/memset8_s/g' include/safe_mem_lib.h
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sed -i 's/memset_s/memset8_s/g' safeclib/memset16_s.c
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sed -i 's/memset_s/memset8_s/g' safeclib/memset32_s.c
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sed -i 's/memset_s/memset8_s/g' safeclib/memset_s.c
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sed -i 's/memset_s/memset8_s/g' safeclib/wmemset_s.c
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sed -i 's/ memset_s/ memset8_s/g' unittests/*.c
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sed -i 's/ wmemset_s/ wmemset8_s/g' unittests/*.c
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'';
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checkPhase = ''
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runHook preCheck
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cd unittests
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./safestring_test
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runHook postCheck
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'';
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doCheck = true;
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installPhase = ''
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runHook preInstall
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mkdir -p $out/lib
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cp ../libsafestring_static.a $out/lib/libsafestring.a
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mkdir -p $out/
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cp -r ../../include $out/
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runHook postInstall
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'';
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meta = {
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homepage = "https://github.com/intel/safestringlib";
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description = "Safer replacements for C library functions that prevent serious security vulnerabilities";
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license = lib.licenses.mit;
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platforms = lib.platforms.unix;
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maintainers = with lib.maintainers; [ apraga ];
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};
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}
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