bolt-llm: Test association between phenotype and genotypes
This commit is contained in:
Jason Bacon
parent
d9992a9107
commit
d1fcda1329
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The BOLT-LMM algorithm computes statistics for testing association between
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phenotype and genotypes using a linear mixed model (LMM) [1]. By default,
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BOLT-LMM assumes a Bayesian mixture-of-normals prior for the random effect
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attributed to SNPs other than the one being tested.
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# $NetBSD$
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#
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###########################################################
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# Generated by fbsd2pkg #
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# Wed Sep 20 05:34:25 CDT 2017 #
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###########################################################
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DISTNAME= BOLT-LMM_v${PORTVERSION}
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PKGNAME= bolt-llm-${PORTVERSION}
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CATEGORIES= biology
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MASTER_SITES= https://data.broadinstitute.org/alkesgroup/BOLT-LMM/downloads/
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MAINTAINER= bacon4000@gmail.com
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HOMEPAGE= https://data.broadinstitute.org/alkesgroup/BOLT-LMM/
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COMMENT= Statistics for testing association between phenotype and genotypes
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# Check this
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LICENSE= gnu-gpl-v3
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USE_LANGUAGES= c c++ fortran
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USE_TOOLS+= gmake
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WRKSRC= ${WRKDIR}/${DISTNAME}/src
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CXXFLAGS= -fopenmp
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BUILD_TARGET= bolt
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PORTVERSION= 2.3
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INSTALLATION_DIRS= bin
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# FIXME: Use openblas when available for better performance
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.include "../../math/nlopt/buildlink3.mk"
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.include "../../math/blas/buildlink3.mk"
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.include "../../math/lapack/buildlink3.mk"
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.include "../../devel/boost-libs/buildlink3.mk"
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.include "../../devel/zlib/buildlink3.mk"
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.include "../../mk/bsd.pkg.mk"
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@ -0,0 +1,2 @@
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@comment $NetBSD$
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bin/bolt
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@ -0,0 +1,9 @@
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$NetBSD$
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SHA1 (BOLT-LMM_v2.3.tar.gz) = 4f2caf427cbcbe58175e6e5c711c3d8b0c66a9d6
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RMD160 (BOLT-LMM_v2.3.tar.gz) = d0d207f2993d00607f256edb0e9cda57aa0bd800
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SHA512 (BOLT-LMM_v2.3.tar.gz) = a396bb6699fbb87327901a8db46faa45705405160f318796f887b8cd6edd495f10fa460201a4eead57b2bc34adb45f44d26dd59ae12ed2240d4d46b6b6e959e6
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Size (BOLT-LMM_v2.3.tar.gz) = 336986328 bytes
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SHA1 (patch-FileUtils.cpp) = 258138822f610ab38f9cf3cf0ad03ca49b67ad1c
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SHA1 (patch-Makefile) = f960889320bdcd8e158cd509ae87b65672169ed5
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SHA1 (patch-StringUtils.cpp) = f0a5c3375a95391235d85fc9431524236e39910f
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@ -0,0 +1,14 @@
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$NetBSD$
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# Unused variable
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--- FileUtils.cpp.orig 2017-09-20 10:29:18 UTC
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+++ FileUtils.cpp
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@@ -275,7 +275,7 @@ namespace FileUtils {
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uint Layout = (flags>>2)&0xf; cout << "Layout: " << Layout << endl;
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assert(Layout==1 || Layout==2); // REQUIRE Layout==1 or Layout==2
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- uint SampleIdentifiers = flags>>31; //cout << "SampleIdentifiers: " << SampleIdentifiers << endl;
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+ // uint SampleIdentifiers = flags>>31; cout << "SampleIdentifiers: " << SampleIdentifiers << endl;
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fseek(fin, offset+4, SEEK_SET);
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// check first SNP
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@ -0,0 +1,118 @@
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$NetBSD$
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# Respect env
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--- Makefile.orig 2017-08-03 00:14:08.000000000 +0000
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+++ Makefile
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@@ -1,28 +1,33 @@
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### modify these paths to local Boost and NLopt install directories
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-BOOST_INSTALL_DIR = /home/pl88/boost_1_58_0/install
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-NLOPT_INSTALL_DIR = /groups/price/poru/HSPH_SVN/src/BOLT-LMM/nlopt-2.4.2
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+BOOST_INSTALL_DIR ?= ${LOCALBASE}
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+# NLOPT_INSTALL_DIR ?= ${LOCALBASE}
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+
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+MKDIR ?= mkdir
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+DESTDIR ?= .
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+PREFIX ?= /usr/local
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+INSTALL ?= install
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MKLROOT = /groups/price/poru/external_software/intel/mkl
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INTELROOT = /groups/price/poru/external_software/intel
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-ZLIB_STATIC_DIR = /opt/zlib-1.2.8/lib # probably unnecessary on most systems
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-GLIBC_STATIC_DIR = /home/pl88/glibc-static/usr/lib64
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+ZLIB_STATIC_DIR ?= /usr/lib
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+GLIBC_STATIC_DIR ?= /home/pl88/glibc-static/usr/lib64
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ifeq ($(strip ${linking}),)
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linking = dynamic
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endif
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-# CC = g++
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-CC = /groups/price/poru/external_software/intel/bin/icpc
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+# CXX = g++
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+CXX ?= /groups/price/poru/external_software/intel/bin/icpc
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ifeq (${debug},true)
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- CFLAGS += -g
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+ CXXFLAGS += -g
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else
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- CFLAGS += -O2
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+ CXXFLAGS += -O2
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endif
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-CFLAGS += -msse -msse2
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-CFLAGS += -DUSE_SSE -DMEASURE_DGEMM -DVERBOSE
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-CFLAGS += -Wall
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+CXXFLAGS += -msse -msse2
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+CXXFLAGS += -DUSE_SSE -DMEASURE_DGEMM -DVERBOSE
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+CXXFLAGS += -Wall
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# add Boost include and lib paths
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@@ -51,7 +56,7 @@ ifneq ($(strip ${ZLIB_STATIC_DIR}),)
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endif
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# add MKL paths (if not compiling with g++, i.e., compiling with icpc)
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-ifneq (${CC},g++)
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+ifneq (${CXX},${CXX})
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CPATHS += -I${MKLROOT}/include
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ifeq (${linking},dynamic)
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LPATHS += -L${MKLROOT}/lib/intel64 -Wl,-rpath,${MKLROOT}/lib/intel64 # for libmkl*
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@@ -60,28 +65,28 @@ ifneq (${CC},g++)
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endif
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# add flags for static linking; build LAPACK/MKL component of link line
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-ifeq (${CC},g++)
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- CFLAGS += -fopenmp
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- LFLAGS += -fopenmp
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- LLAPACK = -llapack -lgfortran
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+ifeq (${CXX},${CXX})
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+ CXXFLAGS += -fopenmp
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+ LDFLAGS += -fopenmp
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+ LLAPACK = -llapack -lblas -lgfortran
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ifeq (${linking},static)
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- LFLAGS += -static
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+ LDFLAGS += -static
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LPATHS += -L${GLIBC_STATIC_DIR} -L${ZLIB_STATIC_DIR}
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else ifeq (${linking},static-except-glibc)
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- LFLAGS += -static-libgcc -static-libstdc++
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+ LDFLAGS += -static-libgcc -static-libstdc++
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LPATHS += -L${ZLIB_STATIC_DIR}
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endif
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else
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- CFLAGS += -DUSE_MKL #-DUSE_MKL_MALLOC
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- CFLAGS += -qopenmp
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- LFLAGS += -qopenmp
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- CFLAGS += -Wunused-variable -Wpointer-arith -Wuninitialized -Wreturn-type -Wcheck -Wshadow
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+ CXXFLAGS += -DUSE_MKL #-DUSE_MKL_MALLOC
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+ CXXFLAGS += -qopenmp
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+ LDFLAGS += -qopenmp
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+ CXXFLAGS += -Wunused-variable -Wpointer-arith -Wuninitialized -Wreturn-type -Wcheck -Wshadow
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ifeq (${linking},static)
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- LFLAGS += -static
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+ LDFLAGS += -static
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LPATHS += -L${GLIBC_STATIC_DIR} -L${ZLIB_STATIC_DIR}
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LLAPACK = -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_intel_thread.a -Wl,--end-group
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else ifeq (${linking},static-except-glibc)
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- LFLAGS += -static-intel -static-libstdc++ -static-libgcc
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+ LDFLAGS += -static-intel -static-libstdc++ -static-libgcc
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LPATHS += -L${ZLIB_STATIC_DIR}
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LLAPACK = -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_intel_thread.a -Wl,--end-group
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else
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@@ -110,11 +115,15 @@ OMAIN = BoltMain.o $O
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.PHONY: clean
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%.o: %.cpp
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- ${CC} ${CFLAGS} ${CPATHS} -o $@ -c $<
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+ ${CXX} ${CXXFLAGS} ${CPATHS} -o $@ -c $<
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$T: ${OMAIN}
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- ${CC} ${LFLAGS} -o $T ${OMAIN} $L
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+ ${CXX} ${LDFLAGS} -o $T ${OMAIN} $L
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clean:
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rm -f *.o
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rm -f $T
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+
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+install:
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+ ${MKDIR} ${DESTDIR}${PREFIX}/bin
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+ ${INSTALL} -c -s $T ${DESTDIR}${PREFIX}/bin
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@ -0,0 +1,13 @@
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$NetBSD$
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# Missing header
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--- StringUtils.cpp.orig 2017-08-02 23:43:24 UTC
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+++ StringUtils.cpp
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@@ -22,6 +22,7 @@
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#include <cstdio>
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#include <iostream>
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#include <sstream>
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+#include <sys/types.h> // uint
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#include "StringUtils.hpp"
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