bolt-lmm: Clean up and install data and examples

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: bolt-lmm: Clean up and install data and examples
From: Jason Bacon <bacon4000%gmail.com@localhost>
Date: Sat, 11 Nov 2017 20:12:53 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Sat Nov 11 14:12:53 2017 -0600
Changeset:	2a440a592c468429a37ed3a3fde1845b8782880f

Modified Files:
	bolt-lmm/Makefile
	bolt-lmm/PLIST
	bolt-lmm/distinfo
Added Files:
	bolt-lmm/files/Makefile
	bolt-lmm/patches/patch-example_run__example.sh
	bolt-lmm/patches/patch-example_run__example__reml2.sh
	bolt-lmm/patches/patch-src_FileUtils.cpp
	bolt-lmm/patches/patch-src_Makefile
	bolt-lmm/patches/patch-src_StringUtils.cpp
Removed Files:
	bolt-lmm/patches/patch-FileUtils.cpp
	bolt-lmm/patches/patch-Makefile
	bolt-lmm/patches/patch-StringUtils.cpp

Log Message:
bolt-lmm: Clean up and install data and examples

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=2a440a592c468429a37ed3a3fde1845b8782880f

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 bolt-lmm/Makefile                                  |  23 +++-
 bolt-lmm/PLIST                                     |  36 ++++++
 bolt-lmm/distinfo                                  |   8 +-
 bolt-lmm/files/Makefile                            |   5 +
 bolt-lmm/patches/patch-FileUtils.cpp               |  14 ---
 bolt-lmm/patches/patch-Makefile                    | 118 --------------------
 bolt-lmm/patches/patch-StringUtils.cpp             |  13 ---
 bolt-lmm/patches/patch-example_run__example.sh     |  13 +++
 .../patches/patch-example_run__example__reml2.sh   |  13 +++
 bolt-lmm/patches/patch-src_FileUtils.cpp           |  14 +++
 bolt-lmm/patches/patch-src_Makefile                | 124 +++++++++++++++++++++
 bolt-lmm/patches/patch-src_StringUtils.cpp         |  13 +++
 12 files changed, 240 insertions(+), 154 deletions(-)

diffs:
diff --git a/bolt-lmm/Makefile b/bolt-lmm/Makefile
index da918fb2b6..11c7a77f9f 100644
--- a/bolt-lmm/Makefile
+++ b/bolt-lmm/Makefile
@@ -6,7 +6,7 @@
 ###########################################################
 
 DISTNAME=	BOLT-LMM_v${PORTVERSION}
-PKGNAME=	bolt-llm-${PORTVERSION}
+PKGNAME=	bolt-lmm-${PORTVERSION}
 CATEGORIES=	biology
 MASTER_SITES=	https://data.broadinstitute.org/alkesgroup/BOLT-LMM/downloads/
 
@@ -18,16 +18,27 @@ COMMENT=	Statistics for testing association between phenotype and genotypes
 LICENSE=	gnu-gpl-v3
 
 USE_LANGUAGES=	c c++ fortran
-USE_TOOLS+=	gmake
-
-WRKSRC=		${WRKDIR}/${DISTNAME}/src
+USE_TOOLS+=	gmake pax
 
 CXXFLAGS=	-fopenmp
-BUILD_TARGET=	 bolt
 
 PORTVERSION=	2.3
+DATADIR=	share/bolt-lmm
+EXAMPLESDIR=	share/examples/bolt-lmm
+
+INSTALLATION_DIRS=	bin ${DATADIR} ${EXAMPLESDIR}
+
+post-patch:
+	${RM} ${WRKSRC}/example/*.orig
+
+pre-build:
+	${CP} ${FILESDIR}/Makefile ${WRKSRC}
 
-INSTALLATION_DIRS=	bin
+post-install:
+	cd ${WRKSRC} && pax -rw tables ${DESTDIR}${PREFIX}/${DATADIR}
+	cd ${WRKSRC}/example && pax -rw * ${DESTDIR}${PREFIX}/${EXAMPLESDIR}
+	${CHMOD} a+x ${DESTDIR}${PREFIX}/${EXAMPLESDIR}/*.sh
+	${CHMOD} g-w ${DESTDIR}${PREFIX}/${EXAMPLESDIR}/*
 
 # FIXME: Use openblas when available for better performance
 .include "../../math/nlopt/buildlink3.mk"
diff --git a/bolt-lmm/PLIST b/bolt-lmm/PLIST
index 773027c62d..3a59534188 100644
--- a/bolt-lmm/PLIST
+++ b/bolt-lmm/PLIST
@@ -1,2 +1,38 @@
 @comment $NetBSD$
 bin/bolt
+share/bolt-lmm/tables/LDSCORE.1000G_EUR.tab.gz
+share/bolt-lmm/tables/genetic_map_hg17_withX.txt.gz
+share/bolt-lmm/tables/genetic_map_hg18_withX.txt.gz
+share/bolt-lmm/tables/genetic_map_hg19_withX.txt.gz
+share/bolt-lmm/tables/genetic_map_hg38_withX.txt.gz
+share/examples/bolt-lmm/EUR_subset.bed
+share/examples/bolt-lmm/EUR_subset.bim
+share/examples/bolt-lmm/EUR_subset.dosage.chr17first100
+share/examples/bolt-lmm/EUR_subset.dosage.chr22last100.gz
+share/examples/bolt-lmm/EUR_subset.dosage.indivs
+share/examples/bolt-lmm/EUR_subset.dosage2.chr17first100.gz
+share/examples/bolt-lmm/EUR_subset.dosage2.chr17first100.map
+share/examples/bolt-lmm/EUR_subset.dosage2.chr17second100
+share/examples/bolt-lmm/EUR_subset.dosage2.chr17second100.map
+share/examples/bolt-lmm/EUR_subset.dosage2.chr22last100.gz
+share/examples/bolt-lmm/EUR_subset.dosage2.chr22last100.map
+share/examples/bolt-lmm/EUR_subset.dosage2FileList.txt
+share/examples/bolt-lmm/EUR_subset.exclude
+share/examples/bolt-lmm/EUR_subset.fam
+share/examples/bolt-lmm/EUR_subset.impute2.chr17first100.gz
+share/examples/bolt-lmm/EUR_subset.impute2.chr17second100
+share/examples/bolt-lmm/EUR_subset.impute2.chr22last100.gz
+share/examples/bolt-lmm/EUR_subset.impute2.indivs
+share/examples/bolt-lmm/EUR_subset.impute2FileList.txt
+share/examples/bolt-lmm/EUR_subset.modelSnps
+share/examples/bolt-lmm/EUR_subset.modelSnps2
+share/examples/bolt-lmm/EUR_subset.pheno.covars
+share/examples/bolt-lmm/EUR_subset.remove
+share/examples/bolt-lmm/example.dosage2Snps.stats
+share/examples/bolt-lmm/example.dosageSnps.stats
+share/examples/bolt-lmm/example.impute2Snps.stats
+share/examples/bolt-lmm/example.log
+share/examples/bolt-lmm/example.stats
+share/examples/bolt-lmm/example_reml2.log
+share/examples/bolt-lmm/run_example.sh
+share/examples/bolt-lmm/run_example_reml2.sh
diff --git a/bolt-lmm/distinfo b/bolt-lmm/distinfo
index da9d6c738d..61d390929a 100644
--- a/bolt-lmm/distinfo
+++ b/bolt-lmm/distinfo
@@ -4,6 +4,8 @@ SHA1 (BOLT-LMM_v2.3.tar.gz) = 4f2caf427cbcbe58175e6e5c711c3d8b0c66a9d6
 RMD160 (BOLT-LMM_v2.3.tar.gz) = d0d207f2993d00607f256edb0e9cda57aa0bd800
 SHA512 (BOLT-LMM_v2.3.tar.gz) = a396bb6699fbb87327901a8db46faa45705405160f318796f887b8cd6edd495f10fa460201a4eead57b2bc34adb45f44d26dd59ae12ed2240d4d46b6b6e959e6
 Size (BOLT-LMM_v2.3.tar.gz) = 336986328 bytes
-SHA1 (patch-FileUtils.cpp) = 258138822f610ab38f9cf3cf0ad03ca49b67ad1c
-SHA1 (patch-Makefile) = 5268bd92b382eda5615958064314c8a2abf62668
-SHA1 (patch-StringUtils.cpp) = f0a5c3375a95391235d85fc9431524236e39910f
+SHA1 (patch-example_run__example.sh) = e75940a782efd6003a21df0ac2f33a87e6fd18e0
+SHA1 (patch-example_run__example__reml2.sh) = 783c9bbbbc2da7e5f2e17782648da82bb4bfd232
+SHA1 (patch-src_FileUtils.cpp) = d4404507f52d7c2c7a6a50336e7045d3b80b3cc4
+SHA1 (patch-src_Makefile) = e53762b5ca6e8a4d4cf35c5293d3a3bd42efff1f
+SHA1 (patch-src_StringUtils.cpp) = 846adf026fb0485d7393dd9ffa1aec8707d3a5f8
diff --git a/bolt-lmm/files/Makefile b/bolt-lmm/files/Makefile
new file mode 100644
index 0000000000..595214a88d
--- /dev/null
+++ b/bolt-lmm/files/Makefile
@@ -0,0 +1,5 @@
+all:
+	cd src && ${MAKE} all
+
+install:
+	cd src && ${MAKE} install
diff --git a/bolt-lmm/patches/patch-FileUtils.cpp b/bolt-lmm/patches/patch-FileUtils.cpp
deleted file mode 100644
index 7806a59216..0000000000
--- a/bolt-lmm/patches/patch-FileUtils.cpp
+++ /dev/null
@@ -1,14 +0,0 @@
-$NetBSD$
-
-# Unused variable
---- FileUtils.cpp.orig	2017-09-20 10:29:18 UTC
-+++ FileUtils.cpp
-@@ -275,7 +275,7 @@ namespace FileUtils {
-     uint Layout = (flags>>2)&0xf; cout << "Layout: " << Layout << endl;
-     assert(Layout==1 || Layout==2); // REQUIRE Layout==1 or Layout==2
- 
--    uint SampleIdentifiers = flags>>31; //cout << "SampleIdentifiers: " << SampleIdentifiers << endl;
-+    // uint SampleIdentifiers = flags>>31; cout << "SampleIdentifiers: " << SampleIdentifiers << endl;
-     fseek(fin, offset+4, SEEK_SET);
- 
-     // check first SNP
diff --git a/bolt-lmm/patches/patch-Makefile b/bolt-lmm/patches/patch-Makefile
deleted file mode 100644
index a9063f3acf..0000000000
--- a/bolt-lmm/patches/patch-Makefile
+++ /dev/null
@@ -1,118 +0,0 @@
-$NetBSD$
-
-# Respect env
---- Makefile.orig	2017-08-03 00:14:08.000000000 +0000
-+++ Makefile
-@@ -1,28 +1,33 @@
- ### modify these paths to local Boost and NLopt install directories
--BOOST_INSTALL_DIR = /home/pl88/boost_1_58_0/install
--NLOPT_INSTALL_DIR = /groups/price/poru/HSPH_SVN/src/BOLT-LMM/nlopt-2.4.2
-+BOOST_INSTALL_DIR ?= ${LOCALBASE}
-+# NLOPT_INSTALL_DIR ?= ${LOCALBASE}
-+
-+MKDIR ?=	mkdir
-+DESTDIR ?=	.
-+PREFIX ?=	/usr/local
-+INSTALL ?=	install
- 
- MKLROOT = /groups/price/poru/external_software/intel/mkl
- INTELROOT = /groups/price/poru/external_software/intel
--ZLIB_STATIC_DIR = /opt/zlib-1.2.8/lib # probably unnecessary on most systems
--GLIBC_STATIC_DIR = /home/pl88/glibc-static/usr/lib64
-+ZLIB_STATIC_DIR ?= /usr/lib
-+GLIBC_STATIC_DIR ?= /home/pl88/glibc-static/usr/lib64
- 
- ifeq ($(strip ${linking}),)
- 	linking = dynamic
- endif
- 
--# CC = g++
--CC = /groups/price/poru/external_software/intel/bin/icpc
-+# CXX = g++
-+CXX ?= /groups/price/poru/external_software/intel/bin/icpc
- 
- ifeq (${debug},true)
--	CFLAGS += -g
-+	CXXFLAGS += -g
- else
--	CFLAGS += -O2
-+	CXXFLAGS += -O2
- endif
- 
--CFLAGS += -msse -msse2
--CFLAGS += -DUSE_SSE -DMEASURE_DGEMM -DVERBOSE
--CFLAGS += -Wall
-+CXXFLAGS += -msse -msse2
-+CXXFLAGS += -DUSE_SSE -DMEASURE_DGEMM -DVERBOSE
-+CXXFLAGS += -Wall
- 
- 
- # add Boost include and lib paths
-@@ -51,7 +56,7 @@ ifneq ($(strip ${ZLIB_STATIC_DIR}),)
- endif
- 
- # add MKL paths (if not compiling with g++, i.e., compiling with icpc)
--ifneq (${CC},g++)
-+ifneq (${CXX},${CXX})
- 	CPATHS += -I${MKLROOT}/include
- 	ifeq (${linking},dynamic)
- 		LPATHS += -L${MKLROOT}/lib/intel64 -Wl,-rpath,${MKLROOT}/lib/intel64 # for libmkl*
-@@ -60,28 +65,28 @@ ifneq (${CC},g++)
- endif
- 
- # add flags for static linking; build LAPACK/MKL component of link line
--ifeq (${CC},g++)
--	CFLAGS += -fopenmp
--	LFLAGS += -fopenmp
--	LLAPACK = -llapack -lgfortran
-+ifeq (${CXX},${CXX})
-+	CXXFLAGS += -fopenmp
-+	LDFLAGS += -fopenmp
-+	LLAPACK = -llapack -lopenblas -lgfortran
- 	ifeq (${linking},static)
--		LFLAGS += -static
-+		LDFLAGS += -static
- 		LPATHS += -L${GLIBC_STATIC_DIR} -L${ZLIB_STATIC_DIR}
- 	else ifeq (${linking},static-except-glibc)
--		LFLAGS += -static-libgcc -static-libstdc++
-+		LDFLAGS += -static-libgcc -static-libstdc++
- 		LPATHS += -L${ZLIB_STATIC_DIR}
- 	endif
- else
--	CFLAGS += -DUSE_MKL #-DUSE_MKL_MALLOC
--	CFLAGS += -qopenmp
--	LFLAGS += -qopenmp
--	CFLAGS += -Wunused-variable -Wpointer-arith -Wuninitialized -Wreturn-type -Wcheck -Wshadow
-+	CXXFLAGS += -DUSE_MKL #-DUSE_MKL_MALLOC
-+	CXXFLAGS += -qopenmp
-+	LDFLAGS += -qopenmp
-+	CXXFLAGS += -Wunused-variable -Wpointer-arith -Wuninitialized -Wreturn-type -Wcheck -Wshadow
- 	ifeq (${linking},static)
--		LFLAGS += -static
-+		LDFLAGS += -static
- 		LPATHS += -L${GLIBC_STATIC_DIR} -L${ZLIB_STATIC_DIR}
- 		LLAPACK = -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_intel_thread.a -Wl,--end-group
- 	else ifeq (${linking},static-except-glibc)
--		LFLAGS += -static-intel -static-libstdc++ -static-libgcc
-+		LDFLAGS += -static-intel -static-libstdc++ -static-libgcc
- 		LPATHS += -L${ZLIB_STATIC_DIR}
- 		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
- 	else
-@@ -110,11 +115,15 @@ OMAIN = BoltMain.o $O
- .PHONY: clean
- 
- %.o: %.cpp
--	${CC} ${CFLAGS} ${CPATHS} -o $@ -c $<
-+	${CXX} ${CXXFLAGS} ${CPATHS} -o $@ -c $<
- 
- $T: ${OMAIN}
--	${CC} ${LFLAGS} -o $T ${OMAIN} $L
-+	${CXX} ${LDFLAGS} -o $T ${OMAIN} $L
- 
- clean:
- 	rm -f *.o
- 	rm -f $T
-+
-+install:
-+	${MKDIR} ${DESTDIR}${PREFIX}/bin
-+	${INSTALL} -c -s $T ${DESTDIR}${PREFIX}/bin
diff --git a/bolt-lmm/patches/patch-StringUtils.cpp b/bolt-lmm/patches/patch-StringUtils.cpp
deleted file mode 100644
index 9aa25f0c38..0000000000
--- a/bolt-lmm/patches/patch-StringUtils.cpp
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD$
-
-# Missing header
---- StringUtils.cpp.orig	2017-08-02 23:43:24 UTC
-+++ StringUtils.cpp
-@@ -22,6 +22,7 @@
- #include <cstdio>
- #include <iostream>
- #include <sstream>
-+#include <sys/types.h>	// uint
- 
- #include "StringUtils.hpp"
- 
diff --git a/bolt-lmm/patches/patch-example_run__example.sh b/bolt-lmm/patches/patch-example_run__example.sh
new file mode 100644
index 0000000000..f8071fb6ab
--- /dev/null
+++ b/bolt-lmm/patches/patch-example_run__example.sh
@@ -0,0 +1,13 @@
+$NetBSD$
+
+# Use PATH
+--- example/run_example.sh.orig	2017-11-11 20:04:21.998666384 +0000
++++ example/run_example.sh
+@@ -1,4 +1,6 @@
+-../bolt \
++#!/bin/sh -e
++
++bolt \
+     --bfile=EUR_subset \
+     --remove=EUR_subset.remove \
+     --exclude=EUR_subset.exclude \
diff --git a/bolt-lmm/patches/patch-example_run__example__reml2.sh b/bolt-lmm/patches/patch-example_run__example__reml2.sh
new file mode 100644
index 0000000000..da24a40967
--- /dev/null
+++ b/bolt-lmm/patches/patch-example_run__example__reml2.sh
@@ -0,0 +1,13 @@
+$NetBSD$
+
+# Use PATH
+--- example/run_example_reml2.sh.orig	2017-11-11 20:04:45.202815471 +0000
++++ example/run_example_reml2.sh
+@@ -1,4 +1,6 @@
+-../bolt \
++#!/bin/sh -e
++
++bolt \
+     --bfile=EUR_subset \
+     --phenoFile=EUR_subset.pheno.covars \
+     --phenoCol=PHENO \
diff --git a/bolt-lmm/patches/patch-src_FileUtils.cpp b/bolt-lmm/patches/patch-src_FileUtils.cpp
new file mode 100644
index 0000000000..b76542db3c
--- /dev/null
+++ b/bolt-lmm/patches/patch-src_FileUtils.cpp
@@ -0,0 +1,14 @@
+$NetBSD$
+
+# Temporary fix
+--- src/FileUtils.cpp.orig	2017-08-02 23:43:24.000000000 +0000
++++ src/FileUtils.cpp
+@@ -275,7 +275,7 @@ namespace FileUtils {
+     uint Layout = (flags>>2)&0xf; cout << "Layout: " << Layout << endl;
+     assert(Layout==1 || Layout==2); // REQUIRE Layout==1 or Layout==2
+ 
+-    uint SampleIdentifiers = flags>>31; //cout << "SampleIdentifiers: " << SampleIdentifiers << endl;
++    // uint SampleIdentifiers = flags>>31; cout << "SampleIdentifiers: " << SampleIdentifiers << endl;
+     fseek(fin, offset+4, SEEK_SET);
+ 
+     // check first SNP
diff --git a/bolt-lmm/patches/patch-src_Makefile b/bolt-lmm/patches/patch-src_Makefile
new file mode 100644
index 0000000000..614d76a3b5
--- /dev/null
+++ b/bolt-lmm/patches/patch-src_Makefile
@@ -0,0 +1,124 @@
+$NetBSD$
+
+# Standardize make vars
+--- src/Makefile.orig	2017-08-03 00:14:08.000000000 +0000
++++ src/Makefile
+@@ -1,28 +1,33 @@
+ ### modify these paths to local Boost and NLopt install directories
+-BOOST_INSTALL_DIR = /home/pl88/boost_1_58_0/install
+-NLOPT_INSTALL_DIR = /groups/price/poru/HSPH_SVN/src/BOLT-LMM/nlopt-2.4.2
++BOOST_INSTALL_DIR ?= ${LOCALBASE}
++# NLOPT_INSTALL_DIR ?= ${LOCALBASE}
++
++MKDIR ?=	mkdir
++DESTDIR ?=	.
++PREFIX ?=	/usr/local
++INSTALL ?=	install
+ 
+ MKLROOT = /groups/price/poru/external_software/intel/mkl
+ INTELROOT = /groups/price/poru/external_software/intel
+-ZLIB_STATIC_DIR = /opt/zlib-1.2.8/lib # probably unnecessary on most systems
+-GLIBC_STATIC_DIR = /home/pl88/glibc-static/usr/lib64
++ZLIB_STATIC_DIR ?= /usr/lib
++GLIBC_STATIC_DIR ?= /home/pl88/glibc-static/usr/lib64
+ 
+ ifeq ($(strip ${linking}),)
+ 	linking = dynamic
+ endif
+ 
+-# CC = g++
+-CC = /groups/price/poru/external_software/intel/bin/icpc
++# CXX = g++
++CXX ?= /groups/price/poru/external_software/intel/bin/icpc
+ 
+ ifeq (${debug},true)
+-	CFLAGS += -g
++	CXXFLAGS += -g
+ else
+-	CFLAGS += -O2
++	CXXFLAGS += -O2
+ endif
+ 
+-CFLAGS += -msse -msse2
+-CFLAGS += -DUSE_SSE -DMEASURE_DGEMM -DVERBOSE
+-CFLAGS += -Wall
++CXXFLAGS += -msse -msse2
++CXXFLAGS += -DUSE_SSE -DMEASURE_DGEMM -DVERBOSE
++CXXFLAGS += -Wall
+ 
+ 
+ # add Boost include and lib paths
+@@ -51,7 +56,7 @@ ifneq ($(strip ${ZLIB_STATIC_DIR}),)
+ endif
+ 
+ # add MKL paths (if not compiling with g++, i.e., compiling with icpc)
+-ifneq (${CC},g++)
++ifneq (${CXX},${CXX})
+ 	CPATHS += -I${MKLROOT}/include
+ 	ifeq (${linking},dynamic)
+ 		LPATHS += -L${MKLROOT}/lib/intel64 -Wl,-rpath,${MKLROOT}/lib/intel64 # for libmkl*
+@@ -60,28 +65,28 @@ ifneq (${CC},g++)
+ endif
+ 
+ # add flags for static linking; build LAPACK/MKL component of link line
+-ifeq (${CC},g++)
+-	CFLAGS += -fopenmp
+-	LFLAGS += -fopenmp
+-	LLAPACK = -llapack -lgfortran
++ifeq (${CXX},${CXX})
++	CXXFLAGS += -fopenmp
++	LDFLAGS += -fopenmp
++	LLAPACK = -llapack -lopenblas -lgfortran
+ 	ifeq (${linking},static)
+-		LFLAGS += -static
++		LDFLAGS += -static
+ 		LPATHS += -L${GLIBC_STATIC_DIR} -L${ZLIB_STATIC_DIR}
+ 	else ifeq (${linking},static-except-glibc)
+-		LFLAGS += -static-libgcc -static-libstdc++
++		LDFLAGS += -static-libgcc -static-libstdc++
+ 		LPATHS += -L${ZLIB_STATIC_DIR}
+ 	endif
+ else
+-	CFLAGS += -DUSE_MKL #-DUSE_MKL_MALLOC
+-	CFLAGS += -qopenmp
+-	LFLAGS += -qopenmp
+-	CFLAGS += -Wunused-variable -Wpointer-arith -Wuninitialized -Wreturn-type -Wcheck -Wshadow
++	CXXFLAGS += -DUSE_MKL #-DUSE_MKL_MALLOC
++	CXXFLAGS += -qopenmp
++	LDFLAGS += -qopenmp
++	CXXFLAGS += -Wunused-variable -Wpointer-arith -Wuninitialized -Wreturn-type -Wcheck -Wshadow
+ 	ifeq (${linking},static)
+-		LFLAGS += -static
++		LDFLAGS += -static
+ 		LPATHS += -L${GLIBC_STATIC_DIR} -L${ZLIB_STATIC_DIR}
+ 		LLAPACK = -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_intel_thread.a -Wl,--end-group
+ 	else ifeq (${linking},static-except-glibc)
+-		LFLAGS += -static-intel -static-libstdc++ -static-libgcc
++		LDFLAGS += -static-intel -static-libstdc++ -static-libgcc
+ 		LPATHS += -L${ZLIB_STATIC_DIR}
+ 		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
+ 	else
+@@ -107,14 +112,20 @@ T = bolt
+ O = Bolt.o BoltParams.o BoltParEstCV.o BoltReml.o CovariateBasis.o DataMatrix.o FileUtils.o Jackknife.o LDscoreCalibration.o MapInterpolater.o MatrixUtils.o MemoryUtils.o NonlinearOptMulti.o NumericUtils.o PhenoBuilder.o RestrictSnpSet.o SnpData.o SnpInfo.o SpectrumTools.o StatsUtils.o StringUtils.o Timer.o
+ OMAIN = BoltMain.o $O
+ 
+-.PHONY: clean
++.PHONY: clean all
++
++all: $T
+ 
+ %.o: %.cpp
+-	${CC} ${CFLAGS} ${CPATHS} -o $@ -c $<
++	${CXX} ${CXXFLAGS} ${CPATHS} -o $@ -c $<
+ 
+ $T: ${OMAIN}
+-	${CC} ${LFLAGS} -o $T ${OMAIN} $L
++	${CXX} ${LDFLAGS} -o $T ${OMAIN} $L
+ 
+ clean:
+ 	rm -f *.o
+ 	rm -f $T
++
++install:
++	${MKDIR} ${DESTDIR}${PREFIX}/bin
++	${INSTALL} -c -s $T ${DESTDIR}${PREFIX}/bin
diff --git a/bolt-lmm/patches/patch-src_StringUtils.cpp b/bolt-lmm/patches/patch-src_StringUtils.cpp
new file mode 100644
index 0000000000..8266b7077c
--- /dev/null
+++ b/bolt-lmm/patches/patch-src_StringUtils.cpp
@@ -0,0 +1,13 @@
+$NetBSD$
+
+# Missing header
+--- src/StringUtils.cpp.orig	2017-08-02 23:43:24.000000000 +0000
++++ src/StringUtils.cpp
+@@ -22,6 +22,7 @@
+ #include <cstdio>
+ #include <iostream>
+ #include <sstream>
++#include <sys/types.h>	// uint
+ 
+ #include "StringUtils.hpp"
+
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