biology/bolt-lmm: Upgrade to 2.3.4

Remove previously upstreamed patches
New Makefile patch that preserves default behavior and should be palatable
to upstream

7 files changed, 63 insertions, 120 deletions

diff --git a/biology/bolt-lmm/Makefile b/biology/bolt-lmm/Makefile
index 1d9a822d9d11..616d24986b07 100644
--- a/biology/bolt-lmm/Makefile
+++ b/biology/bolt-lmm/Makefile
@@ -1,8 +1,7 @@
 # $FreeBSD$
 
 PORTNAME=	bolt-lmm
-DISTVERSION=	2.3.2
-PORTREVISION=	2
+DISTVERSION=	2.3.4
 CATEGORIES=	biology
 MASTER_SITES=	https://data.broadinstitute.org/alkesgroup/BOLT-LMM/downloads/
 DISTNAME=	BOLT-LMM_v${PORTVERSION}
@@ -21,11 +20,19 @@ LIB_DEPENDS=	libnlopt.so:math/nlopt \
 # both merely add a GCC requirement.
 USES=		compiler:gcc-c++11-lib gmake
 
-BUILD_WRKSRC=	${WRKDIR}/${DISTNAME}/src
-INSTALL_WRKSRC=	${WRKDIR}/${DISTNAME}/src
-CXXFLAGS_i386=	-DUSE_SSE -msse -msse2
-CXXFLAGS_amd64=	-DUSE_SSE
+BUILD_WRKSRC=		${WRKDIR}/${DISTNAME}/src
+INSTALL_WRKSRC=		${WRKDIR}/${DISTNAME}/src
+CXXFLAGS_i386=		-DUSE_SSE -msse -msse2
+CXXFLAGS_amd64=		-DUSE_SSE
 CXXFLAGS_powerpc64=	-DNO_WARN_X86_INTRINSICS -mvsx
+MAKE_ARGS=		BOOST_INSTALL_DIR=${LOCALBASE} \
+			NLOPT_INSTALL_DIR=${LOCALBASE} \
+			ZLIB_STATIC_DIR=/usr/lib \
+			LIBSTDCXX_STATIC_DIR=/usr/lib \
+			GLIBC_STATIC_DIR=/usr/lib \
+			SSEFLAGS="" \
+			MEMCPY="" \
+			LLAPACK="-lopenblas -lgfortran"
 
 PORTEXAMPLES=	*
 
diff --git a/biology/bolt-lmm/distinfo b/biology/bolt-lmm/distinfo
index 18551a76e51a..618a36d60050 100644
--- a/biology/bolt-lmm/distinfo
+++ b/biology/bolt-lmm/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1558717810
-SHA256 (BOLT-LMM_v2.3.2.tar.gz) = ee505a04138f6c80bfefad4df4b81a2d07e72114dd8329d187c97543f5a0521f
-SIZE (BOLT-LMM_v2.3.2.tar.gz) = 335057533
+TIMESTAMP = 1565528176
+SHA256 (BOLT-LMM_v2.3.4.tar.gz) = 2477faff5028ff8fee5d8f4e6b0cab6d0752b268fd508fe64530a66807d9b0c0
+SIZE (BOLT-LMM_v2.3.4.tar.gz) = 335128004
diff --git a/biology/bolt-lmm/files/patch-src_Jackknife.cpp b/biology/bolt-lmm/files/patch-src_Jackknife.cpp
deleted file mode 100644
index 6d6a970889c3..000000000000
--- a/biology/bolt-lmm/files/patch-src_Jackknife.cpp
+++ /dev/null
@@ -1,13 +0,0 @@
---- src/Jackknife.cpp.orig	2019-08-03 00:15:27 UTC
-+++ src/Jackknife.cpp
-@@ -28,8 +28,8 @@ namespace Jackknife {
-   using std::make_pair;
- 
-   double stddev(const vector <double> &x, int n) {
--    for (int i = 0; i < n; i++) if (isnan(x[i])) return NAN;
--    for (int i = 0; i < n; i++) if (isinf(x[i])) return INFINITY;
-+    for (int i = 0; i < n; i++) if (std::isnan(x[i])) return NAN;
-+    for (int i = 0; i < n; i++) if (std::isinf(x[i])) return INFINITY;
-     double s = 0.0, s2 = 0.0;
-     for (int i = 0; i < n; i++) {
-       s += x[i];
diff --git a/biology/bolt-lmm/files/patch-src_LDscoreCalibration.cpp b/biology/bolt-lmm/files/patch-src_LDscoreCalibration.cpp
deleted file mode 100644
index 51a1ef896340..000000000000
--- a/biology/bolt-lmm/files/patch-src_LDscoreCalibration.cpp
+++ /dev/null
@@ -1,24 +0,0 @@
---- src/LDscoreCalibration.cpp.orig	2019-08-03 00:18:05 UTC
-+++ src/LDscoreCalibration.cpp
-@@ -201,8 +201,8 @@ namespace LDscoreCalibration {
- 	snps[m].MAF >= minMAF &&      // MAF threshold
- 	statsRef[m] > 0 &&            // ref stat available
- 	statsCur[m] > 0 &&            // cur stat available
--	!isnan(LDscores[m]) &&   // LD Score available
--	!isnan(LDscoresChip[m]); // LD Score weight available
-+	!std::isnan(LDscores[m]) &&   // LD Score available
-+	!std::isnan(LDscoresChip[m]); // LD Score weight available
-     
-     // perform outlier removal
-     double outlierChisqThresh = std::max(MIN_OUTLIER_CHISQ_THRESH, N * outlierVarFracThresh);
-@@ -256,8 +256,8 @@ namespace LDscoreCalibration {
-       maskSnps[m] =
- 	snps[m].MAF >= minMAF &&      // MAF threshold
- 	stats[m] > 0 &&               // stat available
--	!isnan(LDscores[m]) &&   // LD Score available
--	!isnan(LDscoresChip[m]); // LD Score weight available
-+	!std::isnan(LDscores[m]) &&   // LD Score available
-+	!std::isnan(LDscoresChip[m]); // LD Score weight available
-     
-     // perform outlier removal
-     double outlierChisqThresh = std::max(MIN_OUTLIER_CHISQ_THRESH, N * outlierVarFracThresh);
diff --git a/biology/bolt-lmm/files/patch-src_Makefile b/biology/bolt-lmm/files/patch-src_Makefile
index 7cd1f25f5420..cf667e25edd4 100644
--- a/biology/bolt-lmm/files/patch-src_Makefile
+++ b/biology/bolt-lmm/files/patch-src_Makefile
@@ -1,21 +1,27 @@
---- src/Makefile.orig	2018-03-13 02:44:52 UTC
+--- src/Makefile.orig	2019-08-11 03:05:04 UTC
 +++ src/Makefile
-@@ -1,29 +1,28 @@
+@@ -1,31 +1,35 @@
++
  ### modify these paths to local Boost and NLopt install directories
 -BOOST_INSTALL_DIR = /home/pl88/boost_1_58_0/install
 -NLOPT_INSTALL_DIR = /n/groups/price/poru/HSPH_SVN/src/BOLT-LMM/nlopt-2.4.2
-+BOOST_INSTALL_DIR ?= ${LOCALBASE}
-+# Redundant on FreeBSD NLOPT_INSTALL_DIR = /n/groups/price/poru/HSPH_SVN/src/BOLT-LMM/nlopt-2.4.2
++### by setting them in the environment or make command line args
++### which will override variables set with ?=
  
- INTELROOT = /n/groups/price/poru/external_software/intel_mkl_2018
- MKLROOT = ${INTELROOT}/mkl
+-INTELROOT = /n/groups/price/poru/external_software/intel_mkl_2019u4
+-MKLROOT = ${INTELROOT}/mkl
 -ZLIB_STATIC_DIR = /n/groups/price/poru/external_software/zlib/zlib-1.2.11 # probably unnecessary on most systems
 -LIBSTDCXX_STATIC_DIR = /n/groups/price/poru/external_software/libstdc++/usr/lib/gcc/x86_64-redhat-linux/4.8.5/
 -GLIBC_STATIC_DIR = /home/pl88/glibc-static/usr/lib64
-+ZLIB_STATIC_DIR ?= /usr/lib
-+LIBSTDCXX_STATIC_DIR ?= /usr/lib
-+GLIBC_STATIC_DIR ?= /usr/lib
- 
++BOOST_INSTALL_DIR ?= /home/pl88/boost_1_58_0/install
++NLOPT_INSTALL_DIR ?= /n/groups/price/poru/HSPH_SVN/src/BOLT-LMM/nlopt-2.4.2
+ 
++INTELROOT ?= /n/groups/price/poru/external_software/intel_mkl_2019u4
++MKLROOT ?= ${INTELROOT}/mkl
++ZLIB_STATIC_DIR ?= /n/groups/price/poru/external_software/zlib/zlib-1.2.11 # probably unnecessary on most systems
++LIBSTDCXX_STATIC_DIR ?= /n/groups/price/poru/external_software/libstdc++/usr/lib/gcc/x86_64-redhat-linux/4.8.5/
++GLIBC_STATIC_DIR ?= /home/pl88/glibc-static/usr/lib64
++
  ifeq ($(strip ${linking}),)
  	linking = dynamic
  endif
@@ -36,33 +42,25 @@
 -CFLAGS += -msse -msse2
 -CFLAGS += -DUSE_SSE -DMEASURE_DGEMM -DVERBOSE
 -CFLAGS += -Wall
-+CXXFLAGS += -DMEASURE_DGEMM -DVERBOSE
-+CXXFLAGS += -Wall
- 
++# Set SSEFLAGS to empty string in the env or make command line if building on
++# systems with no SSE such as PowerPC
++SSEFLAGS ?= -msse -msse2 -DUSE_SSE
++CXXFLAGS += ${SSEFLAGS} -DMEASURE_DGEMM -DVERBOSE -Wall
  
+-
  # add Boost include and lib paths
-@@ -38,9 +37,9 @@ endif
- # add NLopt include and lib paths
- ifneq ($(strip ${NLOPT_INSTALL_DIR}),)
- 	CPATHS += -I${NLOPT_INSTALL_DIR}/api
--	LPATHS += -L${NLOPT_INSTALL_DIR}/.libs
-+	LPATHS += -L${NLOPT_INSTALL_DIR}/libs
- 	ifeq (${linking},dynamic)
--		LPATHS += -Wl,-rpath,${NLOPT_INSTALL_DIR}/.libs
-+		LPATHS += -Wl,-rpath,${NLOPT_INSTALL_DIR}/libs
- 	endif
- endif
- 
-@@ -52,7 +51,7 @@ ifneq ($(strip ${ZLIB_STATIC_DIR}),)
+ ifneq ($(strip ${BOOST_INSTALL_DIR}),)
+ 	CPATHS += -I${BOOST_INSTALL_DIR}/include
+@@ -52,7 +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},${CXX})
++ifeq (${CXX},icpc)
  	CPATHS += -I${MKLROOT}/include
- 	ifeq (${linking},dynamic)
- 		LPATHS += -L${MKLROOT}/lib/intel64 -Wl,-rpath,${MKLROOT}/lib/intel64 # for libmkl*
-@@ -61,28 +60,28 @@ ifneq (${CC},g++)
+ 	ifeq (${linking},static)
+ 		LPATHS += -L${INTELROOT}/lib/intel64 '-Wl,-rpath,$$ORIGIN/lib' # for libiomp5.so (now packaged with binary)
+@@ -65,34 +69,34 @@ ifneq (${CC},g++)
  endif
  
  # add flags for static linking; build LAPACK/MKL component of link line
@@ -70,10 +68,10 @@
 -	CFLAGS += -fopenmp
 -	LFLAGS += -fopenmp
 -	LLAPACK = -llapack -lgfortran
-+ifeq (${CXX},${CXX})
++ifneq (${CXX},icpc)
 +	CXXFLAGS += -fopenmp
 +	LDFLAGS += -fopenmp
-+	LLAPACK = -lopenblas -lgfortran
++	LLAPACK ?= -llapack -lgfortran
  	ifeq (${linking},static)
 -		LFLAGS += -static
 +		LDFLAGS += -static
@@ -92,39 +90,47 @@
 +	CXXFLAGS += -qopenmp
 +	LDFLAGS += -qopenmp
 +	CXXFLAGS += -Wunused-variable -Wpointer-arith -Wuninitialized -Wreturn-type -Wcheck -Wshadow
+ 	LIOMP5 = -liomp5
+ 	LDL = -ldl
  	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
+ 		LLAPACK = -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_intel_thread.a ${MKLROOT}/lib/intel64/libmkl_core.a -Wl,--end-group
  	else ifeq (${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
+ 		LLAPACK = -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_intel_thread.a ${MKLROOT}/lib/intel64/libmkl_core.a -Wl,--end-group
+ 	else ifeq (${linking},static-except-glibc-intel)
+-		LFLAGS += -static-libstdc++ -static-libgcc
++		LDFLAGS += -static-libstdc++ -static-libgcc
+ 		LPATHS += -L${ZLIB_STATIC_DIR}
+ 		LLAPACK = -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core
  	else
-@@ -95,7 +94,8 @@ else
+@@ -105,7 +109,7 @@ else
  endif
  
  # build link line (minus flags)
 -LLIBS = -lboost_program_options -lboost_iostreams -lz -lnlopt
 +LLIBS = -lnlopt -lboost_program_options -lboost_iostreams -lz
-+# LLIBS = /usr/local/lib/libboost_program_options.a -lnlopt -lboost_iostreams -lz
  ifeq (${linking},static-except-glibc)
- 	L = -L${LIBSTDCXX_STATIC_DIR} ${LPATHS} -Wl,--wrap=memcpy -Wl,-Bstatic ${LLIBS} ${LLAPACK} -Wl,-Bdynamic -lpthread -lm
- else
-@@ -105,16 +105,18 @@ endif
+ 	L = -L${LIBSTDCXX_STATIC_DIR} ${LPATHS} -Wl,--wrap=memcpy -Wl,-Bstatic ${LLIBS} ${LLAPACK} -Wl,-Bdynamic ${LIOMP5} -lpthread -lm ${LDL}
+ else ifeq (${linking},static-except-glibc-intel)
+@@ -117,16 +121,20 @@ endif
  
  
  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 memcpy.o
-+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
++# Set to empty string in env or make command line to use system memcpy
++MEMCPY ?= memcpy.o
++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 ${MEMCPY}
  OMAIN = BoltMain.o $O
  
 -.PHONY: clean
 +.PHONY: clean all
  
-+all: $T
++all: ${T}
 +
  %.o: %.cpp
 -	${CC} ${CFLAGS} ${CPATHS} -o $@ -c $<
diff --git a/biology/bolt-lmm/files/patch-src_SnpData.cpp b/biology/bolt-lmm/files/patch-src_SnpData.cpp
deleted file mode 100644
index 5763ee62879c..000000000000
--- a/biology/bolt-lmm/files/patch-src_SnpData.cpp
+++ /dev/null
@@ -1,20 +0,0 @@
---- src/SnpData.cpp.orig	2019-08-03 00:23:17 UTC
-+++ src/SnpData.cpp
-@@ -996,7 +996,7 @@ namespace LMM {
-     for (int w = 0; w < W; w++)
-       if (isProximal(m, mp, windows[w].first, windows[w].second)) {
- 	foundProximal = true;
--	if (!isnan(r2)) {
-+	if (!std::isnan(r2)) {
- 	  for (int a = 0; a < A; a++) {
- 	    double weight = pow((snps[mp].MAF * (1-snps[mp].MAF)), alphaMAFdeps[a]);
- 	    LDscores[w*A+a] += weight * r2;
-@@ -1048,7 +1048,7 @@ namespace LMM {
-       if (snps[mp].chrom != snps[m].chrom) {
- 	fillSnpRow(&mpRow[0], mp);
- 	double r2 = compute_r2(&mRow[0], &mpRow[0], Nstride);
--	if (!isnan(r2)) {
-+	if (!std::isnan(r2)) {
- 	  totOffChrom_r2s += r2;
- 	  numOffChrom_r2s++;
- 	}
diff --git a/biology/bolt-lmm/files/patch-src_StatsUtils.cpp b/biology/bolt-lmm/files/patch-src_StatsUtils.cpp
deleted file mode 100644
index 7e4e35d33963..000000000000
--- a/biology/bolt-lmm/files/patch-src_StatsUtils.cpp
+++ /dev/null
@@ -1,13 +0,0 @@
---- src/StatsUtils.cpp.orig	2019-08-03 00:24:37 UTC
-+++ src/StatsUtils.cpp
-@@ -33,8 +33,8 @@ namespace StatsUtils {
-     if (n <= 1) return NAN;
-     double s = 0.0, s2 = 0.0;
-     for (uint64 i = 0; i < n; i++) {
--      if (isnan(x[i])) return NAN;
--      if (isinf(x[i])) return INFINITY;
-+      if (std::isnan(x[i])) return NAN;
-+      if (std::isinf(x[i])) return INFINITY;
-       s += x[i];
-       s2 += x[i]*x[i];
-     }