From 93f42ee115245cb7515267cd3a0b3aa054c04f00 Mon Sep 17 00:00:00 2001
From: "Jason W. Bacon" <jwb@FreeBSD.org>
Date: Tue, 14 Jan 2020 22:35:36 +0000
Subject: [PATCH] biology/gemma: Unbreak build

Conflict between cblas.h and gsl_cblas.h
---
 biology/gemma/Makefile                       | 12 ++++------
 biology/gemma/files/Makefile                 |  2 +-
 biology/gemma/files/patch-src_fastopenblas.h | 15 ++++++++++++
 biology/gemma/files/patch-src_gemma.cpp      | 24 +++++++++++++++++++-
 4 files changed, 44 insertions(+), 9 deletions(-)
 create mode 100644 biology/gemma/files/patch-src_fastopenblas.h

diff --git a/biology/gemma/Makefile b/biology/gemma/Makefile
index ada67a32f052..6dec370bd0fc 100644
--- a/biology/gemma/Makefile
+++ b/biology/gemma/Makefile
@@ -2,7 +2,7 @@
 
 PORTNAME=	gemma
 DISTVERSION=	0.98.1
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	biology
 
 MAINTAINER=	jwb@FreeBSD.org
@@ -11,8 +11,7 @@ COMMENT=	Genome-wide Efficient Mixed Model Association
 LICENSE=	GPLv3
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
-LIB_DEPENDS=	libcblas.so:math/cblas \
-		libgsl.so:math/gsl
+LIB_DEPENDS=	libgsl.so:math/gsl
 
 USES=		blaslapack:openblas compiler:c++11-lang eigen:3 gmake \
 		localbase:ldflags
@@ -21,13 +20,12 @@ GH_ACCOUNT=	genetics-statistics
 GH_PROJECT=	GEMMA
 
 MAKEFILE=	${FILESDIR}/Makefile
-CXXFLAGS+=	-I${LOCALBASE}/include/eigen3 -DOPENBLAS -DOPENBLAS_LEGACY
-LDFLAGS+=	-lopenblas
+# Assuming openblas is built with pthreads, not openmp
+CXXFLAGS+=	-I${LOCALBASE}/include/eigen3 -DOPENBLAS -pthread
+LDFLAGS+=	-lopenblasp -pthread
 
 OPTIONS_DEFINE=	EXAMPLES
 
-BROKEN=		Conflict between math/gsl and math/cblas constant redeclarations
-
 pre-configure:
 	@${REINPLACE_CMD} -e 's|../bin/gemma|../gemma|' ${WRKSRC}/test/*.sh
 
diff --git a/biology/gemma/files/Makefile b/biology/gemma/files/Makefile
index e70996bcde6c..56519ee79dc0 100644
--- a/biology/gemma/files/Makefile
+++ b/biology/gemma/files/Makefile
@@ -1,7 +1,7 @@
 
 GEMMA_VERSION = $(shell cat ./VERSION)
 VGEN		= scripts/gen_version_info.sh
-CXXFLAGS	+= -DHAVE_INLINE -pthread -Wall -std=gnu++11
+CXXFLAGS	+= -DHAVE_INLINE -Wall -std=gnu++11
 CXXFLAGS 	+= -DNDEBUG -Icontrib/catch-1.9.7 -Isrc
 
 SRC_DIR		= ./src
diff --git a/biology/gemma/files/patch-src_fastopenblas.h b/biology/gemma/files/patch-src_fastopenblas.h
new file mode 100644
index 000000000000..32d2c4b1b94c
--- /dev/null
+++ b/biology/gemma/files/patch-src_fastopenblas.h
@@ -0,0 +1,15 @@
+--- src/fastopenblas.h.orig	2018-12-11 05:34:29 UTC
++++ src/fastopenblas.h
+@@ -23,10 +23,12 @@
+ 
+ #include <assert.h>
+ #include <iostream>
++/* Conflicts with gsl_cblas.h, included from gsl_matrix.h
+ extern "C"
+ {
+    #include <cblas.h>   // For OpenBlas / Atlas
+ }
++*/
+ #include "gsl/gsl_matrix.h"
+ 
+ void fast_cblas_dgemm(const enum CBLAS_ORDER Order,
diff --git a/biology/gemma/files/patch-src_gemma.cpp b/biology/gemma/files/patch-src_gemma.cpp
index 09272489a8be..ce4f026b7f26 100644
--- a/biology/gemma/files/patch-src_gemma.cpp
+++ b/biology/gemma/files/patch-src_gemma.cpp
@@ -1,5 +1,18 @@
---- src/gemma.cpp.orig	2019-04-18 21:03:48 UTC
+--- src/gemma.cpp.orig	2018-12-11 05:34:29 UTC
 +++ src/gemma.cpp
+@@ -75,9 +75,9 @@ void gemma_gsl_error_handler (const char * reason,
+   std::raise(SIGINT); // keep the stack trace for gdb
+ }
+ 
+-#if defined(OPENBLAS) && !defined(OPENBLAS_LEGACY)
+-#include <openblas_config.h>
+-#endif
++//#if defined(OPENBLAS) && !defined(OPENBLAS_LEGACY)
++//#include <openblas_config.h>
++//#endif
+ 
+ void GEMMA::PrintHeader(void) {
+ 
 @@ -154,7 +154,7 @@ void GEMMA::PrintHelp(size_t option) {
  
    if (option == 0) {
@@ -164,3 +177,12 @@
           << endl;
      cout << endl;
    }
+@@ -3148,7 +3148,7 @@ void GEMMA::WriteLog(int argc, char **argv, PARAM &cPa
+ #ifdef OPENBLAS
+ 
+   #ifndef OPENBLAS_LEGACY
+-  outfile << "## OpenBlas         =" << OPENBLAS_VERSION << " - " << openblas_get_config() << endl;
++  //outfile << "## OpenBlas         =" << OPENBLAS_VERSION << " - " << openblas_get_config() << endl;
+   outfile << "##   arch           = " << openblas_get_corename() << endl;
+   outfile << "##   threads        = " << openblas_get_num_threads() << endl;
+   #else