svn commit: r523074 - in head/biology/gemma: . files
Jason W. Bacon
jwb at FreeBSD.org
Tue Jan 14 22:35:37 UTC 2020
Author: jwb
Date: Tue Jan 14 22:35:36 2020
New Revision: 523074
URL: https://svnweb.freebsd.org/changeset/ports/523074
Log:
biology/gemma: Unbreak build
Conflict between cblas.h and gsl_cblas.h
Added:
head/biology/gemma/files/patch-src_fastopenblas.h (contents, props changed)
Modified:
head/biology/gemma/Makefile
head/biology/gemma/files/Makefile
head/biology/gemma/files/patch-src_gemma.cpp
Modified: head/biology/gemma/Makefile
==============================================================================
--- head/biology/gemma/Makefile Tue Jan 14 22:33:48 2020 (r523073)
+++ head/biology/gemma/Makefile Tue Jan 14 22:35:36 2020 (r523074)
@@ -2,7 +2,7 @@
PORTNAME= gemma
DISTVERSION= 0.98.1
-PORTREVISION= 2
+PORTREVISION= 3
CATEGORIES= biology
MAINTAINER= jwb at 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
@@ -21,12 +20,11 @@ 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
Modified: head/biology/gemma/files/Makefile
==============================================================================
--- head/biology/gemma/files/Makefile Tue Jan 14 22:33:48 2020 (r523073)
+++ head/biology/gemma/files/Makefile Tue Jan 14 22:35:36 2020 (r523074)
@@ -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
Added: head/biology/gemma/files/patch-src_fastopenblas.h
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/gemma/files/patch-src_fastopenblas.h Tue Jan 14 22:35:36 2020 (r523074)
@@ -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,
Modified: head/biology/gemma/files/patch-src_gemma.cpp
==============================================================================
--- head/biology/gemma/files/patch-src_gemma.cpp Tue Jan 14 22:33:48 2020 (r523073)
+++ head/biology/gemma/files/patch-src_gemma.cpp Tue Jan 14 22:35:36 2020 (r523074)
@@ -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
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