biology/gcta: Update to 1.94.1

Too many changes since v1.26 to list here
Changes: https://yanglab.westlake.edu.cn/software/gcta/#Download

Reported by:    pkg-fallout

biology/gcta/Makefile

@@ -1,34 +1,40 @@
 PORTNAME=	gcta
-DISTVERSION=	1.26.0
-PORTREVISION=	4
+DISTVERSIONPREFIX=	v
+DISTVERSION=	1.94.1
 CATEGORIES=	biology
-MASTER_SITES=	https://cnsgenomics.com/software/gcta/pre_gcta/:main \
-		https://gitlab.com/libeigen/eigen/-/archive/${EIGEN_VERSION}/:eigen
-DISTFILES=	${PORTNAME}_${DISTVERSION}_src${EXTRACT_SUFX}:main \
-		eigen-${EIGEN_VERSION}.tar.gz:eigen
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Genome-wide Complex Trait Analysis
 WWW=		https://cnsgenomics.com/software/gcta/index.html
 
 LICENSE=	GPLv3
-LICENSE_FILE=	${WRKSRC}/GNU_General_Public_License_v3.txt
+LICENSE_FILE=	${WRKSRC}/LICENSE
 
-LIB_DEPENDS=	libopenblas.so:math/openblas
+BUILD_DEPENDS=	boost-libs>0:devel/boost-libs \
+		spectra>0:math/spectra
+LIB_DEPENDS=	libgsl.so:math/gsl \
+		libopenblas.so:math/openblas \
+		libsqlite3.so:databases/sqlite3 \
+		libzstd.so:archivers/zstd
 
-USES=		compiler:c++11-lang dos2unix gmake localbase:ldflags zip
+USES=		cmake eigen:3 localbase:ldflags
+USE_GITHUB=	yes
 
-CXXFLAGS+=	-I${WRKDIR}/eigen-${EIGEN_VERSION} -fopenmp
-LDFLAGS+=	-lopenblas
+GH_ACCOUNT=	jianyangqt
+GH_TUPLE=	zhilizheng:plink-ng:3744540:plink/submods/plink-ng
 
-INSTALL_TARGET=	install-strip
-PLIST_FILES=	bin/gcta
+CONFIGURE_ENV+=	EIGEN3_INCLUDE_DIR=${LOCALBASE}/include/eigen3 \
+		BOOST_INCLUDE_DIR=${LOCALBASE}/include/boost \
+		OPENBLAS=${LOCALBASE} \
+		SPECTRA_INCLUDE_DIR=${LOCALBASE}/include/Spectra
 
-EIGEN_VERSION=	3.3.9
+LDFLAGS+=	-fopenmp
 
-do-extract:
-	@${UNZIP_NATIVE_CMD} -d ${WRKSRC} ${DISTDIR}/${PORTNAME}_${DISTVERSION}_src${EXTRACT_SUFX}
-	@cd ${WRKDIR} && \
-		${TAR} xzf ${DISTDIR}/eigen-${EIGEN_VERSION}.tar.gz
+PLIST_FILES=	bin/gcta64 bin/gcta
+
+do-install:
+	@${MKDIR} ${STAGEDIR}${PREFIX}/bin
+	${INSTALL_PROGRAM} ${BUILD_WRKSRC}/gcta64 ${STAGEDIR}${PREFIX}/bin
+	${RLN} ${STAGEDIR}${PREFIX}/bin/gcta64 ${STAGEDIR}${PREFIX}/bin/gcta
 
 .include <bsd.port.mk>

biology/gcta/distinfo

@@ -1,5 +1,5 @@
-TIMESTAMP = 1657137653
-SHA256 (gcta_1.26.0_src.zip) = 554c48f421c93cbaf64b1c300ca507d8e7a56086b5c7d857227fbd4048f42acf
-SIZE (gcta_1.26.0_src.zip) = 198045
-SHA256 (eigen-3.3.9.tar.gz) = 7985975b787340124786f092b3a07d594b2e9cd53bbfe5f3d9b1daee7d55f56f
-SIZE (eigen-3.3.9.tar.gz) = 2142379
+TIMESTAMP = 1697202096
+SHA256 (jianyangqt-gcta-v1.94.1_GH0.tar.gz) = d38841587bef016d7885cc1b3287d7ed0373bd370674130e814e2c5e6a90bfbf
+SIZE (jianyangqt-gcta-v1.94.1_GH0.tar.gz) = 1101577
+SHA256 (zhilizheng-plink-ng-3744540_GH0.tar.gz) = dfa4879bc6bcbe24411451748c7c5dc803e42cafa55b008134f0d123cd933222
+SIZE (zhilizheng-plink-ng-3744540_GH0.tar.gz) = 3222588

biology/gcta/files/patch-CMakeLists.txt

@@ -0,0 +1,98 @@
+--- CMakeLists.txt.orig	2022-08-03 06:01:52 UTC
++++ CMakeLists.txt
+@@ -3,7 +3,7 @@ SET(CMAKE_INCLUDE_CURRENT_DIR ON)
+ SET(PROJECT_NAME_STR GCTA2)
+ PROJECT(${PROJECT_NAME_STR} C CXX)
+ SET(CMAKE_INCLUDE_CURRENT_DIR ON)
+-SET(CMAKE_CXX_STANDARD 11)
++SET(CMAKE_CXX_STANDARD 14)
+ SET(CMAKE_C_STANDARD 11)
+
+ # get system architecture
+@@ -16,8 +16,8 @@ endif()
+     MESSAGE(FATAL_ERROR "Use the Visual Studio project file which located in gcta_win64 directory")
+ endif()
+
+-if("${CMAKE_SYSTEM_NAME}" MATCHES "Linux" OR "${CMAKE_SYSTEM_NAME}" MATCHES "Darwin")
+-    MESSAGE("Linux and Mac are supported.")
++if("${CMAKE_SYSTEM_NAME}" MATCHES "FreeBSD" OR "${CMAKE_SYSTEM_NAME}" MATCHES "Linux" OR "${CMAKE_SYSTEM_NAME}" MATCHES "Darwin")
++    MESSAGE("FreeBSD, Linux and Mac are supported.")
+ else()
+     MESSAGE("Your system: ${CMAKE_SYSTEM_NAME}")
+     MESSAGE(FATAL_ERROR "Only Linux and Mac are currently supported.")
+@@ -43,18 +43,18 @@ INCLUDE_DIRECTORIES("${EIGEN3_INCLUDE_DIR}")
+ ENDIF()
+ INCLUDE_DIRECTORIES("${EIGEN3_INCLUDE_DIR}")
+
+-SET(SPECTRA_LIB "$ENV{SPECTRA_LIB}")
+-IF(NOT SPECTRA_LIB)
+-    MESSAGE(FATAL_ERROR "Specify environment variable SPECTRA_LIB to the location of Spectra package")
++SET(SPECTRA_INCLUDE_DIR "$ENV{SPECTRA_INCLUDE_DIR}")
++IF(NOT SPECTRA_INCLUDE_DIR)
++    MESSAGE(FATAL_ERROR "Specify environment variable SPECTRA_INCLUDE_DIR to the location of Spectra package")
+ ENDIF()
+-INCLUDE_DIRECTORIES("${SPECTRA_LIB}")
++INCLUDE_DIRECTORIES("${SPECTRA_INCLUDE_DIR}")
+
+
+-SET(BOOST_LIB "$ENV{BOOST_LIB}")
+-IF(NOT BOOST_LIB)
+-    MESSAGE(FATAL_ERROR "Specify environment variable BOOST_LIB to the location of BOOST library")
++SET(BOOST_INCLUDE_DIR "$ENV{BOOST_INCLUDE_DIR}")
++IF(NOT BOOST_INCLUDE_DIR)
++    MESSAGE(FATAL_ERROR "Specify environment variable BOOST_INCLUDE_DIR to the location of BOOST headers")
+ ENDIF()
+-INCLUDE_DIRECTORIES("${BOOST_LIB}")
++INCLUDE_DIRECTORIES("${BOOST_INCLUDE_DIR}")
+
+
+ # PLINK2.0 pgen library;
+@@ -63,13 +63,28 @@ message(STATUS "ARCHITECTURE:${CMAKE_LIBRARY_ARCHITECT
+
+
+ message(STATUS "ARCHITECTURE:${CMAKE_LIBRARY_ARCHITECTURE}")
+-if(CMAKE_LIBRARY_ARCHITECTURE STREQUAL "aarch64")
++if("${CMAKE_SYSTEM_NAME}" MATCHES "FreeBSD")
+     SET(OPENBLAS "$ENV{OPENBLAS}")
+     IF(NOT OPENBLAS)
+         MESSAGE(FATAL_ERROR "Specify environment variable OPENBLAS to the location of OPENBLAS package")
+     ENDIF()
+     INCLUDE_DIRECTORIES("${OPENBLAS}/include")
+
++    find_library(lib_openblas NAMES openblas PATHS "${OPENBLAS}" "${LOCALBASE}/lib")
++    set(BLAS_LIB ${lib_openblas})
++
++    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread")
++    set(CMAKE_CXX_FLAGS_RELEASE  "${CMAKE_CXX_FLAGS_RELEASE} -DNDEBUG")
++    set(CMAKE_CXX_FLAGS_DEBUG  "${CMAKE_CXX_FLAGS_DEBUG} -O0 -g")
++    add_compile_options(-fopenmp)
++
++elseif(CMAKE_LIBRARY_ARCHITECTURE STREQUAL "aarch64")
++    SET(OPENBLAS "$ENV{OPENBLAS}")
++    IF(NOT OPENBLAS)
++        MESSAGE(FATAL_ERROR "Specify environment variable OPENBLAS to the location of OPENBLAS package")
++    ENDIF()
++    INCLUDE_DIRECTORIES("${OPENBLAS}/include")
++
+     find_library(lib_openblas NAMES openblas PATHS "${OPENBLAS}" "${OPENBLAS}/lib")
+     set(BLAS_LIB ${lib_openblas})
+
+@@ -169,6 +184,8 @@ if(APPLE)
+ if(APPLE)
+     link_directories(${MKLROOT}/lib)
+     link_directories(/usr/local/lib)
++elseif("${CMAKE_SYSTEM_NAME}" MATCHES "FreeBSD")
++    link_directories(${LOCALBASE}/lib)
+ else(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+     #linux
+     link_directories(${MKLROOT}/../../../lib/intel64)
+@@ -179,6 +196,9 @@ if(APPLE)
+ if(APPLE)
+     # iomp5
+     target_link_libraries(gcta64 ${libs_list} Pgenlib mainV1 z ${BLAS_LIB} sqlite3 zstd_s omp pthread m dl )
++elseif("${CMAKE_SYSTEM_NAME}" MATCHES "FreeBSD")
++    # FIXME: Clean this up
++    target_link_libraries(gcta64 mainV1 ${libs_list} Pgenlib gsl z sqlite3 zstd -Wl,--start-group ${BLAS_LIB} -Wl,--end-group -Wl,--whole-archive -lpthread -Wl,--no-whole-archive m dl)
+ else()
+     if (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+         # error keeps only

biology/gcta/files/patch-include_cpu.h

@@ -0,0 +1,18 @@
+--- include/cpu.h.orig	2023-10-13 13:09:13 UTC
++++ include/cpu.h
+@@ -13,7 +13,7 @@
+   #define GCTA_ARCH_i386 0
+ #endif
+
+-#if GCTA_ARCH_x86_64 || GCTA_ARCH_i386
++#if !defined(__FreeBSD__) && (GCTA_ARCH_x86_64 || GCTA_ARCH_i386)
+   #define GCTA_CPU_x86 1
+ #else
+   #define GCTA_CPU_x86 0
+@@ -50,4 +50,4 @@
+   #include <lapack.h>
+ #endif
+
+-#endif  //END GCTA_CPU_H
+\ No newline at end of file
++#endif  //END GCTA_CPU_H

biology/gcta/files/patch-include_cpu__f77blas.h

@@ -0,0 +1,18 @@
+--- include/cpu_f77blas.h.orig	2023-10-13 13:10:15 UTC
++++ include/cpu_f77blas.h
+@@ -13,7 +13,7 @@
+   #define GCTA_ARCH_i386 0
+ #endif
+
+-#if GCTA_ARCH_x86_64 || GCTA_ARCH_i386
++#if !defined(__FreeBSD__) && (GCTA_ARCH_x86_64 || GCTA_ARCH_i386)
+   #define GCTA_CPU_x86 1
+ #else
+   #define GCTA_CPU_x86 0
+@@ -46,4 +46,4 @@
+   #include <f77blas.h>
+ #endif
+
+-#endif  //END GCTA_F77BLAS_CPU_H
+\ No newline at end of file
++#endif  //END GCTA_F77BLAS_CPU_H

biology/gcta/files/patch-main_option.cpp

@@ -0,0 +1,28 @@
+--- main/option.cpp.orig	2023-10-13 13:49:25 UTC
++++ main/option.cpp
+@@ -1112,10 +1112,10 @@ void option(int option_num, char* option_str[])
+
+ #ifdef _WIN32
+ 	    if(chbuf != '\\') ref_ld_dirt = ref_ld_dirt + '\\';
+-#elif defined __linux__ || defined __APPLE__
++#elif defined __FreeBSD__ || defined __linux__ || defined __APPLE__
+ 	    if(chbuf != '/') ref_ld_dirt = ref_ld_dirt + '/';
+ #else
+-#error Only Windows, Mac and Linux are supported.
++#error Only FreeBSD, Windows, Mac and Linux are supported.
+ #endif
+             LOGGER << "--ref-ld-chr " << ref_ld_dirt << endl;
+         } else if (strcmp(argv[i], "--w-ld-chr") == 0) {
+@@ -1124,10 +1124,10 @@ void option(int option_num, char* option_str[])
+             chbuf = w_ld_dirt.back();
+ #ifdef _WIN32
+             if(chbuf != '\\') w_ld_dirt = w_ld_dirt + '\\';
+-#elif defined __linux__ || defined __APPLE__
++#elif defined __FreeBSD__ || defined __linux__ || defined __APPLE__
+             if(chbuf != '/') w_ld_dirt = w_ld_dirt + '/';
+ #else
+-#error Only Windows, Mac and Linux are supported.
++#error Only FreeBSD, Windows, Mac and Linux are supported.
+ #endif
+
+             LOGGER << "--w-ld-chr " << w_ld_dirt << endl;