Adding metadata

7 files changed, 0 insertions, 224 deletions

diff --git a/sci-biology/geneathome/Manifest b/sci-biology/geneathome/Manifest
deleted file mode 100644
index 806447644dd0..000000000000
--- a/sci-biology/geneathome/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST geneathome-1.10.tar.gz 73686241 BLAKE2B 4a4e9930e3faeaf0b6d687d26adb3267af1a70096397e9e4001066a7029a854b95cd35b6779a0e6bcf6c9cb3ad662b5f9e6adf4ab9d608ed2d73c65d3dadc10b SHA512 c8c1bb65f0021d9c9d9f14375212c458694dbb21abbfa90f6b8fb958bc6d86a522bbe13846b5930f6df0a4e755256f2016c5edd4447ae147cb1381eccce06b9e
diff --git a/sci-biology/geneathome/files/app_info.xml b/sci-biology/geneathome/files/app_info.xml
deleted file mode 100644
index 82ce7a9cd93a..000000000000
--- a/sci-biology/geneathome/files/app_info.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<app_info>
-<app>
-	<name>gene_pcim</name>
-	<user_friendly_name>gene@home PC-IM</user_friendly_name>
-</app>
-
-<file_info>
-	<name>gene_pcim_v@PV@</name>
-	<sticky/>
-	<executable/>
-</file_info>
-
-<app_version>
-	<app_name>gene_pcim</app_name>
-	<version_num>110</version_num>
-	<plan_class>avx</plan_class>
-	<file_ref>
-		<file_name>gene_pcim_v@PV@</file_name>
-		<main_program/>
-	</file_ref>
-</app_version>
-</app_info>
diff --git a/sci-biology/geneathome/files/geneathome-1.10-include.patch b/sci-biology/geneathome/files/geneathome-1.10-include.patch
deleted file mode 100644
index 9130b88e30e5..000000000000
--- a/sci-biology/geneathome/files/geneathome-1.10-include.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-Fixes build with GCC 13.
-
---- a/src/simd/Vector.hpp
-+++ b/src/simd/Vector.hpp
-@@ -23,6 +23,7 @@
- 
- #include <type_traits>
- #include <cassert>
-+#include <cstdint>
- 
- // std::negation requires C++17, so defined own one
- template<typename B>
diff --git a/sci-biology/geneathome/files/geneathome-1.10-iostream.patch b/sci-biology/geneathome/files/geneathome-1.10-iostream.patch
deleted file mode 100644
index 24d47cee4038..000000000000
--- a/sci-biology/geneathome/files/geneathome-1.10-iostream.patch
+++ /dev/null
@@ -1,82 +0,0 @@
-Fixes "inlining failed in call to ..."
-
---- a/src/main.cpp
-+++ b/src/main.cpp
-@@ -22,8 +22,8 @@ int appMain(int argc, char* argv[]);
- 
- #if defined(__i386__) || defined (__x86_64__)
- 
-+#include <iostream>
- #include <cpuid.h>
--#include <stdio.h>
- 
- __attribute__((target("no-avx,no-sse")))
- bool checkRequiredInstructionSets() {
-@@ -34,14 +34,14 @@ bool checkRequiredInstructionSets() {
- 	unsigned int a, b, c, d;
- 
- 	if (!__get_cpuid(1, &a, &b, &c, &d)) {
--		fprintf(stderr, "CPUID instruction is not supported by your CPU!\n");
-+		std::cerr << "CPUID instruction is not supported by your CPU!\n";
- 		return false;
- 	}
- 
- #ifdef __SSE2__
- 	//printf("Checking for SSE2 support\n");
- 	if (0 == (d & bit_SSE2)) {
--		fprintf(stderr, "SSE2 instructions are not supported by your CPU!\n");
-+		std::cerr << "SSE2 instructions are not supported by your CPU!\n";
- 		return false;
- 	}
- #endif
-@@ -49,13 +49,13 @@ bool checkRequiredInstructionSets() {
- #ifdef __AVX__
- 	//printf("Checking for AVX support\n");
- 	if (0 == (c & bit_AVX)) {
--		fprintf(stderr, "AVX instructions are not supported by your CPU!\n");
-+		std::cerr << "AVX instructions are not supported by your CPU!\n";
- 		return false;
- 	}
- 
- 	// AVX also needs OS support, check for it
- 	if (0 == (c & bit_OSXSAVE)) {
--		fprintf(stderr, "OSXSAVE instructions are not supported by your CPU!\n");
-+		std::cerr << "OSXSAVE instructions are not supported by your CPU!\n";
- 		return false;
- 	}
- 
-@@ -63,7 +63,7 @@ bool checkRequiredInstructionSets() {
- 	unsigned int ecx = 0; // _XCR_XFEATURE_ENABLED_MASK
- 	__asm__ ("xgetbv" : "=a" (eax), "=d" (edx) : "c" (ecx));
- 	if (0x6 != (eax & 0x6)) { // XSTATE_SSE | XSTATE_YMM
--		fprintf(stderr, "AVX instructions are not supported by your OS!\n");
-+		std::cerr << "AVX instructions are not supported by your OS!\n";
- 		return false;
- 	}
- #endif
-@@ -71,7 +71,7 @@ bool checkRequiredInstructionSets() {
- #ifdef __FMA__
- 	//printf("Checking for FMA support\n");
- 	if (0 == (c & bit_FMA)) {
--		fprintf(stderr, "FMA instructions are not supported by your CPU!\n");
-+		std::cerr << "FMA instructions are not supported by your CPU!\n";
- 		return false;
- 	}
- #endif
-@@ -79,14 +79,14 @@ bool checkRequiredInstructionSets() {
- #ifdef __AVX2__
- 	//printf("Checking for AVX2 support\n");
- 	if (__get_cpuid_max(0, 0) < 7) {
--		fprintf(stderr, "Extended CPUID 0x7 instruction is not supported by your CPU!\n");
-+		std::cerr << "Extended CPUID 0x7 instruction is not supported by your CPU!\n";
- 		return false;
- 	}
- 
- 	__cpuid_count(7, 0, a, b, c, d);
- 
- 	if (0 == (b & bit_AVX2)) {
--		fprintf(stderr, "AVX2 instructions are not supported by your CPU!\n");
-+		std::cerr << "AVX2 instructions are not supported by your CPU!\n";
- 		return false;
- 	}
- #endif
diff --git a/sci-biology/geneathome/files/geneathome-1.10-makefile.patch b/sci-biology/geneathome/files/geneathome-1.10-makefile.patch
deleted file mode 100644
index 7025b694df36..000000000000
--- a/sci-biology/geneathome/files/geneathome-1.10-makefile.patch
+++ /dev/null
@@ -1,44 +0,0 @@
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -22,20 +22,16 @@
- BOINC_DIR ?= ../../..
- BOINC_API_DIR ?= $(BOINC_DIR)/api
- BOINC_LIB_DIR ?= $(BOINC_DIR)/lib
--BOINC_ZIP_DIR ?= $(BOINC_DIR)/zip
--BOINC_LIBS ?= $(BOINC_API_DIR)/libboinc_api.a $(BOINC_LIB_DIR)/libboinc.a
-+BOINC_LIBS ?= -lboinc_api -lboinc
- 
- ifdef BOINC_STUB
- BOINC_DIR = ../boinc_stub
- BOINC_LIBS =
- endif
- 
--FREETYPE_DIR = /usr/include/freetype2
--CPPFLAGS += -I$(BOINC_DIR) -I$(BOINC_LIB_DIR) -I$(BOINC_API_DIR) -I$(BOINC_ZIP_DIR) -I$(FREETYPE_DIR) -Isimd
--CFLAGS += -c -O3 $(ARCH) -Wall -Wextra -pedantic -Werror $(VARIANTFLAGS)  -MMD -MP
--CXXFLAGS += $(CFLAGS) -std=gnu++11
--LDFLAGS += $(ARCH) -L/usr/X11R6/lib -L. -static
--LIBS ?= -static-libgcc -static-libstdc++ -pthread -Wl,-Bstatic -lbz2
-+CPPFLAGS += -I$(BOINC_DIR) -Isimd
-+CXXFLAGS += -std=gnu++11
-+LIBS ?= -pthread -lbz2
- CXXSOURCES = BoincFile.cpp Graph.cpp boinc_functions.cpp utility.cpp pc.cpp main.cpp
- CSOURCES = erf.c
- OBJECTS = $(CXXSOURCES:.cpp=.o) $(CSOURCES:.c=.o)
-@@ -44,13 +40,13 @@
- all: $(EXECUTABLE)
- 
- $(EXECUTABLE): $(OBJECTS)
--	$(CXX) $(LDFLAGS) $(OBJECTS) -o $@ $(LIBS) $(BOINC_LIBS)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) $(LIBS) $(BOINC_LIBS)
- 
- .cpp.o:
--	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $< -o $@
-+	$(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $< -o $@
- 
- .c.o:
--	$(CC) $(CPPFLAGS) $(CFLAGS) $< -o $@
-+	$(CC) -c $(CPPFLAGS) $(CFLAGS) $< -o $@
- 
- clean:
- 	rm -rf ../bin/$(EXECUTABLE) *.o *~ *.d
diff --git a/sci-biology/geneathome/geneathome-1.10-r5.ebuild b/sci-biology/geneathome/geneathome-1.10-r5.ebuild
deleted file mode 100644
index 64c1db7d3acd..000000000000
--- a/sci-biology/geneathome/geneathome-1.10-r5.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-BOINC_MASTER_URL="https://gene.disi.unitn.it/test/"
-BOINC_INVITATION_CODE="science@tn"
-BOINC_HELPTEXT=\
-"gene@home is a part of TN-Grid BOINC project."
-
-inherit boinc-app edo toolchain-funcs
-
-MY_PN="pc-boinc"
-COMMIT="3186afba409a"
-
-DESCRIPTION="BOINC application for expanding Gene Regulatory Networks (GRN)"
-HOMEPAGE+=" https://bitbucket.org/francesco-asnicar/pc-boinc"
-SRC_URI="https://bitbucket.org/francesco-asnicar/${MY_PN}/get/${COMMIT}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}/francesco-asnicar-${MY_PN}-${COMMIT}"
-
-LICENSE="sunpro public-domain"
-SLOT="0"
-KEYWORDS="~amd64 ~arm64 ~x86"
-
-DEPEND="app-arch/bzip2"
-RDEPEND="${DEPEND}"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-1.10-include.patch
-	"${FILESDIR}"/${PN}-1.10-iostream.patch
-	"${FILESDIR}"/${PN}-1.10-makefile.patch
-)
-
-DOCS=( Readme.md )
-
-boinc-app_add_deps
-
-src_compile() {
-	tc-export CC CXX
-
-	emake -C src BOINC_DIR="${ESYSROOT}"/usr/include/boinc
-}
-
-src_test() {
-	edo bash ./test_run.sh
-	edo bash ./test_run2.sh
-}
-
-src_install() {
-	doappinfo "${FILESDIR}"/app_info.xml
-
-	exeinto $(get_project_root)
-	exeopts -m 0755 --owner root --group boinc
-	newexe bin/pc "gene_pcim_v${PV}"
-}
diff --git a/sci-biology/geneathome/metadata.xml b/sci-biology/geneathome/metadata.xml
deleted file mode 100644
index 7ad3b4b682c6..000000000000
--- a/sci-biology/geneathome/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<upstream>
-		<remote-id type="bitbucket">francesco-asnicar/pc-boinc</remote-id>
-	</upstream>
-	<!-- maintainer-needed -->
-</pkgmetadata>