[gentoo-commits] repo/proj/guru:master commit in: sci-biology/geneathome/files/, sci-biology/geneathome/

[gentoo-commits] repo/proj/guru:master commit in: sci-biology/geneathome/files/, sci-biology/geneathome/

[Michał Górny]

commit:     eb4a3bc46231713ffee75e71f37b828971a8bfec
Author:     Anna Vyalkova <cyber <AT> sysrq <DOT> in>
AuthorDate: Thu May 20 12:29:59 2021 +0000
Commit:     Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Thu May 20 12:47:26 2021 +0000
URL:        https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=eb4a3bc4

sci-biology/geneathome: fix wrong filename

Signed-off-by: Anna Vyalkova <cyber <AT> sysrq.in>

 sci-biology/geneathome/files/{app_config.xml => app_info.xml} | 0
 sci-biology/geneathome/geneathome-1.10.ebuild                 | 2 +-
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/geneathome/files/app_config.xml b/sci-biology/geneathome/files/app_info.xml
similarity index 100%
rename from sci-biology/geneathome/files/app_config.xml
rename to sci-biology/geneathome/files/app_info.xml

diff --git a/sci-biology/geneathome/geneathome-1.10.ebuild b/sci-biology/geneathome/geneathome-1.10.ebuild
index cf16befe5..b82d1dce5 100644
--- a/sci-biology/geneathome/geneathome-1.10.ebuild
+++ b/sci-biology/geneathome/geneathome-1.10.ebuild
@@ -64,7 +64,7 @@ src_test() {
 
 src_install() {
 	insinto /var/lib/boinc/projects/gene.disi.unitn.it_test
-	doins "${FILESDIR}"/app_config.xml
+	doins "${FILESDIR}"/app_info.xml
 	exeinto /var/lib/boinc/projects/gene.disi.unitn.it_test
 	newexe bin/pc "gene_pcim_v${PV}"
 }

[gentoo-commits] repo/proj/guru:master commit in: sci-biology/geneathome/files/, sci-biology/geneathome/

[Florian Schmaus]

commit:     9ea5a49aa158bcc842b65e236b64241a7e49272f
Author:     Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Sun Jun 11 12:13:21 2023 +0000
Commit:     Florian Schmaus <flow <AT> gentoo <DOT> org>
CommitDate: Sun Jun 11 12:14:34 2023 +0000
URL:        https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=9ea5a49a

sci-biology/geneathome: fix build with gcc 13

Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>

 .../geneathome/files/geneathome-1.10-include.patch | 12 ++++
 .../files/geneathome-1.10-iostream.patch           | 82 ++++++++++++++++++++++
 ...kefile.patch => geneathome-1.10-makefile.patch} |  0
 ...me-1.10-r3.ebuild => geneathome-1.10-r4.ebuild} | 15 ++--
 4 files changed, 99 insertions(+), 10 deletions(-)

diff --git a/sci-biology/geneathome/files/geneathome-1.10-include.patch b/sci-biology/geneathome/files/geneathome-1.10-include.patch
new file mode 100644
index 000000000..9130b88e3
--- /dev/null
+++ b/sci-biology/geneathome/files/geneathome-1.10-include.patch
@@ -0,0 +1,12 @@
+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
new file mode 100644
index 000000000..24d47cee4
--- /dev/null
+++ b/sci-biology/geneathome/files/geneathome-1.10-iostream.patch
@@ -0,0 +1,82 @@
+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/makefile.patch b/sci-biology/geneathome/files/geneathome-1.10-makefile.patch
similarity index 100%
rename from sci-biology/geneathome/files/makefile.patch
rename to sci-biology/geneathome/files/geneathome-1.10-makefile.patch

diff --git a/sci-biology/geneathome/geneathome-1.10-r3.ebuild b/sci-biology/geneathome/geneathome-1.10-r4.ebuild
similarity index 77%
rename from sci-biology/geneathome/geneathome-1.10-r3.ebuild
rename to sci-biology/geneathome/geneathome-1.10-r4.ebuild
index c25cf8755..64c1db7d3 100644
--- a/sci-biology/geneathome/geneathome-1.10-r3.ebuild
+++ b/sci-biology/geneathome/geneathome-1.10-r4.ebuild
@@ -25,21 +25,16 @@ KEYWORDS="~amd64 ~arm64 ~x86"
 DEPEND="app-arch/bzip2"
 RDEPEND="${DEPEND}"
 
-PATCHES=( "${FILESDIR}"/makefile.patch )
+PATCHES=(
+	"${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_prepare() {
-	default
-
-	# error: inlining failed in call to ‘always_inline’ ‘int fprintf(FILE*, const char*, ...)’: target specific option mismatch
-	sed  -i src/main.cpp \
-		-e 's/stdio.h/iostream/' \
-		-e 's/fprintf(stderr, \(.*\))/std::cerr << \1/g' || die
-}
-
 src_compile() {
 	tc-export CC CXX