From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (2048 bits) server-digest SHA256) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id CADB215810F for ; Sun, 11 Jun 2023 12:14:47 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 15BB9E0784; Sun, 11 Jun 2023 12:14:47 +0000 (UTC) Received: from smtp.gentoo.org (woodpecker.gentoo.org [140.211.166.183]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id E7C6DE0784 for ; Sun, 11 Jun 2023 12:14:46 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id B1C3B341288 for ; Sun, 11 Jun 2023 12:14:45 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 1AA96A5C for ; Sun, 11 Jun 2023 12:14:44 +0000 (UTC) From: "Anna Vyalkova" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Anna Vyalkova" Message-ID: <1686485674.9ea5a49aa158bcc842b65e236b64241a7e49272f.cybertailor@gentoo> Subject: [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/geneathome/files/, sci-biology/geneathome/ X-VCS-Repository: repo/proj/guru X-VCS-Files: sci-biology/geneathome/files/geneathome-1.10-include.patch sci-biology/geneathome/files/geneathome-1.10-iostream.patch sci-biology/geneathome/files/geneathome-1.10-makefile.patch sci-biology/geneathome/files/makefile.patch sci-biology/geneathome/geneathome-1.10-r3.ebuild sci-biology/geneathome/geneathome-1.10-r4.ebuild X-VCS-Directories: sci-biology/geneathome/files/ sci-biology/geneathome/ X-VCS-Committer: cybertailor X-VCS-Committer-Name: Anna Vyalkova X-VCS-Revision: 9ea5a49aa158bcc842b65e236b64241a7e49272f X-VCS-Branch: dev Date: Sun, 11 Jun 2023 12:14:44 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: 6d92dbe2-6a09-4dbd-a976-a26d9afcde21 X-Archives-Hash: d80dd206e9974ed25666eb303c757cf9 commit: 9ea5a49aa158bcc842b65e236b64241a7e49272f Author: Anna (cybertailor) Vyalkova sysrq in> AuthorDate: Sun Jun 11 12:13:21 2023 +0000 Commit: Anna Vyalkova sysrq in> 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 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 + #include ++#include + + // std::negation requires C++17, so defined own one + template 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 + #include +-#include + + __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