Received: from localhost (localhost [127.0.0.1]) by mail.netbsd.org (Postfix) with ESMTP id A2C2B84D45 for ; Sat, 20 May 2023 11:27:28 +0000 (UTC) X-Virus-Scanned: amavisd-new at netbsd.org Received: from mail.netbsd.org ([IPv6:::1]) by localhost (mail.netbsd.org [IPv6:::1]) (amavisd-new, port 10025) with ESMTP id 0uJI-lH_Ump9 for ; Sat, 20 May 2023 11:27:27 +0000 (UTC) Received: from cvs.NetBSD.org (ivanova.netbsd.org [199.233.217.197]) by mail.netbsd.org (Postfix) with ESMTP id 618C084CED for ; Sat, 20 May 2023 11:27:27 +0000 (UTC) Received: by cvs.NetBSD.org (Postfix, from userid 500) id 5A8CAFA87; Sat, 20 May 2023 11:27:27 +0000 (UTC) Content-Transfer-Encoding: 7bit Content-Type: multipart/mixed; boundary="_----------=_1684582047262710" MIME-Version: 1.0 Date: Sat, 20 May 2023 11:27:27 +0000 From: "Jason Bacon" Subject: CVS commit: pkgsrc/biology/canu To: pkgsrc-changes@NetBSD.org Approved: commit_and_comment Reply-To: bacon@netbsd.org X-Mailer: log_accum Message-Id: <20230520112727.5A8CAFA87@cvs.NetBSD.org> This is a multi-part message in MIME format. --_----------=_1684582047262710 Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Module Name: pkgsrc Committed By: bacon Date: Sat May 20 11:27:27 UTC 2023 Modified Files: pkgsrc/biology/canu: Makefile PLIST distinfo pkgsrc/biology/canu/patches: patch-Makefile patch-pipelines_canu_Defaults.pm patch-pipelines_canu_Execution.pm patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp patch-utility_src_parasail_internal__sse.h patch-utility_src_utility_align-ssw.H patch-utility_src_utility_files.H patch-utility_src_utility_logging.H patch-utility_src_utility_system.H patch-utility_src_utility_types.H Log Message: biology/canu: Hacks to support Darwin x86 OpenMP support needs improvement Darwin aarch64 still blocked by glib2 build issues No changes to binaries on other platforms To generate a diff of this commit: cvs rdiff -u -r1.19 -r1.20 pkgsrc/biology/canu/Makefile cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/canu/PLIST cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/canu/distinfo cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/canu/patches/patch-Makefile \ pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm \ pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm cvs rdiff -u -r1.1 -r1.2 \ pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp \ pkgsrc/biology/canu/patches/patch-utility_src_parasail_internal__sse.h \ pkgsrc/biology/canu/patches/patch-utility_src_utility_align-ssw.H \ pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H \ pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H \ pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H \ pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H Please note that diffs are not public domain; they are subject to the copyright notices on the relevant files. --_----------=_1684582047262710 Content-Disposition: inline Content-Length: 12080 Content-Transfer-Encoding: binary Content-Type: text/x-diff; charset=us-ascii Modified files: Index: pkgsrc/biology/canu/Makefile diff -u pkgsrc/biology/canu/Makefile:1.19 pkgsrc/biology/canu/Makefile:1.20 --- pkgsrc/biology/canu/Makefile:1.19 Thu May 18 18:17:32 2023 +++ pkgsrc/biology/canu/Makefile Sat May 20 11:27:27 2023 @@ -1,4 +1,4 @@ -# $NetBSD: Makefile,v 1.19 2023/05/18 18:17:32 bacon Exp $ +# $NetBSD: Makefile,v 1.20 2023/05/20 11:27:27 bacon Exp $ DISTNAME= canu-2.2 CATEGORIES= biology java @@ -13,17 +13,6 @@ LICENSE= gnu-gpl-v2 DEPENDS+= gnuplot>0:../../graphics/gnuplot -# Makefile compiles directly into ${DESTDIR}${PREFIX} -SUBST_CLASSES+= optimize -SUBST_STAGE.optimize= pre-configure -SUBST_SED.optimize+= -e 's|-g3||g' -SUBST_SED.optimize+= -e 's|-O3||g' -SUBST_SED.optimize+= -e 's|-O4||g' -SUBST_SED.optimize+= -e 's|-funroll-loops||g' -SUBST_SED.optimize+= -e 's|-fexpensive-optimizations||g' -SUBST_SED.optimize+= -e 's|-finline-functions||g' -SUBST_FILES.optimize+= Makefile - SUBST_CLASSES+= perl SUBST_STAGE.perl= pre-configure SUBST_SED.perl+= -e 's|$$FindBin::RealBin/../lib/site_perl|${PREFIX}/${SITE_PERL_REL}|g' @@ -55,7 +44,7 @@ MAKE_ENV+= DESTDIR=${WRKSRC} TMP_INST= ${WRKSRC}/build SITE_PERL_REL= lib/perl5/site_perl JAVAJARDIR= share/java/classes -INSTALLATION_DIRS= bin ${JAVAJARDIR} +INSTALLATION_DIRS= bin lib/perl5 ${JAVAJARDIR} post-extract: ${CHMOD} -R g-w ${WRKDIR} @@ -70,6 +59,15 @@ do-install: cd ${TMP_INST}/lib/perl5 && ${PAX} -wr * ${DESTDIR}${PREFIX}/lib/perl5 cd ${TMP_INST}/share && ${PAX} -wr * ${DESTDIR}${PREFIX}/share +.include "../../mk/bsd.prefs.mk" + +# Xcode supports -Xpreprocessor -fopenmp, but does not supply OpenMP libs +# parallel/openmp installs an entire llvm +# Maybe a libomp package would suffice? +.if ${OPSYS} == Darwin +.include "../../parallel/openmp/buildlink3.mk" +.endif + .include "../../devel/boost-libs/buildlink3.mk" .include "../../devel/simde/buildlink3.mk" .include "../../lang/perl5/module.mk" Index: pkgsrc/biology/canu/PLIST diff -u pkgsrc/biology/canu/PLIST:1.2 pkgsrc/biology/canu/PLIST:1.3 --- pkgsrc/biology/canu/PLIST:1.2 Thu May 18 18:17:32 2023 +++ pkgsrc/biology/canu/PLIST Sat May 20 11:27:27 2023 @@ -1,4 +1,4 @@ -@comment $NetBSD: PLIST,v 1.2 2023/05/18 18:17:32 bacon Exp $ +@comment $NetBSD: PLIST,v 1.3 2023/05/20 11:27:27 bacon Exp $ bin/alignGFA bin/bogart bin/canu Index: pkgsrc/biology/canu/distinfo diff -u pkgsrc/biology/canu/distinfo:1.5 pkgsrc/biology/canu/distinfo:1.6 --- pkgsrc/biology/canu/distinfo:1.5 Thu May 18 18:17:32 2023 +++ pkgsrc/biology/canu/distinfo Sat May 20 11:27:27 2023 @@ -1,9 +1,9 @@ -$NetBSD: distinfo,v 1.5 2023/05/18 18:17:32 bacon Exp $ +$NetBSD: distinfo,v 1.6 2023/05/20 11:27:27 bacon Exp $ BLAKE2s (canu-2.2.tar.xz) = 5b585a2e0a31c2181817798b5f267dd4cf43c3ffeba4b0a04ffc8021a4603aed SHA512 (canu-2.2.tar.xz) = af08874a319dd5fd6bbe666c8a5d0a43b7c0caaaca3a3cbf4d3fe022d6d6b8c14cd967c2e26f4fbf571129be240dcb65e92fe61fad1e51d554f15254d0b6ce8f Size (canu-2.2.tar.xz) = 2400192 bytes -SHA1 (patch-Makefile) = aa83003677cbb12558e438c776402ec48df0598d +SHA1 (patch-Makefile) = 54a3a216948fea81cfeb6ce91458126adc2ad8da SHA1 (patch-pipelines_canu_Defaults.pm) = 5ecea8ebac667499916b0243f34dc25838992444 SHA1 (patch-pipelines_canu_Execution.pm) = 75c019a93f5b6a4491191b4f32931ac0b8435421 SHA1 (patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp) = fd219645141ebe9d6f23153a2a2b0f56abc103af Index: pkgsrc/biology/canu/patches/patch-Makefile diff -u pkgsrc/biology/canu/patches/patch-Makefile:1.2 pkgsrc/biology/canu/patches/patch-Makefile:1.3 --- pkgsrc/biology/canu/patches/patch-Makefile:1.2 Thu May 18 18:17:32 2023 +++ pkgsrc/biology/canu/patches/patch-Makefile Sat May 20 11:27:27 2023 @@ -1,11 +1,61 @@ -$NetBSD: patch-Makefile,v 1.2 2023/05/18 18:17:32 bacon Exp $ +$NetBSD: patch-Makefile,v 1.3 2023/05/20 11:27:27 bacon Exp $ -# Template Makefile requires platform-specific defaults for each OS -# To be sent upstream following commit +# Portability ---- Makefile.orig 2018-10-22 16:47:31.000000000 +0000 +--- Makefile.orig 2021-08-04 00:21:51.000000000 +0000 +++ Makefile -@@ -545,6 +545,40 @@ endif +@@ -418,12 +418,12 @@ endif + ifeq ($(origin CXXFLAGS), undefined) + ifeq ($(BUILDOPTIMIZED), 1) + else +- CXXFLAGS += -g3 ++ CXXFLAGS += + endif + + ifeq ($(BUILDDEBUG), 1) + else +- CXXFLAGS += -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer ++ CXXFLAGS += -fomit-frame-pointer + endif + + ifeq ($(BUILDJEMALLOC), 1) +@@ -497,27 +497,8 @@ endef + ifeq (${OSTYPE}, Darwin) + $(foreach suffix,mp-9 9 mp-8 8 mp-7 7,$(eval $(call TEST_COMPILER,${suffix}))) + +- ifneq ($(shell echo `$(CXX) --version 2>&1 | grep -c clang`), 0) +- CPATH := $(shell echo `which $(CXX)`) +- CLANG := $(shell echo `$(CXX) --version 2>&1 | grep clang`) +- space := +- +- $(warning ) +- ifeq ($(CXX), $(CPATH)) +- $(warning Compiler '$(CXX)' reports version '$(CLANG)'.) +- else +- $(warning Compiler '$(CXX)' at '$(CPATH)' reports version '$(CLANG)'.) +- endif +- $(warning ) +- $(warning Canu cannot be compiled with this compiler. Please install GCC and/or) +- $(warning specify a non-Clang compiler on the command line, e.g.,) # Quite the evil trick to get +- $(warning $(space) make CC=/path/to/gcc CXX=/path/to/g++); # this line indented! +- $(warning ) +- $(error unsupported compiler) +- endif +- +- CXXFLAGS += -fopenmp -pthread -fPIC -m64 -Wno-format +- LDFLAGS += -fopenmp -pthread -lm ++ CXXFLAGS += -std=c++11 -Xpreprocessor -fopenmp -pthread -fPIC -m64 -Wno-format ++ LDFLAGS += -L${PREFIX}/lib -lomp -pthread -lm + endif + + +@@ -559,11 +540,45 @@ else + #LDFLAGS += -lprofiler + + # callgrind +- #CXXFLAGS += -g3 -Wa,--gstabs -save-temps ++ #CXXFLAGS += -Wa,--gstabs -save-temps + endif endif @@ -29,16 +79,16 @@ $NetBSD: patch-Makefile,v 1.2 2023/05/18 + #LDFLAGS += -lprofiler + + # callgrind -+ #CXXFLAGS += -g3 -Wa,--gstabs -save-temps ++ #CXXFLAGS += -Wa,--gstabs -save-temps + + ifeq ($(BUILDOPTIMIZED), 1) + else -+ CXXFLAGS += -g3 ++ CXXFLAGS += + endif + + ifeq ($(BUILDDEBUG), 1) + else -+ CXXFLAGS += -O3 -finline-functions -fomit-frame-pointer ++ CXXFLAGS += -fomit-frame-pointer + endif +endif + Index: pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm diff -u pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm:1.2 pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm:1.3 --- pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm:1.2 Thu May 18 18:17:32 2023 +++ pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm Sat May 20 11:27:27 2023 @@ -1,4 +1,4 @@ -$NetBSD: patch-pipelines_canu_Defaults.pm,v 1.2 2023/05/18 18:17:32 bacon Exp $ +$NetBSD: patch-pipelines_canu_Defaults.pm,v 1.3 2023/05/20 11:27:27 bacon Exp $ # Better task limit control under slurm Index: pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm diff -u pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm:1.2 pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm:1.3 --- pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm:1.2 Thu May 18 18:17:32 2023 +++ pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm Sat May 20 11:27:27 2023 @@ -1,4 +1,4 @@ -$NetBSD: patch-pipelines_canu_Execution.pm,v 1.2 2023/05/18 18:17:32 bacon Exp $ +$NetBSD: patch-pipelines_canu_Execution.pm,v 1.3 2023/05/20 11:27:27 bacon Exp $ # Better task limit control under slurm Index: pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp diff -u pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp:1.1 pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp:1.2 --- pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp:1.1 Thu May 18 18:17:32 2023 +++ pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp Sat May 20 11:27:27 2023 @@ -1,4 +1,4 @@ -$NetBSD: patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp,v 1.1 2023/05/18 18:17:32 bacon Exp $ +$NetBSD: patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp,v 1.2 2023/05/20 11:27:27 bacon Exp $ # Portability Index: pkgsrc/biology/canu/patches/patch-utility_src_parasail_internal__sse.h diff -u pkgsrc/biology/canu/patches/patch-utility_src_parasail_internal__sse.h:1.1 pkgsrc/biology/canu/patches/patch-utility_src_parasail_internal__sse.h:1.2 --- pkgsrc/biology/canu/patches/patch-utility_src_parasail_internal__sse.h:1.1 Thu May 18 18:17:32 2023 +++ pkgsrc/biology/canu/patches/patch-utility_src_parasail_internal__sse.h Sat May 20 11:27:27 2023 @@ -1,4 +1,4 @@ -$NetBSD: patch-utility_src_parasail_internal__sse.h,v 1.1 2023/05/18 18:17:32 bacon Exp $ +$NetBSD: patch-utility_src_parasail_internal__sse.h,v 1.2 2023/05/20 11:27:27 bacon Exp $ # Portability Index: pkgsrc/biology/canu/patches/patch-utility_src_utility_align-ssw.H diff -u pkgsrc/biology/canu/patches/patch-utility_src_utility_align-ssw.H:1.1 pkgsrc/biology/canu/patches/patch-utility_src_utility_align-ssw.H:1.2 --- pkgsrc/biology/canu/patches/patch-utility_src_utility_align-ssw.H:1.1 Thu May 18 18:17:32 2023 +++ pkgsrc/biology/canu/patches/patch-utility_src_utility_align-ssw.H Sat May 20 11:27:27 2023 @@ -1,4 +1,4 @@ -$NetBSD: patch-utility_src_utility_align-ssw.H,v 1.1 2023/05/18 18:17:32 bacon Exp $ +$NetBSD: patch-utility_src_utility_align-ssw.H,v 1.2 2023/05/20 11:27:27 bacon Exp $ # Portability Index: pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H diff -u pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H:1.1 pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H:1.2 --- pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H:1.1 Thu May 18 18:17:32 2023 +++ pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H Sat May 20 11:27:27 2023 @@ -1,4 +1,4 @@ -$NetBSD: patch-utility_src_utility_files.H,v 1.1 2023/05/18 18:17:32 bacon Exp $ +$NetBSD: patch-utility_src_utility_files.H,v 1.2 2023/05/20 11:27:27 bacon Exp $ # Portability Index: pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H diff -u pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H:1.1 pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H:1.2 --- pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H:1.1 Thu May 18 18:17:32 2023 +++ pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H Sat May 20 11:27:27 2023 @@ -1,4 +1,4 @@ -$NetBSD: patch-utility_src_utility_logging.H,v 1.1 2023/05/18 18:17:32 bacon Exp $ +$NetBSD: patch-utility_src_utility_logging.H,v 1.2 2023/05/20 11:27:27 bacon Exp $ # Portability Index: pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H diff -u pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H:1.1 pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H:1.2 --- pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H:1.1 Thu May 18 18:17:32 2023 +++ pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H Sat May 20 11:27:27 2023 @@ -1,4 +1,4 @@ -$NetBSD: patch-utility_src_utility_system.H,v 1.1 2023/05/18 18:17:32 bacon Exp $ +$NetBSD: patch-utility_src_utility_system.H,v 1.2 2023/05/20 11:27:27 bacon Exp $ # Portability Index: pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H diff -u pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H:1.1 pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H:1.2 --- pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H:1.1 Thu May 18 18:17:32 2023 +++ pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H Sat May 20 11:27:27 2023 @@ -1,4 +1,4 @@ -$NetBSD: patch-utility_src_utility_types.H,v 1.1 2023/05/18 18:17:32 bacon Exp $ +$NetBSD: patch-utility_src_utility_types.H,v 1.2 2023/05/20 11:27:27 bacon Exp $ # Portability --_----------=_1684582047262710--