head 1.4; access; symbols pkgsrc-2026Q1:1.4.0.24 pkgsrc-2026Q1-base:1.4 pkgsrc-2025Q4:1.4.0.22 pkgsrc-2025Q4-base:1.4 pkgsrc-2025Q3:1.4.0.20 pkgsrc-2025Q3-base:1.4 pkgsrc-2025Q2:1.4.0.18 pkgsrc-2025Q2-base:1.4 pkgsrc-2025Q1:1.4.0.16 pkgsrc-2025Q1-base:1.4 pkgsrc-2024Q4:1.4.0.14 pkgsrc-2024Q4-base:1.4 pkgsrc-2024Q3:1.4.0.12 pkgsrc-2024Q3-base:1.4 pkgsrc-2024Q2:1.4.0.10 pkgsrc-2024Q2-base:1.4 pkgsrc-2024Q1:1.4.0.8 pkgsrc-2024Q1-base:1.4 pkgsrc-2023Q4:1.4.0.6 pkgsrc-2023Q4-base:1.4 pkgsrc-2023Q3:1.4.0.4 pkgsrc-2023Q3-base:1.4 pkgsrc-2023Q2:1.4.0.2 pkgsrc-2023Q2-base:1.4 pkgsrc-2023Q1:1.1.0.34 pkgsrc-2023Q1-base:1.1 pkgsrc-2022Q4:1.1.0.32 pkgsrc-2022Q4-base:1.1 pkgsrc-2022Q3:1.1.0.30 pkgsrc-2022Q3-base:1.1 pkgsrc-2022Q2:1.1.0.28 pkgsrc-2022Q2-base:1.1 pkgsrc-2022Q1:1.1.0.26 pkgsrc-2022Q1-base:1.1 pkgsrc-2021Q4:1.1.0.24 pkgsrc-2021Q4-base:1.1 pkgsrc-2021Q3:1.1.0.22 pkgsrc-2021Q3-base:1.1 pkgsrc-2021Q2:1.1.0.20 pkgsrc-2021Q2-base:1.1 pkgsrc-2021Q1:1.1.0.18 pkgsrc-2021Q1-base:1.1 pkgsrc-2020Q4:1.1.0.16 pkgsrc-2020Q4-base:1.1 pkgsrc-2020Q3:1.1.0.14 pkgsrc-2020Q3-base:1.1 pkgsrc-2020Q2:1.1.0.12 pkgsrc-2020Q2-base:1.1 pkgsrc-2020Q1:1.1.0.8 pkgsrc-2020Q1-base:1.1 pkgsrc-2019Q4:1.1.0.10 pkgsrc-2019Q4-base:1.1 pkgsrc-2019Q3:1.1.0.6 pkgsrc-2019Q3-base:1.1 pkgsrc-2019Q2:1.1.0.4 pkgsrc-2019Q2-base:1.1 pkgsrc-2019Q1:1.1.0.2 pkgsrc-2019Q1-base:1.1; locks; strict; comment @# @; 1.4 date 2023.05.20.14.42.11; author bacon; state Exp; branches; next 1.3; commitid 8RILFeKtJELCaIpE; 1.3 date 2023.05.20.11.27.27; author bacon; state Exp; branches; next 1.2; commitid dYMeBtIFfV0k5HpE; 1.2 date 2023.05.18.18.17.32; author bacon; state Exp; branches; next 1.1; commitid n0kkHuV914heqtpE; 1.1 date 2019.01.07.02.33.17; author bacon; state Exp; branches; next ; commitid HfnComiKFLAHnN6B; desc @@ 1.4 log @biology/canu: Fix build on Darwin aarch64 Replace SIMDE with upstream source hacks from FreeBSD port Should also work on powerpc, but untested No changes to existing binaries @ text @$NetBSD$ # Portability --- Makefile.orig 2021-08-04 00:21:51.000000000 +0000 +++ Makefile @@@@ -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 +ifeq (${OSTYPE}, NetBSD) + CC ?= gcc + CXX ?= g++ + + # GCC + CXXFLAGS += -pthread -fopenmp -fPIC + LDFLAGS += -pthread -fopenmp -lm -lexecinfo + + #CXXFLAGS += -Wall -Wextra -Wformat -Wno-unused -Wno-parentheses + CXXFLAGS += -Wall -Wextra -Wformat -Wno-unused-function -Wno-unused-parameter -Wno-unused-variable -Wno-char-subscripts -Wno-write-strings -Wno-sign-compare -Wno-format-truncation + + # Google Performance Tools malloc and heapchecker (HEAPCHECK=normal) + #CXXFLAGS += + #LDFLAGS += -ltcmalloc + + # Google Performance Tools cpu profiler (CPUPROFILE=/path) + #CXXFLAGS += + #LDFLAGS += -lprofiler + + # callgrind + #CXXFLAGS += -Wa,--gstabs -save-temps + + ifeq ($(BUILDOPTIMIZED), 1) + else + CXXFLAGS += + endif + + ifeq ($(BUILDDEBUG), 1) + else + CXXFLAGS += -fomit-frame-pointer + endif +endif + + ifneq (,$(findstring CYGWIN, ${OSTYPE})) CC ?= gcc CXX ?= g++ @ 1.3 log @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 @ text @@ 1.2 log @biology/canu: Update to 2.2 Numerous new features, enhancements, and bug fixes since 1.8 Enabled support for aarch64 May work on other 64-bit platforms, but untested Changes: https://github.com/marbl/canu/releases @ text @d3 1 a3 2 # Template Makefile requires platform-specific defaults for each OS # To be sent upstream following commit d5 1 a5 1 --- Makefile.orig 2018-10-22 16:47:31.000000000 +0000 d7 52 a58 1 @@@@ -545,6 +545,40 @@@@ endif d82 1 a82 1 + #CXXFLAGS += -g3 -Wa,--gstabs -save-temps d86 1 a86 1 + CXXFLAGS += -g3 d91 1 a91 1 + CXXFLAGS += -O3 -finline-functions -fomit-frame-pointer @ 1.1 log @biology/canu: import canu-1.8 Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). Canu is a hierarchical assembly pipeline which runs in four steps: Detect overlaps in high-noise sequences using MHAP Generate corrected sequence consensus Trim corrected sequences Assemble trimmed corrected sequences @ text @@