Date: Sun, 22 Mar 2026 12:59:38 +0000 From: Jason W. Bacon <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: f3a8e8b50e62 - main - biology/fastp: Update to 1.2.0 Message-ID: <69bfe7ba.421e1.8a1187d@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=f3a8e8b50e6241bc719508b807d62d5222553a4f commit f3a8e8b50e6241bc719508b807d62d5222553a4f Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2026-03-22 12:55:42 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2026-03-22 12:55:42 +0000 biology/fastp: Update to 1.2.0 Numerous improvements and fixes since 0.26.0 Changes: https://github.com/OpenGene/fastp/commits/master/ Reported by: hayzam@alchemilla.io Reviewed by: jwb Tested by: jwb --- biology/fastp/Makefile | 5 ++- biology/fastp/distinfo | 6 +-- biology/fastp/files/patch-Makefile | 79 +++++++++++++++++++++++--------------- 3 files changed, 55 insertions(+), 35 deletions(-) diff --git a/biology/fastp/Makefile b/biology/fastp/Makefile index 7d91034eb87c..36ede673577f 100644 --- a/biology/fastp/Makefile +++ b/biology/fastp/Makefile @@ -1,6 +1,6 @@ PORTNAME= fastp DISTVERSIONPREFIX= v -DISTVERSION= 0.26.0 +DISTVERSION= 1.2.0 CATEGORIES= biology MAINTAINER= hayzam@alchemilla.io @@ -11,7 +11,8 @@ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libdeflate.so:archivers/libdeflate \ - libisal.so:devel/isa-l + libisal.so:devel/isa-l \ + libhwy.so:devel/highway USES= gmake localbase:ldflags USE_GITHUB= yes diff --git a/biology/fastp/distinfo b/biology/fastp/distinfo index 6abdf5196be5..c7039f9e2bf7 100644 --- a/biology/fastp/distinfo +++ b/biology/fastp/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1749236354 -SHA256 (OpenGene-fastp-v0.26.0_GH0.tar.gz) = ab5396f448bece92e599e4d3acc48751fc46f0f43333ca271d229aa95dc47c4e -SIZE (OpenGene-fastp-v0.26.0_GH0.tar.gz) = 166500 +TIMESTAMP = 1773759010 +SHA256 (OpenGene-fastp-v1.2.0_GH0.tar.gz) = fd7e20923e8f748803d54d9e0fabf44a44c748822a65062999e4b7edec6b8da6 +SIZE (OpenGene-fastp-v1.2.0_GH0.tar.gz) = 125582 diff --git a/biology/fastp/files/patch-Makefile b/biology/fastp/files/patch-Makefile index 09efd133c6d8..527c69f39def 100644 --- a/biology/fastp/files/patch-Makefile +++ b/biology/fastp/files/patch-Makefile @@ -1,40 +1,58 @@ ---- Makefile.orig 2025-06-06 00:03:48 UTC -+++ Makefile -@@ -7,6 +7,8 @@ LIBRARY_DIRS ?= - INCLUDE_DIRS ?= - LIBRARY_DIRS ?= +--- Makefile.orig 2026-03-10 03:34:23.000000000 +0000 ++++ Makefile 2026-03-17 16:26:48.654370000 +0000 +@@ -2,6 +2,8 @@ + DIR_SRC := ./src + DIR_OBJ := ./obj -+STRIP ?= strip ++STRIP ?= strip + - SRC := $(wildcard ${DIR_SRC}/*.cpp) - OBJ := $(patsubst %.cpp,${DIR_OBJ}/%.o,$(notdir ${SRC})) - -@@ -15,15 +17,21 @@ CXX ?= g++ + PREFIX ?= /usr/local + BINDIR ?= $(PREFIX)/bin + INCLUDE_DIRS ?= +@@ -15,26 +17,29 @@ BIN_TARGET := ${TARGET} CXX ?= g++ --CXXFLAGS := -std=c++11 -pthread -g -O3 -MD -MP -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) ${CXXFLAGS} -+# Optional flags that the user can override by setting CXXFLAGS in the -+# env or make argument. -pthread is a link flag, and serves no purpose -+# in the compile command. It is handled by -lpthread in LIBS. +-CXXFLAGS := -std=c++11 -pthread -g -O3 -MD -MP -I. -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) ${CXXFLAGS} +CXXFLAGS ?= -g -O3 -MD -MP -+# Required flags -+CXXFLAGS += -std=c++11 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) - LIBS := -lisal -ldeflate -lpthread - STATIC_FLAGS := -static -Wl,--no-as-needed -pthread --LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS) $(LD_FLAGS) -+# Append required flags to standard LDFLAGS from env -+LDFLAGS += $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS) - STATIC_LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(STATIC_FLAGS) $(LIBS) $(STATIC_LD_FLAGS) ++CXXFLAGS += -std=c++11 -I. -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) + LIBS := -lisal -ldeflate -lhwy -lpthread + UNAME_S := $(shell uname -s) + ifeq ($(UNAME_S),Linux) +- # Linux: fully static binary +- LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) -static -Wl,--no-as-needed -pthread $(LIBS) $(LD_FLAGS) ++# Linux: fully static binary ++LD_FLAGS := $(LDFLAGS) $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) -static -Wl,--no-as-needed -pthread $(LIBS) ++else ifeq ($(UNAME_S),Darwin) ++# macOS: link 3rd-party libs statically via .a when available, fallback to dynamic ++FIND_STATIC = $(firstword $(foreach d,$(LIBRARY_DIRS),$(wildcard $(d)/lib$(1).a)) $(wildcard /usr/local/lib/lib$(1).a /opt/homebrew/lib/lib$(1).a)) ++STATIC_LIBS := ++DYNAMIC_LIBS := ++$(foreach lib,isal deflate hwy,\ ++ $(if $(call FIND_STATIC,$(lib)),\ ++ $(eval STATIC_LIBS += $(call FIND_STATIC,$(lib))),\ ++ $(eval DYNAMIC_LIBS += -l$(lib)))) ++LD_FLAGS := $(LDFLAGS) $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(STATIC_LIBS) $(DYNAMIC_LIBS) -lpthread + else +- # macOS: link 3rd-party libs statically via .a when available, fallback to dynamic +- FIND_STATIC = $(firstword $(foreach d,$(LIBRARY_DIRS),$(wildcard $(d)/lib$(1).a)) $(wildcard /usr/local/lib/lib$(1).a /opt/homebrew/lib/lib$(1).a)) +- STATIC_LIBS := +- DYNAMIC_LIBS := +- $(foreach lib,isal deflate hwy,\ +- $(if $(call FIND_STATIC,$(lib)),\ +- $(eval STATIC_LIBS += $(call FIND_STATIC,$(lib))),\ +- $(eval DYNAMIC_LIBS += -l$(lib)))) +- LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(STATIC_LIBS) $(DYNAMIC_LIBS) -lpthread $(LD_FLAGS) ++# Other Unix-like systems (e.g. FreeBSD): use normal dynamic linking ++LD_FLAGS := $(LDFLAGS) $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS) + endif +- ${BIN_TARGET}:${OBJ} -- $(CXX) $(OBJ) -o $@ $(LD_FLAGS) -+ $(CXX) $(OBJ) -o $@ $(LDFLAGS) + $(CXX) $(OBJ) -o $@ $(LD_FLAGS) - static:${OBJ} - $(CXX) $(OBJ) -o ${BIN_TARGET} $(STATIC_LD_FLAGS) -@@ -38,8 +46,15 @@ clean: +@@ -47,8 +52,16 @@ @rm -rf $(DIR_OBJ) @rm -f $(TARGET) @@ -43,11 +61,12 @@ +# unless DESTDIR is supplied by the user. install: - install $(TARGET) $(BINDIR)/$(TARGET) -+ install $(TARGET) $(DESTDIR)$(BINDIR)/$(TARGET) ++ mkdir -p $(DESTDIR)$(BINDIR) ++ install $(TARGET) $(DESTDIR)$(BINDIR) @echo "Installed." -+ + +# Many package managers use install-strip target if debugging is not enabled +install-strip: install + $(STRIP) $(DESTDIR)$(BINDIR)/$(TARGET) - ++ -include $(OBJ:.o=.d)home | help
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