git: f3a8e8b50e62 - main - biology/fastp: Update to 1.2.0
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Date: Sun, 22 Mar 2026 12:59:38 UTC
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)