git: ccb32a8ebf02 - main - biology/fastp: Update to 1.4.0

Go to: [ bottom of page ] [ top of archives ] [ this month ]
From: Joseph Mingrone <jrm_at_FreeBSD.org>
Date: Fri, 16 Oct 2026 16:49:26 UTC
The branch main has been updated by jrm:

URL: https://cgit.FreeBSD.org/ports/commit/?id=ccb32a8ebf02e153711fc6fbe71080c31f1c56e7

commit ccb32a8ebf02e153711fc6fbe71080c31f1c56e7
Author:     hayzamjs <hayzam@alchemilla.io>
AuthorDate: 2026-10-16 15:49:49 +0000
Commit:     Joseph Mingrone <jrm@FreeBSD.org>
CommitDate: 2026-10-16 16:48:01 +0000

    biology/fastp: Update to 1.4.0
    
    Changelog: https://github.com/OpenGene/fastp/releases/tag/v1.4.0
    
    Reviewed by:    jrm
    Differential Revision:  https://reviews.freebsd.org/D60778
---
 biology/fastp/Makefile             | 13 +++----
 biology/fastp/distinfo             |  6 +--
 biology/fastp/files/patch-Makefile | 77 ++++++++++----------------------------
 3 files changed, 29 insertions(+), 67 deletions(-)

diff --git a/biology/fastp/Makefile b/biology/fastp/Makefile
index 36ede673577f..9c51bb4f6b2e 100644
--- a/biology/fastp/Makefile
+++ b/biology/fastp/Makefile
@@ -1,7 +1,7 @@
-PORTNAME=		fastp
+PORTNAME=	fastp
 DISTVERSIONPREFIX=	v
-DISTVERSION=		1.2.0
-CATEGORIES=		biology
+DISTVERSION=	1.4.0
+CATEGORIES=	biology
 
 MAINTAINER=	hayzam@alchemilla.io
 COMMENT=	Ultra-fast all-in-one FASTQ preprocessor
@@ -11,12 +11,11 @@ LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 LIB_DEPENDS=	libdeflate.so:archivers/libdeflate \
-		libisal.so:devel/isa-l \
-		libhwy.so:devel/highway
+		libhwy.so:devel/highway \
+		libisal.so:devel/isa-l
 
-USES=		gmake localbase:ldflags
+USES=		gmake localbase:ldflags pkgconfig
 USE_GITHUB=	yes
-
 GH_ACCOUNT=	OpenGene
 
 ALL_TARGET=	fastp
diff --git a/biology/fastp/distinfo b/biology/fastp/distinfo
index c7039f9e2bf7..eeb10d046c86 100644
--- a/biology/fastp/distinfo
+++ b/biology/fastp/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1773759010
-SHA256 (OpenGene-fastp-v1.2.0_GH0.tar.gz) = fd7e20923e8f748803d54d9e0fabf44a44c748822a65062999e4b7edec6b8da6
-SIZE (OpenGene-fastp-v1.2.0_GH0.tar.gz) = 125582
+TIMESTAMP = 1792161239
+SHA256 (OpenGene-fastp-v1.4.0_GH0.tar.gz) = 28c0537e9d1f32f5a5c404562e6a282bf373b034a4c3a3610d9aa31d6429b550
+SIZE (OpenGene-fastp-v1.4.0_GH0.tar.gz) = 117999
diff --git a/biology/fastp/files/patch-Makefile b/biology/fastp/files/patch-Makefile
index 527c69f39def..6f7c54630aed 100644
--- a/biology/fastp/files/patch-Makefile
+++ b/biology/fastp/files/patch-Makefile
@@ -1,72 +1,35 @@
---- 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
-+
- PREFIX ?= /usr/local
- BINDIR ?= $(PREFIX)/bin
- INCLUDE_DIRS ?=
-@@ -15,26 +17,29 @@
+--- Makefile.orig	2026-10-07 00:49:32 UTC
++++ Makefile
+@@ -24,7 +24,8 @@ CXX ?= g++
  BIN_TARGET := ${TARGET}
  
  CXX ?= g++
--CXXFLAGS := -std=c++11 -pthread -g -O3 -MD -MP -I. -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) ${CXXFLAGS}
+-CXXFLAGS := -std=c++11 -pthread -g -O3 -MD -MP -I. -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) $(HWY_CFLAGS) $(ISAL_CFLAGS) $(DEFLATE_CFLAGS) ${CXXFLAGS}
 +CXXFLAGS ?= -g -O3 -MD -MP
-+CXXFLAGS += -std=c++11 -I. -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir))
++CXXFLAGS += -std=c++11 -pthread -I. -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) $(HWY_CFLAGS) $(ISAL_CFLAGS) $(DEFLATE_CFLAGS)
  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)
+ PKG_LDFLAGS := $(HWY_LIBS) $(ISAL_LIBS) $(DEFLATE_LIBS)
+@@ -38,7 +39,10 @@ $(foreach lib,isal deflate hwy,\
+     $(eval STATIC_LIBS += $(call FIND_STATIC,$(lib))),\
+     $(eval DYNAMIC_LIBS += -l$(lib))))
  
-@@ -47,8 +52,16 @@
- 	@rm -rf $(DIR_OBJ)
+-ifeq ($(UNAME_S),Linux)
++ifeq ($(UNAME_S),FreeBSD)
++  # Respect linker flags and use shared libraries.
++  LD_FLAGS := $(LDFLAGS) $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(PKG_LDFLAGS) $(LIBS)
++else ifeq ($(UNAME_S),Linux)
+   ifeq ($(DYNAMIC_LIBS),)
+     # All .a found: fully static binary (default for Linux)
+     LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(PKG_LDFLAGS) -static -Wl,--no-as-needed -pthread $(LIBS) $(LD_FLAGS)
+@@ -72,8 +76,8 @@ install:
  	@rm -f $(TARGET)
  
-+# Respect DESTDIR for staged installs (used by most package managers).
-+# DESTDIR is empty by default, so this will install directly to BINDIR
-+# unless DESTDIR is supplied by the user.
  install:
+-	mkdir -p $(BINDIR)
 -	install $(TARGET) $(BINDIR)/$(TARGET)
 +	mkdir -p $(DESTDIR)$(BINDIR)
-+	install $(TARGET) $(DESTDIR)$(BINDIR)
++	install $(TARGET) $(DESTDIR)$(BINDIR)/$(TARGET)
  	@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)