From b902f8f425a4f7e3e8196c3f30857f7208c3d0ee Mon Sep 17 00:00:00 2001 From: "Jason W. Bacon" Date: Sat, 7 Jun 2025 07:28:25 -0500 Subject: [PATCH] biology/fastp: Update to 0.26.0 Improve adapter detection and trimming Changes: https://github.com/OpenGene/fastp/releases New maintainer: hayzam@alchemilla.io Reported by: portscout --- biology/fastp/Makefile | 4 ++-- biology/fastp/distinfo | 6 +++--- biology/fastp/files/patch-Makefile | 15 +++++++++------ 3 files changed, 14 insertions(+), 11 deletions(-) diff --git a/biology/fastp/Makefile b/biology/fastp/Makefile index fadcb2fbec61..7d91034eb87c 100644 --- a/biology/fastp/Makefile +++ b/biology/fastp/Makefile @@ -1,9 +1,9 @@ PORTNAME= fastp DISTVERSIONPREFIX= v -DISTVERSION= 0.25.0 +DISTVERSION= 0.26.0 CATEGORIES= biology -MAINTAINER= jwb@FreeBSD.org +MAINTAINER= hayzam@alchemilla.io COMMENT= Ultra-fast all-in-one FASTQ preprocessor WWW= https://github.com/OpenGene/fastp diff --git a/biology/fastp/distinfo b/biology/fastp/distinfo index 8d1d45fdddba..6abdf5196be5 100644 --- a/biology/fastp/distinfo +++ b/biology/fastp/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1748779414 -SHA256 (OpenGene-fastp-v0.25.0_GH0.tar.gz) = 55fa7d9b8166200e901ff59a1825ba6455ec1a322d9465ce40aae6d145c3146f -SIZE (OpenGene-fastp-v0.25.0_GH0.tar.gz) = 164959 +TIMESTAMP = 1749236354 +SHA256 (OpenGene-fastp-v0.26.0_GH0.tar.gz) = ab5396f448bece92e599e4d3acc48751fc46f0f43333ca271d229aa95dc47c4e +SIZE (OpenGene-fastp-v0.26.0_GH0.tar.gz) = 166500 diff --git a/biology/fastp/files/patch-Makefile b/biology/fastp/files/patch-Makefile index 5e68e39804a1..09efd133c6d8 100644 --- a/biology/fastp/files/patch-Makefile +++ b/biology/fastp/files/patch-Makefile @@ -1,4 +1,4 @@ ---- Makefile.orig 2025-04-16 10:13:35 UTC +--- Makefile.orig 2025-06-06 00:03:48 UTC +++ Makefile @@ -7,6 +7,8 @@ LIBRARY_DIRS ?= INCLUDE_DIRS ?= @@ -9,14 +9,15 @@ SRC := $(wildcard ${DIR_SRC}/*.cpp) OBJ := $(patsubst %.cpp,${DIR_OBJ}/%.o,$(notdir ${SRC})) -@@ -15,15 +17,20 @@ CXX ?= g++ +@@ -15,15 +17,21 @@ CXX ?= g++ BIN_TARGET := ${TARGET} CXX ?= g++ -CXXFLAGS := -std=c++11 -pthread -g -O3 -MD -MP -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) ${CXXFLAGS} +# Optional flags that the user can override by setting CXXFLAGS in the -+# env or make argument -+CXXFLAGS ?= -g -O3 ++# env or make argument. -pthread is a link flag, and serves no purpose ++# in the compile command. It is handled by -lpthread in LIBS. ++CXXFLAGS ?= -g -O3 -MD -MP +# Required flags +CXXFLAGS += -std=c++11 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) LIBS := -lisal -ldeflate -lpthread @@ -33,11 +34,13 @@ static:${OBJ} $(CXX) $(OBJ) -o ${BIN_TARGET} $(STATIC_LD_FLAGS) -@@ -38,8 +45,13 @@ clean: +@@ -38,8 +46,15 @@ clean: @rm -rf $(DIR_OBJ) @rm -f $(TARGET) -+# Respect DESTDIR for staged installs (used by most package managers) ++# 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: - install $(TARGET) $(BINDIR)/$(TARGET) + install $(TARGET) $(DESTDIR)$(BINDIR)/$(TARGET)