Date: Wed, 20 Oct 2021 16:37:54 GMT 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: f6c6c5a37954 - main - biology/fastp: Update to 0.23.1 Message-ID: <202110201637.19KGbsqD013587@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=f6c6c5a37954173f208f39515fdf79d1dc6e2689 commit f6c6c5a37954173f208f39515fdf79d1dc6e2689 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2021-10-20 16:35:11 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2021-10-20 16:37:39 +0000 biology/fastp: Update to 0.23.1 Performance improvements, more reproducible output Fix seg fault when running with no args --- biology/fastp/Makefile | 7 +++-- biology/fastp/distinfo | 6 ++--- biology/fastp/files/patch-Makefile | 47 ++++++++++++++++++++++------------ biology/fastp/files/patch-src_main.cpp | 17 ++++++++++++ 4 files changed, 56 insertions(+), 21 deletions(-) diff --git a/biology/fastp/Makefile b/biology/fastp/Makefile index 2b8ec0278e58..904ebb18ad56 100644 --- a/biology/fastp/Makefile +++ b/biology/fastp/Makefile @@ -1,6 +1,6 @@ PORTNAME= fastp DISTVERSIONPREFIX= v -DISTVERSION= 0.22.0 +DISTVERSION= 0.23.1 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -9,7 +9,10 @@ COMMENT= Ultra-fast all-in-one FASTQ preprocessor LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE -USES= compiler:c++11-lang gmake +LIB_DEPENDS= libdeflate.so:archivers/libdeflate \ + libisal.so:devel/isa-l + +USES= compiler:c++11-lang gmake localbase:ldflags USE_GITHUB= yes GH_ACCOUNT= OpenGene diff --git a/biology/fastp/distinfo b/biology/fastp/distinfo index 3ecec1406b78..a6994823ad4b 100644 --- a/biology/fastp/distinfo +++ b/biology/fastp/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1630006835 -SHA256 (OpenGene-fastp-v0.22.0_GH0.tar.gz) = a7ef81cc39daed7ac6bfc254697345c448095539e1b5b45f3a8ab286098be456 -SIZE (OpenGene-fastp-v0.22.0_GH0.tar.gz) = 141257 +TIMESTAMP = 1634739193 +SHA256 (OpenGene-fastp-v0.23.1_GH0.tar.gz) = 32cb16ea1199a5f722d3c5caa24d1aaace4b24f6efa0fd774f227d8a80ebb8f3 +SIZE (OpenGene-fastp-v0.23.1_GH0.tar.gz) = 163190 diff --git a/biology/fastp/files/patch-Makefile b/biology/fastp/files/patch-Makefile index 595fdc96c6e6..da927edbe011 100644 --- a/biology/fastp/files/patch-Makefile +++ b/biology/fastp/files/patch-Makefile @@ -1,42 +1,57 @@ ---- Makefile.orig 2020-04-08 07:26:52 UTC +--- Makefile.orig 2021-10-19 02:19:29 UTC +++ Makefile -@@ -3,9 +3,11 @@ DIR_SRC := ./src +@@ -2,11 +2,13 @@ DIR_INC := ./inc + DIR_SRC := ./src DIR_OBJ := ./obj - PREFIX ?= /usr/local -+DESTDIR ?= - BINDIR ?= $(PREFIX)/bin - INCLUDE_DIRS ?= - LIBRARY_DIRS ?= -+STRIP_CMD ?= strip +-PREFIX ?= /usr/local +-BINDIR ?= $(PREFIX)/bin +-INCLUDE_DIRS ?= +-LIBRARY_DIRS ?= ++PREFIX ?= /usr/local ++BINDIR ?= $(PREFIX)/bin ++INCLUDE_DIRS ?= ++LIBRARY_DIRS ?= ++STRIP ?= strip ++ SRC := $(wildcard ${DIR_SRC}/*.cpp) OBJ := $(patsubst %.cpp,${DIR_OBJ}/%.o,$(notdir ${SRC})) -@@ -15,13 +17,14 @@ TARGET := fastp + +@@ -15,15 +17,19 @@ TARGET := fastp BIN_TARGET := ${TARGET} CXX ?= g++ --CXXFLAGS := -std=c++11 -g -O3 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) ${CXXFLAGS} +-CXXFLAGS := -std=c++11 -pthread -g -O3 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) ${CXXFLAGS} ++# Optional flags that the user can override by setting CXXFLAGS in the ++# env or make argument +CXXFLAGS ?= -g -O3 ++# Required flags +CXXFLAGS += -std=c++11 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) - LIBS := -lz -lpthread + 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) - +- ${BIN_TARGET}:${OBJ} - $(CXX) $(OBJ) -o $@ $(LD_FLAGS) + $(CXX) $(OBJ) -o $@ $(LDFLAGS) - ${DIR_OBJ}/%.o:${DIR_SRC}/%.cpp make_obj_dir - $(CXX) -c $< -o $@ $(CXXFLAGS) -@@ -38,5 +41,8 @@ make_obj_dir: + static:${OBJ} + $(CXX) $(OBJ) -o ${BIN_TARGET} $(STATIC_LD_FLAGS) +@@ -49,6 +55,11 @@ make_obj_dir: + mkdir $(DIR_OBJ) ; \ fi ++# Respect DESTDIR for staged installs (used by most package managers) install: - install $(TARGET) $(BINDIR)/$(TARGET) + install $(TARGET) $(DESTDIR)$(BINDIR)/$(TARGET) @echo "Installed." + ++# Many package managers use install-strip target if debugging is not enabled +install-strip: install -+ $(STRIP_CMD) $(DESTDIR)$(BINDIR)/$(TARGET) ++ $(STRIP) $(DESTDIR)$(BINDIR)/$(TARGET) diff --git a/biology/fastp/files/patch-src_main.cpp b/biology/fastp/files/patch-src_main.cpp new file mode 100644 index 000000000000..28e5bf918991 --- /dev/null +++ b/biology/fastp/files/patch-src_main.cpp @@ -0,0 +1,17 @@ +--- src/main.cpp.orig 2021-10-19 02:19:29 UTC ++++ src/main.cpp +@@ -1,4 +1,5 @@ + #include <stdio.h> ++#include <sysexits.h> + #include "fastqreader.h" + #include "unittest.h" + #include <time.h> +@@ -18,7 +19,7 @@ int main(int argc, char* argv[]){ + if(argc == 1) { + cerr << "fastp: an ultra-fast all-in-one FASTQ preprocessor" << endl << "version " << FASTP_VER << endl; + //cerr << "fastp --help to see the help"<<endl; +- //return 0; ++ return EX_USAGE; + } + if (argc == 2 && strcmp(argv[1], "test")==0){ + UnitTest tester;
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