git: f6c6c5a37954 - main - biology/fastp: Update to 0.23.1

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;