CVS commit: pkgsrc/biology/fastp

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/biology/fastp
From: "Jason Bacon" <bacon%netbsd.org@localhost>
Date: Thu, 1 Jun 2023 13:03:53 +0000

Module Name:    pkgsrc
Committed By:   bacon
Date:           Thu Jun  1 13:03:53 UTC 2023

Modified Files:
        pkgsrc/biology/fastp: Makefile PLIST distinfo
        pkgsrc/biology/fastp/patches: patch-Makefile
Added Files:
        pkgsrc/biology/fastp/patches: patch-src_main.cpp

Log Message:
biology/fastp: Update to 0.22.0

Adds deduplication subcommand
Changes: https://github.com/OpenGene/fastp/releases
Holding off on 0.23, which depends on the non-portable Intel isa-l,
which does not build on Darwin aarch64


To generate a diff of this commit:
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/fastp/Makefile
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/fastp/PLIST
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/fastp/distinfo
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/fastp/patches/patch-Makefile
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/fastp/patches/patch-src_main.cpp

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/biology/fastp/Makefile
diff -u pkgsrc/biology/fastp/Makefile:1.2 pkgsrc/biology/fastp/Makefile:1.3
--- pkgsrc/biology/fastp/Makefile:1.2   Mon May 25 05:18:35 2020
+++ pkgsrc/biology/fastp/Makefile       Thu Jun  1 13:03:53 2023
@@ -1,6 +1,8 @@
-# $NetBSD: Makefile,v 1.2 2020/05/25 05:18:35 rillig Exp $
+# $NetBSD: Makefile,v 1.3 2023/06/01 13:03:53 bacon Exp $
 
-DISTNAME=      fastp-0.20.0
+# 0.22.0 is the last release that doesn't depend on the non-portable
+# Intel isa-l library
+DISTNAME=      fastp-0.22.0
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=OpenGene/}
 GITHUB_TAG=    v${PKGVERSION_NOREV}
@@ -15,12 +17,6 @@ USE_TOOLS+=          gmake
 BUILD_TARGET=          fastp
 PTHREAD_AUTO_VARS=     yes
 
-# src/stats.cpp: In member function 'void Stats::statRead(Read*)':
-# src/stats.cpp:248:29: error: array subscript has type 'char' [-Werror=char-subscripts]
-#              mCycleQ30Bases[b][i]++;
-# Maybe fix this later.
-BUILDLINK_TRANSFORM+=  rm:-Werror=char-subscripts
-
 post-install:
        ${STRIP} ${DESTDIR}${PREFIX}/bin/fastp
 

Index: pkgsrc/biology/fastp/PLIST
diff -u pkgsrc/biology/fastp/PLIST:1.1 pkgsrc/biology/fastp/PLIST:1.2
--- pkgsrc/biology/fastp/PLIST:1.1      Sat May  4 16:15:25 2019
+++ pkgsrc/biology/fastp/PLIST  Thu Jun  1 13:03:53 2023
@@ -1,2 +1,2 @@
-@comment $NetBSD: PLIST,v 1.1 2019/05/04 16:15:25 bacon Exp $
+@comment $NetBSD: PLIST,v 1.2 2023/06/01 13:03:53 bacon Exp $
 bin/fastp

Index: pkgsrc/biology/fastp/distinfo
diff -u pkgsrc/biology/fastp/distinfo:1.3 pkgsrc/biology/fastp/distinfo:1.4
--- pkgsrc/biology/fastp/distinfo:1.3   Tue Oct 26 10:03:38 2021
+++ pkgsrc/biology/fastp/distinfo       Thu Jun  1 13:03:53 2023
@@ -1,6 +1,7 @@
-$NetBSD: distinfo,v 1.3 2021/10/26 10:03:38 nia Exp $
+$NetBSD: distinfo,v 1.4 2023/06/01 13:03:53 bacon Exp $
 
-BLAKE2s (fastp-0.20.0.tar.gz) = 1096c02c241da76f04cbf485abd3a348b1c87af88e7ba3adb2fe5b0ff811c327
-SHA512 (fastp-0.20.0.tar.gz) = 33349b761283a42fb9eaf045ab7f839d5ec335fb394e277519b87f8c95cf682027ab183b174a1b82d908a3e4d1d65ac63a88c30efea04d93a08f559c1a7a732c
-Size (fastp-0.20.0.tar.gz) = 139422 bytes
-SHA1 (patch-Makefile) = 52fa55ead7d384b8c758e7a2d14680a53f61e623
+BLAKE2s (fastp-0.22.0.tar.gz) = fbeed45925f33bde6020054e68affd30b076a81a43f383650cf5c8b6e0d09e7d
+SHA512 (fastp-0.22.0.tar.gz) = 661e61c78fd77347e23380bb0da79e4269ef0acf7350e2b95dd104b85083db55e12b52330bb8fbcaf25554f22d649315db05e083704b8bdabf1e5fb345e34c41
+Size (fastp-0.22.0.tar.gz) = 141257 bytes
+SHA1 (patch-Makefile) = d55955d62ede0e5fad1be39c937fedb7e79b746d
+SHA1 (patch-src_main.cpp) = d28fb587c72b59f4c86bc51fd66874344a9dd43d

Index: pkgsrc/biology/fastp/patches/patch-Makefile
diff -u pkgsrc/biology/fastp/patches/patch-Makefile:1.1 pkgsrc/biology/fastp/patches/patch-Makefile:1.2
--- pkgsrc/biology/fastp/patches/patch-Makefile:1.1     Sat May  4 16:15:25 2019
+++ pkgsrc/biology/fastp/patches/patch-Makefile Thu Jun  1 13:03:53 2023
@@ -1,31 +1,30 @@
-$NetBSD: patch-Makefile,v 1.1 2019/05/04 16:15:25 bacon Exp $
+$NetBSD: patch-Makefile,v 1.2 2023/06/01 13:03:53 bacon Exp $
 
-# Add destdir support, install-strip, and respect LDFLAGS
+# Respect env
 
---- Makefile.orig      2019-04-17 03:23:22.000000000 +0000
+--- Makefile.orig      2021-08-24 14:00:31.000000000 +0000
 +++ Makefile
-@@ -3,9 +3,11 @@ DIR_SRC := ./src
- DIR_OBJ := ./obj
- 
- PREFIX ?= /usr/local
-+DESTDIR ?=
- BINDIR ?= $(PREFIX)/bin
+@@ -7,6 +7,8 @@ BINDIR ?= $(PREFIX)/bin
  INCLUDE_DIRS ?=
  LIBRARY_DIRS ?=
-+STRIP ?= strip
  
++STRIP ?= strip
++
  SRC := $(wildcard ${DIR_SRC}/*.cpp)
  OBJ := $(patsubst %.cpp,${DIR_OBJ}/%.o,$(notdir ${SRC}))
-@@ -15,13 +17,14 @@ TARGET := fastp
+ 
+@@ -15,13 +17,17 @@ TARGET := fastp
  BIN_TARGET := ${TARGET}
  
  CXX ?= g++
 -CXXFLAGS := -std=c++11 -g -O3 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) ${CXXFLAGS}
--LIBS := -lz -lpthread
--LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS) $(LD_FLAGS)
++# Optional flags that the user can override by setting CXXFLAGS in the
++# env or make argument
 +CXXFLAGS ?= -g -O3
++# Required flags
 +CXXFLAGS += -std=c++11 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir))
-+LIBS := -lz
+ LIBS := -lz -lpthread
+-LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS) $(LD_FLAGS)
 +LDFLAGS += $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS)
  
  
@@ -35,14 +34,17 @@ $NetBSD: patch-Makefile,v 1.1 2019/05/04
  
  ${DIR_OBJ}/%.o:${DIR_SRC}/%.cpp make_obj_dir
        $(CXX) -c $< -o $@ $(CXXFLAGS)
-@@ -38,5 +41,9 @@ make_obj_dir:
+@@ -43,6 +49,12 @@ make_obj_dir:
+               mkdir $(DIR_OBJ) ; \
        fi
  
++# Respect DESTDIR for staged installs (used by most package managers)
  install:
 -      install $(TARGET) $(BINDIR)/$(TARGET)
-+      install -d $(DESTDIR)$(BINDIR)
++      mkdir $(DESTDIR)$(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)

Added files:

Index: pkgsrc/biology/fastp/patches/patch-src_main.cpp
diff -u /dev/null pkgsrc/biology/fastp/patches/patch-src_main.cpp:1.1
--- /dev/null   Thu Jun  1 13:03:53 2023
+++ pkgsrc/biology/fastp/patches/patch-src_main.cpp     Thu Jun  1 13:03:53 2023
@@ -0,0 +1,21 @@
+$NetBSD: patch-src_main.cpp,v 1.1 2023/06/01 13:03:53 bacon Exp $
+
+# Make sure main() returns a value
+
+--- 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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