CVS commit: pkgsrc/biology/vsearch

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Fri Dec 17 19:20:44 UTC 2021

Modified Files:
        pkgsrc/biology/vsearch: Makefile PLIST distinfo
        pkgsrc/biology/vsearch/patches: patch-configure.ac
            patch-src_Makefile.am
Added Files:
        pkgsrc/biology/vsearch: patch-src_Makefile.am
Removed Files:
        pkgsrc/biology/vsearch/patches: patch-man_Makefile.am

Log Message:
biology/vsearch: Update to 2.18.0

Add powerpc64 support
Numerous fixes and enhancements since 2.13

Changes: https://github.com/torognes/vsearch/tags


To generate a diff of this commit:
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/vsearch/Makefile
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/vsearch/PLIST
cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/vsearch/distinfo
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/vsearch/patch-src_Makefile.am
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/vsearch/patches/patch-configure.ac \
    pkgsrc/biology/vsearch/patches/patch-src_Makefile.am
cvs rdiff -u -r1.1 -r0 pkgsrc/biology/vsearch/patches/patch-man_Makefile.am

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

Modified files:

Index: pkgsrc/biology/vsearch/Makefile
diff -u pkgsrc/biology/vsearch/Makefile:1.3 pkgsrc/biology/vsearch/Makefile:1.4
--- pkgsrc/biology/vsearch/Makefile:1.3 Sun Apr 25 07:51:24 2021
+++ pkgsrc/biology/vsearch/Makefile     Fri Dec 17 19:20:44 2021
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.3 2021/04/25 07:51:24 mrg Exp $
+# $NetBSD: Makefile,v 1.4 2021/12/17 19:20:44 bacon Exp $
 
-DISTNAME=      vsearch-2.13.4
+DISTNAME=      vsearch-2.18.0
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=torognes/}
 GITHUB_TAG=    v${PKGVERSION_NOREV}
@@ -11,13 +11,15 @@ COMMENT=    Versatile open-source tool for 
 LICENSE=       gnu-gpl-v3
 
 # Works on powerpc64, but only in little endian mode
-ONLY_FOR_PLATFORM=     *-*-aarch64* *-*-x86_64
+ONLY_FOR_PLATFORM=     *-*-aarch64* *-*-powerpc64 *-*-x86_64
 
 USE_LANGUAGES=         c c++
 USE_TOOLS+=            autoconf automake autoreconf gmake
 GNU_CONFIGURE=         yes
 CONFIGURE_ARGS+=       --disable-pdfman
 
+CXXFLAGS+=     -std=c++11
+
 pre-configure:
        cd ${WRKSRC} && autoreconf -fi
 

Index: pkgsrc/biology/vsearch/PLIST
diff -u pkgsrc/biology/vsearch/PLIST:1.2 pkgsrc/biology/vsearch/PLIST:1.3
--- pkgsrc/biology/vsearch/PLIST:1.2    Sat May 11 14:27:18 2019
+++ pkgsrc/biology/vsearch/PLIST        Fri Dec 17 19:20:44 2021
@@ -1,3 +1,3 @@
-@comment $NetBSD: PLIST,v 1.2 2019/05/11 14:27:18 bacon Exp $
+@comment $NetBSD: PLIST,v 1.3 2021/12/17 19:20:44 bacon Exp $
 bin/vsearch
 man/man1/vsearch.1

Index: pkgsrc/biology/vsearch/distinfo
diff -u pkgsrc/biology/vsearch/distinfo:1.5 pkgsrc/biology/vsearch/distinfo:1.6
--- pkgsrc/biology/vsearch/distinfo:1.5 Tue Oct 26 10:03:44 2021
+++ pkgsrc/biology/vsearch/distinfo     Fri Dec 17 19:20:44 2021
@@ -1,8 +1,7 @@
-$NetBSD: distinfo,v 1.5 2021/10/26 10:03:44 nia Exp $
+$NetBSD: distinfo,v 1.6 2021/12/17 19:20:44 bacon Exp $
 
-BLAKE2s (vsearch-2.13.4.tar.gz) = 16fd625aa53e9b9d5b062c9db71dc201c7d458dc97fe82915e37ba6ca794b706
-SHA512 (vsearch-2.13.4.tar.gz) = 31cc321f96309385414f3847a4cb29a5b3e43e42870b3f41e34fa0e6b3a928b2dd306edeff896ffa6bca85ecea776b33655611fa62749e9b29e86bf1adbe7de3
-Size (vsearch-2.13.4.tar.gz) = 234364 bytes
-SHA1 (patch-configure.ac) = 536a8565514cf9b43f4f8892d1cba0444f752c5e
-SHA1 (patch-man_Makefile.am) = e2e536f46b32eb191c2b930dcdd927a9bf11e833
-SHA1 (patch-src_Makefile.am) = bcdd1bbe9f04197084825e2c3560ba27a750f124
+BLAKE2s (vsearch-2.18.0.tar.gz) = 48ca99858b157da943eca273d4a4f25e94aa7c64ecf4c7373821c30cdfbc38c5
+SHA512 (vsearch-2.18.0.tar.gz) = 9da21685fe64743ccf43f209bdd5b586c8f7faaae9f1a204634b713d7ba8a86478f31b24bdda7820fba97318d4408c803a6b3eed1e37189907fbd5882183d781
+Size (vsearch-2.18.0.tar.gz) = 252014 bytes
+SHA1 (patch-configure.ac) = 23aa28454d5f58222b10302cbd01ceaf0e7dca3f
+SHA1 (patch-src_Makefile.am) = fb76ec48d5292aaa276a0b6105e19ccc0abb03df

Index: pkgsrc/biology/vsearch/patches/patch-configure.ac
diff -u pkgsrc/biology/vsearch/patches/patch-configure.ac:1.2 pkgsrc/biology/vsearch/patches/patch-configure.ac:1.3
--- pkgsrc/biology/vsearch/patches/patch-configure.ac:1.2       Sat May 11 14:27:18 2019
+++ pkgsrc/biology/vsearch/patches/patch-configure.ac   Fri Dec 17 19:20:44 2021
@@ -1,15 +1,15 @@
-$NetBSD: patch-configure.ac,v 1.2 2019/05/11 14:27:18 bacon Exp $
+$NetBSD: patch-configure.ac,v 1.3 2021/12/17 19:20:44 bacon Exp $
 
-# Respect build env
+# Respect pkgsrc env
 
---- configure.ac.orig  2019-05-09 20:58:52 UTC
+--- configure.ac.orig  2021-08-27 10:35:25.000000000 +0000
 +++ configure.ac
 @@ -14,9 +14,6 @@ MACOSX_DEPLOYMENT_TARGET="10.9"
  
  # Set default gcc and g++ options
  
 -CFLAGS='-g'
--CXXFLAGS='-g'
+-CXXFLAGS='-g -std=c++11'
 -
  # Checks for programs.
  AC_PROG_CXX
Index: pkgsrc/biology/vsearch/patches/patch-src_Makefile.am
diff -u pkgsrc/biology/vsearch/patches/patch-src_Makefile.am:1.2 pkgsrc/biology/vsearch/patches/patch-src_Makefile.am:1.3
--- pkgsrc/biology/vsearch/patches/patch-src_Makefile.am:1.2    Sat May 11 14:27:18 2019
+++ pkgsrc/biology/vsearch/patches/patch-src_Makefile.am        Fri Dec 17 19:20:44 2021
@@ -1,14 +1,14 @@
-$NetBSD: patch-src_Makefile.am,v 1.2 2019/05/11 14:27:18 bacon Exp $
+$NetBSD: patch-src_Makefile.am,v 1.3 2021/12/17 19:20:44 bacon Exp $
 
-# Respect build env
+# Respect pkgsrc env
 
---- src/Makefile.am.orig       2019-04-30 11:57:32 UTC
+--- src/Makefile.am.orig       2021-12-17 18:04:20.932004483 +0000
 +++ src/Makefile.am
 @@ -1,12 +1,12 @@
  bin_PROGRAMS = $(top_builddir)/bin/vsearch
  
  if TARGET_PPC
--AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -mcpu=power8
+-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -mcpu=powerpc64le -maltivec
 +AM_CXXFLAGS=-Wall -Wsign-compare
  else
  if TARGET_AARCH64

Added files:

Index: pkgsrc/biology/vsearch/patch-src_Makefile.am
diff -u /dev/null pkgsrc/biology/vsearch/patch-src_Makefile.am:1.1
--- /dev/null   Fri Dec 17 19:20:44 2021
+++ pkgsrc/biology/vsearch/patch-src_Makefile.am        Fri Dec 17 19:20:44 2021
@@ -0,0 +1,22 @@
+$NetBSD: patch-src_Makefile.am,v 1.1 2021/12/17 19:20:44 bacon Exp $
+
+# Respect build env
+
+--- src/Makefile.am.orig       2019-04-30 11:57:32 UTC
++++ src/Makefile.am
+@@ -1,12 +1,12 @@
+ bin_PROGRAMS = $(top_builddir)/bin/vsearch
+ 
+ if TARGET_PPC
+-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -mcpu=power8
++AM_CXXFLAGS=-Wall -Wsign-compare
+ else
+ if TARGET_AARCH64
+-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -march=armv8-a+simd -mtune=generic
++AM_CXXFLAGS=-Wall -Wsign-compare
+ else
+-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -march=x86-64 -mtune=generic
++AM_CXXFLAGS=-Wall -Wsign-compare
+ endif
+ endif
+