CVS commit: pkgsrc/biology/bwa

["Havard Eidnes" <he%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   he
Date:           Wed Dec 27 23:44:02 UTC 2017

Modified Files:
        pkgsrc/biology/bwa: Makefile distinfo
Added Files:
        pkgsrc/biology/bwa/patches: patch-kopen.c

Log Message:
Re-add patch to bring timeval definition and select prototype into scope.
Bump PKGREVISION.


To generate a diff of this commit:
cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/bwa/Makefile \
    pkgsrc/biology/bwa/distinfo
cvs rdiff -u -r0 -r1.3 pkgsrc/biology/bwa/patches/patch-kopen.c

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

Modified files:

Index: pkgsrc/biology/bwa/Makefile
diff -u pkgsrc/biology/bwa/Makefile:1.5 pkgsrc/biology/bwa/Makefile:1.6
--- pkgsrc/biology/bwa/Makefile:1.5     Sun Dec 17 14:30:36 2017
+++ pkgsrc/biology/bwa/Makefile Wed Dec 27 23:44:01 2017
@@ -1,7 +1,8 @@
-# $NetBSD: Makefile,v 1.5 2017/12/17 14:30:36 bacon Exp $
+# $NetBSD: Makefile,v 1.6 2017/12/27 23:44:01 he Exp $
 
 DISTNAME=      bwa-0.7.17
 CATEGORIES=    biology
+PKGREVISION=   1
 GITHUB_TAG=     v${PKGVERSION_NOREV}
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=lh3/}
 
Index: pkgsrc/biology/bwa/distinfo
diff -u pkgsrc/biology/bwa/distinfo:1.5 pkgsrc/biology/bwa/distinfo:1.6
--- pkgsrc/biology/bwa/distinfo:1.5     Sun Dec 17 14:30:36 2017
+++ pkgsrc/biology/bwa/distinfo Wed Dec 27 23:44:01 2017
@@ -1,7 +1,8 @@
-$NetBSD: distinfo,v 1.5 2017/12/17 14:30:36 bacon Exp $
+$NetBSD: distinfo,v 1.6 2017/12/27 23:44:01 he Exp $
 
 SHA1 (bwa-0.7.17.tar.gz) = 77f9aac723110227ea51cb42011336d291d03723
 RMD160 (bwa-0.7.17.tar.gz) = d26a266387dee4fc9fcf6eef4f7ffcc076495c22
 SHA512 (bwa-0.7.17.tar.gz) = 114e61b7cc5edcb67172d1eca7be1fa670ea33dd48b5c02c98318e254871363775c0dab327fd7ee7023200a5fedc745fa01cbe0fd9550d783f091d4df6926f48
 Size (bwa-0.7.17.tar.gz) = 232593 bytes
 SHA1 (patch-Makefile) = 72ac08d92540a88da08bf4d988ca3f6132327a6a
+SHA1 (patch-kopen.c) = ecc92efa3ebe4da484aa6760e23de9437b000644

Added files:

Index: pkgsrc/biology/bwa/patches/patch-kopen.c
diff -u /dev/null pkgsrc/biology/bwa/patches/patch-kopen.c:1.3
--- /dev/null   Wed Dec 27 23:44:02 2017
+++ pkgsrc/biology/bwa/patches/patch-kopen.c    Wed Dec 27 23:44:01 2017
@@ -0,0 +1,15 @@
+$NetBSD: patch-kopen.c,v 1.3 2017/12/27 23:44:01 he Exp $
+
+Add includes for getting timevals and select prototype into scope.
+
+--- kopen.c.orig       2017-10-23 17:10:17.000000000 +0000
++++ kopen.c
+@@ -12,6 +12,8 @@
+ #include <netdb.h>
+ #include <arpa/inet.h>
+ #include <sys/socket.h>
++#include <sys/time.h>
++#include <sys/select.h>
+ #endif
+ 
+ #ifdef USE_MALLOC_WRAPPERS