Attachment 148204 Details for Bug 194309 – Unified diff

Unified diff

plinkseq-diff.txt (text/plain), 5.13 KB, created by Jason W. Bacon on 2014-10-11 22:04:19 UTC

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Creator: Jason W. Bacon

Created: 2014-10-11 22:04:19 UTC

Size: 5.13 KB

patch

obsolete

>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/plinkseq/Makefile /usr/wip/biology/plinkseq/Makefile
>--- /usr/ports/biology/plinkseq/Makefile	2014-10-04 10:12:44.000000000 -0500
>+++ /usr/wip/biology/plinkseq/Makefile	2014-10-11 16:43:52.000000000 -0500
>@@ -2,29 +2,39 @@
> # $FreeBSD: head/biology/plinkseq/Makefile 369969 2014-10-04 15:12:44Z sunpoet $
> 
> PORTNAME=	plinkseq
>-PORTVERSION=	0.08
>-PORTREVISION=	3
>+PORTVERSION=	0.10
> CATEGORIES=	biology science
>-MASTER_SITES=	http://atgu.mgh.harvard.edu/${PORTNAME}/dist/version-${PORTVERSION}/
>+MASTER_SITES=	http://psychgen.u.hpc.mssm.edu/plinkseq_downloads/
>+# Default DISTNAME is correct, so leave it alone.
>+DISTFILES=	${PORTNAME}-src-${PORTVERSION}.tgz
> 
> MAINTAINER=	jwbacon@tds.net
> COMMENT=	Toolset for working with human genetic variation data
> 
> LICENSE=	GPLv2
> 
>-LIB_DEPENDS=	libprotobuf.so:${PORTSDIR}/devel/protobuf
>-
>-USES=		dos2unix libtool shebangfix
>-SHEBANG_FILES=	${WRKSRC}/browser/pbrowse.in ${WRKSRC}/index/index.in
>-USE_LDCONFIG=	yes
>-GNU_CONFIGURE=	yes
>-CONFIGURE_ARGS+=--with-protobuf=${LOCALBASE}
>+USES=		libtool gmake
> 
> post-patch:
>-	${REINPLACE_CMD} -e 's|PF_INET|AF_INET|g' ${WRKSRC}/browser/mongoose.c
>-	${REINPLACE_CMD} -e 's|-ldl||g' \
>-		${WRKSRC}/browser/Makefile.in \
>-		${WRKSRC}/client/Makefile.in \
>-		${WRKSRC}/index/Makefile.in
>+	${REINPLACE_CMD} \
>+		-e 's|PF_INET|AF_INET|g' \
>+		${WRKSRC}/sources/mongoose/sources/lib/mongoose.c
>+	${REINPLACE_CMD} \
>+		-e 's|g++|${CXX}|g' \
>+		-e 's|gcc|${CC}|g' \
>+		-e 's|CXXFLAGS = -O3|CXXFLAGS = ${CXXFLAGS}|g' \
>+		-e 's|ALL_CFLAGS =-O3|ALL_CFLAGS = ${CFLAGS}|g' \
>+		${WRKSRC}/config_defs.Makefile
>+	${REINPLACE_CMD} \
>+		-e 's| -ldl||g' \
>+		-e 's| $$(STATIC_FLAG)||g' \
>+		${WRKSRC}/Makefile
>+
>+do-install:
>+.for f in behead browser gcol mm mongoose pdas pseq smp tab2vcf
>+	${INSTALL_PROGRAM} ${WRKSRC}/build/execs/${f} ${STAGEDIR}${PREFIX}/bin
>+.endfor
>+	${INSTALL_DATA} ${WRKSRC}/sources/plinkseq/build/lib/libplinkseq.a \
>+		${STAGEDIR}${PREFIX}/lib
> 
> .include <bsd.port.mk>
>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/plinkseq/distinfo /usr/wip/biology/plinkseq/distinfo
>--- /usr/ports/biology/plinkseq/distinfo	2012-09-27 04:59:25.000000000 -0500
>+++ /usr/wip/biology/plinkseq/distinfo	2014-10-11 16:07:53.000000000 -0500
>@@ -1,2 +1,2 @@
>-SHA256 (plinkseq-0.08.tar.gz) = 6bde88925a82a79c6fa2401a197865cf6d659163fd5f11c5fb426701b54bb24f
>-SIZE (plinkseq-0.08.tar.gz) = 2991871
>+SHA256 (plinkseq-src-0.10.tgz) = e9d4705acf8b22eddba0c48cf502e3bd4236f3b60b010f39f94deecf37e94b58
>+SIZE (plinkseq-src-0.10.tgz) = 6090698
>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/plinkseq/files/patch-pp.pb.h /usr/wip/biology/plinkseq/files/patch-pp.pb.h
>--- /usr/ports/biology/plinkseq/files/patch-pp.pb.h	2013-03-21 09:09:22.000000000 -0500
>+++ /usr/wip/biology/plinkseq/files/patch-pp.pb.h	1969-12-31 18:00:00.000000000 -0600
>@@ -1,17 +0,0 @@
>---- lib/pp.pb.h.orig	2013-03-21 21:46:21.000000000 +0800
>-+++ lib/pp.pb.h	2013-03-21 21:46:33.000000000 +0800
>-@@ -8,12 +8,12 @@
>- 
>- #include <google/protobuf/stubs/common.h>
>- 
>--#if GOOGLE_PROTOBUF_VERSION < 2004000
>-+#if GOOGLE_PROTOBUF_VERSION < 2005000
>- #error This file was generated by a newer version of protoc which is
>- #error incompatible with your Protocol Buffer headers.  Please update
>- #error your headers.
>- #endif
>--#if 2004001 < GOOGLE_PROTOBUF_MIN_PROTOC_VERSION
>-+#if 2005001 < GOOGLE_PROTOBUF_MIN_PROTOC_VERSION
>- #error This file was generated by an older version of protoc which is
>- #error incompatible with your Protocol Buffer headers.  Please
>- #error regenerate this file with a newer version of protoc.
>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/plinkseq/files/patch-variant.pb.h /usr/wip/biology/plinkseq/files/patch-variant.pb.h
>--- /usr/ports/biology/plinkseq/files/patch-variant.pb.h	2013-03-21 09:09:22.000000000 -0500
>+++ /usr/wip/biology/plinkseq/files/patch-variant.pb.h	1969-12-31 18:00:00.000000000 -0600
>@@ -1,17 +0,0 @@
>---- lib/variant.pb.h.orig	2013-03-21 21:45:44.000000000 +0800
>-+++ lib/variant.pb.h	2013-03-21 21:45:55.000000000 +0800
>-@@ -8,12 +8,12 @@
>- 
>- #include <google/protobuf/stubs/common.h>
>- 
>--#if GOOGLE_PROTOBUF_VERSION < 2004000
>-+#if GOOGLE_PROTOBUF_VERSION < 2005000
>- #error This file was generated by a newer version of protoc which is
>- #error incompatible with your Protocol Buffer headers.  Please update
>- #error your headers.
>- #endif
>--#if 2004001 < GOOGLE_PROTOBUF_MIN_PROTOC_VERSION
>-+#if 2005001 < GOOGLE_PROTOBUF_MIN_PROTOC_VERSION
>- #error This file was generated by an older version of protoc which is
>- #error incompatible with your Protocol Buffer headers.  Please
>- #error regenerate this file with a newer version of protoc.
>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/plinkseq/pkg-plist /usr/wip/biology/plinkseq/pkg-plist
>--- /usr/ports/biology/plinkseq/pkg-plist	2014-07-22 17:12:15.000000000 -0500
>+++ /usr/wip/biology/plinkseq/pkg-plist	2014-10-11 16:07:23.000000000 -0500
>@@ -1,12 +1,10 @@
> bin/behead
>+bin/browser
> bin/gcol
>-bin/index
>-bin/index.cgi
>+bin/mm
> bin/mongoose
>-bin/pbrowse
>-bin/pbrowse.cgi
>+bin/pdas
> bin/pseq
>+bin/smp
> bin/tab2vcf
>-lib/libplinkseq.so
>-lib/libplinkseq.so.0
>-lib/libplinkseq.so.0.0.0
>+lib/libplinkseq.a

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