Attachment 190628 Details for Bug 225682 – update for biology/seqan-apps

[patch] update for biology/seqan-apps

update_biology_seqan-apps.patch (text/plain), 2.92 KB, created by Hannes Hauswedell on 2018-02-14 17:12:33 UTC

(hide)

Description:

Filename:

MIME Type:

Creator: Hannes Hauswedell

Created: 2018-02-14 17:12:33 UTC

Size: 2.92 KB

patch

obsolete

>diff -ru seqan-appsOld/distinfo seqan-apps/distinfo
>--- seqan-appsOld/distinfo	2016-09-14 21:38:58.000000000 +0200
>+++ seqan-apps/distinfo	2018-02-14 17:54:28.261623000 +0100
>@@ -1,3 +1,3 @@
>-TIMESTAMP = 1473848209
>-SHA256 (seqan-seqan-seqan-v2.2.0_GH0.tar.gz) = 6add074932c2723ef1fb658c88f906bdd6ced1fc34cb16a7410251ffc4cb8cc8
>-SIZE (seqan-seqan-seqan-v2.2.0_GH0.tar.gz) = 110936119
>+TIMESTAMP = 1517833288
>+SHA256 (seqan-seqan-seqan-v2.4.0_GH0.tar.gz) = d7084d17729214003e84818e0280a16f223c8f1c6a30eeef040c27e0c0047bd7
>+SIZE (seqan-seqan-seqan-v2.4.0_GH0.tar.gz) = 109626901
>Only in seqan-apps: distinfo.orig
>diff -ru seqan-appsOld/Makefile seqan-apps/Makefile
>--- seqan-appsOld/Makefile	2018-01-18 05:11:02.000000000 +0100
>+++ seqan-apps/Makefile	2018-02-14 18:06:39.749270000 +0100
>@@ -2,34 +2,34 @@
> # $FreeBSD: head/biology/seqan-apps/Makefile 459315 2018-01-18 04:11:02Z jbeich $
> 
> PORTNAME=	seqan-apps
>-PORTVERSION=	2.2.0
> DISTVERSIONPREFIX=	seqan-v
>-PORTREVISION=	9
>+DISTVERSION=	2.4.0
> CATEGORIES=	biology
> 
> MAINTAINER=	h2+fbsdports@fsfe.org
>-COMMENT=	Official Bioinformatic applications based on the SeqAn library
>+COMMENT=	Official bioinformatic applications based on the SeqAn library
> 
> LICENSE=	BSD3CLAUSE LGPL3 GPLv3
> LICENSE_COMB=	multi
> 
> BUILD_DEPENDS=	boost-libs>0:devel/boost-libs
> 
>-BROKEN_aarch64=		fails to compile: Error: unknown mnemonic rep -- rep
>-BROKEN_armv6=		fails to compile: Error: bad instruction rep
>-BROKEN_armv7=		fails to compile: Error: bad instruction rep
>-BROKEN_powerpc64=	fails to compile: Error: unrecognized opcode: rep
>-
>+# once #199603 is resolved, add c++14-lang:
>+# USES=		cmake:outsource compiler:openmp,c++14-lang
>+USES=		cmake:outsource compiler:openmp
> USE_GITHUB=	yes
> GH_ACCOUNT=	seqan
> GH_PROJECT=	seqan
>-
>-# once #199603 is resolved, do the following instead of USE_GCC
>-# USES=		cmake:outsource compiler:openmp,c++14-lang
>-USES=		cmake:outsource
> CMAKE_ARGS=	-DSEQAN_BUILD_SYSTEM="SEQAN_RELEASE_APPS"
> 
>-USE_GCC=	yes
>+OPTIONS_RADIO=		ARCH
>+OPTIONS_RADIO_ARCH=	SSE4 AVX2 NATIVE
>+SSE4_DESC= 		Use SSE4 and POPCNT instructions
>+SSE4_CMAKE_ON=		-DSEQAN_ARCH_SSE4:BOOL=TRUE
>+AVX2_DESC= 		Use SSE4, AVX2 and POPCNT instructions
>+AVX2_CMAKE_ON=		-DSEQAN_ARCH_AVX2:BOOL=TRUE
>+NATIVE_DESC=		Use all available instruction sets (-march=native)
>+NATIVE_CMAKE_ON=	-DSEQAN_ARCH_NATIVE:BOOL=TRUE
> 
> .include <bsd.port.pre.mk>
> 
>Only in seqan-apps: Makefile.orig
>diff -ru seqan-appsOld/pkg-plist seqan-apps/pkg-plist
>--- seqan-appsOld/pkg-plist	2016-05-10 02:52:04.000000000 +0200
>+++ seqan-apps/pkg-plist	2018-02-14 17:54:28.262215000 +0100
>@@ -48,6 +48,7 @@
> bin/tree_recon
> bin/yara_indexer
> bin/yara_mapper
>+man/man1/sak.1.gz
> share/doc/alf/LICENSE
> share/doc/alf/README
> share/doc/alf/example/small.fasta
>@@ -117,7 +118,6 @@
> share/doc/sak/LICENSE
> share/doc/sak/README
> share/doc/sak/README.sak.txt
>-share/doc/sak/man/sak.1
> share/doc/sam2matrix/LICENSE
> share/doc/sam2matrix/README
> share/doc/samcat/LICENSE
>Only in seqan-apps: pkg-plist.orig

Flags:

h2+fbsdports: maintainer-approval+

Actions: View | Diff

Attachments on bug 225682: 190337 | 190338 | 190502 | 190503 | 190628