svn commit: r451982 - in head/biology: ariadne biococoa crux plink ssaha tRNAscan-SE

[Dan Langille]

biology/biococoa did not get marked as BROKEN.  Is that intentional?

I discovered this while investigating FreshPorts fallout for https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=223037 <https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=223037>

-- 
Dan Langille - BSDCan / PGCon
dan at langille.org


> On Oct 13, 2017, at 7:14 AM, Baptiste Daroussin <bapt at FreeBSD.org> wrote:
> 
> Author: bapt
> Date: Fri Oct 13 11:14:53 2017
> New Revision: 451982
> URL: https://svnweb.freebsd.org/changeset/ports/451982
> 
> Log:
>  Mark as broken ports with no public distfiles
> 
> Modified:
>  head/biology/ariadne/Makefile
>  head/biology/biococoa/Makefile
>  head/biology/crux/Makefile
>  head/biology/plink/Makefile
>  head/biology/ssaha/Makefile
>  head/biology/tRNAscan-SE/Makefile
> 
> Modified: head/biology/ariadne/Makefile
> ==============================================================================
> --- head/biology/ariadne/Makefile	Fri Oct 13 11:14:32 2017	(r451981)
> +++ head/biology/ariadne/Makefile	Fri Oct 13 11:14:53 2017	(r451982)
> @@ -11,6 +11,8 @@ COMMENT=	Programs to compare protein sequences and pro
> 
> WRKSRC=		${WRKDIR}/SRC-${PORTVERSION}
> 
> +BROKEN=		No public distfiles
> +
> PLIST_FILES+=	bin/ariadne bin/prospero
> USES=		gmake tar:Z
> PORTDOCS=	README
> 
> Modified: head/biology/biococoa/Makefile
> ==============================================================================
> --- head/biology/biococoa/Makefile	Fri Oct 13 11:14:32 2017	(r451981)
> +++ head/biology/biococoa/Makefile	Fri Oct 13 11:14:53 2017	(r451982)
> @@ -4,7 +4,7 @@ PORTNAME=	biococoa
> PORTVERSION=	2.2.2
> PORTREVISION=	3
> CATEGORIES=	biology gnustep
> -MASTER_SITES=	http://bioinformatics.org/biococoa/downloads/ DEBIAN/pool/main/b/biococoa.app
> +MASTER_SITES=	http://bioinformatics.org/biococoa/downloads/
> DISTNAME=	biococoa-${PORTVERSION}-src
> EXTRACT_SUFX=	.tgz
> 
> 
> Modified: head/biology/crux/Makefile
> ==============================================================================
> --- head/biology/crux/Makefile	Fri Oct 13 11:14:32 2017	(r451981)
> +++ head/biology/crux/Makefile	Fri Oct 13 11:14:53 2017	(r451982)
> @@ -13,6 +13,7 @@ COMMENT=	Software toolkit for phylogenetic inference
> LICENSE=	BSD2CLAUSE BSD3CLAUSE
> LICENSE_COMB=	multi
> 
> +BROKEN=		No public distfiles
> BROKEN_aarch64=		Fails to link: ImportError: /lib/libgcc_s.so.1: version GCC_4.5.0 required by /usr/local/lib/gcc5/libgfortran.so.3 not found
> BROKEN_armv6=		Fails to link: ImportError: /usr/local/lib/gcc49/libgfortran.so.3: Undefined symbol "__aeabi_ldivmod"
> 
> 
> Modified: head/biology/plink/Makefile
> ==============================================================================
> --- head/biology/plink/Makefile	Fri Oct 13 11:14:32 2017	(r451981)
> +++ head/biology/plink/Makefile	Fri Oct 13 11:14:53 2017	(r451982)
> @@ -11,6 +11,8 @@ DISTNAME=	${PORTNAME}-${PORTVERSION}-src
> MAINTAINER=	bacon4000 at gmail.com
> COMMENT=	Whole genome association analysis toolset
> 
> +BROKEN=		no public distfiles
> +
> LICENSE=	GPLv2
> 
> LIB_DEPENDS=	liblapack.so:math/lapack
> 
> Modified: head/biology/ssaha/Makefile
> ==============================================================================
> --- head/biology/ssaha/Makefile	Fri Oct 13 11:14:32 2017	(r451981)
> +++ head/biology/ssaha/Makefile	Fri Oct 13 11:14:53 2017	(r451982)
> @@ -11,6 +11,8 @@ DISTNAME=	${PORTNAME}_v${PORTVERSION:S/.//}
> MAINTAINER=	ports at FreeBSD.org
> COMMENT=	Very fast matching and alignment of DNA sequences
> 
> +BROKEN=		No public distfiles
> +
> NO_WRKSUBDIR=	yes
> BUILD_WRKSRC=		${WRKSRC}/Binary
> 
> 
> Modified: head/biology/tRNAscan-SE/Makefile
> ==============================================================================
> --- head/biology/tRNAscan-SE/Makefile	Fri Oct 13 11:14:32 2017	(r451981)
> +++ head/biology/tRNAscan-SE/Makefile	Fri Oct 13 11:14:53 2017	(r451982)
> @@ -10,6 +10,8 @@ MASTER_SITES=	ftp://selab.janelia.org/pub/software/tRN
> MAINTAINER=	ports at FreeBSD.org
> COMMENT=	Improved tool for transfer RNA detection
> 
> +BROKEN=		No public distfiles
> +
> USES=		perl5 tar:Z
> MAKE_ARGS=	BINDIR="${PREFIX}/bin" \
> 		LIBDIR="${DATADIR}" \
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