Date: Thu, 18 Jan 2024 18:29:34 GMT From: Muhammad Moinur Rahman <bofh@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: b8f4ba2ca32b - main - biology/sim4: Remove expired port Message-ID: <202401181829.40IITYeu083872@gitrepo.freebsd.org>
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The branch main has been updated by bofh: URL: https://cgit.FreeBSD.org/ports/commit/?id=b8f4ba2ca32b0e3e1424741f4b74bebf337518bd commit b8f4ba2ca32b0e3e1424741f4b74bebf337518bd Author: Muhammad Moinur Rahman <bofh@FreeBSD.org> AuthorDate: 2024-01-18 18:26:28 +0000 Commit: Muhammad Moinur Rahman <bofh@FreeBSD.org> CommitDate: 2024-01-18 18:29:13 +0000 biology/sim4: Remove expired port 2024-01-17 biology/sim4: Upstream last update was in 2005 --- MOVED | 1 + biology/Makefile | 1 - biology/sim4/Makefile | 29 ----------------------------- biology/sim4/distinfo | 2 -- biology/sim4/pkg-descr | 8 -------- 5 files changed, 1 insertion(+), 40 deletions(-) diff --git a/MOVED b/MOVED index 67dca30a0c52..4d717786f2d4 100644 --- a/MOVED +++ b/MOVED @@ -2951,3 +2951,4 @@ x11-toolkits/p5-Gtk2-TrayIcon||2024-01-17|Has expired: Upstream marked this modu editors/led||2024-01-17|Has expired: Last upstream release was in 2002 reconsider using editors/nano editors/jove||2024-01-18|Has expired: No upstream update in last 23 years editors/impress||2024-01-18|Has expired: Upstream last release was in 2000 +biology/sim4||2024-01-18|Has expired: Upstream last update was in 2005 diff --git a/biology/Makefile b/biology/Makefile index 11fc752f7b4c..447996cf7556 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -223,7 +223,6 @@ SUBDIR += seqtk SUBDIR += seqwish SUBDIR += sigviewer - SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += snpeff diff --git a/biology/sim4/Makefile b/biology/sim4/Makefile deleted file mode 100644 index 9b31b89ce721..000000000000 --- a/biology/sim4/Makefile +++ /dev/null @@ -1,29 +0,0 @@ -PORTNAME= sim4 -PORTVERSION= 2003.09.21 -PORTREVISION= 1 -CATEGORIES= biology -MASTER_SITES= http://globin.cse.psu.edu/ftp/dist/sim4/ -DISTNAME= ${PORTNAME}.${PORTVERSION:S/./-/g} - -MAINTAINER= ports@FreeBSD.org -COMMENT= Algorithm for aligning expressed DNA with genomic sequences -WWW= http://globin.cse.psu.edu/ - -LICENSE= GPLv2 - -DEPRECATED= Upstream last update was in 2005 -EXPIRATION_DATE= 2024-01-17 - -WRKSRC= ${WRKDIR}/sim4.${PORTVERSION:S/./-/g} - -ALL_TARGET= sim4 -PLIST_FILES= bin/sim4 - -post-patch: - ${REINPLACE_CMD} -e 's|^CC=|CC?=|g ; \ - s|^CFLAGS=|CFLAGS+=|g' ${WRKSRC}/Makefile - -do-install: - ${INSTALL_PROGRAM} ${WRKSRC}/sim4 ${STAGEDIR}${PREFIX}/bin - -.include <bsd.port.mk> diff --git a/biology/sim4/distinfo b/biology/sim4/distinfo deleted file mode 100644 index a8098bd717a5..000000000000 --- a/biology/sim4/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -SHA256 (sim4.2003-09-21.tar.gz) = 0d65166c1d1951e1d0b83e5d221f23f07462b9d8c46ea0d0569f66e35a5229ee -SIZE (sim4.2003-09-21.tar.gz) = 60814 diff --git a/biology/sim4/pkg-descr b/biology/sim4/pkg-descr deleted file mode 100644 index 10ca6fb4ed29..000000000000 --- a/biology/sim4/pkg-descr +++ /dev/null @@ -1,8 +0,0 @@ -This package implements the Sim4 algorithm for aligning expressed DNA -with genomic sequences, described in the paper: - -L. Florea, G. Hartzell, Z. Zhang, G. Rubin, and W. Miller (1998) -"A computer program for aligning a cDNA sequence with a genomic DNA sequence." -Genome Research 8, 967-974. - -Port maintained by the FreeBSD bio-porters mailing list.
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