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authorbapt <bapt@FreeBSD.org>2012-10-26 07:05:56 +0800
committerbapt <bapt@FreeBSD.org>2012-10-26 07:05:56 +0800
commitb9188470ffb3f05bde694d4d1c25b9860cd1cd03 (patch)
tree79c19af554e3cc39ac10ad0222588e84a1a0b30a /biology
parent4d5d86ee578830528ae200e0ea23d2048eaafc2c (diff)
downloadfreebsd-ports-gnome-b9188470ffb3f05bde694d4d1c25b9860cd1cd03.tar.gz
freebsd-ports-gnome-b9188470ffb3f05bde694d4d1c25b9860cd1cd03.tar.zst
freebsd-ports-gnome-b9188470ffb3f05bde694d4d1c25b9860cd1cd03.zip
2012-10-20 chinese/wangttf: No more public distfiles
2012-10-20 chinese/stardict-dict-zh_TW: No more public distfiles 2012-10-20 chinese/stardict-dict-zh_CN: No more public distfiles 2012-10-20 chinese/mingunittf: No more public distfiles 2012-10-20 chinese/dfsongsd: No more public distfiles 2012-10-20 biology/dna-qc: No more public distfiles Feature safe: yes
Diffstat (limited to 'biology')
-rw-r--r--biology/Makefile1
-rw-r--r--biology/dna-qc/Makefile55
-rw-r--r--biology/dna-qc/distinfo2
-rw-r--r--biology/dna-qc/files/patch-hybridize.c12
-rw-r--r--biology/dna-qc/pkg-descr5
-rw-r--r--biology/dna-qc/pkg-plist25
6 files changed, 0 insertions, 100 deletions
diff --git a/biology/Makefile b/biology/Makefile
index 4956b22f782c..935b8c6c59d3 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -18,7 +18,6 @@
SUBDIR += clustalw
SUBDIR += consed
SUBDIR += crux
- SUBDIR += dna-qc
SUBDIR += dotter
SUBDIR += embassy
SUBDIR += emboss
diff --git a/biology/dna-qc/Makefile b/biology/dna-qc/Makefile
deleted file mode 100644
index 76aab5a81edf..000000000000
--- a/biology/dna-qc/Makefile
+++ /dev/null
@@ -1,55 +0,0 @@
-# New ports collection makefile for: dna-qc
-# Date created: 25 Novemeber 2001
-# Whom: Tony Maher <tonym@biolateral.com.au>
-#
-# $FreeBSD$
-#
-
-PORTNAME= dna-qc
-PORTVERSION= 1993.07.26
-CATEGORIES= biology
-MASTER_SITES= ftp://ftp.tigr.org/pub/software/qc/
-DISTNAME= qc
-EXTRACT_SUFX= .tar.Z
-
-MAINTAINER= ports@FreeBSD.org
-COMMENT= A quality control algorithm for DNA sequencing projects
-
-DEPRECATED= No more public distfiles
-EXPIRATION_DATE= 2012-10-20
-
-NO_WRKSUBDIR= true
-
-EXAMPLES= README script.compare script.limits \
- bact.all chromosomeIII.all human.all worm.all
-PROGRAMS= counter hybridize normalize random_clip random_line
-
-.include <bsd.port.pre.mk>
-
-.if ${ARCH} == "alpha"
-BROKEN= Does not compile
-.endif
-
-post-patch:
- @${REINPLACE_CMD} -e 's,^CFLAGS,#CFLAGS,' ${WRKSRC}/Makefile
- @${REINPLACE_CMD} -e 's,malloc.h,stdlib.h,' ${WRKSRC}/normalize.c
- @${REINPLACE_CMD} -e 's,fname\*,fname,' ${WRKSRC}/random_line.c
- @${REINPLACE_CMD} -e 's,static void allocate_pool,void allocate_pool,' \
- ${WRKSRC}/stringpool.c
-
-do-install:
-.for file in ${PROGRAMS}
- ${INSTALL_PROGRAM} ${WRKSRC}/${file} ${PREFIX}/bin
- ${STRIP_CMD} ${PREFIX}/bin/${file}
-.endfor
-.if !defined(NOPORTDOCS)
- @${MKDIR} ${DOCSDIR}
- ${INSTALL_DATA} ${WRKSRC}/qc_doc/* ${DOCSDIR}
- ${INSTALL_DATA} ${WRKSRC}/surprize_doc/* ${DOCSDIR}
- @${MKDIR} ${EXAMPLESDIR}
-.for file in ${EXAMPLES}
- ${INSTALL_DATA} ${WRKSRC}/${file} ${EXAMPLESDIR}
-.endfor
-.endif
-
-.include <bsd.port.post.mk>
diff --git a/biology/dna-qc/distinfo b/biology/dna-qc/distinfo
deleted file mode 100644
index 75b04ae97a1e..000000000000
--- a/biology/dna-qc/distinfo
+++ /dev/null
@@ -1,2 +0,0 @@
-SHA256 (qc.tar.Z) = e17258a7b47fd2b6b53cd1794df3acd760a4cdfbfdb8573389dbb1076883ad27
-SIZE (qc.tar.Z) = 1084013
diff --git a/biology/dna-qc/files/patch-hybridize.c b/biology/dna-qc/files/patch-hybridize.c
deleted file mode 100644
index 45dae76fc31e..000000000000
--- a/biology/dna-qc/files/patch-hybridize.c
+++ /dev/null
@@ -1,12 +0,0 @@
-$FreeBSD$
-
---- hybridize.c.orig Sat Nov 24 21:25:04 2001
-+++ hybridize.c Sat Nov 24 21:25:35 2001
-@@ -54,6 +54,7 @@
- extern unsigned array_to_base_4();
- extern unsigned string_to_base_4();
- extern int dna2i();
-+double logl();
- int *read_file();
-
- main(argc, argv)
diff --git a/biology/dna-qc/pkg-descr b/biology/dna-qc/pkg-descr
deleted file mode 100644
index e9a85e146525..000000000000
--- a/biology/dna-qc/pkg-descr
+++ /dev/null
@@ -1,5 +0,0 @@
-"relevant reference:
-White, O., T. Dunning, G. Sutton, M. Adams, J. C. Venter, and C.
-Fields (1993). A quality control algorithm for DNA sequencing
-projects. Nucleic Acids Research (in press)."
-- from the README file
diff --git a/biology/dna-qc/pkg-plist b/biology/dna-qc/pkg-plist
deleted file mode 100644
index b9e9afbcf6b3..000000000000
--- a/biology/dna-qc/pkg-plist
+++ /dev/null
@@ -1,25 +0,0 @@
-bin/counter
-bin/hybridize
-bin/normalize
-bin/random_clip
-bin/random_line
-%%PORTDOCS%%%%DOCSDIR%%/qc_algorithm.ps.Z
-%%PORTDOCS%%%%DOCSDIR%%/qc_fig1.ps.Z
-%%PORTDOCS%%%%DOCSDIR%%/qc_fig2a.ps.Z
-%%PORTDOCS%%%%DOCSDIR%%/qc_fig2b.ps.Z
-%%PORTDOCS%%%%DOCSDIR%%/qc_fig2c.ps.Z
-%%PORTDOCS%%%%DOCSDIR%%/qc_fig3.ps.Z
-%%PORTDOCS%%%%DOCSDIR%%/qc_fig4.ps.Z
-%%PORTDOCS%%%%DOCSDIR%%/qc_fig5.ps.Z
-%%PORTDOCS%%%%DOCSDIR%%/qc_fig6.ps.Z
-%%PORTDOCS%%%%DOCSDIR%%/qc_fig7.ps.Z
-%%PORTDOCS%%%%DOCSDIR%%/surprize.ps.Z
-%%PORTDOCS%%share/examples/dna-qc/README
-%%PORTDOCS%%share/examples/dna-qc/bact.all
-%%PORTDOCS%%share/examples/dna-qc/chromosomeIII.all
-%%PORTDOCS%%share/examples/dna-qc/human.all
-%%PORTDOCS%%share/examples/dna-qc/script.compare
-%%PORTDOCS%%share/examples/dna-qc/script.limits
-%%PORTDOCS%%share/examples/dna-qc/worm.all
-%%PORTDOCS%%@dirrm share/examples/dna-qc
-%%PORTDOCS%%@dirrm %%DOCSDIR%%