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non port: biology/seqio/Makefile

Number of commits found: 13

Wednesday, 7 Sep 2022
21:10 Stefan E├čer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.

This commit implements such a proposal and moves one of the WWW: entries
of each pkg-descr file into the respective port's Makefile. A heuristic
attempts to identify the most relevant URL in case there is more than
one WWW: entry in some pkg-descr file. URLs that are not moved into the
Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr
files in order to preserve them.

There are 1256 ports that had no WWW: entries in pkg-descr files. These
ports will not be touched in this commit.

The portlint port has been adjusted to expect a WWW entry in each port
Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as
deprecated.

Approved by:		portmgr (tcberner)
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 b7f0544
Wednesday, 20 Jul 2022
14:20 Tobias C. Berner (tcberner) search for other commits by this committer
biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
  *  Johann Visagie <johann@egenetics.com>
  *  Johann Visagie <wjv@FreeBSD.org>
  *  Mauricio Herrera Cuadra <mauricio@arareko.net>
  *  Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
  *  Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@niid.go.jp>
  *  Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Razi Khaja <razi@genet.sickkids.on.ca>
  *  Reed A. Cartwright <cartwright@asu.edu>
  *  Ryo MIYAMOTO
  *  Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
  *  Sangwoo Shim <sangwoos@gmail.com>
  *  Sunpoet Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Tassilo Philipp <tphilipp@potion-studios.com>
  *  Tony Maher
  *  Tony Maher <tonym@biolateral.com.au>
  *  Wen Heping <wen@FreeBSD.org>
  *  Wen Heping <wenheping@gmail.com>
  *  Yonatan <onatan@gmail.com>
  *  Yuri Victorovich <yuri@rawbw.com>
  *  ballen
  *  barnhart@genetics.wustl.edu
  *  camson@bilateral.com.au
  *  chuynh@biolateral.com.au
  *  dbader@eece.unm.edu
  *  frankch@waru.life.nthu.edu.tw
  *  h2
  *  lentferj
  *  maho@FreeBSD.org
  *  mzaki@biol.s.u-tokyo.ac.jp
  *  tonym
  *  wen@FreeBSD.org

With hat:	portmgr
commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 37526bb
Tuesday, 6 Apr 2021
14:31 Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb 305f148
Sunday, 26 Nov 2017
09:00 amdmi3 search for other commits by this committer
- Switch to options helpers
Original commitRevision:454906 
Sunday, 16 Feb 2014
11:42 ehaupt search for other commits by this committer
Support staging
Original commitRevision:344538 
Friday, 20 Sep 2013
15:55 bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
Original commitRevision:327709 
Wednesday, 19 Jun 2013
13:30 bsam search for other commits by this committer
Forced commit to show previous changes:
-----
. NOPORTDOCS -> PORT_OPTIONS:MDOCS;
. NOPORTEXAMPLES -> PORT_OPTIONS:MEXAMPLES;
. use PLIST_FILES, PORTEXAMPLES and PORTDOCS;
. get rid of pkg-plist;
. use plain install commands instead of .for loops;
. remove unnecessary mkdir command (the following one creates a subdirectory);
. mute mkdirs;
. trim Makefile headers;
. remove the indefinite article from COMMENT.
-----
Original commitRevision:321248 
13:09 bsam search for other commits by this committer
Index: Makefile
===================================================================
--- Makefile	(revision 321238)
+++ Makefile	(working copy)
@@ -1,9 +1,5 @@
-# New ports collection makefile for:	seqio
-# Date created:				17 August 2001
-# Whom:					Tony Maher
-#
+# Created by: Tony Maher
 # $FreeBSD$
-#

 PORTNAME=	seqio
 PORTVERSION=	1.2.2
@@ -13,38 +9,32 @@
 DISTNAME=	${PORTNAME}

 MAINTAINER=	ports@FreeBSD.org
-COMMENT=	A set of C functions which can read/write biological sequence files
+COMMENT=	Set of C functions which can read/write biological sequence files

 WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}

 EXAMPLES=	example1.c example2.c example3.c example4.c seqio.c \
 		seqio.h Makefile
 PROGRAMS=	fmtseq grepseq idxseq typeseq wcseq
+PLIST_FILES+=	${PROGRAMS:S,^,bin/,}
+PORTEXAMPLES=	*
+PORTDOCS=	*

+OPTIONS_DEFINE=	DOCS EXAMPLES
+
+.include <bsd.port.options.mk>
+
 do-install:
-	cd ${WRKSRC}; \
-	for file in ${PROGRAMS}; do \
-		${INSTALL_PROGRAM} $$file ${PREFIX}/bin; \
-	done
-.if !defined(NOPORTEXAMPLES)
-	${MKDIR} ${EXAMPLESDIR}
-	cd ${WRKSRC}; \
-	for file in ${EXAMPLES}; do \
-		${INSTALL_DATA} $$file ${EXAMPLESDIR}; \
-	done
+	${INSTALL_PROGRAM} ${PROGRAMS:S,^,${WRKSRC}/,} ${PREFIX}/bin
+.if ${PORT_OPTIONS:MEXAMPLES}
+	@${MKDIR} ${EXAMPLESDIR}
+	${INSTALL_DATA} ${EXAMPLES:S,^,${WRKSRC}/,} ${EXAMPLESDIR}
 .endif
-.if !defined(NOPORTDOCS)
-	${MKDIR} ${DOCSDIR}
-	${MKDIR} ${DOCSDIR}/html
+.if ${PORT_OPTIONS:MDOCS}
+	@${MKDIR} ${DOCSDIR}/html
 	${INSTALL_DATA} ${WRKSRC}/bioseq.txt ${DOCSDIR}
-	cd ${WRKSRC}/doc; \
-	for file in *.doc; do \
-		${INSTALL_DATA} $$file ${DOCSDIR}; \
-	done
-	cd ${WRKSRC}/html; \
-	for file in *.html; do \
-		${INSTALL_DATA} $$file ${DOCSDIR}/html; \
-	done
+	${INSTALL_DATA} ${WRKSRC}/doc/*.doc ${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/html/*.html ${DOCSDIR}/html
 .endif

 .include <bsd.port.mk>
Original commitRevision:321246 
Saturday, 12 Jul 2008
06:28 itetcu search for other commits by this committer
- respect NOPORTEXAMPLES/NOPORTDOCS and fix plist
- bump PORTREVISION

Prompted by:    QA Tindy run
Original commit
Tuesday, 26 Dec 2006
12:46 linimon search for other commits by this committer
Reset tonymaher@optusnet.com.au due to maintainer-timeouts and no response
to email.

Hat:            portmgr
Original commit
Monday, 9 Jan 2006
03:25 edwin search for other commits by this committer
Fix maintainer address

    From: Tony Maher <anthony.maher@uts.edu.au>
    To: Edwin Groothuis <edwin@FreeBSD.org>
    Subject: Re: ports/91537: maths/xgobi - download site moved/maintainer
addressupdate

    Actually I need  modify all my ports to use OptusNet rather than
    Biolateral.  Is there an easy way to do this or should I submit a
    separate 1-line patch and PR for each port?

    biology/crimap
    biology/dna-qc
    biology/flip
    biology/primer3
    biology/seqio
    biology/wise
    math/xgobi
    net/generic-nqs

Submitted by:   Tony Maher <anthony.maher@uts.edu.au>
Original commit
Friday, 21 Feb 2003
11:01 knu search for other commits by this committer
De-pkg-comment.
Original commit
Wednesday, 22 Aug 2001
13:07 wjv search for other commits by this committer
Add seqio 1.2.2, a set of C functions which can read/write   biological sequence
files.    
Original commit

Number of commits found: 13