[gentoo-commits] repo/gentoo:master commit in: sci-biology/ariadne/, profiles/, sci-biology/ariadne/files/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/ariadne/, profiles/, sci-biology/ariadne/files/

[Aaron Bauman]

commit:     9a4dd523d67483752a9734dce98106c3d80ddd98
Author:     Aaron Bauman <bman <AT> gentoo <DOT> org>
AuthorDate: Wed Nov 20 17:12:06 2019 +0000
Commit:     Aaron Bauman <bman <AT> gentoo <DOT> org>
CommitDate: Wed Nov 20 17:27:43 2019 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9a4dd523

sci-biology/ariadne: drop last-rited package

Signed-off-by: Aaron Bauman <bman <AT> gentoo.org>

 profiles/package.mask                              |  7 ----
 sci-biology/ariadne/Manifest                       |  1 -
 sci-biology/ariadne/ariadne-1.3-r3.ebuild          | 46 ----------------------
 sci-biology/ariadne/files/ariadne-1.3-gcc4.patch   | 10 -----
 .../ariadne/files/ariadne-1.3-implicits.patch      | 23 -----------
 sci-biology/ariadne/metadata.xml                   | 20 ----------
 6 files changed, 107 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 19d22417f5f..b12fa738ecf 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -341,13 +341,6 @@ www-servers/thin
 # Removal in 30 days.  Bug #697376.
 app-text/scrollkeeper
 
-# Michał Górny <mgorny@gentoo.org> (2019-10-19)
-# Upstream homepage and sources are gone.  The license raises doubt
-# as to whether we can redistribute it.  No new releases since being
-# added in 2005.
-# Removal in 30 days.  Bug #694926.
-sci-biology/ariadne
-
 # Michał Górny <mgorny@gentoo.org> (2019-10-19)
 # Unmaintained package with incorrect LICENSE and a failing build
 # (#679204).

diff --git a/sci-biology/ariadne/Manifest b/sci-biology/ariadne/Manifest
deleted file mode 100644
index b70c215d27b..00000000000
--- a/sci-biology/ariadne/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ariadne-1.3.tar.Z 69427 BLAKE2B 97277e78a2f8c2fd70117f40159d1c47b6c0e2b2c2b491dcc22b50d9842da128aeb3a03ec501d97391c38b8bfcdc3a903fa07770bf1030e5a46247ea14733cc4 SHA512 6c803f945bbcf36c08407e907ad716dc7cd01c7bed555777af46a5dc626b56ca3d1de7d16cab82bfa8bd5a91e06f42c590c0489594251405999459459e9c7289

diff --git a/sci-biology/ariadne/ariadne-1.3-r3.ebuild b/sci-biology/ariadne/ariadne-1.3-r3.ebuild
deleted file mode 100644
index 0103c6d3648..00000000000
--- a/sci-biology/ariadne/ariadne-1.3-r3.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs
-
-DESCRIPTION="Protein sequences and profiles comparison"
-HOMEPAGE="http://www.well.ox.ac.uk/ariadne/"
-SRC_URI="http://www.well.ox.ac.uk/${PN}/${P}.tar.Z"
-
-LICENSE="ARIADNE"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="static-libs"
-
-DEPEND=">=sci-biology/ncbi-tools-0.20041020-r1"
-RDEPEND="${DEPEND}"
-
-S=${WORKDIR}/SRC-${PV}
-
-PATCHES=(
-	"${FILESDIR}"/${P}-gcc4.patch
-	"${FILESDIR}"/${P}-implicits.patch
-)
-
-src_prepare() {
-	default
-	sed -i -e "s/\$(CFLAGS)/\$(LDFLAGS) &/" Makefile || die #359045
-	sed -e "s/blosum62/BLOSUM62/" -i prospero.c || die
-}
-
-src_compile() {
-	emake CC="$(tc-getCC)" OPTIMISE="${CFLAGS}"
-}
-
-src_install() {
-	dobin Linux/{ariadne,prospero}
-
-	use static-libs && dolib.a Linux/libseq.a
-
-	insinto /usr/include/${PN}
-	doins Include/*.h
-
-	einstalldocs
-}

diff --git a/sci-biology/ariadne/files/ariadne-1.3-gcc4.patch b/sci-biology/ariadne/files/ariadne-1.3-gcc4.patch
deleted file mode 100644
index 8bda75cb4f3..00000000000
--- a/sci-biology/ariadne/files/ariadne-1.3-gcc4.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- a/cl.c
-+++ b/cl.c
-@@ -658,6 +658,7 @@
-       fclose(fp);
-       if ( ! stat( filename, &buf ) )
- 	{
-+	  char *ctime(), *t;
- 	  sprintf( date, "%s", ctime(&buf.st_mtime) );
- 	  t = date;
- 	  while ( *t )

diff --git a/sci-biology/ariadne/files/ariadne-1.3-implicits.patch b/sci-biology/ariadne/files/ariadne-1.3-implicits.patch
deleted file mode 100644
index 31c442b1226..00000000000
--- a/sci-biology/ariadne/files/ariadne-1.3-implicits.patch
+++ /dev/null
@@ -1,23 +0,0 @@
-topalign.c:96:5: warning: implicit declaration of function ‘toupper’
-prospero.c:63:3: warning: implicit declaration of function ‘strcpy’
-
---- SRC-1.3/prospero.c
-+++ SRC-1.3/prospero.c
-@@ -26,6 +26,7 @@
- */
- 
- #include<stdio.h>
-+#include<string.h>
- #include<math.h>
- #include"cl.h"
- #include"seq_util.h"
---- SRC-1.3/topalign.c
-+++ SRC-1.3/topalign.c
-@@ -26,6 +26,7 @@
- */
- 
- #include<stdio.h>
-+#include<ctype.h>
- #include<math.h>
- #include"seq_util.h"
- #include"ariadne.h"

diff --git a/sci-biology/ariadne/metadata.xml b/sci-biology/ariadne/metadata.xml
deleted file mode 100644
index d0e8e0be55e..00000000000
--- a/sci-biology/ariadne/metadata.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>
-		ARIADNE is a package of two programs, ariadne and prospero, that
-		compare protein sequences and profiles using the Smith-Waterman
-		algorithm, and assesses statistical significance using a new accurate
-		formula, described in Mott, 2000, "Accurate Formula for P-values of
-		gapped local sequence and profile alignments" J. Mol Biol. 300:649-659.
-		The sequence/profile comparison algorithms used in ARIADNE are
-		standard, and are probably not the fastest implementations available.
-		The novel part is the method for determining statistical significance,
-		which will give thresholds of significance that are accurate to within
-		5% 95% of the time.
-	</longdescription>
-</pkgmetadata>