From 1a7c939f8f1087c8031e2621e53bd3bda0f043af Mon Sep 17 00:00:00 2001
From: David Seifert <soap@gentoo.org>
Date: Sat, 26 Sep 2020 12:00:48 +0200
Subject: sci-biology/bwa: Remove old 0.7.16a

Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: David Seifert <soap@gentoo.org>
---
 sci-biology/bwa/Manifest                        |  1 -
 sci-biology/bwa/bwa-0.7.16a.ebuild              | 36 -------------------------
 sci-biology/bwa/files/bwa-0.7.15-Makefile.patch | 27 -------------------
 sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch  |  7 -----
 4 files changed, 71 deletions(-)
 delete mode 100644 sci-biology/bwa/bwa-0.7.16a.ebuild
 delete mode 100644 sci-biology/bwa/files/bwa-0.7.15-Makefile.patch
 delete mode 100644 sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch

(limited to 'sci-biology')

diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest
index 4b69e7f04038..5f912dc43cf0 100644
--- a/sci-biology/bwa/Manifest
+++ b/sci-biology/bwa/Manifest
@@ -1,2 +1 @@
-DIST bwa-0.7.16a.tar.bz2 190773 BLAKE2B e1064381b6b1aa4c9b78d12222c7b783a55676a163b94ad8596a2af64c9b0d60bbebd8e840aaa13b25e1ca4f10466c2c39c99830f1ca58e558d724d1ad583944 SHA512 8bbe223f79efd328d66adb88baf995e894f5944aad912ac1b464dc84dc9b4e22ddf77b60dcbe468e0eedc344ee58d08dc498777f0d2794a2c1e0ddd33dad606d
 DIST bwa-0.7.17.tar.gz 232593 BLAKE2B fa48aad72a47547d66c767e2e2a5aadfcfc7c77c517410812230f51a2222ee66bb04383b068036b696af0a57b04b35e97bed11e3c44793aa899a8c0807f3df5e SHA512 114e61b7cc5edcb67172d1eca7be1fa670ea33dd48b5c02c98318e254871363775c0dab327fd7ee7023200a5fedc745fa01cbe0fd9550d783f091d4df6926f48
diff --git a/sci-biology/bwa/bwa-0.7.16a.ebuild b/sci-biology/bwa/bwa-0.7.16a.ebuild
deleted file mode 100644
index b29bf210169a..000000000000
--- a/sci-biology/bwa/bwa-0.7.16a.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner"
-HOMEPAGE="https://bio-bwa.sourceforge.net/"
-SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-
-RDEPEND="dev-lang/perl"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-0.7.15-Makefile.patch
-	"${FILESDIR}"/${PN}-0.7.16a-gcc-10.patch
-)
-DOCS=( NEWS.md README-alt.md README.md )
-
-src_configure() {
-	tc-export CC AR
-}
-
-src_install() {
-	dobin bwa
-
-	exeinto /usr/libexec/${PN}
-	doexe qualfa2fq.pl xa2multi.pl
-
-	einstalldocs
-	doman bwa.1
-}
diff --git a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch
deleted file mode 100644
index 39b437a02897..000000000000
--- a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch
+++ /dev/null
@@ -1,27 +0,0 @@
---- bwa-0.7.13/Makefile
-+++ bwa-0.7.13/Makefile
-@@ -1,8 +1,8 @@
--CC=			gcc
-+CC?=			gcc
- #CC=			clang --analyze
--CFLAGS=		-g -Wall -Wno-unused-function -O2
-+CFLAGS?=		-g -Wall -Wno-unused-function -O2
- WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
--AR=			ar
-+AR?=			ar
- DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)
- LOBJS=		utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o
- AOBJS=		QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
-@@ -26,10 +26,10 @@
- all:$(PROG)
- 
- bwa:libbwa.a $(AOBJS) main.o
--		$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
-+		$(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
- 
- bwamem-lite:libbwa.a example.o
--		$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
-+		$(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
- 
- libbwa.a:$(LOBJS)
- 		$(AR) -csru $@ $(LOBJS)
diff --git a/sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch b/sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch
deleted file mode 100644
index 40056ffeaaa9..000000000000
--- a/sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch
+++ /dev/null
@@ -1,7 +0,0 @@
---- a/rle.h
-+++ b/rle.h
-@@ -32,3 +32,3 @@ extern "C" {
- 
--const uint8_t rle_auxtab[8];
-+extern const uint8_t rle_auxtab[8];
- 
-- 
cgit v1.2.3-65-gdbad