From 8eccda982236f2cfe9188bdcaffd9168134f39a9 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Fri, 27 Jan 2023 13:58:28 +0000 Subject: gentoo auto-resync : 27:01:2023 - 13:58:28 --- sci-biology/phrap/Manifest | 4 - .../files/phrap-1.080812-fix-build-system.patch | 100 --------------------- sci-biology/phrap/metadata.xml | 8 -- sci-biology/phrap/phrap-1.080812-r2.ebuild | 47 ---------- 4 files changed, 159 deletions(-) delete mode 100644 sci-biology/phrap/Manifest delete mode 100644 sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch delete mode 100644 sci-biology/phrap/metadata.xml delete mode 100644 sci-biology/phrap/phrap-1.080812-r2.ebuild (limited to 'sci-biology/phrap') diff --git a/sci-biology/phrap/Manifest b/sci-biology/phrap/Manifest deleted file mode 100644 index 4fe85ddfb7b0..000000000000 --- a/sci-biology/phrap/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -AUX phrap-1.080812-fix-build-system.patch 3600 BLAKE2B 29a7846cd6394d17b35e525220b8ead461a22ab0f1301ae5668da36605649c07f23040c4c134424802d4da6e0c3b48fbbb05ec5708de50b33f024e4ba702ac49 SHA512 536ad862b9b8ce0fbc7ab67bc48db597e7d4b8c66018a5abefe5a59f4fbc30a4a76c94f4c13f5af7d42a422a22f5181d8f015b797d37f175238c3d4170adf21c -DIST phrap-1.080812-distrib.tar.gz 317350 BLAKE2B 9cc53d05184b4a55a9a80e6112498f91a622b98a853b255daedd57c892b7c2bb8ef3091ed3d141e297864c158b7e03d02313a272448d2e0fb80e1c51a906e00a SHA512 6b125b9a99b6180eb5de16bccfe068abefdb59237fd3295924c418749f2f2d6e39cdbcecc6786e42738846975334c4d8a645eae8fd0fcbda6b0e99241deb15ca -EBUILD phrap-1.080812-r2.ebuild 962 BLAKE2B 42c56565cc83f792878f8dac26badf57a7307d63dae27684a7799c6607521b5e564d0b21f49a7669ed291e0facd502b9745aec1a643226e9ac9ec8e0031d9d76 SHA512 abbc494349976d3a6371a424b4a6bce60e30f7963db4d05976a59c88cf0def994b690f8746d34db683629eb171322ebbcb2aa9325e746adeec9afd575468bc92 -MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de diff --git a/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch b/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch deleted file mode 100644 index 6d30c2ce326a..000000000000 --- a/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch +++ /dev/null @@ -1,100 +0,0 @@ -* Fix perl shebang to be portable -* Make build system honour LDFLAGS - ---- a/makefile -+++ b/makefile -@@ -25,9 +25,8 @@ - # Makefile for swat, phrap, cross_match, phrapview; also swprobs (currently inactivated) - #CC= icc - #CFLAGS= -O2 -wd266,880 --CC= cc --CFLAGS= -O2 --LFLAGS= -lm -+CC ?= cc -+LIBS = -lm - - SWATOBJS= swat.o weibull.o - -@@ -96,46 +95,46 @@ - chmod a+x phrapview - - swat: makefile $(SWATOBJS) $(SWOBJS) -- $(CC) $(CFLAGS) -o $@ $(SWATOBJS) $(SWOBJS) $(LFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(SWATOBJS) $(SWOBJS) $(LIBS) - chmod o-r swat - - alpha_swat: makefile $(ALPHOBJS) $(SWOBJS) -- $(CC) $(CFLAGS) -o $@ $(ALPHOBJS) $(SWOBJS) $(LFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(ALPHOBJS) $(SWOBJS) $(LIBS) - chmod o-r alpha_swat - - swat_counts: makefile $(COUNOBJS) $(SWOBJS) -- $(CC) $(CFLAGS) -o $@ $(COUNOBJS) $(SWOBJS) $(LFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(COUNOBJS) $(SWOBJS) $(LIBS) - chmod o-r swat_counts - - swprobs: makefile $(PROBOBJS) -- $(CC) $(CFLAGS) -o $@ $(PROBOBJS) $(LFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(PROBOBJS) $(LIBS) - - phrap: makefile phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) -- $(CC) $(CFLAGS) -o $@ phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(LFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(LIBS) - chmod o-r phrap - - gcphrap: makefile gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) -- $(CC) $(CFLAGS) -o $@ gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LIBS) - chmod o-r gcphrap - - cross_match: makefile cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) -- $(CC) $(CFLAGS) -o $@ cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(LFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(LIBS) - chmod o-r cross_match - - gccross_match: makefile gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) -- $(CC) $(CFLAGS) -o $@ gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LIBS) - chmod o-r gccross_match - - cluster: makefile $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) -- $(CC) $(CFLAGS) -o $@ $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) $(LFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) $(LIBS) - chmod o-r cluster - - loco: makefile $(LOCOOBJS) $(SWOBJS) -- $(CC) $(CFLAGS) -o $@ $(LOCOOBJS) $(SWOBJS) $(LFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(LOCOOBJS) $(SWOBJS) $(LIBS) - chmod o-r loco - - erf_test: $(ERFOBJS) -- $(CC) $(CFLAGS) -o $@ $(ERFOBJS) $(LFLAGS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(ERFOBJS) $(LIBS) - - loco.o: swat.h - -@@ -228,7 +227,7 @@ - anomalies.o: swat.h - - fast_smith_wat.s: fast_smith_wat.c -- cc -S -machine_code -source_listing -O3 fast_smith_wat.c -+ $(CC) $(CFLAGS) -S -machine_code -source_listing fast_smith_wat.c - #N.B. fast_smith_wat.s MUST BE EDITTED BEFORE USE!!! - - tig_node.o: swat.h ---- a/phrapview -+++ b/phrapview -@@ -1,4 +1,4 @@ --#!/usr/local/bin/perl -w -+#!/usr/bin/env perl - - - #/***************************************************************************** -@@ -25,6 +25,7 @@ - # - #*****************************************************************************/ - -+use warnings; - use strict; - use Tk; - #phrapview version 0.960731 diff --git a/sci-biology/phrap/metadata.xml b/sci-biology/phrap/metadata.xml deleted file mode 100644 index ccdff086e20b..000000000000 --- a/sci-biology/phrap/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ - - - - - sci-biology@gentoo.org - Gentoo Biology Project - - diff --git a/sci-biology/phrap/phrap-1.080812-r2.ebuild b/sci-biology/phrap/phrap-1.080812-r2.ebuild deleted file mode 100644 index 08ea5a1fb71f..000000000000 --- a/sci-biology/phrap/phrap-1.080812-r2.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs - -DESCRIPTION="Shotgun assembly and alignment utilities" -HOMEPAGE="http://www.phrap.org/" -SRC_URI="phrap-${PV}-distrib.tar.gz" - -LICENSE="phrap" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND=" - dev-lang/perl - dev-perl/Tk" - -S="${WORKDIR}" - -RESTRICT="fetch" -PATCHES=( "${FILESDIR}/${PN}-1.080812-fix-build-system.patch" ) - -pkg_nofetch() { - einfo "Please visit http://www.phrap.org/phredphrapconsed.html and obtain the file" - einfo "\"distrib.tar.gz\", then rename it to \"phrap-${PV}-distrib.tar.gz\"" - einfo "and put it into your DISTDIR directory." -} - -src_compile() { - emake CC="$(tc-getCC)" \ - CFLAGS="${CFLAGS}" \ - LDFLAGS="${LDFLAGS}" -} - -src_install() { - dobin cross_match loco phrap phrapview swat - newbin cluster cluster_phrap - - local i - for i in {general,phrap,swat}.doc; do - newdoc ${i} ${i}.txt - done -} -- cgit v1.2.3