commit: 52964cfbf139e8676669ca563b7e421cf8188187 Author: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> AuthorDate: Fri Jan 27 11:02:44 2023 +0000 Commit: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> CommitDate: Fri Jan 27 11:07:29 2023 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=52964cfb
sci-biology/phrap: treeclean Signed-off-by: Jakov Smolić <jsmolic <AT> gentoo.org> profiles/package.mask | 1 - sci-biology/phrap/Manifest | 1 - .../files/phrap-1.080812-fix-build-system.patch | 100 --------------------- sci-biology/phrap/metadata.xml | 8 -- sci-biology/phrap/phrap-1.080812-r2.ebuild | 47 ---------- 5 files changed, 157 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 6496beff8e24..d442ec3896a7 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -708,7 +708,6 @@ app-eselect/eselect-sh # GCC and Clang (-fcommon), license prohibits distributing, EAPI 6, # last release 8 years ago. Removal on 2023-01-25. sci-biology/consed -sci-biology/phrap # Ionen Wolkens <[email protected]> (2022-12-24) # Upstream dropped wxGTK support in >=games-emulation/pcsx2-1.7.3773, diff --git a/sci-biology/phrap/Manifest b/sci-biology/phrap/Manifest deleted file mode 100644 index 12d65a0b5974..000000000000 --- a/sci-biology/phrap/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST phrap-1.080812-distrib.tar.gz 317350 BLAKE2B 9cc53d05184b4a55a9a80e6112498f91a622b98a853b255daedd57c892b7c2bb8ef3091ed3d141e297864c158b7e03d02313a272448d2e0fb80e1c51a906e00a SHA512 6b125b9a99b6180eb5de16bccfe068abefdb59237fd3295924c418749f2f2d6e39cdbcecc6786e42738846975334c4d8a645eae8fd0fcbda6b0e99241deb15ca 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) $(CFLAGS) -S -machine_code -source_listing fast_smith_wat.c - #N.B. fast_smith_wat.s MUST BE EDITTED BEFORE USE!!! - - tig_node.o: swat.h ---- a/phrapview -+++ b/phrapview -@@ -1,4 +1,4 @@ --#!/usr/local/bin/perl -w -+#!/usr/bin/env perl - - - #/***************************************************************************** -@@ -25,6 +25,7 @@ - # - #*****************************************************************************/ - -+use warnings; - use strict; - use Tk; - #phrapview version 0.960731 diff --git a/sci-biology/phrap/metadata.xml b/sci-biology/phrap/metadata.xml deleted file mode 100644 index ccdff086e20b..000000000000 --- a/sci-biology/phrap/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/phrap/phrap-1.080812-r2.ebuild b/sci-biology/phrap/phrap-1.080812-r2.ebuild deleted file mode 100644 index 08ea5a1fb71f..000000000000 --- a/sci-biology/phrap/phrap-1.080812-r2.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs - -DESCRIPTION="Shotgun assembly and alignment utilities" -HOMEPAGE="http://www.phrap.org/"; -SRC_URI="phrap-${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 -}
