commit: 718c86792641e4203877c23d69e9d4dcb0274388 Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Sat Mar 6 10:02:43 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Sat Mar 6 10:02:43 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=718c8679
sci-biology/bowtie: drop old Package-Manager: Portage-3.0.16, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> .../bowtie/bowtie-1.2.2_beta20190219.ebuild | 81 ---------------------- .../files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch | 17 ----- .../files/bowtie-1.2.2-fix-Intel-compilation.patch | 32 --------- .../files/bowtie-1.2.2-fix-isa-return-type.patch | 22 ------ .../bowtie/files/bowtie-1.2.2-unbundle-seqan.patch | 14 ---- .../bowtie/files/bowtie-1.2.2-void2int.patch | 16 ----- 6 files changed, 182 deletions(-) diff --git a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild deleted file mode 100644 index f7a1b92d4..000000000 --- a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild +++ /dev/null @@ -1,81 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit flag-o-matic toolchain-funcs git-r3 - -DESCRIPTION="Popular short read aligner for Next-generation sequencing data" -HOMEPAGE="http://bowtie-bio.sourceforge.net/"; -EGIT_REPO_URI="https://github.com/BenLangmead/bowtie.git"; -EGIT_BRANCH="bug_fixes" -COMMIT="f253e204f5ba4565d14ae1b300ea6cb10dfe4660" - -LICENSE="Artistic" -SLOT="1" -KEYWORDS="~amd64 ~x86" - -IUSE="examples +tbb" - -RDEPEND="tbb? ( dev-cpp/tbb )" -DEPEND="${RDEPEND} - app-arch/unzip" -# sci-biology/seqan:1.4" - -DOCS=( AUTHORS NEWS TUTORIAL doc/README ) -HTML_DOCS=( doc/{manual.html,style.css} ) - -PATCHES=( "${FILESDIR}/bowtie-1.2.2-fix-isa-return-type.patch" ) -# not needed -# "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b -# -# still to be considered -#PATCHES=( -# "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch" -# "${FILESDIR}/${P}-unbundle-seqan.patch" -# "${FILESDIR}/${P}-fix-setBegin-call.patch" -# "${FILESDIR}/${P}-seqan-popcount.patch" -# "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch" -# "${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch" -# "${FILESDIR}/${P}-spelling.patch" -# "${FILESDIR}/${P}-tbb-tinythread-missing.patch" -#) - -src_prepare() { - default - - # remove bundled library of headers, use system seqan 1.4 - # rm -rf SeqAn-1.1/ third_party/ || die - - # innocuous non-security flags, prevent log pollution - append-cxxflags \ - -Wno-unused-local-typedefs \ - -Wno-unused-but-set-variable \ - -Wno-unused-variable -} - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CFLAGS="" \ - CXXFLAGS="" \ - EXTRA_FLAGS="${LDFLAGS}" \ - RELEASE_FLAGS="${CXXFLAGS}" \ - WITH_TBB="$(usex tbb 1 0)" -} - -src_install() { - dobin ${PN} ${PN}-* - - exeinto /usr/libexec/${PN} - doexe scripts/* - - newman MANUAL ${PN}.1 - einstalldocs - - if use examples; then - insinto /usr/share/${PN} - doins -r genomes indexes - fi -} diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch b/sci-biology/bowtie/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch deleted file mode 100644 index 4bcd61ba3..000000000 --- a/sci-biology/bowtie/files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch +++ /dev/null @@ -1,17 +0,0 @@ -Description: Change class name of _Context_LSS - New version 1.4 of SeQan uses a different name of the class. -Forwarded: no -Author: Gert Wollny <[email protected]> -Last-Update: 2014-100-06 - ---- bowtie-1.2.2/diff_sample.h 2017-11-03 01:25:56.000000000 +0100 -+++ bowtie-1.2.2/diff_sample.h 2019-02-18 12:50:37.894674282 +0100 -@@ -979,7 +979,7 @@ - { - Timer timer(cout, " Invoking Larsson-Sadakane on ranks time: ", this->verbose()); - VMSG_NL(" Invoking Larsson-Sadakane on ranks"); -- _Context_LSS<TIndexOff> c; -+ ContextLss_<TIndexOff> c; - c.suffixsort( - (TIndexOff*)begin(_isaPrime, Standard()), - (TIndexOff*)begin(sPrime, Standard()), diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch b/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch deleted file mode 100644 index 75942efb5..000000000 --- a/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch +++ /dev/null @@ -1,32 +0,0 @@ -fix compilation errors with Intel compilers: -error: no operator "=" matches these operands -author: Ward Poelmans ---- bowtie-1.2.2/hit.h 2018-01-24 12:57:47.135575442 +0100 -+++ bowtie-1.2.2/hit.h 2018-01-24 12:57:58.615869774 +0100 -@@ -640,10 +640,26 @@ - s.moveTo(btString); - } - -+ batch(const batch &other) -+ { -+ batchId = other.batchId; -+ isWritten = other.isWritten; -+ btString = other.btString; -+ } -+ - bool operator<(const batch& other) const { - return batchId < other.batchId; - } - -+ batch& operator=(batch&& other) { -+ if (&other != this) { -+ batchId = other.batchId; -+ isWritten = other.isWritten; -+ other.btString.moveTo(btString); -+ } -+ return *this; -+ } -+ - batch& operator=(batch& other) { - if (&other != this) { - batchId = other.batchId; diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch b/sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch deleted file mode 100644 index de19e42a8..000000000 --- a/sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch +++ /dev/null @@ -1,22 +0,0 @@ -From 58c6ac97b1938909881877ef83167f5eff0e8ab1 Mon Sep 17 00:00:00 2001 -From: Rone Charles <[email protected]> -Date: Tue, 4 Sep 2018 21:06:39 -0400 -Subject: [PATCH] Fix isa return type - ---- - ebwt.h | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/ebwt.h b/ebwt.h -index fe6300cc..8f886b8d 100644 ---- a/ebwt.h -+++ b/ebwt.h -@@ -862,7 +862,7 @@ class Ebwt { - TIndexOffU* ftab() const { return _ftab; } - TIndexOffU* eftab() const { return _eftab; } - TIndexOffU* offs() const { return _offs; } -- uint32_t* isa() const { return _isa; } /* check */ -+ TIndexOffU* isa() const { return _isa; } /* check */ - TIndexOffU* plen() const { return _plen; } - TIndexOffU* rstarts() const { return _rstarts; } - uint8_t* ebwt() const { return _ebwt; } diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-unbundle-seqan.patch b/sci-biology/bowtie/files/bowtie-1.2.2-unbundle-seqan.patch deleted file mode 100644 index b1a5f98f5..000000000 --- a/sci-biology/bowtie/files/bowtie-1.2.2-unbundle-seqan.patch +++ /dev/null @@ -1,14 +0,0 @@ ---- bowtie-1.2.2/Makefile 2019-02-18 13:26:29.490835084 +0100 -+++ bowtie-1.2.2/Makefile 2019-02-18 13:28:36.864742545 +0100 -@@ -5,10 +5,7 @@ - prefix = /usr/local - bindir = $(prefix)/bin - --SEQAN_DIR = ./SeqAn-1.1 --# treat SeqAn as a sysdir to suppress warnings --SEQAN_INC = -isystem $(SEQAN_DIR) --INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) $(SEQAN_INC) -I third_party -+INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) `pkg-config --cflags seqan-1.4` -I third_party - CPP = g++ - CXX = $(CPP) - CC = gcc diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-void2int.patch b/sci-biology/bowtie/files/bowtie-1.2.2-void2int.patch deleted file mode 100644 index 822b673ae..000000000 --- a/sci-biology/bowtie/files/bowtie-1.2.2-void2int.patch +++ /dev/null @@ -1,16 +0,0 @@ -#The latest Intel compiler (2016,2017) complains about the incompatibility of "void *" argument -#being incompatible with parameter of type "int *" -#M. Fujinaga ([email protected]) ---- processor_support.h 2017-02-02 21:48:42.436432756 +0000 -+++ processor_support.h 2017-02-02 21:48:54.419309743 +0000 -@@ -44,8 +44,8 @@ - - try { - #if ( defined(USING_INTEL_COMPILER) || defined(USING_MSC_COMPILER) ) -- __cpuid((void *) ®s,0); // test if __cpuid() works, if not catch the exception -- __cpuid((void *) ®s,0x1); // POPCNT bit is bit 23 in ECX -+ __cpuid((int *) ®s,0); // test if __cpuid() works, if not catch the exception -+ __cpuid((int *) ®s,0x1); // POPCNT bit is bit 23 in ECX - #elif defined(USING_GCC_COMPILER) - __get_cpuid(0x1, ®s.EAX, ®s.EBX, ®s.ECX, ®s.EDX); - #else
