[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/
commit: b3c6b97c03059d44b801c71c3ccf7a6165593149
Author: David Seifert gentoo org>
AuthorDate: Sun Aug 1 16:40:42 2021 +
Commit: David Seifert gentoo org>
CommitDate: Sun Aug 1 16:40:42 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b3c6b97c
sci-biology/bowtie: drop 2.2.9
Closes: https://bugs.gentoo.org/722870
Signed-off-by: David Seifert gentoo.org>
sci-biology/bowtie/Manifest| 1 -
sci-biology/bowtie/bowtie-2.2.9.ebuild | 61 --
.../bowtie/files/bowtie-2.2.9-fix-c++14.patch | 29 --
3 files changed, 91 deletions(-)
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index 96d35e2bfd2..e6270339582 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1,2 +1 @@
-DIST bowtie2-2.2.9-source.zip 5734235 BLAKE2B
ec48e09fe05403d1085bb4e0c6ef1325b8912da0a8c942061c34f3381c6dd7ccdcc64c4bcdbb18c1da84ac57e1e34cc866fe79809c33c2769a8d75ecde7d0846
SHA512
ead8f7641f3231638d986f9e500bc4ec7afe1e542048465bfcc2e93e2b2d2e499f0dd8aa5c1e3e21df285c9d195b187682eb7e12be4a408f6c50fb97c0e0a205
DIST bowtie2-2.4.4-source.zip 10515984 BLAKE2B
be4ceb9d3155d2a9a1f580e5032251b04b89ce0c8c9c89fc3551b34fe3bd71a683362488be7aad6daef24734c6f95c19223f20e67f198f745c4432381243039c
SHA512
1b5dadd7e41b90bb9b05f50bfa171fe219cfd03aa8bb6f800de4baaffeb975eef6efc4fb8b49cb0d18833f74a1741cbe1556b87388f59188e04a55dcee6a02da
diff --git a/sci-biology/bowtie/bowtie-2.2.9.ebuild
b/sci-biology/bowtie/bowtie-2.2.9.ebuild
deleted file mode 100644
index 0bacb8ca25d..000
--- a/sci-biology/bowtie/bowtie-2.2.9.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs
-
-DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/";
-SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
-
-LICENSE="GPL-3"
-SLOT="2"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="examples cpu_flags_x86_sse2 +tbb"
-
-RDEPEND="dev-lang/perl
- tbb? ( dev-cpp/tbb )"
-DEPEND="${RDEPEND}
- app-arch/unzip"
-
-S="${WORKDIR}/${PN}2-${PV}"
-
-DOCS=( AUTHORS NEWS TUTORIAL )
-HTML_DOCS=( doc/{manual.html,style.css} )
-PATCHES=( "${FILESDIR}/${PN}-2.2.9-fix-c++14.patch" )
-
-pkg_pretend() {
- if ! use cpu_flags_x86_sse2 ; then
- eerror "This package requires a CPU supporting the SSE2
instruction set."
- die "SSE2 support missing"
- fi
-}
-
-src_compile() {
- emake \
- CC="$(tc-getCC)" \
- CPP="$(tc-getCXX)" \
- CXX="$(tc-getCXX)" \
- CFLAGS="" \
- CXXFLAGS="" \
- EXTRA_FLAGS="${LDFLAGS}" \
- RELEASE_FLAGS="${CXXFLAGS} -msse2" \
- WITH_TBB="$(usex tbb 1 0)"
-}
-
-src_install() {
- dobin ${PN}2 ${PN}2-*
-
- exeinto /usr/libexec/${PN}2
- doexe scripts/*
-
- newman MANUAL ${PN}2.1
- einstalldocs
-
- if use examples; then
- insinto /usr/share/${PN}2
- doins -r example
- fi
-}
diff --git a/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch
b/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch
deleted file mode 100644
index cd2a67b6a52..000
--- a/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch
+++ /dev/null
@@ -1,29 +0,0 @@
-Fix building with C++14, which errors out due to differing semantics between
C++98
-and C++14 with regards to allowing destructors to throw exceptions.
-See also: https://bugs.gentoo.org/show_bug.cgi?id=593966
-
a/blockwise_sa.h
-+++ b/blockwise_sa.h
-@@ -87,7 +87,11 @@
- _logger(__logger)
- { }
-
-- virtual ~BlockwiseSA() { }
-+ virtual ~BlockwiseSA()
-+#if __cplusplus >= 201103L
-+ noexcept(false)
-+#endif
-+ { }
-
- /**
-* Get the next suffix; compute the next bucket if necessary.
-@@ -216,6 +220,9 @@
- { _randomSrc.init(__seed); reset(); }
-
- ~KarkkainenBlockwiseSA()
-+#if __cplusplus >= 201103L
-+noexcept(false)
-+#endif
- {
- #ifdef WITH_TBB
- tbb_grp.wait();
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/
commit: a4da0209640e967dbbc8cd85820ff8858e34f872
Author: David Seifert gentoo org>
AuthorDate: Sun Sep 18 22:39:18 2016 +
Commit: David Seifert gentoo org>
CommitDate: Sun Sep 18 22:39:56 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a4da0209
sci-biology/bowtie: Allow for compiling with GCC 6
Gentoo-bug: 593966
Package-Manager: portage-2.3.0
sci-biology/bowtie/bowtie-2.2.9.ebuild | 3 ++-
.../bowtie/files/bowtie-2.2.9-fix-c++14.patch | 29 ++
2 files changed, 31 insertions(+), 1 deletion(-)
diff --git a/sci-biology/bowtie/bowtie-2.2.9.ebuild
b/sci-biology/bowtie/bowtie-2.2.9.ebuild
index 6e66420..8544512 100644
--- a/sci-biology/bowtie/bowtie-2.2.9.ebuild
+++ b/sci-biology/bowtie/bowtie-2.2.9.ebuild
@@ -4,7 +4,7 @@
EAPI=6
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/";
@@ -25,6 +25,7 @@ S="${WORKDIR}/${PN}2-${PV}"
DOCS=( AUTHORS NEWS TUTORIAL )
HTML_DOCS=( doc/{manual.html,style.css} )
+PATCHES=( "${FILESDIR}/${PN}-2.2.9-fix-c++14.patch" )
pkg_pretend() {
if ! use cpu_flags_x86_sse2 ; then
diff --git a/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch
b/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch
new file mode 100644
index ..cd2a67b
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch
@@ -0,0 +1,29 @@
+Fix building with C++14, which errors out due to differing semantics between
C++98
+and C++14 with regards to allowing destructors to throw exceptions.
+See also: https://bugs.gentoo.org/show_bug.cgi?id=593966
+
+--- a/blockwise_sa.h
b/blockwise_sa.h
+@@ -87,7 +87,11 @@
+ _logger(__logger)
+ { }
+
+- virtual ~BlockwiseSA() { }
++ virtual ~BlockwiseSA()
++#if __cplusplus >= 201103L
++ noexcept(false)
++#endif
++ { }
+
+ /**
+* Get the next suffix; compute the next bucket if necessary.
+@@ -216,6 +220,9 @@
+ { _randomSrc.init(__seed); reset(); }
+
+ ~KarkkainenBlockwiseSA()
++#if __cplusplus >= 201103L
++noexcept(false)
++#endif
+ {
+ #ifdef WITH_TBB
+ tbb_grp.wait();
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/
commit: 1e3f5d88f730c5d04b64095114d2e48c1ec4ba58
Author: David Seifert gentoo org>
AuthorDate: Sat Apr 9 18:26:28 2016 +
Commit: David Seifert gentoo org>
CommitDate: Sat Apr 9 18:57:05 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1e3f5d88
sci-biology/bowtie: unbundle SeqAn, import Debian patches
* EAPI=6
Package-Manager: portage-2.2.28
sci-biology/bowtie/bowtie-1.1.2-r1.ebuild | 75
.../files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch | 17 +
.../files/bowtie-1.1.2-fix-setBegin-call.patch | 42 +++
.../bowtie/files/bowtie-1.1.2-seqan-popcount.patch | 24 ++
.../bowtie-1.1.2-seqan-rename-ChunkPool.patch | 382 +
.../bowtie-1.1.2-seqan-rename-fill-to-resize.patch | 85 +
.../bowtie/files/bowtie-1.1.2-spelling.patch | 48 +++
.../bowtie/files/bowtie-1.1.2-unbundle-seqan.patch | 27 ++
8 files changed, 700 insertions(+)
diff --git a/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild
b/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild
new file mode 100644
index 000..e0b4358
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild
@@ -0,0 +1,75 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit flag-o-matic toolchain-funcs
+
+DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/";
+SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
+
+LICENSE="Artistic"
+SLOT="1"
+KEYWORDS="~amd64 ~x86 ~x64-macos"
+
+IUSE="examples +tbb"
+
+RDEPEND="tbb? ( dev-cpp/tbb )"
+DEPEND="${RDEPEND}
+ sci-biology/seqan:1.4
+ app-arch/unzip"
+
+DOCS=( AUTHORS NEWS TUTORIAL doc/README )
+HTML_DOCS=( doc/{manual.html,style.css} )
+
+PATCHES=(
+ "${FILESDIR}/${P}-_ContextLss-1.1-1.4.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"
+ "${FILESDIR}/${P}-unbundle-seqan.patch"
+)
+
+src_prepare() {
+ default
+
+ # remove bundled libraries, 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-1.1.2-_ContextLss-1.1-1.4.patch
b/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch
new file mode 100644
index 000..78b9c01
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch
@@ -0,0 +1,17 @@
+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
+Last-Update: 2014-100-06
+
+--- a/diff_sample.h
b/diff_sample.h
+@@ -856,7 +856,7 @@ void DifferenceCoverSample::build(
+ {
+ Timer timer(cout, " Invoking Larsson-Sadakane on ranks time:
", this->verbose());
+ VMSG_NL(" Invoking Larsson-Sadakane on ranks");
+- _Context_LSS c;
++ ContextLss_ c;
+ c.suffixsort(
+ (TIndexOff*)begin(_isaPrime, Standard()),
+ (TIndexOff*)begin(sPrime, Standard()),
diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch
b/sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch
new file mode 100644
index 000..af7f7f6
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch
@@ -0,0 +1,42 @@
+Description: Proper type-casting in using seqan::_setBegin().
+ Required by newer versions of GCC.
+Forwarded: no
+Author: Ognyan Kulev
+Last-Update: 2013-04-18
+
+--- a/pat.h
b/pat.h
+@@ -82,20 +82,20 @@ struct ReadBuf {
+ ~ReadBuf() {
+ clearAll(); reset();
+ // Prevent seqan from trying to free buffers
+- _setBegin(patFw, NULL);
+- _setBegin(patRc, NULL);
+- _setBegin(qual, NULL);
+- _setBegin(patFwRev, NULL);
+- _setBegin(patRcRev, NULL);
+-
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/
commit: 50fe91c03b9c8431a871463ee75ae68bdfc8a171
Author: Ted Tanberry gmail com>
AuthorDate: Sun Oct 11 08:04:43 2015 +
Commit: Justin Lecher gentoo org>
CommitDate: Wed Oct 14 12:47:58 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=50fe91c0
sci-biology/bowtie: bring back stable bowtie-0.12.8
bowtie-0.12.8 is the only stable variant and removing it
breaks the stable depgraph.
sci-biology/bowtie/Manifest| 1 +
sci-biology/bowtie/bowtie-0.12.8.ebuild| 44 +
.../bowtie/files/bowtie-0.12.8-gcc-47.patch| 45 ++
3 files changed, 90 insertions(+)
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index 1291400..c692c89 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1,2 +1,3 @@
+DIST bowtie-0.12.8-src.zip 15569919 SHA256
f074a0f25e156976c4951fd69651d60caab925af9829054d107ec8b19af3082d SHA512
824eddd7db24177f7e15b90fb93a0426c2b8cee4dbcac2707f4cc7e7e42bafcad3775382b79d9b4d679e0c4b5c17a1b79ad134e91a968037336b34c6262e9c48
WHIRLPOOL
7056444822e7a0de619dcab933a7870ebe7db52008f3dbb2dd72aa189325d7ca4c353133d77150ec67c414e005a834458538f57746b13fd20f06bc7289869800
DIST bowtie-1.1.2-src.zip 7713258 SHA256
b1e9ccc825207efd1893d9e33244c681bcb89b9b2b811eb95a9f5a92eab637ae SHA512
3d3d69bc3a865bb577b5a91440215d0d5b606c7a8751d565e606e36adbfbdef695b1718ae81cd3e2682a39ca7784c4d00976441e7618264ad99b04c7f53c36e8
WHIRLPOOL
08cb824bf7a1ddfbe6692de67191aacf44776d7d4e0ab66bd2a13ecfffd087bc28cdde4c7285c781fa4759de0a239e68f87b702bcc2e24c9b81fda5804360ce7
DIST bowtie2-2.2.6-source.zip 5728779 SHA256
1000e90cdd90c3ca43c69d0d0ad951e190d36a6981a546f430a90ce86d64bfc8 SHA512
3ab5a5475cf214affd91e0d1782fd2d6dedccd979e3c809b5dfb272726d99ff1c7b59d92e387b187a7c2e43557786a1085186ccb96588de91212caf2eb94ce4f
WHIRLPOOL
4fb02b3a0d76bbee0fe9abf91a71405922568bc38e593d5740df6279bad6f8b668df0debb0a81f3d3c23623558f34d842dd662a6838cf2d7f0fc8945fd00a298
diff --git a/sci-biology/bowtie/bowtie-0.12.8.ebuild
b/sci-biology/bowtie/bowtie-0.12.8.ebuild
new file mode 100644
index 000..c26c986
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-0.12.8.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="An ultrafast memory-efficient short read aligner"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/";
+SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86 ~x64-macos"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+# NB: Bundles code from Maq (http://maq.sf.net) and the SeqAn library
(http://www.seqan.de)
+# TODO: properly report system CFLAGS in -DCOMPILE_OPTIONS
+
+src_prepare() {
+ epatch "${FILESDIR}"/${P}-gcc-47.patch
+}
+
+src_compile() {
+ unset CFLAGS
+ emake \
+ CC="$(tc-getCC)" \
+ CPP="$(tc-getCXX)" \
+ CXX="$(tc-getCXX)" \
+ EXTRA_FLAGS="${LDFLAGS}" \
+ RELEASE_FLAGS=""
+}
+
+src_install() {
+ dobin bowtie bowtie-*
+ exeinto /usr/share/${PN}/scripts
+ doexe scripts/*
+ newman MANUAL bowtie.1
+ dodoc AUTHORS NEWS TUTORIAL
+}
diff --git a/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch
b/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch
new file mode 100644
index 000..3c8a1e1
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch
@@ -0,0 +1,45 @@
+ alphabet.h | 24
+ 1 files changed, 12 insertions(+), 12 deletions(-)
+
+diff --git a/alphabet.h b/alphabet.h
+index b464ddf..08d0281 100644
+--- a/alphabet.h
b/alphabet.h
+@@ -38,6 +38,18 @@ static inline TStr reverseComplement(const TStr& s, bool
color) {
+ return s_rc;
+ }
+
++/// Reverse a string in-place
++template
++static inline void reverseInPlace(TStr& s) {
++ typedef typename Value::Type TVal;
++ size_t len = length(s);
++ for(size_t i = 0; i < (len>>1); i++) {
++ TVal tmp = s[i];
++ s[i] = s[len-i-1];
++ s[len-i-1] = tmp;
++ }
++}
++
+ /**
+ * Reverse-complement s in-place. Ns go to Ns.
+ */
+@@ -69,18 +81,6 @@ static inline void reverseComplementInPlace(TStr& s, bool
color) {
+ }
+ }
+
+-/// Reverse a string in-place
+-template
+-static inline void reverseInPlace(TStr& s) {
+- typedef typename Value::Type TVal;
+- size_t len = length(s);
+- for(size_t i = 0; i < (len>>1); i++) {
+- TVal tmp = s[i];
+- s[i] = s[len-i-1];
+- s[len-i-1] = tmp;
+- }
+-}
+-
+ /**
+ * Return the reverse-complement of s.
+ */
