* [gentoo-commits] repo/gentoo:master commit in: sci-biology/recon/files/, sci-biology/recon/
@ 2017-02-25 16:15 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2017-02-25 16:15 UTC (permalink / raw
To: gentoo-commits
commit: 960abf9442aca3794235dc9f15e92005e9d0d77d
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Feb 25 16:14:33 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Feb 25 16:14:33 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=960abf94
sci-biology/recon: Version bump to 1.08
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/recon/Manifest | 1 +
.../recon/files/recon-1.08-buffer-overflow.patch | 11 +++++
.../recon/files/recon-1.08-perl-shebangs.patch | 19 +++++++++
sci-biology/recon/recon-1.08.ebuild | 48 ++++++++++++++++++++++
4 files changed, 79 insertions(+)
diff --git a/sci-biology/recon/Manifest b/sci-biology/recon/Manifest
index d779bd4735..c27ca97b51 100644
--- a/sci-biology/recon/Manifest
+++ b/sci-biology/recon/Manifest
@@ -1 +1,2 @@
+DIST RECON-1.08.tar.gz 108477 SHA256 699765fa49d18dbfac9f7a82ecd054464b468cb7521abe9c2bd8caccf08ee7d8 SHA512 68672312f31751fa93250bbe337ae57f11dc4b1994c7dd5249dca916012c2df83a03c925cb631709e081c72055ef5bffd0846bc252d8c3c6247ae5ef61b160c9 WHIRLPOOL e9a60353e4f6bbe37883c648a7c8f5d363c780d03a681dd2d6803d2e65a1eb5f9b8fb02a85721636e7a792b53628a00f21d57d1c4066fb8b91b2fb1d4c383763
DIST RECON1.06.tar.gz 109484 SHA256 6e106adb546952ecdfe7e9c1b56a4a80581383446c63abbe0c61c53af0e67461 SHA512 0df3ecb4b569d087ffce6b4f326f6c8686e78b08864dff09b7441d4f4067e72baf80ecb211366c23f7b49ed123426f612347309ceb5ae052d9bb371070525d32 WHIRLPOOL d1f66533d16bc1b5cb4cc51b35278a25c5cd1b797a4178987a873757f9b8f591527f84d65a0dfd4f8b165c35bf336c94f8c465235a3ebc101992e5af970cccec
diff --git a/sci-biology/recon/files/recon-1.08-buffer-overflow.patch b/sci-biology/recon/files/recon-1.08-buffer-overflow.patch
new file mode 100644
index 0000000000..e6bf54e7c2
--- /dev/null
+++ b/sci-biology/recon/files/recon-1.08-buffer-overflow.patch
@@ -0,0 +1,11 @@
+--- a/src/eledef.c
++++ b/src/eledef.c
+@@ -385,7 +385,7 @@ void ele_def(int method, FILE *frags, float cutoff, EPROT_t **all_epp, int *ecp,
+
+ void img_charge(IPROT_t **shadow, int ct, FILE *input) {
+ int i=0, pos=0;
+- char line[151];
++ char line[256];
+ int scan_flag;
+ MSP_t msp;
+
diff --git a/sci-biology/recon/files/recon-1.08-perl-shebangs.patch b/sci-biology/recon/files/recon-1.08-perl-shebangs.patch
new file mode 100644
index 0000000000..769fe4a93c
--- /dev/null
+++ b/sci-biology/recon/files/recon-1.08-perl-shebangs.patch
@@ -0,0 +1,19 @@
+Make Perl shebangs Prefix friendly
+See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/
+
+--- a/scripts/MSPCollect.pl
++++ b/scripts/MSPCollect.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+
+ if (!@ARGV) {
+ die "usage: MSPCollect BLAST_output_file\n";
+--- a/scripts/recon.pl
++++ b/scripts/recon.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+
+ $path = "";
+
diff --git a/sci-biology/recon/recon-1.08.ebuild b/sci-biology/recon/recon-1.08.ebuild
new file mode 100644
index 0000000000..8d934d014f
--- /dev/null
+++ b/sci-biology/recon/recon-1.08.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit toolchain-funcs
+
+DESCRIPTION="Automated de novo identification of repeat families from genomic sequences"
+HOMEPAGE="http://www.repeatmasker.org/RepeatModeler.html"
+SRC_URI="http://www.repeatmasker.org/${P^^}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="examples"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-lang/perl"
+
+S=${WORKDIR}/${P^^}
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-1.08-buffer-overflow.patch
+ "${FILESDIR}"/${PN}-1.08-perl-shebangs.patch
+)
+
+src_prepare() {
+ default
+ sed -i "s|$path = \"\";|$path = \"${EPREFIX}/usr/libexec/${PN}\";|" scripts/recon.pl || die
+}
+
+src_compile() {
+ emake CC="$(tc-getCC)" CFLAGS="${CFLAGS}" -C src
+}
+
+src_install() {
+ dobin scripts/*
+
+ exeinto /usr/libexec/${PN}
+ doexe src/{edgeredef,eledef,eleredef,famdef,imagespread}
+
+ newdoc {00,}README
+
+ if use examples; then
+ insinto /usr/share/${PN}
+ doins -r Demos
+ fi
+}
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/recon/files/, sci-biology/recon/
@ 2017-02-25 17:13 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2017-02-25 17:13 UTC (permalink / raw
To: gentoo-commits
commit: adeefddadbab83e8ab35a0a7d6dcf1e6f2698b05
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Feb 25 16:35:43 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Feb 25 17:13:02 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=adeefdda
sci-biology/recon: Remove old
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Closes: https://github.com/gentoo/gentoo/pull/4076
sci-biology/recon/Manifest | 1 -
sci-biology/recon/files/1.06-buffer-overflow.patch | 13 --------
sci-biology/recon/files/recon-1.06-respect.patch | 24 -------------
sci-biology/recon/recon-1.06-r1.ebuild | 36 --------------------
sci-biology/recon/recon-1.06-r2.ebuild | 39 ----------------------
5 files changed, 113 deletions(-)
diff --git a/sci-biology/recon/Manifest b/sci-biology/recon/Manifest
index c27ca97b51..2e55e8cb1e 100644
--- a/sci-biology/recon/Manifest
+++ b/sci-biology/recon/Manifest
@@ -1,2 +1 @@
DIST RECON-1.08.tar.gz 108477 SHA256 699765fa49d18dbfac9f7a82ecd054464b468cb7521abe9c2bd8caccf08ee7d8 SHA512 68672312f31751fa93250bbe337ae57f11dc4b1994c7dd5249dca916012c2df83a03c925cb631709e081c72055ef5bffd0846bc252d8c3c6247ae5ef61b160c9 WHIRLPOOL e9a60353e4f6bbe37883c648a7c8f5d363c780d03a681dd2d6803d2e65a1eb5f9b8fb02a85721636e7a792b53628a00f21d57d1c4066fb8b91b2fb1d4c383763
-DIST RECON1.06.tar.gz 109484 SHA256 6e106adb546952ecdfe7e9c1b56a4a80581383446c63abbe0c61c53af0e67461 SHA512 0df3ecb4b569d087ffce6b4f326f6c8686e78b08864dff09b7441d4f4067e72baf80ecb211366c23f7b49ed123426f612347309ceb5ae052d9bb371070525d32 WHIRLPOOL d1f66533d16bc1b5cb4cc51b35278a25c5cd1b797a4178987a873757f9b8f591527f84d65a0dfd4f8b165c35bf336c94f8c465235a3ebc101992e5af970cccec
diff --git a/sci-biology/recon/files/1.06-buffer-overflow.patch b/sci-biology/recon/files/1.06-buffer-overflow.patch
deleted file mode 100644
index 29d220c731..0000000000
--- a/sci-biology/recon/files/1.06-buffer-overflow.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/src/eledef.c b/src/eledef.c
-index 964890b..a001ec4 100644
---- a/src/eledef.c
-+++ b/src/eledef.c
-@@ -385,7 +385,7 @@ void ele_def(int method, FILE *frags, float cutoff, EPROT_t **all_epp, int *ecp,
-
- void img_charge(IPROT_t **shadow, int ct, FILE *input) {
- int i=0, pos=0;
-- char line[100];
-+ char line[256];
- int scan_flag;
- MSP_t msp;
-
diff --git a/sci-biology/recon/files/recon-1.06-respect.patch b/sci-biology/recon/files/recon-1.06-respect.patch
deleted file mode 100644
index a02038d847..0000000000
--- a/sci-biology/recon/files/recon-1.06-respect.patch
+++ /dev/null
@@ -1,24 +0,0 @@
- src/Makefile | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/src/Makefile b/src/Makefile
-index 36ef59b..e45a0f2 100644
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -13,14 +13,14 @@ MANDIR = $(HOME)/man
- #SRCDIR = .
-
- ## your compiler
--CC = gcc
-+CC ?= gcc
- #CC = cc # for SGI Origin200 compiler#
-
- ## any special compiler flags you want
- # -pedantic clashes with -DMEMDEBUG??
- #
- #CFLAGS = -g -Wall -pedantic
--CFLAGS = -O
-+CFLAGS ?= -O
- #CFLAGS = -g
- #CFLAGS = -TARG:exc_max -64 -Ofast=ip27 #specific SGI Origin200 compiler#
-
diff --git a/sci-biology/recon/recon-1.06-r1.ebuild b/sci-biology/recon/recon-1.06-r1.ebuild
deleted file mode 100644
index 86e820f49e..0000000000
--- a/sci-biology/recon/recon-1.06-r1.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="4"
-
-inherit eutils
-
-DESCRIPTION="Automated de novo identification of repeat families from genomic sequences"
-HOMEPAGE="http://selab.janelia.org/recon.html http://www.repeatmasker.org/RepeatModeler.html"
-SRC_URI="http://www.repeatmasker.org/RECON${PV}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE="examples"
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/RECON${PV}"
-
-src_prepare() {
- epatch "${FILESDIR}"/${PV}-buffer-overflow.patch
- sed -i 's|$path = "";|$path = "/usr/libexec/'${PN}'";|' scripts/recon.pl || die
-}
-
-src_compile() {
- emake -C src
-}
-
-src_install() {
- dobin scripts/*
- exeinto /usr/libexec/${PN}
- doexe src/{edgeredef,eledef,eleredef,famdef,imagespread}
- dodoc 00README
- insinto /usr/share/${PN}
- use examples && doins -r Demos
-}
diff --git a/sci-biology/recon/recon-1.06-r2.ebuild b/sci-biology/recon/recon-1.06-r2.ebuild
deleted file mode 100644
index 12a9207c9f..0000000000
--- a/sci-biology/recon/recon-1.06-r2.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="4"
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Automated de novo identification of repeat families from genomic sequences"
-HOMEPAGE="http://selab.janelia.org/recon.html http://www.repeatmasker.org/RepeatModeler.html"
-SRC_URI="http://www.repeatmasker.org/RECON${PV}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE="examples"
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/RECON${PV}"
-
-src_prepare() {
- epatch \
- "${FILESDIR}"/${PV}-buffer-overflow.patch \
- "${FILESDIR}"/${P}-respect.patch
- sed -i 's|$path = "";|$path = "/usr/libexec/'${PN}'";|' scripts/recon.pl || die
- tc-export CC
-}
-
-src_compile() {
- emake -C src
-}
-
-src_install() {
- dobin scripts/*
- exeinto /usr/libexec/${PN}
- doexe src/{edgeredef,eledef,eleredef,famdef,imagespread}
- dodoc 00README
- insinto /usr/share/${PN}
- use examples && doins -r Demos
-}
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/recon/files/, sci-biology/recon/
@ 2022-07-07 19:58 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2022-07-07 19:58 UTC (permalink / raw
To: gentoo-commits
commit: e00ee2933cf56d8a51e0abb0326ff4138e646cfe
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Jul 7 19:57:10 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Jul 7 19:57:10 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e00ee293
sci-biology/recon: update EAPI 6 -> 8
Closes: https://bugs.gentoo.org/716082
Signed-off-by: David Seifert <soap <AT> gentoo.org>
.../recon-1.08-Wimplicit-function-declaration.patch | 20 ++++++++++++++++++++
.../{recon-1.08.ebuild => recon-1.08-r1.ebuild} | 16 ++++++++--------
2 files changed, 28 insertions(+), 8 deletions(-)
diff --git a/sci-biology/recon/files/recon-1.08-Wimplicit-function-declaration.patch b/sci-biology/recon/files/recon-1.08-Wimplicit-function-declaration.patch
new file mode 100644
index 000000000000..9eba16e4a410
--- /dev/null
+++ b/sci-biology/recon/files/recon-1.08-Wimplicit-function-declaration.patch
@@ -0,0 +1,20 @@
+--- a/src/bolts.h
++++ b/src/bolts.h
+@@ -3,6 +3,7 @@
+ #include <stdio.h>
+ #include <math.h>
+ #include <stdlib.h>
++#include <stdint.h>
+
+
+ #define NAME_LEN 50
+--- a/src/seqlist.h
++++ b/src/seqlist.h
+@@ -1,6 +1,7 @@
+
+ #include "bolts.h"
+ #include "string.h"
++#include <ctype.h>
+
+ #ifndef _seqlist_h
+ #define _seqlist_h
diff --git a/sci-biology/recon/recon-1.08.ebuild b/sci-biology/recon/recon-1.08-r1.ebuild
similarity index 75%
rename from sci-biology/recon/recon-1.08.ebuild
rename to sci-biology/recon/recon-1.08-r1.ebuild
index a96403c812be..dd79dd43c496 100644
--- a/sci-biology/recon/recon-1.08.ebuild
+++ b/sci-biology/recon/recon-1.08-r1.ebuild
@@ -1,31 +1,31 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=8
inherit toolchain-funcs
DESCRIPTION="Automated de novo identification of repeat families from genomic sequences"
HOMEPAGE="http://www.repeatmasker.org/RepeatModeler.html"
SRC_URI="http://www.repeatmasker.org/${P^^}.tar.gz"
+S="${WORKDIR}/${P^^}"
LICENSE="GPL-2"
SLOT="0"
-IUSE="examples"
KEYWORDS="~amd64 ~x86"
+IUSE="examples"
RDEPEND="dev-lang/perl"
-S=${WORKDIR}/${P^^}
-
PATCHES=(
"${FILESDIR}"/${PN}-1.08-buffer-overflow.patch
"${FILESDIR}"/${PN}-1.08-perl-shebangs.patch
+ "${FILESDIR}"/${PN}-1.08-Wimplicit-function-declaration.patch
)
src_prepare() {
default
- sed -i "s|$path = \"\";|$path = \"${EPREFIX}/usr/libexec/${PN}\";|" scripts/recon.pl || die
+ sed -i "s|$path = \"\";|$path = \"${EPREFIX}/usr/libexec/recon\";|" scripts/recon.pl || die
}
src_compile() {
@@ -35,13 +35,13 @@ src_compile() {
src_install() {
dobin scripts/*
- exeinto /usr/libexec/${PN}
+ exeinto /usr/libexec/recon
doexe src/{edgeredef,eledef,eleredef,famdef,imagespread}
newdoc {00,}README
if use examples; then
- insinto /usr/share/${PN}
+ insinto /usr/share/recon
doins -r Demos
fi
}
^ permalink raw reply related [flat|nested] 3+ messages in thread
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