* [gentoo-commits] proj/sci:master commit in: sci-chemistry/shiftx/files/, sci-chemistry/shiftx/
@ 2013-06-20 12:51 Justin Lecher
0 siblings, 0 replies; 2+ messages in thread
From: Justin Lecher @ 2013-06-20 12:51 UTC (permalink / raw
To: gentoo-commits
commit: bd6d9729719a12de85a3ae16f2cbfe984f6b36f6
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jun 20 11:54:00 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jun 20 12:51:01 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bd6d9729
sci-chemistry/shiftx: Fix patch and add patch for buffer overflow fix
Package-Manager: portage-2.2.0_alpha182
---
sci-chemistry/shiftx/ChangeLog | 4 ++++
sci-chemistry/shiftx/files/1.1-Makefile.patch | 15 ++++++++++-----
sci-chemistry/shiftx/files/1.1-bfr-overflow.patch | 16 ++++++++++++++++
sci-chemistry/shiftx/metadata.xml | 2 +-
sci-chemistry/shiftx/shiftx-1.1.ebuild | 4 +++-
5 files changed, 34 insertions(+), 7 deletions(-)
diff --git a/sci-chemistry/shiftx/ChangeLog b/sci-chemistry/shiftx/ChangeLog
index e588d4f..85e5049 100644
--- a/sci-chemistry/shiftx/ChangeLog
+++ b/sci-chemistry/shiftx/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 20 Jun 2013; Justin Lecher <jlec@gentoo.org> shiftx-1.1.ebuild,
+ files/1.1-Makefile.patch, +files/1.1-bfr-overflow.patch, metadata.xml:
+ Fix patch and add patch for buffer overflow fix
+
16 Jun 2013; Justin Lecher <jlec@gentoo.org> shiftx-1.1.ebuild, metadata.xml:
Bump to EAPI=5 and fix license
diff --git a/sci-chemistry/shiftx/files/1.1-Makefile.patch b/sci-chemistry/shiftx/files/1.1-Makefile.patch
index 1678752..f208d08 100644
--- a/sci-chemistry/shiftx/files/1.1-Makefile.patch
+++ b/sci-chemistry/shiftx/files/1.1-Makefile.patch
@@ -1,17 +1,22 @@
---- Makefile 2004-08-03 20:33:20.000000000 +0200
-+++ Makefile.new 2009-06-14 10:49:40.000000000 +0200
+ Makefile | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index 5401c07..ffd8157 100644
+--- a/Makefile
++++ b/Makefile
@@ -6,8 +6,8 @@
# E-Mail: anip@redpoll.pharmacy.ualberta.ca
#
#CC=gcc -Xcpluscomm -cckr
-CC=/usr/bin/gcc
--CFLAGS=-O3
+-CFLAGS=-O
+#CC=/usr/bin/gcc
-+#CFLAGS=-O3
++#CFLAGS=-O
SYSLIB=
INCLUDES=-I/usr/include
LIBS=$(SYSLIB) -lm
-@@ -25,7 +25,7 @@
+@@ -25,7 +25,7 @@ OBJS=Main.o Nn.o Ssbond.o Residue.o Hetatm.o Vector.o Torison.o Cs.o Phipsi.o \
all: shiftx
shiftx: $(OBJS)
diff --git a/sci-chemistry/shiftx/files/1.1-bfr-overflow.patch b/sci-chemistry/shiftx/files/1.1-bfr-overflow.patch
new file mode 100644
index 0000000..68507a3
--- /dev/null
+++ b/sci-chemistry/shiftx/files/1.1-bfr-overflow.patch
@@ -0,0 +1,16 @@
+ Display.c | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/Display.c b/Display.c
+index 671d3ee..9a03c48 100644
+--- a/Display.c
++++ b/Display.c
+@@ -85,7 +85,7 @@ DISPLAY_DATA *CreateDisplayData( int len, int prop, int nuc )
+ void display_selected_nucleus( DISPLAY_DATA *d )
+ {
+ int i, j;
+- char nucleus[5];
++ char nucleus[8];
+
+ /* Print Header Information */
+
diff --git a/sci-chemistry/shiftx/metadata.xml b/sci-chemistry/shiftx/metadata.xml
index 9ac9ffd..51fdeda 100644
--- a/sci-chemistry/shiftx/metadata.xml
+++ b/sci-chemistry/shiftx/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
-<herd>sci-chemistry</herd>
+ <herd>sci-chemistry</herd>
</pkgmetadata>
diff --git a/sci-chemistry/shiftx/shiftx-1.1.ebuild b/sci-chemistry/shiftx/shiftx-1.1.ebuild
index 5f26ed3..5d3cc0f 100644
--- a/sci-chemistry/shiftx/shiftx-1.1.ebuild
+++ b/sci-chemistry/shiftx/shiftx-1.1.ebuild
@@ -17,7 +17,9 @@ IUSE=""
S="${WORKDIR}"/${PN}
-PATCHES=( "${FILESDIR}"/${PV}-Makefile.patch )
+PATCHES=(
+ "${FILESDIR}"/${PV}-Makefile.patch
+ "${FILESDIR}"/${PV}-bfr-overflow.patch )
DOCS="README FEATURES *.pdb *.out"
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/shiftx/files/, sci-chemistry/shiftx/
@ 2020-09-28 10:01 Horea Christian
0 siblings, 0 replies; 2+ messages in thread
From: Horea Christian @ 2020-09-28 10:01 UTC (permalink / raw
To: gentoo-commits
commit: 147e93b9e5f88467c7658850f251a32a68c8c24a
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Sep 28 10:00:45 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Sep 28 10:00:45 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=147e93b9
sci-chemistry/shiftx: removed discontinued package
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-chemistry/shiftx/files/1.1-Makefile.patch | 27 -----------------
sci-chemistry/shiftx/files/1.1-bfr-overflow.patch | 16 ----------
sci-chemistry/shiftx/metadata.xml | 8 -----
sci-chemistry/shiftx/shiftx-1.1.ebuild | 37 -----------------------
4 files changed, 88 deletions(-)
diff --git a/sci-chemistry/shiftx/files/1.1-Makefile.patch b/sci-chemistry/shiftx/files/1.1-Makefile.patch
deleted file mode 100644
index f208d087f..000000000
--- a/sci-chemistry/shiftx/files/1.1-Makefile.patch
+++ /dev/null
@@ -1,27 +0,0 @@
- Makefile | 6 +++---
- 1 file changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 5401c07..ffd8157 100644
---- a/Makefile
-+++ b/Makefile
-@@ -6,8 +6,8 @@
- # E-Mail: anip@redpoll.pharmacy.ualberta.ca
- #
- #CC=gcc -Xcpluscomm -cckr
--CC=/usr/bin/gcc
--CFLAGS=-O
-+#CC=/usr/bin/gcc
-+#CFLAGS=-O
- SYSLIB=
- INCLUDES=-I/usr/include
- LIBS=$(SYSLIB) -lm
-@@ -25,7 +25,7 @@ OBJS=Main.o Nn.o Ssbond.o Residue.o Hetatm.o Vector.o Torison.o Cs.o Phipsi.o \
- all: shiftx
-
- shiftx: $(OBJS)
-- $(CC) $(OBJS) $(CFLAGS) $(LIBS) -o $@
-+ $(CC) $(CFLAGS) $(LDFLAGS) $(OBJS) $(LIBS) -o $@
-
- Main.o: Main.c main.h states.h nn.h ssbond.h residue.h hetatm.h cs.h \
- phipsi.h torison.h hydrogens.h rings.h es.h proline.h hbond.h \
diff --git a/sci-chemistry/shiftx/files/1.1-bfr-overflow.patch b/sci-chemistry/shiftx/files/1.1-bfr-overflow.patch
deleted file mode 100644
index 68507a364..000000000
--- a/sci-chemistry/shiftx/files/1.1-bfr-overflow.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- Display.c | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/Display.c b/Display.c
-index 671d3ee..9a03c48 100644
---- a/Display.c
-+++ b/Display.c
-@@ -85,7 +85,7 @@ DISPLAY_DATA *CreateDisplayData( int len, int prop, int nuc )
- void display_selected_nucleus( DISPLAY_DATA *d )
- {
- int i, j;
-- char nucleus[5];
-+ char nucleus[8];
-
- /* Print Header Information */
-
diff --git a/sci-chemistry/shiftx/metadata.xml b/sci-chemistry/shiftx/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/shiftx/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-chemistry@gentoo.org</email>
- <name>Gentoo Chemistry Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/shiftx/shiftx-1.1.ebuild b/sci-chemistry/shiftx/shiftx-1.1.ebuild
deleted file mode 100644
index c25718308..000000000
--- a/sci-chemistry/shiftx/shiftx-1.1.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Prediction of 1H, 13C and 15N chemical shifts for proteins"
-HOMEPAGE="http://shiftx.wishartlab.com/"
-SRC_URI="http://shiftx.wishartlab.com/download/${PN}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="all-rights-reserved"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="sci-chemistry/shiftx2"
-
-S="${WORKDIR}"/${PN}
-
-DOCS="README FEATURES *.pdb *.out"
-
-src_prepare() {
- epatch \
- "${FILESDIR}"/${PV}-Makefile.patch \
- "${FILESDIR}"/${PV}-bfr-overflow.patch
-}
-
-src_compile() {
- emake CC="$(tc-getCC)"
-}
-
-src_install() {
- dobin ${PN}
- dodoc ${DOCS}
-}
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