commit: 8b50a13b56cc9ac53dd7c6770432e1b2155bdc79
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Apr 14 18:35:30 2017 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Apr 14 18:59:57 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8b50a13b
sci-chemistry/threeV: Bump EAPI to 6
fix format-security problems
Package-Manager: Portage-2.3.5, Repoman-2.3.2
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
.../threeV/files/threeV-1.2-format-security.patch | 198 +++++++++++++++++++++
.../{1.2-gentoo.patch => threeV-1.2-gentoo.patch} | 6 +-
.../{threeV-1.2.ebuild => threeV-1.2-r1.ebuild} | 23 ++-
3 files changed, 216 insertions(+), 11 deletions(-)
diff --git a/sci-chemistry/threeV/files/threeV-1.2-format-security.patch
b/sci-chemistry/threeV/files/threeV-1.2-format-security.patch
new file mode 100644
index 00000000000..b693559900a
--- /dev/null
+++ b/sci-chemistry/threeV/files/threeV-1.2-format-security.patch
@@ -0,0 +1,198 @@
+ cavities.cpp | 8 ++++----
+ channel.cpp | 10 +++++-----
+ fsv_calc.cpp | 8 ++++----
+ solvent.cpp | 8 ++++----
+ tunnel.cpp | 8 ++++----
+ vdw.cpp | 8 ++++----
+ volume.cpp | 8 ++++----
+ 7 files changed, 29 insertions(+), 29 deletions(-)
+
+diff --git a/cavities.cpp b/cavities.cpp
+index 418a1a7..96b6a15 100644
+--- a/cavities.cpp
++++ b/cavities.cpp
+@@ -35,7 +35,7 @@ int main(int argc, char *argv[]) {
+
+ while(argc > 1 && argv[1][0] == '-') {
+ if(argv[1][1] == 'i') {
+- sprintf(file,&argv[2][0]);
++ sprintf(file,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'g') {
+ GRID = atof(&argv[2][0]);
+ } else if(argv[1][1] == 's') {
+@@ -45,11 +45,11 @@ int main(int argc, char *argv[]) {
+ } else if(argv[1][1] == 't') {
+ trim_rad = atof(&argv[2][0]);
+ } else if(argv[1][1] == 'e') {
+- sprintf(ezdfile,&argv[2][0]);
++ sprintf(ezdfile,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'm') {
+- sprintf(mrcfile,&argv[2][0]);
++ sprintf(mrcfile,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'o') {
+- sprintf(pdbfile,&argv[2][0]);
++ sprintf(pdbfile,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'h') {
+ cerr << "./Cavities.exe -i <file> -g <grid spacing> -s <shell radius> "
<< endl
+ << "\t-p <probe radius> -t <trim_probe_rad> " << endl
+diff --git a/channel.cpp b/channel.cpp
+index c5acd20..9040631 100644
+--- a/channel.cpp
++++ b/channel.cpp
+@@ -35,7 +35,7 @@ int main(int argc, char *argv[]) {
+
+ while(argc > 1 && argv[1][0] == '-') {
+ if(argv[1][1] == 'i') {
+- sprintf(file,&argv[2][0]);
++ sprintf(file,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'b') {
+ BIGPROBE = atof(&argv[2][0]);
+ } else if(argv[1][1] == 's') {
+@@ -49,13 +49,13 @@ int main(int argc, char *argv[]) {
+ } else if(argv[1][1] == 'z') {
+ z = atof(&argv[2][0]);
+ } else if(argv[1][1] == 'i') {
+- sprintf(file,&argv[2][0]);
++ sprintf(file,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'o') {
+- sprintf(pdbfile,&argv[2][0]);
++ sprintf(pdbfile,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'e') {
+- sprintf(ezdfile,&argv[2][0]);
++ sprintf(ezdfile,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'm') {
+- sprintf(mrcfile,&argv[2][0]);
++ sprintf(mrcfile,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'g') {
+ GRID = atof(&argv[2][0]);
+ } else if(argv[1][1] == 'h') {
+diff --git a/fsv_calc.cpp b/fsv_calc.cpp
+index 9f81347..ef765b8 100644
+--- a/fsv_calc.cpp
++++ b/fsv_calc.cpp
+@@ -34,7 +34,7 @@ int main(int argc, char *argv[]) {
+
+ while(argc > 1 && argv[1][0] == '-') {
+ if(argv[1][1] == 'i') {
+- sprintf(file,&argv[2][0]);
++ sprintf(file,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 's') {
+ SMPROBE = atof(&argv[2][0]);
+ } else if(argv[1][1] == 'b') {
+@@ -44,11 +44,11 @@ int main(int argc, char *argv[]) {
+ } else if(argv[1][1] == 'g') {
+ GRID = atof(&argv[2][0]);
+ } else if(argv[1][1] == 'o') {
+- sprintf(pdbfile,&argv[2][0]);
++ sprintf(pdbfile,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'e') {
+- sprintf(ezdfile,&argv[2][0]);
++ sprintf(ezdfile,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'm') {
+- sprintf(mrcfile,&argv[2][0]);
++ sprintf(mrcfile,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'h') {
+ cerr << "./FsvCalc.exe -i <file> -b <big_probe> -s <small_probe> " <<
endl
+ << "\t-t <trim probe> -g <gridspace> " << endl
+diff --git a/solvent.cpp b/solvent.cpp
+index d857696..bc9d67f 100644
+--- a/solvent.cpp
++++ b/solvent.cpp
+@@ -34,7 +34,7 @@ int main(int argc, char *argv[]) {
+
+ while(argc > 1 && argv[1][0] == '-') {
+ if(argv[1][1] == 'i') {
+- sprintf(file,&argv[2][0]);
++ sprintf(file,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 's') {
+ SMPROBE = atof(&argv[2][0]);
+ } else if(argv[1][1] == 'b') {
+@@ -42,11 +42,11 @@ int main(int argc, char *argv[]) {
+ } else if(argv[1][1] == 't') {
+ TRIMPROBE = atof(&argv[2][0]);
+ } else if(argv[1][1] == 'e') {
+- sprintf(ezdfile,&argv[2][0]);
++ sprintf(ezdfile,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'm') {
+- sprintf(mrcfile,&argv[2][0]);
++ sprintf(mrcfile,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'o') {
+- sprintf(pdbfile,&argv[2][0]);
++ sprintf(pdbfile,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'g') {
+ GRID = atof(&argv[2][0]);
+ } else if(argv[1][1] == 'h') {
+diff --git a/tunnel.cpp b/tunnel.cpp
+index 0094d05..7472aaa 100644
+--- a/tunnel.cpp
++++ b/tunnel.cpp
+@@ -40,7 +40,7 @@ int main(int argc, char *argv[]) {
+
+ while(argc > 1 && argv[1][0] == '-') {
+ if(argv[1][1] == 'i') {
+- sprintf(file,&argv[2][0]);
++ sprintf(file,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'g') {
+ GRID = atof(&argv[2][0]);
+ } else if(argv[1][1] == 's') {
+@@ -50,11 +50,11 @@ int main(int argc, char *argv[]) {
+ } else if(argv[1][1] == 't') {
+ trim_prb = atof(&argv[2][0]);
+ } else if(argv[1][1] == 'e') {
+- sprintf(ezdfile,&argv[2][0]);
++ sprintf(ezdfile,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'm') {
+- sprintf(mrcfile,&argv[2][0]);
++ sprintf(mrcfile,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'o') {
+- sprintf(pdbfile,&argv[2][0]);
++ sprintf(pdbfile,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'h') {
+ cerr << "./Tunnel.exe -i <file> -g <grid spacing> -p <tunnel probe
radius>" << endl
+ << "\t-e <EZD outfile> -o <PDB outfile> -m <MRC outfile>" << endl
+diff --git a/vdw.cpp b/vdw.cpp
+index 4df73f5..0e26edc 100644
+--- a/vdw.cpp
++++ b/vdw.cpp
+@@ -32,13 +32,13 @@ int main(int argc, char *argv[]) {
+
+ while(argc > 1 && argv[1][0] == '-') {
+ if(argv[1][1] == 'i') {
+- sprintf(file,&argv[2][0]);
++ sprintf(file,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'o') {
+- sprintf(pdbfile,&argv[2][0]);
++ sprintf(pdbfile,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'e') {
+- sprintf(ezdfile,&argv[2][0]);
++ sprintf(ezdfile,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'm') {
+- sprintf(mrcfile,&argv[2][0]);
++ sprintf(mrcfile,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'g') {
+ GRID = atof(&argv[2][0]);
+ } else if(argv[1][1] == 'h') {
+diff --git a/volume.cpp b/volume.cpp
+index a2ca9ad..c304b94 100644
+--- a/volume.cpp
++++ b/volume.cpp
+@@ -32,15 +32,15 @@ int main(int argc, char *argv[]) {
+
+ while(argc > 1 && argv[1][0] == '-') {
+ if(argv[1][1] == 'i') {
+- sprintf(file,&argv[2][0]);
++ sprintf(file,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'p') {
+ PROBE = atof(&argv[2][0]);
+ } else if(argv[1][1] == 'o') {
+- sprintf(pdbfile,&argv[2][0]);
++ sprintf(pdbfile,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'e') {
+- sprintf(ezdfile,&argv[2][0]);
++ sprintf(ezdfile,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'm') {
+- sprintf(mrcfile,&argv[2][0]);
++ sprintf(mrcfile,"%s",&argv[2][0]);
+ } else if(argv[1][1] == 'g') {
+ GRID = atof(&argv[2][0]);
+ } else if(argv[1][1] == 'h') {
diff --git a/sci-chemistry/threeV/files/1.2-gentoo.patch
b/sci-chemistry/threeV/files/threeV-1.2-gentoo.patch
similarity index 97%
rename from sci-chemistry/threeV/files/1.2-gentoo.patch
rename to sci-chemistry/threeV/files/threeV-1.2-gentoo.patch
index 0827551599b..556e928d581 100644
--- a/sci-chemistry/threeV/files/1.2-gentoo.patch
+++ b/sci-chemistry/threeV/files/threeV-1.2-gentoo.patch
@@ -1,7 +1,7 @@
-diff --git a/src/Makefile b/src/Makefile
+diff --git a/Makefile b/Makefile
index a58462c..616f51a 100644
---- a/src/Makefile
-+++ b/src/Makefile
+--- a/Makefile
++++ b/Makefile
@@ -1,7 +1,7 @@
-CC = g++
-EXT=$(shell ./cpuflags.pl --opt )
diff --git a/sci-chemistry/threeV/threeV-1.2.ebuild
b/sci-chemistry/threeV/threeV-1.2-r1.ebuild
similarity index 58%
rename from sci-chemistry/threeV/threeV-1.2.ebuild
rename to sci-chemistry/threeV/threeV-1.2-r1.ebuild
index 8ed375a4876..1d4a1e1f346 100644
--- a/sci-chemistry/threeV/threeV-1.2.ebuild
+++ b/sci-chemistry/threeV/threeV-1.2-r1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-EAPI="3"
+EAPI=6
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
DESCRIPTION="3V: Voss Volume Voxelator"
HOMEPAGE="http://geometry.molmovdb.org/3v/";
@@ -19,15 +19,22 @@ PDEPEND="sci-chemistry/msms-bin"
S="${WORKDIR}/3v-${PV}/src"
+PATCHES=(
+ "${FILESDIR}"/${P}-gentoo.patch
+ "${FILESDIR}"/${P}-format-security.patch
+)
+
src_prepare() {
- epatch "${FILESDIR}"/${PV}-gentoo.patch
+ default
tc-export CXX
- emake distclean || die
+ emake distclean
+
+ export MAKEOPTS+=" V=1"
}
src_install() {
- emake DESTDIR="${ED}" install || die
+ emake DESTDIR="${ED}" install
- cd ..
- dodoc AUTHORS ChangeLog QUICKSTART README TODO VERSION || die
+ cd .. || die
+ dodoc AUTHORS ChangeLog QUICKSTART README TODO VERSION
}
