Fix for format-security, bug #542276; move to new python eclasses and EAPI=5

(Portage version: 2.2.18/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

4 files changed, 191 insertions, 84 deletions

diff --git a/sci-chemistry/eden/ChangeLog b/sci-chemistry/eden/ChangeLog
index d6e99d1e80b6..247e5b642412 100644
--- a/sci-chemistry/eden/ChangeLog
+++ b/sci-chemistry/eden/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/eden
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/eden/ChangeLog,v 1.19 2013/02/19 15:43:19 jlec Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/eden/ChangeLog,v 1.20 2015/03/11 14:54:19 jlec Exp $
+
+*eden-5.3-r2 (11 Mar 2015)
+
+  11 Mar 2015; Justin Lecher <jlec@gentoo.org> +eden-5.3-r2.ebuild,
+  +files/eden-5.3-format-security.patch, -eden-5.3.ebuild:
+  Fix for format-security, bug #542276; move to new python eclasses and EAPI=5
 
   19 Feb 2013; Justin Lecher <jlec@gentoo.org> eden-5.3-r1.ebuild,
   metadata.xml:
@@ -70,4 +76,3 @@
   +files/makefile-fixes.patch, +metadata.xml, +eden-5.3.ebuild:
   A crystallographic real-space electron-density refinement and optimization
   program.
-
diff --git a/sci-chemistry/eden/eden-5.3-r2.ebuild b/sci-chemistry/eden/eden-5.3-r2.ebuild
new file mode 100644
index 000000000000..93a1594a4519
--- /dev/null
+++ b/sci-chemistry/eden/eden-5.3-r2.ebuild
@@ -0,0 +1,87 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/eden/eden-5.3-r2.ebuild,v 1.1 2015/03/11 14:54:19 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils multilib python-r1 toolchain-funcs
+
+MY_P="${PN}_V${PV}"
+
+DESCRIPTION="A crystallographic real-space electron-density refinement and optimization program"
+HOMEPAGE="http://www.gromacs.org/pipermail/eden-users/"
+SRC_URI="mirror://gentoo/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="double-precision"
+
+RDEPEND="
+	sci-libs/fftw:2.1
+	sci-libs/gsl"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+S="${WORKDIR}/${PN}"
+
+SRC="${S}/source"
+
+pkg_setup() {
+	export EDENHOME="${EPREFIX}/usr/$(get_libdir)/${PN}"
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PV}-makefile-fixes.patch \
+		"${FILESDIR}"/${P}-impl-dec.patch \
+		"${FILESDIR}"/${P}-format-security.patch
+
+	sed -i \
+		-e "s:^\(FFTW.*=\).*:\1 ${EPREFIX}/usr:g" \
+		-e "s:^\(LIB.*=.*\$(FFTW)/\).*:\1$(get_libdir):g" \
+		-e "s:^\(BIN.*=\).*:\1 ${D}usr/bin:g" \
+		-e "s:^\(CFLAGS.*=\).*:\1 ${CFLAGS}:g" \
+		-e "s:-lgsl -lgslcblas:$($(tc-getPKG_CONFIG) --libs gsl):g" \
+		${SRC}/Makefile || die
+
+	if ! use double-precision; then
+		sed -i -e "s:^\(DOUBLESWITCH.*=\).*:\1 OFF:g" ${SRC}/Makefile || die
+		EDEN_EXE="s${PN}"
+	else
+		EDEN_EXE="d${PN}"
+	fi
+}
+
+src_compile() {
+	emake CC=$(tc-getCC) -C ${SRC}
+}
+
+src_install() {
+	emake -C ${SRC} install
+
+	python_foreach_impl python_newscript python/${PN}.py i${PN}
+	python_foreach_impl python_domodule python/FileListDialog.py
+
+	rm python/*py || die
+	insinto ${EDENHOME}/python
+	doins python/*
+
+	insinto ${EDENHOME}/help
+	doins help/*
+
+	insinto ${EDENHOME}/tools
+	doins tools/*
+
+	dodoc manual/UserManual.pdf
+
+	cat >> "${T}"/60${PN} <<- EOF
+	EDENHOME="${EDENHOME}"
+	EOF
+
+	doenvd "${T}"/60${PN}
+
+	dosym ${EDEN_EXE} /usr/bin/${PN}
+}
diff --git a/sci-chemistry/eden/eden-5.3.ebuild b/sci-chemistry/eden/eden-5.3.ebuild
deleted file mode 100644
index bfa7ea368940..000000000000
--- a/sci-chemistry/eden/eden-5.3.ebuild
+++ /dev/null
@@ -1,81 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/eden/eden-5.3.ebuild,v 1.8 2010/06/23 21:00:32 mr_bones_ Exp $
-
-inherit eutils multilib toolchain-funcs
-
-MY_P="${PN}_V${PV}"
-DESCRIPTION="A crystallographic real-space electron-density refinement and optimization program"
-HOMEPAGE="http://www.gromacs.org/pipermail/eden-users"
-SRC_URI="mirror://gentoo/${MY_P}.tar.gz"
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="x86"
-IUSE="double-precision"
-RDEPEND="=sci-libs/fftw-2*
-	sci-libs/gsl"
-
-DEPEND="${RDEPEND}"
-S="${WORKDIR}/${PN}"
-SRC="${S}/source"
-
-src_unpack() {
-	unpack ${A}
-
-	epatch "${FILESDIR}"/makefile-fixes.patch
-
-	sed -i \
-		-e "s:^\(FFTW.*=\).*:\1 /usr:g" \
-		-e "s:^\(LIB.*=.*\$(FFTW)/\).*:\1$(get_libdir):g" \
-		-e "s:^\(BIN.*=\).*:\1 ${D}usr/bin:g" \
-		-e "s:^\(CFLAGS.*=\).*:\1 ${CFLAGS}:g" \
-		${SRC}/Makefile
-
-	if ! use double-precision; then
-		sed -i -e "s:^\(DOUBLESWITCH.*=\).*:\1 OFF:g" ${SRC}/Makefile
-		EXE="seden"
-	else
-		EXE="deden"
-	fi
-}
-
-src_compile() {
-	cd ${SRC}
-	emake CC=$(tc-getCC) || die "emake failed"
-}
-
-src_install() {
-	local EDENHOME="/usr/lib/eden"
-
-	cd ${SRC}
-	dodir /usr/bin
-	make install || die "install failed"
-
-	cd "${S}"
-	exeinto ${EDENHOME}/python
-	doexe python/*
-
-	insinto ${EDENHOME}/help
-	doins help/*
-
-	insinto ${EDENHOME}/tools
-	doins tools/*
-
-	dodoc manual/UserManual.pdf
-
-cat << EOF > "${T}"/eden
-#!/bin/bash
-export EDENHOME="${EDENHOME}"
-${EXE} \$*
-EOF
-
-	dobin "${T}"/eden
-
-cat << EOF > "${T}"/ieden
-#!/bin/bash
-export EDENHOME="${EDENHOME}"
-\${EDENHOME}/python/eden.py
-EOF
-
-	dobin "${T}"/ieden
-}
diff --git a/sci-chemistry/eden/files/eden-5.3-format-security.patch b/sci-chemistry/eden/files/eden-5.3-format-security.patch
new file mode 100644
index 000000000000..04b5ecfddebb
--- /dev/null
+++ b/sci-chemistry/eden/files/eden-5.3-format-security.patch
@@ -0,0 +1,96 @@
+ source/back.c     | 2 +-
+ source/concosts.c | 4 ++--
+ source/count.c    | 4 ++--
+ source/eden.c     | 2 +-
+ source/util.c     | 4 ++--
+ 5 files changed, 8 insertions(+), 8 deletions(-)
+
+diff --git a/source/back.c b/source/back.c
+index fd517b9..185a02b 100644
+--- a/source/back.c
++++ b/source/back.c
+@@ -112,7 +112,7 @@ void	back_main(int argc, char *argv[])
+           ballpark(caller) ;
+ 
+      if (argc > optind+2)
+-	  sprintf(sf_filename, argv[optind+2]) ;
++	  sprintf(sf_filename, "%s", argv[optind+2]) ;
+ 
+   /*********************************************
+   Pull off prefix defining whereabouts of input 
+diff --git a/source/concosts.c b/source/concosts.c
+index d62d2e3..590f073 100644
+--- a/source/concosts.c
++++ b/source/concosts.c
+@@ -452,7 +452,7 @@ void	prepare_singlets(char *filename)
+                       sprintf(message, 
+ 		      "s=%d, p=%d, n=%d, phase=%g, old phase=%g, delta=%g\n", 
+                       s, p, n, phase, *(checks+n), phase-*(checks+n)) ;
+-                      fprintf(fp_log, message) ;
++                      fprintf(fp_log, "%s", message) ;
+                  }
+               } 
+ 		/***********************************************
+@@ -556,7 +556,7 @@ void	prepare_triplets(char *filename)
+ 		 sprintf(message, 
+ "Triplet (%d %d %d) from input (%d %d %d) corresponds to point w/o fobs info!\n",
+ 		   newh, newk, newl, t_h[q], t_k[q], t_l[q]) ;
+-		 fprintf(fp_log, message) ;
++		 fprintf(fp_log, "%s", message) ;
+ 		 legal_triplet = FALSE ;
+               }
+            }
+diff --git a/source/count.c b/source/count.c
+index c3bc390..ca13008 100644
+--- a/source/count.c
++++ b/source/count.c
+@@ -460,12 +460,12 @@ void	print_el_count(char *filename,
+      }
+ 
+      sprintf(message, "\nTotal no. of electrons is %g\n", totnump*volvox) ;
+-     fprintf(fp, message) ;
++     fprintf(fp, "%s", message) ;
+      printTwice(message) ;
+ 
+      sprintf(message, "Count of all remaining electrons: %g %g %g\n", 
+      remainder0*volvox, remainder1*volvox, remainder2*volvox) ;
+-     fprintf(fp, message) ;
++     fprintf(fp, "%s", message) ;
+      printTwice(message) ;
+ 
+      fclose(fp) ;
+diff --git a/source/eden.c b/source/eden.c
+index dea3246..5a9b389 100644
+--- a/source/eden.c
++++ b/source/eden.c
+@@ -319,7 +319,7 @@ int	main(int argc, char *argv[])
+ 
+      get_unique_logname() ;
+ 
+-     sprintf(command_line, argv[0]) ;
++     sprintf(command_line, "%s", argv[0]) ;
+ 
+      for (k = 1; k < argc; k++) { 
+          strcat(command_line, " ") ;
+diff --git a/source/util.c b/source/util.c
+index 6fff179..41c624c 100644
+--- a/source/util.c
++++ b/source/util.c
+@@ -266,7 +266,7 @@ void	printTwice(char *mess)	/* send info to terminal (stdout) and to log */
+  
+ void	prompt(char *mess)	/* Send message to user, await reply */
+ {
+-    fprintf(stdout, mess) ;
++    fprintf(stdout, "%s", mess) ;
+ 
+     while (fgets(terminp, MAXSTRING, stdin) != NULL)  {
+ 	if ((int)strlen(terminp) > 0) 
+@@ -722,7 +722,7 @@ void	start_record()
+      int	k ;
+ 
+      rec_length = k = sprintf(record, "\n") ;
+-     rec_length += sprintf(record+k, timestamp()) ;
++     rec_length += sprintf(record+k, "%s", timestamp()) ;
+      k = rec_length ;
+ 
+      if ((cwd = getcwd(NULL, 120)) == NULL)