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

Package-Manager: portage-2.2.18/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

diff --git a/sci-chemistry/eden/ChangeLog b/sci-chemistry/eden/ChangeLog
index d6e99d1e80b67d8d94cae0aaf9938a80cfa09d07..247e5b6424121cb74edcfd5fc4979d2ea3682186 100644 (file)
--- 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/Manifest b/sci-chemistry/eden/Manifest
index 4ccbadfe39a98d715fe911ea983229230c3c9c03..94469e144cd9b928d805b979321185b3102f156f 100644 (file)
--- a/sci-chemistry/eden/Manifest
+++ b/sci-chemistry/eden/Manifest
@@ -1,18 +1,31 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
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+AUX eden-5.3-format-security.patch 3202 SHA256 098c6fdd0dc433a2a2f3c18df7f9e8307e9a2d1bf21366e75a14343e38fcbff6 SHA512 01e100fe5481a73de2efa6652fe38c19337eae0dc13557ef0ad3e3a4f186becbfb8831aece0a619c08541e1a667e999c47b28438ec431f056c44f12849662c12 WHIRLPOOL 89eaad2e0025c7552642cc6441ad6a3ae9f6563f2f5f00dd5a06756d02a3aa961d622b1b4bc7439947b1f15b836d64781f9ed7057faffb207fe7f87d4ee08bc7
 AUX eden-5.3-impl-dec.patch 899 SHA256 b1760b8deab3bc01661a586a0a8c536449ea6f1f201e9c40fccccfdce07be10e SHA512 e89f1e0c028099e305a79befa558a86bc47d050c1e30394178999c7a1568bae9c3e525953bf152888690e0e1607dd72c522d2995f45b1eccfb9f7bf75e7866c2 WHIRLPOOL 0a2a50d0819346861e899ae17e65746936caf23454cd4e7fe0477b0d1aff0e958ce2c8f6f3179f676ab7a94d1c446d32c7acd0182f3cc2f5103c3485829b9dd0
 AUX makefile-fixes.patch 837 SHA256 6f7612404cccd9e40de19df3f86eb86be9a17fa105eac21e615c0d464f92cc31 SHA512 818fe1d23fa940cb533afcb9e84bdc5c719651005136304ca66d368fc21cf4d7a1facb0a383c9689ab1658632cec30969322fdffccadae941a754900542237e7 WHIRLPOOL adf204b3f1a361dfa426249b6e1ab89b1565d8c9852b03fbe770c429e098ece80b5528464d6c4c1a680960f1cb2d3dc6c7826799b41688dfffd33ebd1e4a96c4
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 EBUILD eden-5.3-r1.ebuild 1974 SHA256 f3435f97da67411fba7626e064397bfca38ae4ca2f13e8c23a7db6f06074400b SHA512 ecb3322f6b1b513fbf51801cac3aed5c3bf02fd744d35c5feab059332e45bed0045b1e7091934e5ad5d0e1b21af49ad1eca585d1a1ad2476f563758d9201fb87 WHIRLPOOL 57e1bafed8bab7067529e057f36f74636d2fba39bd02eeeffef038e0352a2f4a7bfb9779130d1dbd00b534931af94113318a077eebb868e903357a552ba927e0
-EBUILD eden-5.3.ebuild 1641 SHA256 909805cfebadf7de5fd3624f8fb2a41446e3e77f264094cebc90b3527ca9a8d4 SHA512 23b29fdfbe22cab54e93dbe1260531c0e910651407bea83a843ed26ec827f4ab4b79b84a59d6ac2656271e5deb54a6c221d1927c5354436014da667c23941d8b WHIRLPOOL fc59305722d3231df58a41e86ff79f97e4b970bb4fd863daa12d0315951a41e9208ed9a1d1f37ac30f9e681e9cd350b5187c30260702207ece0f6a4d11424183
-MISC ChangeLog 2854 SHA256 f12fb9c952f9cce400058257cdbf1b2a1eecaf1f4eb8100bd3caeef27fe17758 SHA512 4ad07cb5b9e6fedcd07ace02ecdad8c47b36de86fed7783f257417a47b4b85130363730c9138688f3e4f797f0cd932a067155b722a3611ac653d9c9084544ac1 WHIRLPOOL 108768d9d2fedcf07815b84d3c50fb33b20bbca541d301dbc399bc78da430b902d1373a713d7ca234037c02be27d514fbc6a696fd3e743d968646381943feb19
+EBUILD eden-5.3-r2.ebuild 1905 SHA256 47bf04f36feb27fa760a6e831f0c8c279e5fcf26a58619d14213e97a77638b61 SHA512 585336b0312fa6a9bb43f696323ec9b622c22aad7ab7e65a49199b59dbf3a086e26129a64200032c45985d1a002d77ea84a706c416df7c5eb7c332b928b8ea38 WHIRLPOOL 6131777a868855fe909335ec67858247dd57eac6ced855d1114cdb5d67adaad5e7c5edc4adcbb3c848271243394232d4fa130d7994b9060a357b183c5e76d40d
+MISC ChangeLog 3088 SHA256 ff2638468b2bd1850e4aa1063479654c1bfe2c834ecc399545b3ca1259bacde4 SHA512 bfe638dcbff9bfdb328c74c60a08022d38f085483f64ee97686efcfa72627b271b72249fb0a4dcfa696f8b7a654537585e1fc9cf70af71e9558fbd4aa967df76 WHIRLPOOL 993ed639b81c41af6a00af4538ada013359d311c47aeb09c30e35a893394dce0db1aa28f99fbc9248a5edd2e4e3cad93c74197a72a91dd0c29ebe26a85166179
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diff --git a/sci-chemistry/eden/eden-5.3-r2.ebuild b/sci-chemistry/eden/eden-5.3-r2.ebuild
new file mode 100644 (file)
index 0000000..93a1594
--- /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 (file)
index bfa7ea3..0000000
--- 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 (file)
index 0000000..04b5ecf
--- /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)