[med-svn] [phyml] 05/05: Refresh patches

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository phyml.

commit 410decc89916770a87546edea1024755bc2c35eb
Author: Andreas Tille <tille at debian.org>
Date:   Sat Jun 24 11:27:15 2017 +0200

    Refresh patches
---
 debian/patches/fix_declaration_of_temp.patch |  4 ++--
 debian/patches/no-configure-ac-date.patch    |  6 +++---
 debian/patches/no-stdc++.patch               |  6 +++---
 debian/patches/sse_only_if_supported.patch   | 11 +----------
 4 files changed, 9 insertions(+), 18 deletions(-)

diff --git a/debian/patches/fix_declaration_of_temp.patch b/debian/patches/fix_declaration_of_temp.patch
index 5f17bc1..3c23243 100644
--- a/debian/patches/fix_declaration_of_temp.patch
+++ b/debian/patches/fix_declaration_of_temp.patch
@@ -4,7 +4,7 @@ Description: Add missing declaration
 
 --- a/src/utilities.c
 +++ b/src/utilities.c
-@@ -2125,6 +2125,9 @@ matrix *K80_dist(calign *data, phydbl g_
+@@ -2104,6 +2104,9 @@ matrix *K80_dist(calign *data, phydbl g_
          }
      }
    
@@ -12,5 +12,5 @@ Description: Add missing declaration
 +  int temp;
 +#endif
    
-   For(i,data->n_otu-1)
+   for(i=0;i<data->n_otu-1;i++)
      for(j=i+1;j<data->n_otu;j++)
diff --git a/debian/patches/no-configure-ac-date.patch b/debian/patches/no-configure-ac-date.patch
index f2218ad..1b6dce3 100644
--- a/debian/patches/no-configure-ac-date.patch
+++ b/debian/patches/no-configure-ac-date.patch
@@ -9,8 +9,8 @@ Description: Enable reproducible build based on version number
  #                                               -*- Autoconf -*-
  # Process this file with autoconf to produce a configure script.
  
--AC_INIT([PhyML],esyscmd([sh -c "date \"+%Y%m%d\" | tr -d '\n'"]),[s.guindon at auckland.ac.nz])
-+AC_INIT([PhyML],esyscmd([sh -c "dpkg-parsechangelog | egrep '^Version:' | cut -f 2 -d ' ' | tr -d '\n'"]),[s.guindon at auckland.ac.nz])
+-AC_INIT([PhyML],esyscmd([sh -c "echo "3.3." | tr -d '\n' ; date \"+%Y%m%d\" | tr -d '\n'"]),[guindon at lirmm.fr])
++AC_INIT([PhyML],esyscmd([sh -c "echo "3.3." | tr -d '\n' ; dpkg-parsechangelog | egrep '^Version:' | cut -f 2 -d ' ' | tr -d '\n'"]),[guindon at lirmm.fr])
  AM_INIT_AUTOMAKE([foreign])
  m4_ifdef([AM_SILENT_RULES], [AM_SILENT_RULES])
- 
+ AC_CONFIG_MACRO_DIR([m4])
diff --git a/debian/patches/no-stdc++.patch b/debian/patches/no-stdc++.patch
index 4a000ef..9f92c9d 100644
--- a/debian/patches/no-stdc++.patch
+++ b/debian/patches/no-stdc++.patch
@@ -4,12 +4,12 @@ Description: Do not uselessly link against libstdc++
 
 --- a/configure.ac
 +++ b/configure.ac
-@@ -110,7 +110,7 @@ AS_IF([test "x$enable_win" = "xyes"],[CC
+@@ -111,7 +111,7 @@ AM_CONDITIONAL([WANT_WIN], [test "$enabl
  AC_ARG_ENABLE([beagle], [AS_HELP_STRING([--enable-beagle], [Compute likelihoods using BEAGLE library.])], [beagle=yes],[beagle=no])
  AS_IF([test "x$enable_beagle" = "xyes"],[PKG_CHECK_MODULES(BEAGLE, hmsbeagle-1)])
  AS_IF([test "x$enable_beagle" = "xyes"],
--      [CFLAGS="${CFLAGS} ${BEAGLE_CFLAGS} ${BEAGLE_LIBS} -lstdc++ ${ARCH_flag}"],
-+      [CFLAGS="${CFLAGS} ${BEAGLE_CFLAGS} ${BEAGLE_LIBS} ${ARCH_flag}"],
+-      [CFLAGS="${CFLAGS} ${BEAGLE_CFLAGS} ${BEAGLE_LIBS} -lstdc++"],
++      [CFLAGS="${CFLAGS} ${BEAGLE_CFLAGS} ${BEAGLE_LIBS}"],
        [CFLAGS=${CFLAGS}])
  AS_IF([test "x$enable_beagle" = "xyes"], AC_DEFINE([BEAGLE],[1],[BEAGLE tag on]))
  AM_CONDITIONAL([WANT_BEAGLE], [test "$enable_beagle" = yes])
diff --git a/debian/patches/sse_only_if_supported.patch b/debian/patches/sse_only_if_supported.patch
index 2b0fe27..2d2b0ea 100644
--- a/debian/patches/sse_only_if_supported.patch
+++ b/debian/patches/sse_only_if_supported.patch
@@ -7,7 +7,7 @@ Description: Verify architecture whether we comiple on i386 or amd64 and
 
 --- a/configure.ac
 +++ b/configure.ac
-@@ -16,6 +16,16 @@ AC_CANONICAL_HOST
+@@ -17,6 +17,16 @@ AC_CANONICAL_HOST
  
  AC_PROG_CC([gcc])
  
@@ -24,12 +24,3 @@ Description: Verify architecture whether we comiple on i386 or amd64 and
  
  # Checks for libraries.
  AC_CHECK_LIB([m], [log])
-@@ -81,7 +91,7 @@ AC_ARG_ENABLE([gprof],
-                               [Remove optimization options and add profiling informations.])])
- AS_IF([test "x$enable_gprof" = "xyes"],
-       [CFLAGS="-ansi -pedantic -Wall -std=c99 -O0 -g -pg"],
--      [AS_IF([test "x$enable_debug" = "xno"],[CFLAGS="-Wall -O2 -msse -fomit-frame-pointer -funroll-loops ${ARCH_flag}"])])
-+      [AS_IF([test "x$enable_debug" = "xno"],[CFLAGS="-Wall -O2 ${MSSE} -fomit-frame-pointer -funroll-loops ${ARCH_flag}"])])
- 
- AC_ARG_ENABLE([mpi],
-               [AS_HELP_STRING([--enable-mpi],

-- 
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