[med-svn] [phyml] 02/04: Adapt patched to previous version

[Andreas Tille]

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tille pushed a commit to branch master
in repository phyml.

commit 3a8c751573ca68320eaf1c03365351bb3d5cb981
Author: Andreas Tille <tille at debian.org>
Date:   Tue Aug 23 07:50:06 2016 +0200

    Adapt patched to previous version
---
 debian/patches/fix_declaration_of_temp.patch                   | 10 +++++-----
 .../{no-configure-ac-date => no-configure-ac-date.patch}       |  4 ++--
 debian/patches/no-stdc++.patch                                 |  2 +-
 debian/patches/series                                          |  4 ++--
 debian/patches/sse_only_if_supported.patch                     |  4 ++--
 5 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/debian/patches/fix_declaration_of_temp.patch b/debian/patches/fix_declaration_of_temp.patch
index ae73039..5f17bc1 100644
--- a/debian/patches/fix_declaration_of_temp.patch
+++ b/debian/patches/fix_declaration_of_temp.patch
@@ -4,13 +4,13 @@ Description: Add missing declaration
 
 --- a/src/utilities.c
 +++ b/src/utilities.c
-@@ -6190,6 +6190,9 @@ void Swap_Partial_Lk(t_edge *a, t_edge *
-   short int *buff_p_lk_tip;
-   unsigned int *buff_ui;
+@@ -2125,6 +2125,9 @@ matrix *K80_dist(calign *data, phydbl g_
+         }
+     }
    
 +#ifdef BEAGLE
 +  int temp;
 +#endif
    
-   if(side_a == LEFT && side_b == LEFT)
-     {
+   For(i,data->n_otu-1)
+     for(j=i+1;j<data->n_otu;j++)
diff --git a/debian/patches/no-configure-ac-date b/debian/patches/no-configure-ac-date.patch
similarity index 79%
rename from debian/patches/no-configure-ac-date
rename to debian/patches/no-configure-ac-date.patch
index 0ee4163..f2218ad 100644
--- a/debian/patches/no-configure-ac-date
+++ 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 "echo "3.2." | tr -d '\n' ; date \"+%Y%m%d\" | tr -d '\n'"]),[guindon at lirmm.fr])
+-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])
  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 aaccbe7..4a000ef 100644
--- a/debian/patches/no-stdc++.patch
+++ b/debian/patches/no-stdc++.patch
@@ -4,7 +4,7 @@ Description: Do not uselessly link against libstdc++
 
 --- a/configure.ac
 +++ b/configure.ac
-@@ -112,7 +112,7 @@ AM_CONDITIONAL([WANT_WIN], [test "$enabl
+@@ -110,7 +110,7 @@ AS_IF([test "x$enable_win" = "xyes"],[CC
  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"],
diff --git a/debian/patches/series b/debian/patches/series
index 7b2f775..dbb6e17 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,5 +1,5 @@
 sse_only_if_supported.patch
 no-stdc++.patch
-no-configure-ac-date
+no-configure-ac-date.patch
 fix_declaration_of_temp.patch
-fix_wrong_initialisation_of_array.patch
+# fix_wrong_initialisation_of_array.patch
diff --git a/debian/patches/sse_only_if_supported.patch b/debian/patches/sse_only_if_supported.patch
index b4bd66d..2b0fe27 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
-@@ -17,6 +17,16 @@ AC_CANONICAL_HOST
+@@ -16,6 +16,16 @@ AC_CANONICAL_HOST
  
  AC_PROG_CC([gcc])
  
@@ -24,7 +24,7 @@ Description: Verify architecture whether we comiple on i386 or amd64 and
  
  # Checks for libraries.
  AC_CHECK_LIB([m], [log])
-@@ -82,7 +92,7 @@ AC_ARG_ENABLE([gprof],
+@@ -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"],

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