[med-svn] [phyml] 02/02: Normalise 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 c81dfb9861b18246cbc713351ec13685f5f7d5c4
Author: Andreas Tille <tille at debian.org>
Date:   Sat Jun 24 21:09:45 2017 +0200

    Normalise patches
---
 debian/patches/fix_declaration_of_temp.patch       | 27 ++++++++++++++++++++--
 .../fix_wrong_initialisation_of_array.patch        |  7 +++---
 debian/patches/gcc-7.patch                         | 18 ---------------
 debian/patches/series                              |  4 +---
 4 files changed, 30 insertions(+), 26 deletions(-)

diff --git a/debian/patches/fix_declaration_of_temp.patch b/debian/patches/fix_declaration_of_temp.patch
index 3c23243..ee48fee 100644
--- a/debian/patches/fix_declaration_of_temp.patch
+++ b/debian/patches/fix_declaration_of_temp.patch
@@ -1,6 +1,6 @@
 Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 17 Aug 2016 15:30:32 +0200
-Description: Add missing declaration
+Last-Update: Sat, 24 Jun 2017 15:29:56 +0200
+Description: Add missing declaration, fix name of BEAGLE constant
 
 --- a/src/utilities.c
 +++ b/src/utilities.c
@@ -14,3 +14,26 @@ Description: Add missing declaration
    
    for(i=0;i<data->n_otu-1;i++)
      for(j=i+1;j<data->n_otu;j++)
+@@ -6204,7 +6204,10 @@ void Swap_Partial_Lk(t_edge *a, t_edge *
+   int *buff_p_lk_loc, *buff_patt_id;
+   phydbl *buff_p_lk_tip;
+   int *buff_ui;
+-  
++
++#ifdef BEAGLE
++  int temp;
++#endif
+   
+   if(side_a == LEFT && side_b == LEFT)
+     {
+--- a/src/beagle_utils.c
++++ b/src/beagle_utils.c
+@@ -53,7 +53,7 @@ void print_beagle_flags(long inFlags) {
+     if (inFlags & BEAGLE_FLAG_SCALING_ALWAYS)     fprintf(stdout, " SCALING_ALWAYS");
+     if (inFlags & BEAGLE_FLAG_SCALING_DYNAMIC)    fprintf(stdout, " SCALING_DYNAMIC");
+     if (inFlags & BEAGLE_FLAG_SCALERS_RAW)        fprintf(stdout, " SCALERS_RAW");
+-    if (inFlags & BEAGLE_FLAG_SCALERS_log)        fprintf(stdout, " SCALERS_log");
++    if (inFlags & BEAGLE_FLAG_SCALERS_LOG)        fprintf(stdout, " SCALERS_LOG");
+     if (inFlags & BEAGLE_FLAG_VECTOR_NONE)        fprintf(stdout, " VECTOR_NONE");
+     if (inFlags & BEAGLE_FLAG_VECTOR_SSE)         fprintf(stdout, " VECTOR_SSE");
+     if (inFlags & BEAGLE_FLAG_VECTOR_AVX)         fprintf(stdout, " VECTOR_AVX");
diff --git a/debian/patches/fix_wrong_initialisation_of_array.patch b/debian/patches/fix_wrong_initialisation_of_array.patch
index ab60a2e..b97ec4f 100644
--- a/debian/patches/fix_wrong_initialisation_of_array.patch
+++ b/debian/patches/fix_wrong_initialisation_of_array.patch
@@ -1,5 +1,6 @@
 Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 17 Aug 2016 15:30:32 +0200
+        Thomas Schmitt <scdbackup at gmx.net>
+Last-Update: Sat, 24 Jun 2017 15:29:56 +0200
 Description: avoid initialisation an array with a scalar value
  Quoting James Cowgill <jcowgill at debian.org> on debian-mentors list:
  .
@@ -12,13 +13,13 @@ Description: avoid initialisation an array with a scalar value
 
 --- a/src/lk.c
 +++ b/src/lk.c
-@@ -2446,8 +2446,8 @@ void Update_PMat_At_Given_Edge(t_edge *b
+@@ -2260,8 +2260,8 @@ void Update_PMat_At_Given_Edge(t_edge *b
        
        //
        len = MAX(0.0, b_fcus->l->v) * tree->mod->br_len_mult->v;
 -      int p_matrices[1]     = b_fcus->Pij_rr_idx;
 -      double branch_lens[1] = len;
-+      int p_matrices[1]     = { b_fcus->Pij_rr_idx } ;
++      int p_matrices[1]     = { b_fcus->Pij_rr_idx };
 +      double branch_lens[1] = { len };
        int ret = beagleUpdateTransitionMatrices(tree->b_inst,0,p_matrices,NULL,NULL,branch_lens,1);
        if(ret<0)
diff --git a/debian/patches/gcc-7.patch b/debian/patches/gcc-7.patch
deleted file mode 100644
index b2b8bba..0000000
--- a/debian/patches/gcc-7.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-Author: Thomas Schmitt <scdbackup at gmx.net>
-Last-Update: Sat, 24 Jun 2017 15:29:56 +0200
-Description: the compiler wants {}-brackets around the scalar value
-             when it shall initialize a vector
-
---- a/src/lk.c
-+++ b/src/lk.c
-@@ -2260,8 +2260,8 @@ void Update_PMat_At_Given_Edge(t_edge *b
-       
-       //
-       len = MAX(0.0, b_fcus->l->v) * tree->mod->br_len_mult->v;
--      int p_matrices[1]     = b_fcus->Pij_rr_idx;
--      double branch_lens[1] = len;
-+      int p_matrices[1]     = { b_fcus->Pij_rr_idx };
-+      double branch_lens[1] = { len };
-       int ret = beagleUpdateTransitionMatrices(tree->b_inst,0,p_matrices,NULL,NULL,branch_lens,1);
-       if(ret<0)
-         {
diff --git a/debian/patches/series b/debian/patches/series
index bea959f..785dd71 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,6 +2,4 @@ sse_only_if_supported.patch
 no-stdc++.patch
 no-configure-ac-date.patch
 fix_declaration_of_temp.patch
-# fix_wrong_initialisation_of_array.patch
-gcc-7.patch
-beagle.patch
+fix_wrong_initialisation_of_array.patch

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/phyml.git