[med-svn] [Git][med-team/phyml][master] Refresh patches

[Shayan Doust]

Shayan Doust pushed to branch master at Debian Med / phyml


Commits:
e3c15a5b by Shayan Doust at 2020-07-22T17:10:14+01:00
Refresh patches

- - - - -


5 changed files:

- debian/patches/cross.patch
- debian/patches/fix_declaration_of_temp.patch
- debian/patches/fix_wrong_initialisation_of_array.patch
- debian/patches/no-configure-ac-date.patch
- debian/patches/no-march-native.patch


Changes:

=====================================
debian/patches/cross.patch
=====================================
@@ -3,11 +3,9 @@ Last-Update: Tue, 26 Jun 2018 17:32:08 +0200
 Bug-Debian: https://bugs.debian.org/902433
 Description: Use MPI_C to enable cross building
 
-Index: phyml/configure.ac
-===================================================================
 --- phyml.orig/configure.ac
 +++ phyml/configure.ac
-@@ -105,7 +105,7 @@ AS_IF([test "x$enable_gprof" = "xyes"],
+@@ -105,7 +105,7 @@
  AC_ARG_ENABLE([mpi],
                [AS_HELP_STRING([--enable-mpi],
                                [Compile with mpicc instead of gcc.])])
@@ -16,11 +14,9 @@ Index: phyml/configure.ac
  AS_IF([test "x$enable_mpi" = "xyes"],AC_DEFINE([MPI],[1],[MPI tag on]))
  AM_CONDITIONAL([WANT_MPI], [test "$enable_mpi" = yes])
  
-Index: phyml/src/Makefile.am
-===================================================================
 --- phyml.orig/src/Makefile.am
 +++ phyml/src/Makefile.am
-@@ -315,7 +315,8 @@ sse.c sse.h\
+@@ -314,7 +314,8 @@
  avx.c avx.h\
  ancestral.c ancestral.h\
  mpi_boot.c mpi_boot.h


=====================================
debian/patches/fix_declaration_of_temp.patch
=====================================
@@ -2,11 +2,9 @@ Author: Andreas Tille <tille at debian.org>
 Last-Update: Sat, 24 Jun 2017 15:29:56 +0200
 Description: Add missing declaration, fix name of BEAGLE constant
 
-Index: phyml/src/utilities.c
-===================================================================
 --- phyml.orig/src/utilities.c
 +++ phyml/src/utilities.c
-@@ -2198,6 +2198,9 @@ matrix *K80_dist(calign *data, phydbl g_
+@@ -2207,6 +2207,9 @@
          }
      }
    
@@ -16,7 +14,7 @@ Index: phyml/src/utilities.c
    
    for(i=0;i<data->n_otu-1;i++)
      for(j=i+1;j<data->n_otu;j++)
-@@ -6640,7 +6643,10 @@ void Swap_Partial_Lk(t_edge *a, t_edge *
+@@ -6671,7 +6674,10 @@
    int *buff_p_lk_loc, *buff_patt_id;
    phydbl *buff_p_lk_tip;
    int *buff_ui;
@@ -28,11 +26,9 @@ Index: phyml/src/utilities.c
    
    if(side_a == LEFT && side_b == LEFT)
      {
-Index: phyml/src/beagle_utils.c
-===================================================================
 --- phyml.orig/src/beagle_utils.c
 +++ phyml/src/beagle_utils.c
-@@ -53,7 +53,7 @@ void print_beagle_flags(long inFlags) {
+@@ -53,7 +53,7 @@
      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");


=====================================
debian/patches/fix_wrong_initialisation_of_array.patch
=====================================
@@ -11,9 +11,9 @@ Description: avoid initialisation an array with a scalar value
  The quick fix here is probably to wrap the values in curly braces to
  form a correct array initializer.
 
---- a/src/lk.c
-+++ b/src/lk.c
-@@ -2266,8 +2266,8 @@ void Update_PMat_At_Given_Edge(t_edge *b
+--- phyml.orig/src/lk.c
++++ phyml/src/lk.c
+@@ -2259,8 +2259,8 @@
        
        //
        len = MAX(0.0, b_fcus->l->v) * tree->mod->br_len_mult->v;


=====================================
debian/patches/no-configure-ac-date.patch
=====================================
@@ -3,13 +3,13 @@ Last-Update: 2016-03-02
 Description: Enable reproducible build based on version number
  rather than build date
 
---- a/configure.ac
-+++ b/configure.ac
+--- phyml.orig/configure.ac
++++ phyml/configure.ac
 @@ -1,7 +1,7 @@
  #                                               -*- Autoconf -*-
  # Process this file with autoconf to produce a configure script.
  
--AC_INIT([PhyML],esyscmd([sh -c "echo "3.3." | tr -d '\n' ; echo "20190909" | tr -d '\n'"]),[guindon at lirmm.fr])
+-AC_INIT([PhyML],esyscmd([sh -c "echo "3.3." | tr -d '\n' ; echo "20200621" | 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])
  


=====================================
debian/patches/no-march-native.patch
=====================================
@@ -2,11 +2,9 @@ Description: Do not emit -march=native
 Bug-Debian: https://bugs.debian.org/866139
 Author: Graham Inggs <ginggs at debian.org>
 Last-Update: 2017-06-30
-Index: phyml/configure.ac
-===================================================================
 --- phyml.orig/configure.ac
 +++ phyml/configure.ac
-@@ -58,7 +58,7 @@ AC_CHECK_FUNCS([floor pow rint sqrt strc
+@@ -58,7 +58,7 @@
  dnl DEFAULT_VECTOR_FLAG=
  dnl DEFAULT_VECTOR_FLAG="-mavx -mfma"
  dnl DEFAULT_VECTOR_FLAG=-msse3



View it on GitLab: https://salsa.debian.org/med-team/phyml/-/commit/e3c15a5b7238fa78c156c802c7795788bd39e158

-- 
View it on GitLab: https://salsa.debian.org/med-team/phyml/-/commit/e3c15a5b7238fa78c156c802c7795788bd39e158
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200722/9ecd32cf/attachment-0001.html>