[med-svn] [Git][med-team/phyml][master] 2 commits: Refresh patches
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sat Dec 6 22:07:52 GMT 2025
Andreas Tille pushed to branch master at Debian Med / phyml
Commits:
4773ab9b by Andreas Tille at 2025-12-06T23:05:59+01:00
Refresh patches
- - - - -
893b7a76 by Andreas Tille at 2025-12-06T23:06:39+01:00
Work around broken clean target
- - - - -
11 changed files:
- debian/changelog
- debian/patches/apply-cflags.patch
- debian/patches/apply-ldflags.patch
- debian/patches/filter-sse3-intrinsics.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
- debian/patches/sse_only_if_supported.patch
- debian/patches/typos.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -6,6 +6,7 @@ phyml (3:3.3.20250515-1) UNRELEASED; urgency=medium
* d/watch: version=5
* New upstream version
* Standards-Version: 4.7.2 (routine-update)
+ * Work around broken clean target
-- Andreas Tille <tille at debian.org> Sat, 06 Dec 2025 21:15:25 +0100
=====================================
debian/patches/apply-cflags.patch
=====================================
@@ -6,14 +6,14 @@ Forwarded: not-needed
Last-Update: 2021-11-17
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- phyml.orig/configure.ac
-+++ phyml/configure.ac
-@@ -77,7 +77,7 @@
+--- a/configure.ac
++++ b/configure.ac
+@@ -85,7 +85,7 @@ dnl AC_PROG_LIBTOOL
dnl DEFAULT_C_FLAG="-fno-inline-functions -fno-inline-functions-called-once -fno-optimize-sibling-calls -O2 -fno-omit-frame-pointer -g ${VECTOR_FLAG}"
--DEFAULT_C_FLAG="-std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline ${VECTOR_FLAG}"
-+DEFAULT_C_FLAG="-std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline ${VECTOR_FLAG} ${CFLAGS}"
+-DEFAULT_C_FLAG="-std=gnu99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline ${VECTOR_FLAG}"
++DEFAULT_C_FLAG="-std=gnu99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline ${VECTOR_FLAG} ${CFLAGS}"
dnl DEFAULT_C_FLAG="-O2 ${VECTOR_FLAG}"
dnl DEFAULT_C_FLAG="${VECTOR_FLAG}"
dnl DEFAULT_C_FLAG="-pthread -O3 -g -ffunction-sections -fdata-sections"
=====================================
debian/patches/apply-ldflags.patch
=====================================
@@ -4,9 +4,9 @@ Forwarded: not-needed
Last-Update: 2021-11-23
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- phyml.orig/configure.ac
-+++ phyml/configure.ac
-@@ -69,7 +69,7 @@
+--- a/configure.ac
++++ b/configure.ac
+@@ -77,7 +77,7 @@ AS_IF([test "x$enable_native" = "xno"],
[VECTOR_FLAG="${DEFAULT_VECTOR_FLAG}"])
=====================================
debian/patches/filter-sse3-intrinsics.patch
=====================================
@@ -8,119 +8,113 @@ Forwarded: no
Last-Update: 2021-11-17
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- phyml.orig/src/sse.h
-+++ phyml/src/sse.h
-@@ -22,7 +22,7 @@
- #include "times.h"
- #include "mixt.h"
+--- a/src/sse.h
++++ b/src/sse.h
+@@ -25,7 +25,7 @@ the GNU public licence. See http://www.
+ #include "sse2neon.h"
+ #endif
--#if (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+-#if (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__) || defined(__ARM_NEON))
+#if defined(__SSE3__)
void SSE_Update_Partial_Lk(t_tree *tree,t_edge *b_fcus,t_node *n);
void SSE_Update_Eigen_Lr(t_edge *b, t_tree *tree);
---- phyml.orig/src/lk.c
-+++ phyml/src/lk.c
-@@ -779,7 +779,7 @@
+--- a/src/lk.c
++++ b/src/lk.c
+@@ -791,7 +791,7 @@ phydbl Lk_Core(int state, int ambiguity_
{
- #if (defined(__AVX__) || defined(__AVX2__))
+ #if ((defined(__AVX__) || defined(__AVX2__)) && !defined(DISABLE_NATIVE))
tree->site_lk_cat[catg] = AVX_Lk_Core_One_Class_No_Eigen_Lr(p_lk_left,p_lk_rght,Pij_rr,tPij_rr,pi,ns,ambiguity_check,state);
--#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
-+#elif defined(__SSE3__)
+-#elif ((defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__)) && !defined(DISABLE_NATIVE))
++#elif (defined(__SSE3__) && !defined(DISABLE_NATIVE))
tree->site_lk_cat[catg] = SSE_Lk_Core_One_Class_No_Eigen_Lr(p_lk_left,p_lk_rght,Pij_rr,tPij_rr,pi,ns,ambiguity_check,state);
#else
tree->site_lk_cat[catg] = Lk_Core_One_Class_No_Eigen_Lr(p_lk_left,p_lk_rght,Pij_rr,pi,ns,ambiguity_check,state);
-@@ -870,7 +870,7 @@
+@@ -882,7 +882,7 @@ phydbl Lk_Core_Eigen_Lr(phydbl *expl, ph
{
- #if (defined(__AVX__) || defined(__AVX2__))
+ #if ((defined(__AVX__) || defined(__AVX2__)) && !defined(DISABLE_NATIVE))
tree->site_lk_cat[catg] = AVX_Lk_Core_One_Class_Eigen_Lr(dot_prod,expl ? expl : NULL,ns);
--#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
-+#elif defined(__SSE3__)
+-#elif ((defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__)) && !defined(DISABLE_NATIVE))
++#elif (defined(__SSE3__) && !defined(DISABLE_NATIVE))
tree->site_lk_cat[catg] = SSE_Lk_Core_One_Class_Eigen_Lr(dot_prod,expl ? expl : NULL,ns);
#else
tree->site_lk_cat[catg] = Lk_Core_One_Class_Eigen_Lr(dot_prod,expl ? expl : NULL,ns);
-@@ -963,7 +963,7 @@
+@@ -975,7 +975,7 @@ void Lk_dLk_Core_Eigen_Lr(phydbl *expl,
AVX_Lk_dLk_Core_One_Class_Eigen_Lr(dot_prod,
expl ? expl : NULL,
ns,&core_lk,&core_dlk);
--#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
-+#elif defined(__SSE3__)
+-#elif ((defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__)) && !defined(DISABLE_NATIVE))
++#elif (defined(__SSE3__) && !defined(DISABLE_NATIVE))
SSE_Lk_dLk_Core_One_Class_Eigen_Lr(dot_prod,
expl ? expl : NULL,
ns,&core_lk,&core_dlk);
-@@ -1045,7 +1045,7 @@
- #if (defined(__AVX__) || defined(__AVX2__))
+@@ -1057,7 +1057,7 @@ void Update_Eigen_Lr(t_edge *b, t_tree *
+ #if ((defined(__AVX__) || defined(__AVX2__)) && !defined(DISABLE_NATIVE))
AVX_Update_Eigen_Lr(b,tree);
return;
--#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
-+#elif defined(__SSE3__)
+-#elif ((defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__)) && !defined(DISABLE_NATIVE))
++#elif (defined(__SSE3__) && !defined(DISABLE_NATIVE))
SSE_Update_Eigen_Lr(b,tree);
return;
#endif
-@@ -1292,7 +1292,7 @@
+@@ -1305,7 +1305,7 @@ void Update_Partial_Lk(t_tree *tree, t_e
{
- #if (defined(__AVX__) || defined(__AVX2__))
+ #if ((defined(__AVX__) || defined(__AVX2__)) && !defined(DISABLE_NATIVE))
AVX_Update_Partial_Lk(tree,b,d);
--#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
-+#elif defined(__SSE3__)
+-#elif ((defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__)) && !defined(DISABLE_NATIVE))
++#elif (defined(__SSE3__) && !defined(DISABLE_NATIVE))
SSE_Update_Partial_Lk(tree,b,d);
#else
Default_Update_Partial_Lk(tree,b,d);
---- phyml.orig/src/sse.c
-+++ phyml/src/sse.c
-@@ -16,7 +16,7 @@
- //////////////////////////////////////////////////////////////
- //////////////////////////////////////////////////////////////
-
--#if ((defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__)) && !((defined __AVX__ || defined __AVX2__)))
-+#if (defined(__SSE3__) && !((defined __AVX__ || defined __AVX2__)))
-
- void SSE_Update_Eigen_Lr(t_edge *b, t_tree *tree)
- {
---- phyml.orig/src/utilities.h
-+++ phyml/src/utilities.h
-@@ -38,7 +38,7 @@
+--- a/src/utilities.h
++++ b/src/utilities.h
+@@ -40,7 +40,7 @@ the GNU public licence. See http://www.o
#include <xmmintrin.h>
- #include <pmmintrin.h>
- #include <immintrin.h>
+ #elif defined(__ARM_NEON)
+ #include "sse2neon.h"
-#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
-+#elif defined(__SSE3__)
++#elif defined __SSE3__
#include <emmintrin.h>
#include <pmmintrin.h>
#endif
-@@ -122,7 +122,7 @@
+@@ -151,8 +151,8 @@ static inline int isinf_ld(long double x
#if (defined __AVX__ || defined __AVX2__)
#define BYTE_ALIGN 32
--#elif (defined(__SSE__) || defined(__SSE2__) || defined __SSE3__)
-+#elif defined __SSE3__
+-#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__) || \
+- defined(__ARM_NEON))
++#elif defined(__SSE3__) || \
++ defined(__ARM_NEON)
#define BYTE_ALIGN 16
#else
#define BYTE_ALIGN 1
-@@ -772,8 +772,10 @@
-
+@@ -873,10 +873,12 @@ typedef struct __Tree
#if (defined(__AVX__) || defined(__AVX2__))
- __m256d *_tPij1,*_tPij2,*_pmat1plk1,*_pmat2plk2,*_plk0,*_l_ev,*_r_ev,*_prod_left,*_prod_rght;
--#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
-+#elif defined(__SSE3__)
- __m128d *_tPij1,*_tPij2,*_pmat1plk1,*_pmat2plk2,*_plk0,*_l_ev,*_r_ev,*_prod_left,*_prod_rght;
+ __m256d *_tPij1, *_tPij2, *_pmat1plk1, *_pmat2plk2, *_plk0, *_l_ev, *_r_ev,
+ *_prod_left, *_prod_rght;
+-#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__) || \
+- defined(__ARM_NEON))
++#elif defined(__SSE3__) || \
++ defined(__ARM_NEON)
+ __m128d *_tPij1, *_tPij2, *_pmat1plk1, *_pmat2plk2, *_plk0, *_l_ev, *_r_ev,
+ *_prod_left, *_prod_rght;
+#else
+ long *_tPij1,*_tPij2,*_pmat1plk1,*_pmat2plk2,*_plk0,*_l_ev,*_r_ev,*_prod_left,*_prod_rght;
#endif
- phydbl *p_lk_left_pi,*l_ev;
-@@ -2559,7 +2561,7 @@
+ phydbl *p_lk_left_pi, *l_ev;
+@@ -2975,7 +2977,7 @@ int Number_Of_Free_Params(t_tree *mix
#if (defined(__AVX__) || defined(__AVX2__))
#include "avx.h"
--#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
-+#elif defined(__SSE3__)
+-#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__) || \
++#elif (defined(__SSE3__) || \
+ defined(__ARM_NEON))
#include "sse.h"
#endif
-
---- phyml.orig/src/free.c
-+++ phyml/src/free.c
-@@ -378,7 +378,7 @@
+--- a/src/free.c
++++ b/src/free.c
+@@ -410,7 +410,7 @@ void Free_Tree_Lk(t_tree *tree)
Free(tree->p_lk_left_pi);
Free(tree->l_ev);
@@ -129,113 +123,146 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Free(tree->_tPij1);
Free(tree->_tPij2);
Free(tree->_pmat1plk1);
---- phyml.orig/src/make.c
-+++ phyml/src/make.c
-@@ -29,7 +29,7 @@
- const unsigned int ns = tree->mod->ns;
- const unsigned int nsns = ns * ns;
+--- a/src/make.c
++++ b/src/make.c
+@@ -28,8 +28,8 @@ void Make_Tree_For_Lk(t_tree *tree)
+ const unsigned int ns = tree->mod->ns;
+ const unsigned int nsns = ns * ns;
--#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
-+#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE3__))
- const unsigned int sz = (int)BYTE_ALIGN / 8;
+-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || \
+- defined(__SSE2__) || defined(__SSE3__))
++#if (defined(__AVX__) || defined(__AVX2__) || \
++ defined(__SSE3__))
+ const unsigned int sz = (int)BYTE_ALIGN / 8;
const unsigned int ncatg = tree->mod->ras->n_catg;
#endif
-@@ -76,7 +76,7 @@
- tree->_prod_rght = _aligned_malloc(ns / sz * sizeof(__m256d),BYTE_ALIGN);
- tree->big_lk_array = _aligned_malloc(((3*tree->n_otu-2)*tree->data->crunch_len*MAX(tree->mod->ras->n_catg,tree->mod->n_mixt_classes)*tree->mod->ns + 2*(2*tree->n_otu-1)*tree->mod->ras->n_catg*tree->mod->ns*tree->mod->ns) * sizeof(phydbl),BYTE_ALIGN);
+@@ -134,7 +134,7 @@ void Make_Tree_For_Lk(t_tree *tree)
+ sizeof(phydbl),
+ BYTE_ALIGN);
#endif
-#elif (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
+#elif (defined(__SSE3__))
#ifndef WIN32
- if(posix_memalign((void **)&tree->dot_prod,BYTE_ALIGN,(size_t)tree->n_pattern*tree->mod->ns*MAX(tree->mod->ras->n_catg,tree->mod->n_mixt_classes)*sizeof(phydbl))) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
- if(posix_memalign((void **)&tree->expl,BYTE_ALIGN,(size_t)3*MAX(tree->mod->ras->n_catg,tree->mod->n_mixt_classes)*tree->mod->ns*sizeof(phydbl))) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
-@@ -108,7 +108,7 @@
- tree->_prod_rght = _aligned_malloc(ns / sz * sizeof(__m128d),BYTE_ALIGN);
- tree->big_lk_array = _aligned_malloc(((3*tree->n_otu-2)*tree->data->crunch_len*MAX(tree->mod->ras->n_catg,tree->mod->n_mixt_classes)*tree->mod->ns + 2*(2*tree->n_otu-1)*tree->mod->ras->n_catg*tree->mod->ns*tree->mod->ns) * sizeof(phydbl),BYTE_ALIGN);
+ if (posix_memalign(
+ (void **)&tree->dot_prod, BYTE_ALIGN,
+@@ -221,8 +221,8 @@ void Make_Tree_For_Lk(t_tree *tree)
+ sizeof(phydbl),
+ BYTE_ALIGN);
#endif
--#elif (!(defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__)))
-+#elif (!(defined(__AVX__) || defined(__AVX2__) || defined(__SSE3__)))
- tree->dot_prod = (phydbl *)mCalloc(tree->n_pattern*tree->mod->ns*MAX(tree->mod->ras->n_catg,tree->mod->n_mixt_classes),sizeof(phydbl));
- tree->expl = (phydbl *)mCalloc(3*MAX(tree->mod->ras->n_catg,tree->mod->n_mixt_classes)*tree->mod->ns,sizeof(phydbl));
- tree->p_lk_left_pi = (phydbl *)mCalloc(ns,sizeof(phydbl));
-@@ -381,7 +381,7 @@
- {
- b->p_lk_left = NULL;
-
--#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
-+#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE3__))
+-#elif (!(defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || \
+- defined(__SSE2__) || defined(__SSE3__)))
++#elif (!(defined(__AVX__) || defined(__AVX2__) || \
++ defined(__SSE3__)))
+ tree->dot_prod = (phydbl *)mCalloc(
+ tree->data->n_pattern * tree->mod->ns *
+ MAX(tree->mod->ras->n_catg, tree->mod->n_mixt_classes),
+@@ -579,8 +579,8 @@ void Make_Edge_Lk_Left(t_edge *b, t_tree
+ {
+ b->p_lk_left = NULL;
+
+-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || \
+- defined(__SSE2__) || defined(__SSE3__))
++#if (defined(__AVX__) || defined(__AVX2__) || \
++ defined(__SSE3__))
#ifndef WIN32
- if(posix_memalign((void **)&b->p_lk_tip_l,BYTE_ALIGN,(size_t)tree->data->crunch_len*tree->mod->ns*sizeof(phydbl))) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
- #else
-@@ -458,7 +458,7 @@
- }
- else if(b->rght->tax)
- {
--#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
-+#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE3__))
+ if (posix_memalign((void **)&b->p_lk_tip_l, BYTE_ALIGN,
+ (size_t)tree->data->n_pattern * tree->mod->ns *
+@@ -686,8 +686,8 @@ void Make_Edge_Lk_Rght(t_edge *b, t_tree
+ }
+ else if (b->rght->tax)
+ {
+-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || \
+- defined(__SSE2__) || defined(__SSE3__))
++#if (defined(__AVX__) || defined(__AVX2__) || \
++ defined(__SSE3__))
#ifndef WIN32
- if(posix_memalign((void **)&b->p_lk_tip_r,BYTE_ALIGN,(size_t)tree->data->crunch_len*tree->mod->ns*sizeof(phydbl))) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
- #else
-@@ -511,7 +511,7 @@
+ if (posix_memalign((void **)&b->p_lk_tip_r, BYTE_ALIGN,
+ (size_t)tree->data->n_pattern * tree->mod->ns *
+@@ -761,8 +761,8 @@ void Make_Extra_Edge_Lk(t_tree *tree)
+ MAX(tree->mod->ras->n_catg, tree->mod->n_mixt_classes),
+ sizeof(int));
- tree->sum_scale_extra_0 = (int *)mCalloc(tree->data->crunch_len*MAX(tree->mod->ras->n_catg,tree->mod->n_mixt_classes),sizeof(int));
-
--#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
-+#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE3__))
+-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || \
+- defined(__SSE2__) || defined(__SSE3__))
++#if (defined(__AVX__) || defined(__AVX2__) || \
++ defined(__SSE3__))
#ifndef WIN32
- if(posix_memalign((void **)&tree->p_lk_extra_0,BYTE_ALIGN,(size_t)tree->data->crunch_len*MAX(tree->mod->ras->n_catg,tree->mod->n_mixt_classes)*tree->mod->ns*sizeof(phydbl))) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
- #else
-@@ -522,7 +522,7 @@
+ if (posix_memalign(
+ (void **)&tree->p_lk_extra_0, BYTE_ALIGN,
+@@ -785,8 +785,8 @@ void Make_Extra_Edge_Lk(t_tree *tree)
+ sizeof(phydbl));
#endif
-
--#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
-+#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE3__))
+-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || \
+- defined(__SSE2__) || defined(__SSE3__))
++#if (defined(__AVX__) || defined(__AVX2__) || \
++ defined(__SSE3__))
#ifndef WIN32
- if(posix_memalign((void **)&tree->p_lk_tip_extra_0,BYTE_ALIGN,(size_t)tree->data->crunch_len*tree->mod->ns*sizeof(phydbl))) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
- #else
-@@ -540,7 +540,7 @@
-
- tree->sum_scale_extra_1 = (int *)mCalloc(tree->data->crunch_len*MAX(tree->mod->ras->n_catg,tree->mod->n_mixt_classes),sizeof(int));
+ if (posix_memalign((void **)&tree->p_lk_tip_extra_0, BYTE_ALIGN,
+ (size_t)tree->data->n_pattern * tree->mod->ns *
+@@ -813,8 +813,8 @@ void Make_Extra_Edge_Lk(t_tree *tree)
+ MAX(tree->mod->ras->n_catg, tree->mod->n_mixt_classes),
+ sizeof(int));
--#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
-+#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE3__))
+-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || \
+- defined(__SSE2__) || defined(__SSE3__))
++#if (defined(__AVX__) || defined(__AVX2__) || \
++ defined(__SSE3__))
#ifndef WIN32
- if(posix_memalign((void **)&tree->p_lk_extra_1,BYTE_ALIGN,(size_t)tree->data->crunch_len*MAX(tree->mod->ras->n_catg,tree->mod->n_mixt_classes)*tree->mod->ns*sizeof(phydbl))) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
- #else
-@@ -551,7 +551,7 @@
+ if (posix_memalign(
+ (void **)&tree->p_lk_extra_1, BYTE_ALIGN,
+@@ -837,8 +837,8 @@ void Make_Extra_Edge_Lk(t_tree *tree)
+ sizeof(phydbl));
#endif
-
--#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
-+#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE3__))
+-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || \
+- defined(__SSE2__) || defined(__SSE3__))
++#if (defined(__AVX__) || defined(__AVX2__) || \
++ defined(__SSE3__))
#ifndef WIN32
- if(posix_memalign((void **)&tree->p_lk_tip_extra_1,BYTE_ALIGN,(size_t)tree->data->crunch_len*tree->mod->ns*sizeof(phydbl))) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
- #else
-@@ -947,7 +947,7 @@
- mod->Pij_rr = (vect_dbl *)mCalloc(1,sizeof(vect_dbl));
- Init_Vect_Dbl(0,mod->Pij_rr);
+ if (posix_memalign((void **)&tree->p_lk_tip_extra_1, BYTE_ALIGN,
+ (size_t)tree->data->n_pattern * tree->mod->ns *
+@@ -1265,8 +1265,8 @@ void Make_Model_Complete(t_mod *mod)
+ mod->Pij_rr = (vect_dbl *)mCalloc(1, sizeof(vect_dbl));
+ Init_Vect_Dbl(0, mod->Pij_rr);
--#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
-+#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE3__))
+-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || \
+- defined(__SSE2__) || defined(__SSE3__))
++#if (defined(__AVX__) || defined(__AVX2__) || \
++ defined(__SSE3__))
#ifndef WIN32
- if(posix_memalign((void **)&mod->Pij_rr->v,BYTE_ALIGN,(size_t)mod->ras->n_catg*mod->ns*mod->ns*sizeof(phydbl))) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
- #else
-@@ -1061,7 +1061,7 @@
- e_frq->pi = (vect_dbl *)mCalloc(1,sizeof(vect_dbl));
- e_frq->pi->len = ns;
+ if (posix_memalign((void **)&mod->Pij_rr->v, BYTE_ALIGN,
+ (size_t)mod->ras->n_catg * mod->ns * mod->ns *
+@@ -1377,8 +1377,8 @@ t_efrq *Make_Efrq(int ns)
+ e_frq->pi = (vect_dbl *)mCalloc(1, sizeof(vect_dbl));
+ e_frq->pi->len = ns;
--#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
-+#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE3__))
+-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || \
+- defined(__SSE2__) || defined(__SSE3__))
++#if (defined(__AVX__) || defined(__AVX2__) || \
++ defined(__SSE3__))
#ifndef WIN32
- if(posix_memalign((void **)&e_frq->pi->v,BYTE_ALIGN,(size_t)ns*sizeof(phydbl))) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
- #else
-@@ -1184,7 +1184,7 @@
- eig->r_e_vect_im = (phydbl *)mCalloc(ns*ns,sizeof(phydbl));
- eig->q = (phydbl *)mCalloc(ns*ns,sizeof(phydbl));
+ if (posix_memalign((void **)&e_frq->pi->v, BYTE_ALIGN,
+ (size_t)ns * sizeof(phydbl)))
+@@ -1504,8 +1504,8 @@ eigen *Make_Eigen_Struct(int ns)
+ eig->r_e_vect_im = (phydbl *)mCalloc(ns * ns, sizeof(phydbl));
+ eig->q = (phydbl *)mCalloc(ns * ns, sizeof(phydbl));
--#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__))
-+#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE3__))
+-#if (defined(__AVX__) || defined(__AVX2__) || defined(__SSE__) || \
+- defined(__SSE2__) || defined(__SSE3__))
++#if (defined(__AVX__) || defined(__AVX2__) || \
++ defined(__SSE3__))
#ifndef WIN32
- if(posix_memalign((void **)&eig->r_e_vect,BYTE_ALIGN,ns*ns*sizeof(phydbl))) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
- if(posix_memalign((void **)&eig->l_e_vect,BYTE_ALIGN,ns*ns*sizeof(phydbl))) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
+ if (posix_memalign((void **)&eig->r_e_vect, BYTE_ALIGN,
+ ns * ns * sizeof(phydbl)))
+--- a/src/sse.c
++++ b/src/sse.c
+@@ -19,7 +19,7 @@ the GNU public licence. See http://www.o
+ //////////////////////////////////////////////////////////////
+ //////////////////////////////////////////////////////////////
+
+-#if (((defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__) || defined(__ARM_NEON)) && !((defined __AVX__ || defined __AVX2__))) && !defined(DISABLE_NATIVE))
++#if (((defined(__SSE3__) || defined(__ARM_NEON)) && !((defined __AVX__ || defined __AVX2__))) && !defined(DISABLE_NATIVE))
+
+ void SSE_Update_Eigen_Lr(t_edge *b, t_tree *tree)
+ {
=====================================
debian/patches/fix_declaration_of_temp.patch
=====================================
@@ -2,31 +2,38 @@ Author: Andreas Tille <tille at debian.org>
Last-Update: 2017-06-24
Description: Add missing declaration, fix name of BEAGLE constant
---- phyml.orig/src/utilities.c
-+++ phyml/src/utilities.c
-@@ -2203,6 +2203,9 @@
- }
+--- a/src/utilities.c
++++ b/src/utilities.c
+@@ -2466,6 +2466,9 @@ matrix *K80_dist(calign *data, phydbl g_
+ }
}
-
+ }
+#ifdef BEAGLE
+ int temp;
+#endif
-
- for(i=0;i<data->n_otu-1;i++)
- for(j=i+1;j<data->n_otu;j++)
-@@ -6705,6 +6708,9 @@
- int *buff_p_lk_loc, *buff_patt_id;
+
+ for (i = 0; i < data->n_otu - 1; i++)
+ for (j = i + 1; j < data->n_otu; j++)
+@@ -6514,6 +6517,9 @@ void Graft_Subtree(t_edge *target, t_nod
phydbl *buff_p_lk_tip;
- int *buff_ui;
+ int *buff_ui;
+ t_edge *b_up;
+#ifdef BEAGLE
+ int temp;
+#endif
-
- if(side_a == LEFT && side_b == LEFT)
- {
---- phyml.orig/src/beagle_utils.c
-+++ phyml/src/beagle_utils.c
-@@ -53,7 +53,7 @@
+
+ assert(link);
+ assert(tree);
+@@ -14841,4 +14847,4 @@ phydbl BIC(t_tree * tree)
+ tree->mod->bic->v =
+ Number_Of_Free_Params(tree) * log(tree->data->init_len) - 2. * Get_Lk(tree);
+ return (tree->mod->bic->v);
+-}
+\ No newline at end of file
++}
+--- 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");
=====================================
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.
---- phyml.orig/src/lk.c
-+++ phyml/src/lk.c
-@@ -2268,8 +2268,8 @@
+--- a/src/lk.c
++++ b/src/lk.c
+@@ -2338,8 +2338,8 @@ void Update_PMat_At_Given_Edge(t_edge *b
//
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
---- phyml.orig/configure.ac
-+++ phyml/configure.ac
+--- a/configure.ac
++++ b/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 "20220408" | tr -d '\n'"]),[guindon at lirmm.fr])
+-AC_INIT([PhyML],esyscmd([sh -c "echo "3.3." | tr -d '\n' ; echo "20250429" | tr -d '\n'"]),[stephane.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])
AC_CONFIG_SRCDIR([src/main.c],[doc/phyml-manual.tex])
=====================================
debian/patches/no-march-native.patch
=====================================
@@ -2,14 +2,27 @@ 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
---- phyml.orig/configure.ac
-+++ phyml/configure.ac
-@@ -57,7 +57,7 @@
+--- a/configure.ac
++++ b/configure.ac
+@@ -13,9 +13,9 @@ AC_CANONICAL_HOST
+
+ AC_PROG_CC([gcc clang mpicc])
+
+-AS_IF([test "$CC" = "gcc"],[DEFAULT_VECTOR_FLAG="-march=native"])
+-AS_IF([test "$CC" = "clang"],[DEFAULT_VECTOR_FLAG="-mcpu=native"])
+-AS_IF([test "$CC" = "mpicc"],[DEFAULT_VECTOR_FLAG="-march=native"])
++dnl AS_IF([test "$CC" = "gcc"],[DEFAULT_VECTOR_FLAG="-march=native"])
++dnl AS_IF([test "$CC" = "clang"],[DEFAULT_VECTOR_FLAG="-mcpu=native"])
++dnl AS_IF([test "$CC" = "mpicc"],[DEFAULT_VECTOR_FLAG="-march=native"])
+
+ AC_MSG_NOTICE(["$CC"])
+
+@@ -64,7 +64,7 @@ dnl DEFAULT_VECTOR_FLAG=""
dnl DEFAULT_VECTOR_FLAG="-mavx -mfma"
dnl DEFAULT_VECTOR_FLAG="-mavx2"
- dnl DEFAULT_VECTOR_FLAG=-msse4.2
+ dnl DEFAULT_VECTOR_FLAG=-msse3
-DEFAULT_VECTOR_FLAG="-march=native"
+dnl DEFAULT_VECTOR_FLAG="-march=native"
- dnl DEFAULT_VECTOR_FLAG="-march=skylake -mprefer-vector-width=256"
-
+ dnl DEFAULT_VECTOR_FLAG="-mtune=native"
+ dnl DEFAULT_VECTOR_FLAG="-mcpu=native"
=====================================
debian/patches/sse_only_if_supported.patch
=====================================
@@ -5,11 +5,11 @@ Forwarded: guindon at lirmm.fr
Description: Verify architecture whether we comiple on i386 or amd64 and
only in this case use -msse
---- phyml.orig/configure.ac
-+++ phyml/configure.ac
-@@ -13,6 +13,16 @@
+--- a/configure.ac
++++ b/configure.ac
+@@ -19,6 +19,16 @@ AS_IF([test "$CC" = "mpicc"],[DEFAULT_VE
- AC_PROG_CC([gcc])
+ AC_MSG_NOTICE(["$CC"])
+case "${host}" in
+*i386*|*amd64*|*x86_64*)
=====================================
debian/patches/typos.patch
=====================================
@@ -4,9 +4,9 @@ Forwarded: no
Last-Update: 2021-11-23
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- phyml.orig/doc/ref.bib
-+++ phyml/doc/ref.bib
-@@ -856,7 +856,7 @@
+--- a/doc/ref.bib
++++ b/doc/ref.bib
+@@ -856,7 +856,7 @@ Pages = {249,265}
Journal = {Journal of Molecular Evolution},
Note = {{I}nfluence du {V}oisinage sur l'{E}volution d'une {S{\'e}}quence d'{ADN}},
Pages = {278-288},
@@ -15,9 +15,9 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Utilisateur = {Guillaume Andrieu},
Volume = 21,
Year = 1985}
---- phyml.orig/src/ancestral.c
-+++ phyml/src/ancestral.c
-@@ -563,7 +563,7 @@
+--- a/src/ancestral.c
++++ b/src/ancestral.c
+@@ -563,7 +563,7 @@ void Ancestral_Sequences(t_tree *tree, i
PhyML_Fprintf(tree->io->fp_out_ancestral_seq,"\n");
PhyML_Fprintf(tree->io->fp_out_ancestral_seq,"\n");
PhyML_Fprintf(tree->io->fp_out_ancestral_seq,"\n. Ancestral reconstruction is conducted based on the \"Minimum Posterior Expected");
@@ -26,9 +26,9 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
PhyML_Fprintf(tree->io->fp_out_ancestral_seq,"\n. ancestral character states.");
PhyML_Fprintf(tree->io->fp_out_ancestral_seq,"\n");
PhyML_Fprintf(tree->io->fp_out_ancestral_seq,"\n");
---- phyml.orig/src/help.c
-+++ phyml/src/help.c
-@@ -316,7 +316,7 @@
+--- a/src/help.c
++++ b/src/help.c
+@@ -317,7 +317,7 @@ void Usage(void)
#ifndef PHYTIME
PhyML_Printf("%s\n\t--alias_subpatt%s\n",BOLD,FLAT);
PhyML_Printf("\t\t%sSite aliasing is generalized at the subtree level. Sometimes lead to faster calculations.\n",FLAT);
@@ -37,34 +37,34 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
PhyML_Printf("\n");
#endif
---- phyml.orig/src/io.c
-+++ phyml/src/io.c
-@@ -178,7 +178,7 @@
- if((*n_int + n_otu) == (2*n_otu-1))
- {
- PhyML_Fprintf(stderr,"\n. The number of internal nodes in the tree exceeds the number of taxa minus one.");
-- PhyML_Fprintf(stderr,"\n. There probably is a formating problem in the input tree.");
-+ PhyML_Fprintf(stderr,"\n. There probably is a formatting problem in the input tree.");
- Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
- }
-
-@@ -4610,7 +4610,7 @@
-
- if(model == NULL)
- {
-- PhyML_Fprintf(stderr,"\n. Poorly formated XML file.");
-+ PhyML_Fprintf(stderr,"\n. Poorly formatted XML file.");
- PhyML_Fprintf(stderr,"\n. Attribute 'model' is mandatory in a <ratematrix> node.");
- Exit("\n");
+--- a/src/io.c
++++ b/src/io.c
+@@ -192,7 +192,7 @@ void R_rtree(char *s_tree_a, char *s_tre
+ "exceeds the number of taxa minus one.");
+ PhyML_Fprintf(
+ stderr,
+- "\n. There probably is a formating problem in the input tree.");
++ "\n. There probably is a formatting problem in the input tree.");
+ Generic_Exit(__FILE__, __LINE__, __FUNCTION__);
}
---- phyml.orig/src/main.c
-+++ phyml/src/main.c
-@@ -346,7 +346,7 @@
-
- most_likely_tree = Bootstrap_From_String(most_likely_tree,cdata,mod,io);
-- PhyML_Printf("\n\n. Completed the bootstrap analysis succesfully."); fflush(NULL);
-+ PhyML_Printf("\n\n. Completed the bootstrap analysis successfully."); fflush(NULL);
- }
- else
- if(io->ratio_test != NO)
+@@ -5250,7 +5250,7 @@ void Make_Ratematrix_From_XML_Node(xml_n
+
+ if (model == NULL)
+ {
+- PhyML_Fprintf(stderr, "\n. Poorly formated XML file.");
++ PhyML_Fprintf(stderr, "\n. Poorly formatted XML file.");
+ PhyML_Fprintf(stderr,
+ "\n. Attribute 'model' is mandatory in a <ratematrix> node.");
+ Exit("\n");
+--- a/src/main.c
++++ b/src/main.c
+@@ -365,7 +365,7 @@ int main(int argc, char **argv)
+ most_likely_tree =
+ Bootstrap_From_String(most_likely_tree, cdata, mod, io);
+
+- PhyML_Printf("\n\n. Completed the bootstrap analysis succesfully.");
++ PhyML_Printf("\n\n. Completed the bootstrap analysis successfully.");
+ fflush(NULL);
+ }
+ else if (io->ratio_test != NO)
=====================================
debian/rules
=====================================
@@ -57,7 +57,7 @@ override_dh_auto_install:
override_dh_auto_clean:
# save pdf from cleaning
mv doc/phyml-manual.pdf .
- dh_auto_clean
+ dh_auto_clean || true
mv phyml-manual.pdf doc
# remove temporary bin dir for phyml (see above hack)
rm -rf debian/bin
View it on GitLab: https://salsa.debian.org/med-team/phyml/-/compare/f91228c858d63e3f7d6979c92f9dea61d0a8432e...893b7a76eeea04be798bde8d7f9865f4ea5a203f
--
View it on GitLab: https://salsa.debian.org/med-team/phyml/-/compare/f91228c858d63e3f7d6979c92f9dea61d0a8432e...893b7a76eeea04be798bde8d7f9865f4ea5a203f
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