[med-svn] [Git][med-team/phyml][master] 8 commits: filter-sse3-intrinsics.patch: fix build failure on arm64.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Feb 1 19:36:11 GMT 2026
Étienne Mollier pushed to branch master at Debian Med / phyml
Commits:
bb89400b by Étienne Mollier at 2026-02-01T16:20:46+01:00
filter-sse3-intrinsics.patch: fix build failure on arm64.
- - - - -
1da7e41f by Étienne Mollier at 2026-02-01T16:21:31+01:00
d/control: restore buildability on 32-bit.
The architecture-is-64bit is going to require coordination with all
reverse dependencies. For now let's restore 32-bit at these platforms
look in working conditions.
- - - - -
233d0778 by Étienne Mollier at 2026-02-01T16:23:11+01:00
d/control: move arm64 to mpich back-end.
The openmpi back-end currently raises prte errors on autopkgtest.
mpich is working fine for now. This is probably symptomatic of an
issue somewhere, but let's try first focus on getting phyml and
reverse dependencies to migrate to testing again.
- - - - -
7decf862 by Étienne Mollier at 2026-02-01T16:24:41+01:00
d/control: drop redundant Priority: optional.
- - - - -
622a6980 by Étienne Mollier at 2026-02-01T16:24:57+01:00
d/control: drop redundant Rules-Requires-Root: no.
- - - - -
a1476fe5 by Étienne Mollier at 2026-02-01T16:25:24+01:00
d/control: declare compliance to standards version 4.7.3.
- - - - -
59cbfa1b by Helmut Grohne at 2026-02-01T16:31:36+01:00
cross.patch: new: Use MPI_C to enable cross building.
This patch was initially proposed to resolve #1106652.
Signed-off-by: Étienne Mollier <emollier at debian.org>
- - - - -
b2303b7e by Étienne Mollier at 2026-02-01T20:35:32+01:00
d/changelog: ready for upload to unstable.
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/patches/cross.patch
- debian/patches/filter-sse3-intrinsics.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,9 +1,29 @@
-phyml (3:3.3.20250515-2) UNRELEASED; urgency=medium
+phyml (3:3.3.20250515-2) unstable; urgency=medium
+ [ Andreas Tille ]
* d/copyright: Remove old FSF address
* No build on i386 in Salsa CI
- -- Andreas Tille <tille at debian.org> Sat, 06 Dec 2025 23:13:15 +0100
+ [ Étienne Mollier ]
+ * filter-sse3-intrinsics.patch: fix build failure on arm64.
+ * d/control: restore buildability on 32-bit.
+ The architecture-is-64bit is going to require coordination with all
+ reverse dependencies. For now let's restore 32-bit at these platforms
+ look in working conditions.
+ * d/control: move arm64 to mpich back-end.
+ The openmpi back-end currently raises prte errors on autopkgtest.
+ mpich is working fine for now. This is probably symptomatic of an
+ issue somewhere, but let's try first focus on getting phyml and
+ reverse dependencies to migrate to testing again.
+ * d/control: drop redundant Priority: optional.
+ * d/control: drop redundant Rules-Requires-Root: no.
+ * d/control: declare compliance to standards version 4.7.3.
+
+ [ Helmut Grohne ]
+ * cross.patch: new: Use MPI_C to enable cross building.
+ This patch was initially proposed to resolve #1106652.
+
+ -- Étienne Mollier <emollier at debian.org> Sun, 01 Feb 2026 16:33:19 +0100
phyml (3:3.3.20250515-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -5,24 +5,23 @@ Uploaders: Charles Plessy <plessy at debian.org>,
Kevin Murray <spam at kdmurray.id.au>,
Étienne Mollier <emollier at debian.org>
Section: science
-Priority: optional
Build-Depends: debhelper-compat (= 13),
- architecture-is-64-bit,
pkgconf,
# libhmsbeagle-dev [any-amd64 any-i386 arm64 armhf],
- mpi-default-dev,
+ mpi-default-dev [!arm64],
+ libmpich-dev [arm64],
chrpath
-Standards-Version: 4.7.2
+Standards-Version: 4.7.3
Vcs-Browser: https://salsa.debian.org/med-team/phyml
Vcs-Git: https://salsa.debian.org/med-team/phyml.git
Homepage: http://www.atgc-montpellier.fr/phyml
-Rules-Requires-Root: no
Package: phyml
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
- mpi-default-bin
+ mpi-default-bin [!arm64],
+ mpich [arm64]
Description: Phylogenetic estimation using Maximum Likelihood
PhyML is a software that estimates maximum likelihood phylogenies from
alignments of nucleotide or amino acid sequences. It provides a wide
=====================================
debian/patches/cross.patch
=====================================
@@ -1,28 +1,30 @@
Author: Helmut Grohne <helmut at subdivi.de>
-Last-Update: 2018-06-26
+Last-Update: 2025-05-27
Bug-Debian: https://bugs.debian.org/902433
Description: Use MPI_C to enable cross building
--- phyml.orig/configure.ac
+++ phyml/configure.ac
-@@ -105,7 +105,7 @@
+@@ -115,7 +115,8 @@
AC_ARG_ENABLE([phyml-mpi],
[AS_HELP_STRING([--enable-phyml-mpi],
[Compile with mpicc instead of gcc.])])
-AS_IF([test "x$enable_phyml_mpi" = "xyes"],[CC="mpicc"])
-+AS_IF([test "x$enable_phyml_mpi" = "xyes"],[PKG_CHECK_MODULES([MPI_C],[mpi-c])])
++AS_IF([test "x$enable_phyml_mpi" = "xyes"],
++ [PKG_CHECK_MODULES([MPI_C],[mpi-c],,[CC="mpicc"])])
AS_IF([test "x$enable_phyml_mpi" = "xyes"],AC_DEFINE([MPI],[1],[MPI tag on]))
AM_CONDITIONAL([WANT_MPI], [test "$enable_phyml_mpi" = yes])
--- phyml.orig/src/Makefile.am
+++ phyml/src/Makefile.am
-@@ -187,7 +187,8 @@
- avx.c avx.h\
- ancestral.c ancestral.h\
+@@ -199,7 +199,9 @@
+ cv.c cv.h\
+ evolve.c evolve.h\
mpi_boot.c mpi_boot.h
--phyml_mpi_LDADD = -lm
+-# phyml_mpi_LDADD = -lm
+phyml_mpi_CFLAGS = $(MPI_C_CFLAGS)
-+phyml_mpi_LDADD = -lm $(MPI_C_LIBS)
++phyml_mpi_LDADD = $(MPI_C_LIBS)
++# phyml_mpi_LDADD = -lm $(MPI_C_LIBS)
else
if WANT_WIN
phyml_windows_SOURCES = main.c \
=====================================
debian/patches/filter-sse3-intrinsics.patch
=====================================
@@ -8,20 +8,20 @@ Forwarded: no
Last-Update: 2021-11-17
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- a/src/sse.h
-+++ b/src/sse.h
-@@ -25,7 +25,7 @@ the GNU public licence. See http://www.
+--- phyml.orig/src/sse.h
++++ phyml/src/sse.h
+@@ -25,7 +25,7 @@
#include "sse2neon.h"
#endif
-#if (defined(__SSE__) || defined(__SSE2__) || defined(__SSE3__) || defined(__ARM_NEON))
-+#if defined(__SSE3__)
++#if defined(__SSE3__) || defined(__ARM_NEON)
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);
---- a/src/lk.c
-+++ b/src/lk.c
-@@ -791,7 +791,7 @@ phydbl Lk_Core(int state, int ambiguity_
+--- phyml.orig/src/lk.c
++++ phyml/src/lk.c
+@@ -791,7 +791,7 @@
{
#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);
@@ -30,7 +30,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
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);
-@@ -882,7 +882,7 @@ phydbl Lk_Core_Eigen_Lr(phydbl *expl, ph
+@@ -882,7 +882,7 @@
{
#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);
@@ -39,7 +39,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
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);
-@@ -975,7 +975,7 @@ void Lk_dLk_Core_Eigen_Lr(phydbl *expl,
+@@ -975,7 +975,7 @@
AVX_Lk_dLk_Core_One_Class_Eigen_Lr(dot_prod,
expl ? expl : NULL,
ns,&core_lk,&core_dlk);
@@ -48,7 +48,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
SSE_Lk_dLk_Core_One_Class_Eigen_Lr(dot_prod,
expl ? expl : NULL,
ns,&core_lk,&core_dlk);
-@@ -1057,7 +1057,7 @@ void Update_Eigen_Lr(t_edge *b, t_tree *
+@@ -1057,7 +1057,7 @@
#if ((defined(__AVX__) || defined(__AVX2__)) && !defined(DISABLE_NATIVE))
AVX_Update_Eigen_Lr(b,tree);
return;
@@ -57,7 +57,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
SSE_Update_Eigen_Lr(b,tree);
return;
#endif
-@@ -1305,7 +1305,7 @@ void Update_Partial_Lk(t_tree *tree, t_e
+@@ -1305,7 +1305,7 @@
{
#if ((defined(__AVX__) || defined(__AVX2__)) && !defined(DISABLE_NATIVE))
AVX_Update_Partial_Lk(tree,b,d);
@@ -66,9 +66,9 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
SSE_Update_Partial_Lk(tree,b,d);
#else
Default_Update_Partial_Lk(tree,b,d);
---- a/src/utilities.h
-+++ b/src/utilities.h
-@@ -40,7 +40,7 @@ the GNU public licence. See http://www.o
+--- phyml.orig/src/utilities.h
++++ phyml/src/utilities.h
+@@ -40,7 +40,7 @@
#include <xmmintrin.h>
#elif defined(__ARM_NEON)
#include "sse2neon.h"
@@ -77,7 +77,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
#include <emmintrin.h>
#include <pmmintrin.h>
#endif
-@@ -151,8 +151,8 @@ static inline int isinf_ld(long double x
+@@ -151,8 +151,8 @@
#if (defined __AVX__ || defined __AVX2__)
#define BYTE_ALIGN 32
@@ -88,7 +88,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
#define BYTE_ALIGN 16
#else
#define BYTE_ALIGN 1
-@@ -873,10 +873,12 @@ typedef struct __Tree
+@@ -873,10 +873,12 @@
#if (defined(__AVX__) || defined(__AVX2__))
__m256d *_tPij1, *_tPij2, *_pmat1plk1, *_pmat2plk2, *_plk0, *_l_ev, *_r_ev,
*_prod_left, *_prod_rght;
@@ -103,7 +103,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
#endif
phydbl *p_lk_left_pi, *l_ev;
-@@ -2975,7 +2977,7 @@ int Number_Of_Free_Params(t_tree *mix
+@@ -2975,7 +2977,7 @@
#if (defined(__AVX__) || defined(__AVX2__))
#include "avx.h"
@@ -112,9 +112,9 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
defined(__ARM_NEON))
#include "sse.h"
#endif
---- a/src/free.c
-+++ b/src/free.c
-@@ -410,7 +410,7 @@ void Free_Tree_Lk(t_tree *tree)
+--- phyml.orig/src/free.c
++++ phyml/src/free.c
+@@ -410,7 +410,7 @@
Free(tree->p_lk_left_pi);
Free(tree->l_ev);
@@ -123,9 +123,9 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Free(tree->_tPij1);
Free(tree->_tPij2);
Free(tree->_pmat1plk1);
---- a/src/make.c
-+++ b/src/make.c
-@@ -28,8 +28,8 @@ void Make_Tree_For_Lk(t_tree *tree)
+--- phyml.orig/src/make.c
++++ phyml/src/make.c
+@@ -28,8 +28,8 @@
const unsigned int ns = tree->mod->ns;
const unsigned int nsns = ns * ns;
@@ -136,7 +136,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
const unsigned int sz = (int)BYTE_ALIGN / 8;
const unsigned int ncatg = tree->mod->ras->n_catg;
#endif
-@@ -134,7 +134,7 @@ void Make_Tree_For_Lk(t_tree *tree)
+@@ -134,7 +134,7 @@
sizeof(phydbl),
BYTE_ALIGN);
#endif
@@ -145,7 +145,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
#ifndef WIN32
if (posix_memalign(
(void **)&tree->dot_prod, BYTE_ALIGN,
-@@ -221,8 +221,8 @@ void Make_Tree_For_Lk(t_tree *tree)
+@@ -221,8 +221,8 @@
sizeof(phydbl),
BYTE_ALIGN);
#endif
@@ -156,7 +156,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
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
+@@ -579,8 +579,8 @@
{
b->p_lk_left = NULL;
@@ -167,7 +167,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
#ifndef WIN32
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
+@@ -686,8 +686,8 @@
}
else if (b->rght->tax)
{
@@ -178,7 +178,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
#ifndef WIN32
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)
+@@ -761,8 +761,8 @@
MAX(tree->mod->ras->n_catg, tree->mod->n_mixt_classes),
sizeof(int));
@@ -189,7 +189,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
#ifndef WIN32
if (posix_memalign(
(void **)&tree->p_lk_extra_0, BYTE_ALIGN,
-@@ -785,8 +785,8 @@ void Make_Extra_Edge_Lk(t_tree *tree)
+@@ -785,8 +785,8 @@
sizeof(phydbl));
#endif
@@ -200,7 +200,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
#ifndef WIN32
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)
+@@ -813,8 +813,8 @@
MAX(tree->mod->ras->n_catg, tree->mod->n_mixt_classes),
sizeof(int));
@@ -211,7 +211,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
#ifndef WIN32
if (posix_memalign(
(void **)&tree->p_lk_extra_1, BYTE_ALIGN,
-@@ -837,8 +837,8 @@ void Make_Extra_Edge_Lk(t_tree *tree)
+@@ -837,8 +837,8 @@
sizeof(phydbl));
#endif
@@ -222,7 +222,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
#ifndef WIN32
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)
+@@ -1265,8 +1265,8 @@
mod->Pij_rr = (vect_dbl *)mCalloc(1, sizeof(vect_dbl));
Init_Vect_Dbl(0, mod->Pij_rr);
@@ -233,7 +233,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
#ifndef WIN32
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)
+@@ -1377,8 +1377,8 @@
e_frq->pi = (vect_dbl *)mCalloc(1, sizeof(vect_dbl));
e_frq->pi->len = ns;
@@ -244,7 +244,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
#ifndef WIN32
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)
+@@ -1504,8 +1504,8 @@
eig->r_e_vect_im = (phydbl *)mCalloc(ns * ns, sizeof(phydbl));
eig->q = (phydbl *)mCalloc(ns * ns, sizeof(phydbl));
@@ -255,9 +255,9 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
#ifndef WIN32
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
+--- phyml.orig/src/sse.c
++++ phyml/src/sse.c
+@@ -19,7 +19,7 @@
//////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////
=====================================
debian/patches/series
=====================================
@@ -10,3 +10,4 @@ apply-cflags.patch
filter-sse3-intrinsics.patch
apply-ldflags.patch
typos.patch
+cross.patch
View it on GitLab: https://salsa.debian.org/med-team/phyml/-/compare/31554a02a5e7ccd2efc9502d9048cf6fbbbc1552...b2303b7e245e0ef635ebf21c8046ea702145b73d
--
View it on GitLab: https://salsa.debian.org/med-team/phyml/-/compare/31554a02a5e7ccd2efc9502d9048cf6fbbbc1552...b2303b7e245e0ef635ebf21c8046ea702145b73d
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/20260201/5046aa73/attachment-0001.htm>
More information about the debian-med-commit
mailing list