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+	tardir=$(distdir) && $(am__tar) | lzip -c $${LZIP_OPT--9} >$(distdir).tar.lz
+	$(am__post_remove_distdir)
+
+dist-xz: distdir
+	tardir=$(distdir) && $(am__tar) | XZ_OPT=$${XZ_OPT--e} xz -c >$(distdir).tar.xz
+	$(am__post_remove_distdir)
+
+dist-tarZ: distdir
+	@echo WARNING: "Support for distribution archives compressed with" \
+		       "legacy program 'compress' is deprecated." >&2
+	@echo WARNING: "It will be removed altogether in Automake 2.0" >&2
+	tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z
+	$(am__post_remove_distdir)
+
+dist-shar: distdir
+	@echo WARNING: "Support for shar distribution archives is" \
+	               "deprecated." >&2
+	@echo WARNING: "It will be removed altogether in Automake 2.0" >&2
+	shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
+	$(am__post_remove_distdir)
+
+dist-zip: distdir
+	-rm -f $(distdir).zip
+	zip -rq $(distdir).zip $(distdir)
+	$(am__post_remove_distdir)
+
+dist dist-all:
+	$(MAKE) $(AM_MAKEFLAGS) $(DIST_TARGETS) am__post_remove_distdir='@:'
+	$(am__post_remove_distdir)
+
+# This target untars the dist file and tries a VPATH configuration.  Then
+# it guarantees that the distribution is self-contained by making another
+# tarfile.
+distcheck: dist
+	case '$(DIST_ARCHIVES)' in \
+	*.tar.gz*) \
+	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\
+	*.tar.bz2*) \
+	  bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\
+	*.tar.lz*) \
+	  lzip -dc $(distdir).tar.lz | $(am__untar) ;;\
+	*.tar.xz*) \
+	  xz -dc $(distdir).tar.xz | $(am__untar) ;;\
+	*.tar.Z*) \
+	  uncompress -c $(distdir).tar.Z | $(am__untar) ;;\
+	*.shar.gz*) \
+	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\
+	*.zip*) \
+	  unzip $(distdir).zip ;;\
+	esac
+	chmod -R a-w $(distdir)
+	chmod u+w $(distdir)
+	mkdir $(distdir)/_build $(distdir)/_build/sub $(distdir)/_inst
+	chmod a-w $(distdir)
+	test -d $(distdir)/_build || exit 0; \
+	dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
+	  && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
+	  && am__cwd=`pwd` \
+	  && $(am__cd) $(distdir)/_build/sub \
+	  && ../../configure \
+	    $(AM_DISTCHECK_CONFIGURE_FLAGS) \
+	    $(DISTCHECK_CONFIGURE_FLAGS) \
+	    --srcdir=../.. --prefix="$$dc_install_base" \
+	  && $(MAKE) $(AM_MAKEFLAGS) \
+	  && $(MAKE) $(AM_MAKEFLAGS) dvi \
+	  && $(MAKE) $(AM_MAKEFLAGS) check \
+	  && $(MAKE) $(AM_MAKEFLAGS) install \
+	  && $(MAKE) $(AM_MAKEFLAGS) installcheck \
+	  && $(MAKE) $(AM_MAKEFLAGS) uninstall \
+	  && $(MAKE) $(AM_MAKEFLAGS) distuninstallcheck_dir="$$dc_install_base" \
+	        distuninstallcheck \
+	  && chmod -R a-w "$$dc_install_base" \
+	  && ({ \
+	       (cd ../.. && umask 077 && mkdir "$$dc_destdir") \
+	       && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" install \
+	       && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" uninstall \
+	       && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" \
+	            distuninstallcheck_dir="$$dc_destdir" distuninstallcheck; \
+	      } || { rm -rf "$$dc_destdir"; exit 1; }) \
+	  && rm -rf "$$dc_destdir" \
+	  && $(MAKE) $(AM_MAKEFLAGS) dist \
+	  && rm -rf $(DIST_ARCHIVES) \
+	  && $(MAKE) $(AM_MAKEFLAGS) distcleancheck \
+	  && cd "$$am__cwd" \
+	  || exit 1
+	$(am__post_remove_distdir)
+	@(echo "$(distdir) archives ready for distribution: "; \
+	  list='$(DIST_ARCHIVES)'; for i in $$list; do echo $$i; done) | \
+	  sed -e 1h -e 1s/./=/g -e 1p -e 1x -e '$$p' -e '$$x'
+distuninstallcheck:
+	@test -n '$(distuninstallcheck_dir)' || { \
+	  echo 'ERROR: trying to run $@ with an empty' \
+	       '$$(distuninstallcheck_dir)' >&2; \
+	  exit 1; \
+	}; \
+	$(am__cd) '$(distuninstallcheck_dir)' || { \
+	  echo 'ERROR: cannot chdir into $(distuninstallcheck_dir)' >&2; \
+	  exit 1; \
+	}; \
+	test `$(am__distuninstallcheck_listfiles) | wc -l` -eq 0 \
+	   || { echo "ERROR: files left after uninstall:" ; \
+	        if test -n "$(DESTDIR)"; then \
+	          echo "  (check DESTDIR support)"; \
+	        fi ; \
+	        $(distuninstallcheck_listfiles) ; \
+	        exit 1; } >&2
+distcleancheck: distclean
+	@if test '$(srcdir)' = . ; then \
+	  echo "ERROR: distcleancheck can only run from a VPATH build" ; \
+	  exit 1 ; \
+	fi
+	@test `$(distcleancheck_listfiles) | wc -l` -eq 0 \
+	  || { echo "ERROR: files left in build directory after distclean:" ; \
+	       $(distcleancheck_listfiles) ; \
+	       exit 1; } >&2
+check-am: all-am
+check: check-recursive
+all-am: Makefile config.h
+installdirs: installdirs-recursive
+installdirs-am:
+install: install-recursive
+install-exec: install-exec-recursive
+install-data: install-data-recursive
+uninstall: uninstall-recursive
+
+install-am: all-am
+	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-recursive
+install-strip:
+	if test -z '$(STRIP)'; then \
+	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	      install; \
+	else \
+	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	    "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'" install; \
+	fi
+mostlyclean-generic:
+
+clean-generic:
+
+distclean-generic:
+	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+
+maintainer-clean-generic:
+	@echo "This command is intended for maintainers to use"
+	@echo "it deletes files that may require special tools to rebuild."
+clean: clean-recursive
+
+clean-am: clean-generic mostlyclean-am
+
+distclean: distclean-recursive
+	-rm -f $(am__CONFIG_DISTCLEAN_FILES)
+	-rm -f Makefile
+distclean-am: clean-am distclean-generic distclean-hdr distclean-tags
+
+dvi: dvi-recursive
+
+dvi-am:
+
+html: html-recursive
+
+html-am:
+
+info: info-recursive
+
+info-am:
+
+install-data-am:
+
+install-dvi: install-dvi-recursive
+
+install-dvi-am:
+
+install-exec-am:
+
+install-html: install-html-recursive
+
+install-html-am:
+
+install-info: install-info-recursive
+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-recursive
+
+install-pdf-am:
+
+install-ps: install-ps-recursive
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-recursive
+	-rm -f $(am__CONFIG_DISTCLEAN_FILES)
+	-rm -rf $(top_srcdir)/autom4te.cache
+	-rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-recursive
+
+mostlyclean-am: mostlyclean-generic
+
+pdf: pdf-recursive
+
+pdf-am:
+
+ps: ps-recursive
+
+ps-am:
+
+uninstall-am:
+
+.MAKE: $(am__recursive_targets) all install-am install-strip
+
+.PHONY: $(am__recursive_targets) CTAGS GTAGS TAGS all all-am \
+	am--refresh check check-am clean clean-cscope clean-generic \
+	cscope cscopelist-am ctags ctags-am dist dist-all dist-bzip2 \
+	dist-gzip dist-lzip dist-shar dist-tarZ dist-xz dist-zip \
+	distcheck distclean distclean-generic distclean-hdr \
+	distclean-tags distcleancheck distdir distuninstallcheck dvi \
+	dvi-am html html-am info info-am install install-am \
+	install-data install-data-am install-dvi install-dvi-am \
+	install-exec install-exec-am install-html install-html-am \
+	install-info install-info-am install-man install-pdf \
+	install-pdf-am install-ps install-ps-am install-strip \
+	installcheck installcheck-am installdirs installdirs-am \
+	maintainer-clean maintainer-clean-generic mostlyclean \
+	mostlyclean-generic pdf pdf-am ps ps-am tags tags-am uninstall \
+	uninstall-am
+
+.PRECIOUS: Makefile
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:

compile

+#! /bin/sh
+# Wrapper for compilers which do not understand '-c -o'.
+
+scriptversion=2012-10-14.11; # UTC
+
+# Copyright (C) 1999-2014 Free Software Foundation, Inc.
+# Written by Tom Tromey <tromey@cygnus.com>.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+# This file is maintained in Automake, please report
+# bugs to <bug-automake@gnu.org> or send patches to
+# <automake-patches@gnu.org>.
+
+nl='
+'
+
+# We need space, tab and new line, in precisely that order.  Quoting is
+# there to prevent tools from complaining about whitespace usage.
+IFS=" ""	$nl"
+
+file_conv=
+
+# func_file_conv build_file lazy
+# Convert a $build file to $host form and store it in $file
+# Currently only supports Windows hosts. If the determined conversion
+# type is listed in (the comma separated) LAZY, no conversion will
+# take place.
+func_file_conv ()
+{
+  file=$1
+  case $file in
+    / | /[!/]*) # absolute file, and not a UNC file
+      if test -z "$file_conv"; then
+	# lazily determine how to convert abs files
+	case `uname -s` in
+	  MINGW*)
+	    file_conv=mingw
+	    ;;
+	  CYGWIN*)
+	    file_conv=cygwin
+	    ;;
+	  *)
+	    file_conv=wine
+	    ;;
+	esac
+      fi
+      case $file_conv/,$2, in
+	*,$file_conv,*)
+	  ;;
+	mingw/*)
+	  file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'`
+	  ;;
+	cygwin/*)
+	  file=`cygpath -m "$file" || echo "$file"`
+	  ;;
+	wine/*)
+	  file=`winepath -w "$file" || echo "$file"`
+	  ;;
+      esac
+      ;;
+  esac
+}
+
+# func_cl_dashL linkdir
+# Make cl look for libraries in LINKDIR
+func_cl_dashL ()
+{
+  func_file_conv "$1"
+  if test -z "$lib_path"; then
+    lib_path=$file
+  else
+    lib_path="$lib_path;$file"
+  fi
+  linker_opts="$linker_opts -LIBPATH:$file"
+}
+
+# func_cl_dashl library
+# Do a library search-path lookup for cl
+func_cl_dashl ()
+{
+  lib=$1
+  found=no
+  save_IFS=$IFS
+  IFS=';'
+  for dir in $lib_path $LIB
+  do
+    IFS=$save_IFS
+    if $shared && test -f "$dir/$lib.dll.lib"; then
+      found=yes
+      lib=$dir/$lib.dll.lib
+      break
+    fi
+    if test -f "$dir/$lib.lib"; then
+      found=yes
+      lib=$dir/$lib.lib
+      break
+    fi
+    if test -f "$dir/lib$lib.a"; then
+      found=yes
+      lib=$dir/lib$lib.a
+      break
+    fi
+  done
+  IFS=$save_IFS
+
+  if test "$found" != yes; then
+    lib=$lib.lib
+  fi
+}
+
+# func_cl_wrapper cl arg...
+# Adjust compile command to suit cl
+func_cl_wrapper ()
+{
+  # Assume a capable shell
+  lib_path=
+  shared=:
+  linker_opts=
+  for arg
+  do
+    if test -n "$eat"; then
+      eat=
+    else
+      case $1 in
+	-o)
+	  # configure might choose to run compile as 'compile cc -o foo foo.c'.
+	  eat=1
+	  case $2 in
+	    *.o | *.[oO][bB][jJ])
+	      func_file_conv "$2"
+	      set x "$@" -Fo"$file"
+	      shift
+	      ;;
+	    *)
+	      func_file_conv "$2"
+	      set x "$@" -Fe"$file"
+	      shift
+	      ;;
+	  esac
+	  ;;
+	-I)
+	  eat=1
+	  func_file_conv "$2" mingw
+	  set x "$@" -I"$file"
+	  shift
+	  ;;
+	-I*)
+	  func_file_conv "${1#-I}" mingw
+	  set x "$@" -I"$file"
+	  shift
+	  ;;
+	-l)
+	  eat=1
+	  func_cl_dashl "$2"
+	  set x "$@" "$lib"
+	  shift
+	  ;;
+	-l*)
+	  func_cl_dashl "${1#-l}"
+	  set x "$@" "$lib"
+	  shift
+	  ;;
+	-L)
+	  eat=1
+	  func_cl_dashL "$2"
+	  ;;
+	-L*)
+	  func_cl_dashL "${1#-L}"
+	  ;;
+	-static)
+	  shared=false
+	  ;;
+	-Wl,*)
+	  arg=${1#-Wl,}
+	  save_ifs="$IFS"; IFS=','
+	  for flag in $arg; do
+	    IFS="$save_ifs"
+	    linker_opts="$linker_opts $flag"
+	  done
+	  IFS="$save_ifs"
+	  ;;
+	-Xlinker)
+	  eat=1
+	  linker_opts="$linker_opts $2"
+	  ;;
+	-*)
+	  set x "$@" "$1"
+	  shift
+	  ;;
+	*.cc | *.CC | *.cxx | *.CXX | *.[cC]++)
+	  func_file_conv "$1"
+	  set x "$@" -Tp"$file"
+	  shift
+	  ;;
+	*.c | *.cpp | *.CPP | *.lib | *.LIB | *.Lib | *.OBJ | *.obj | *.[oO])
+	  func_file_conv "$1" mingw
+	  set x "$@" "$file"
+	  shift
+	  ;;
+	*)
+	  set x "$@" "$1"
+	  shift
+	  ;;
+      esac
+    fi
+    shift
+  done
+  if test -n "$linker_opts"; then
+    linker_opts="-link$linker_opts"
+  fi
+  exec "$@" $linker_opts
+  exit 1
+}
+
+eat=
+
+case $1 in
+  '')
+     echo "$0: No command.  Try '$0 --help' for more information." 1>&2
+     exit 1;
+     ;;
+  -h | --h*)
+    cat <<\EOF
+Usage: compile [--help] [--version] PROGRAM [ARGS]
+
+Wrapper for compilers which do not understand '-c -o'.
+Remove '-o dest.o' from ARGS, run PROGRAM with the remaining
+arguments, and rename the output as expected.
+
+If you are trying to build a whole package this is not the
+right script to run: please start by reading the file 'INSTALL'.
+
+Report bugs to <bug-automake@gnu.org>.
+EOF
+    exit $?
+    ;;
+  -v | --v*)
+    echo "compile $scriptversion"
+    exit $?
+    ;;
+  cl | *[/\\]cl | cl.exe | *[/\\]cl.exe )
+    func_cl_wrapper "$@"      # Doesn't return...
+    ;;
+esac
+
+ofile=
+cfile=
+
+for arg
+do
+  if test -n "$eat"; then
+    eat=
+  else
+    case $1 in
+      -o)
+	# configure might choose to run compile as 'compile cc -o foo foo.c'.
+	# So we strip '-o arg' only if arg is an object.
+	eat=1
+	case $2 in
+	  *.o | *.obj)
+	    ofile=$2
+	    ;;
+	  *)
+	    set x "$@" -o "$2"
+	    shift
+	    ;;
+	esac
+	;;
+      *.c)
+	cfile=$1
+	set x "$@" "$1"
+	shift
+	;;
+      *)
+	set x "$@" "$1"
+	shift
+	;;
+    esac
+  fi
+  shift
+done
+
+if test -z "$ofile" || test -z "$cfile"; then
+  # If no '-o' option was seen then we might have been invoked from a
+  # pattern rule where we don't need one.  That is ok -- this is a
+  # normal compilation that the losing compiler can handle.  If no
+  # '.c' file was seen then we are probably linking.  That is also
+  # ok.
+  exec "$@"
+fi
+
+# Name of file we expect compiler to create.
+cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'`
+
+# Create the lock directory.
+# Note: use '[/\\:.-]' here to ensure that we don't use the same name
+# that we are using for the .o file.  Also, base the name on the expected
+# object file name, since that is what matters with a parallel build.
+lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d
+while true; do
+  if mkdir "$lockdir" >/dev/null 2>&1; then
+    break
+  fi
+  sleep 1
+done
+# FIXME: race condition here if user kills between mkdir and trap.
+trap "rmdir '$lockdir'; exit 1" 1 2 15
+
+# Run the compile.
+"$@"
+ret=$?
+
+if test -f "$cofile"; then
+  test "$cofile" = "$ofile" || mv "$cofile" "$ofile"
+elif test -f "${cofile}bj"; then
+  test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile"
+fi
+
+rmdir "$lockdir"
+exit $ret
+
+# Local Variables:
+# mode: shell-script
+# sh-indentation: 2
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:

configure.ac

 #                                               -*- Autoconf -*-
 # Process this file with autoconf to produce a configure script.
 
-AC_INIT([PhyML],esyscmd([sh -c "echo "3.3." | tr -d '\n' ; echo "20180214" | tr -d '\n'"]),[guindon@lirmm.fr])
+AC_INIT([PhyML],esyscmd([sh -c "echo "3.3." | tr -d '\n' ; echo "20180621" | tr -d '\n'"]),[guindon@lirmm.fr])
 AM_INIT_AUTOMAKE([foreign])
 
 AC_CONFIG_SRCDIR([src/simu.c],[doc/phyml-manual.tex])
@@ -45,6 +45,8 @@ AC_FUNC_SETVBUF_REVERSED
 AC_FUNC_VPRINTF
 AC_CHECK_FUNCS([floor pow rint sqrt strchr strstr])
 
+dnl DEFAULT_VECTOR_FLAG=-mavx
+dnl DEFAULT_VECTOR_FLAG=-msse3
 DEFAULT_VECTOR_FLAG=-march=native
 AC_ARG_ENABLE([native],
               [AS_HELP_STRING([--disable-native],
@@ -145,7 +147,6 @@ if test "$phycont" = yes; then
    AC_DEFINE([PHYCONT],[1],[PHYCONT tag on])
 fi
 
-
 AC_ARG_ENABLE([rf],[AS_HELP_STRING([--enable-rf],[Compile RF])],[rf=yes],[rf=no])
 AM_CONDITIONAL([WANT_RF], [test "$rf" = yes])
 if test "$rf" = yes; then
@@ -211,6 +212,7 @@ if test "$part" = no; then
 if test "$rwrap" = no; then
 if test "$phycont" = no; then
 if test "$test" = no; then
+if test "$rf" = no; then
 if test "$invitee" = no; then
 if test "$geo" = no; then
 if test "$evolve" = no; then
@@ -230,6 +232,7 @@ fi
 fi
 fi
 fi
+fi
 
 AC_CONFIG_FILES([Makefile src/Makefile doc/Makefile])
 AC_OUTPUT

debian/changelog

+phyml (3:3.3.20180621-2) UNRELEASED; urgency=medium
+
+  * Install test script to user documentation
+
+ -- Andreas Tille <tille@debian.org>  Tue, 26 Jun 2018 18:18:52 +0200
+
+phyml (3:3.3.20180621-1) unstable; urgency=medium
+
+  * New upstream version
+  * d/copyright: Do not exclude non-included files any more
+  * Use MPI_C to enable cross building (thanks for the patch to Helmut Grohne)
+    Closes: #902433
+
+ -- Andreas Tille <tille@debian.org>  Tue, 26 Jun 2018 18:11:00 +0200
+
 phyml (3:3.3.20180214+dfsg-1) unstable; urgency=medium
 
   [ Steffen Moeller ]

debian/copyright

@@ -2,28 +2,6 @@ Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: PhyML
 Upstream-Contact: Stephane Guindon <guindon@stat.auckland.ac.nz>
 Source: https://github.com/stephaneguindon/phyml-downloads/releases
-Files-Excluded: bin/*
-                *~
-                *.aux
-                *.dvi
-                *.idx
-                *.ilg
-                *.ind
-                *.log
-                *.out
-                *.toc
-                aclocal.m4
-                Makefile.in
-                */Makefile
-                */Makefile.in
-                compile
-                config.guess
-                config.sub
-                configure
-                depcomp
-                install-sh
-                ltmain.sh
-                missing
 
 Files: *
 Copyright: Stephane Guindon <guindon@stat.auckland.ac.nz>

debian/docs

 doc/phyml-manual.pdf
+debian/tests/run-unit-test

debian/patches/cross.patch

+Author: Helmut Grohne <helmut@subdivi.de>
+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
+
+--- a/configure.ac
++++ b/configure.ac
+@@ -98,7 +98,7 @@ AS_IF([test "x$enable_gprof" = "xyes"],
+ AC_ARG_ENABLE([mpi],
+               [AS_HELP_STRING([--enable-mpi],
+                               [Compile with mpicc instead of gcc.])])
+-AS_IF([test "x$enable_mpi" = "xyes"],[CC="mpicc"])
++AS_IF([test "x$enable_mpi" = "xyes"],[PKG_CHECK_MODULES([MPI_C],[mpi-c])])
+ AS_IF([test "x$enable_mpi" = "xyes"],AC_DEFINE([MPI],[1],[MPI tag on]))
+ AM_CONDITIONAL([WANT_MPI], [test "$enable_mpi" = yes])
+ 
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -312,7 +312,8 @@ date.c date.h\
+ sse.c sse.h\
+ avx.c avx.h\
+ mpi_boot.c mpi_boot.h
+-phyml_mpi_LDADD = -lm
++phyml_mpi_CFLAGS = $(MPI_C_CFLAGS)
++phyml_mpi_LDADD = -lm $(MPI_C_LIBS)
+ else
+ if WANT_WIN
+ phyml_windows_SOURCES = main.c \

debian/patches/fix_declaration_of_temp.patch

@@ -4,7 +4,7 @@ Description: Add missing declaration, fix name of BEAGLE constant
 
 --- a/src/utilities.c
 +++ b/src/utilities.c
-@@ -2137,6 +2137,9 @@ matrix *K80_dist(calign *data, phydbl g_
+@@ -2138,6 +2138,9 @@ matrix *K80_dist(calign *data, phydbl g_
          }
      }
    
@@ -14,7 +14,7 @@ Description: Add missing declaration, fix name of BEAGLE constant
    
    for(i=0;i<data->n_otu-1;i++)
      for(j=i+1;j<data->n_otu;j++)
-@@ -6288,7 +6291,10 @@ void Swap_Partial_Lk(t_edge *a, t_edge *
+@@ -6385,7 +6388,10 @@ 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;

debian/patches/fix_wrong_initialisation_of_array.patch

@@ -13,7 +13,7 @@ Description: avoid initialisation an array with a scalar value
 
 --- a/src/lk.c
 +++ b/src/lk.c
-@@ -2297,8 +2297,8 @@ void Update_PMat_At_Given_Edge(t_edge *b
+@@ -2302,8 +2302,8 @@ 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

@@ -9,7 +9,7 @@ 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 "3.3." | tr -d '\n' ; echo "20180214" | tr -d '\n'"]),[guindon@lirmm.fr])
+-AC_INIT([PhyML],esyscmd([sh -c "echo "3.3." | tr -d '\n' ; echo "20180621" | tr -d '\n'"]),[guindon@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@lirmm.fr])
  AM_INIT_AUTOMAKE([foreign])
  

debian/patches/no-march-native.patch

@@ -4,10 +4,10 @@ Author: Graham Inggs <ginggs@debian.org>
 Last-Update: 2017-06-30
 --- a/configure.ac
 +++ b/configure.ac
-@@ -55,7 +55,7 @@ AC_FUNC_SETVBUF_REVERSED
- AC_FUNC_VPRINTF
- AC_CHECK_FUNCS([floor pow rint sqrt strchr strstr])
+@@ -57,7 +57,7 @@ AC_CHECK_FUNCS([floor pow rint sqrt strc
  
+ dnl DEFAULT_VECTOR_FLAG=-mavx
+ dnl DEFAULT_VECTOR_FLAG=-msse3
 -DEFAULT_VECTOR_FLAG=-march=native
 +DEFAULT_VECTOR_FLAG=""
  AC_ARG_ENABLE([native],

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 "$enabl
+@@ -114,7 +114,7 @@ AM_CONDITIONAL([WANT_WIN], [test "$enabl
  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"],

debian/patches/series

@@ -4,3 +4,4 @@ no-configure-ac-date.patch
 fix_declaration_of_temp.patch
 fix_wrong_initialisation_of_array.patch
 no-march-native.patch
+cross.patch

debian/watch

 version=4
 
-opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
 https://github.com/stephaneguindon/phyml/releases .*/archive/v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)