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 <[email protected]> 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'"]),[[email protected]]) +-AC_INIT([PhyML],esyscmd([sh -c "echo "3.3." | tr -d '\n' ; echo "20200621" | tr -d '\n'"]),[[email protected]]) +AC_INIT([PhyML],esyscmd([sh -c "echo "3.3." | tr -d '\n' ; dpkg-parsechangelog | egrep '^Version:' | cut -f 2 -d ' ' | tr -d '\n'"]),[[email protected]]) 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 <[email protected]> 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.
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