[med-svn] [Git][med-team/examl][master] 6 commits: routine-update: New upstream version

Michael R. Crusoe gitlab at salsa.debian.org
Mon Jun 1 15:10:37 BST 2020 


Michael R. Crusoe pushed to branch master at Debian Med / examl


Commits:
21a71129 by Michael R. Crusoe at 2020-06-01T15:47:58+02:00
routine-update: New upstream version

- - - - -
60a10856 by Michael R. Crusoe at 2020-06-01T15:47:59+02:00
New upstream version 3.0.22
- - - - -
207a7fd0 by Michael R. Crusoe at 2020-06-01T15:48:01+02:00
Update upstream source from tag 'upstream/3.0.22'

Update to upstream version '3.0.22'
with Debian dir c792c49595fd2191b9c1712d26f5a731d844786b
- - - - -
998cc4d6 by Michael R. Crusoe at 2020-06-01T16:00:31+02:00
Refresh hardening patch, almost all of it was applied upstream.

- - - - -
93bb2fa0 by Michael R. Crusoe at 2020-06-01T16:08:03+02:00
fix SIMDe Built-Using

- - - - -
bd8acb65 by Michael R. Crusoe at 2020-06-01T16:10:06+02:00
release 3.0.22-1 to unstable

- - - - -


8 changed files:

- debian/changelog
- debian/patches/hardening.patch
- debian/rules
- examl/Makefile.AVX.gcc
- examl/Makefile.OMP.AVX.gcc
- examl/Makefile.OMP.SSE3.gcc
- examl/Makefile.SSE3.gcc
- versionHeader/version.h


Changes:

=====================================
debian/changelog
=====================================
@@ -1,10 +1,12 @@
-examl (3.0.21-5) UNRELEASED; urgency=medium
+examl (3.0.22-1) unstable; urgency=medium
 
   * Team upload.
+  * New upstream release.
   * For GPL compliance, document libsimde-dev usage and version number via
     Built-Using
+  * Refresh hardening patch, almost all of it was applied upstream.
 
- -- Michael R. Crusoe <michael.crusoe at gmail.com>  Sun, 19 Apr 2020 14:23:38 +0200
+ -- Michael R. Crusoe <crusoe at debian.org>  Mon, 01 Jun 2020 16:09:49 +0200
 
 examl (3.0.21-4) unstable; urgency=medium
 


=====================================
debian/patches/hardening.patch
=====================================
@@ -3,94 +3,6 @@ Last-Update: Tue, 14 Feb 2017 17:37:55 +0100
 Subject: Enable propagation of hardening options
 Forwarded: https://github.com/stamatak/ExaML/pull/15
 
---- examl.orig/examl/Makefile.AVX.gcc
-+++ examl/examl/Makefile.AVX.gcc
-@@ -8,7 +8,7 @@
- OPT_FLAG_1 = -O1
- OPT_FLAG_2 = -O2
- 
--CFLAGS = $(COMMON_FLAGS) $(OPT_FLAG_2)
-+CFLAGS += $(COMMON_FLAGS) $(OPT_FLAG_2)
- 
- LIBRARIES = -lm -mavx
- 
-@@ -21,13 +21,13 @@
- GLOBAL_DEPS = axml.h globalVariables.h ../versionHeader/version.h
- 
- examl-AVX : $(objs)
--	$(CC) -o examl-AVX $(objs) $(LIBRARIES) 
-+	$(CC) -o examl-AVX $(objs) $(LIBRARIES) $(LDFLAGS)
- 
- avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
--	$(CC) $(CFLAGS) -mavx -c -o avxLikelihood.o avxLikelihood.c
-+	$(CC) $(CFLAGS) $(CPPFLAGS) -mavx -c -o avxLikelihood.o avxLikelihood.c
- 
- models.o : models.c $(GLOBAL_DEPS)
--	 $(CC) $(COMMON_FLAGS) $(OPT_FLAG_1) -c -o models.o models.c
-+	$(CC) $(CFLAGS) $(COMMON_FLAGS) $(OPT_FLAG_1) $(CPPFLAGS) -c -o models.o models.c
- 
- bipartitionList.o : bipartitionList.c $(GLOBAL_DEPS)
- evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
---- examl.orig/examl/Makefile.OMP.AVX.gcc
-+++ examl/examl/Makefile.OMP.AVX.gcc
-@@ -8,7 +8,7 @@
- OPT_FLAG_1 = -O1
- OPT_FLAG_2 = -O2
- 
--CFLAGS = $(COMMON_FLAGS) $(OPT_FLAG_2)
-+CFLAGS += $(COMMON_FLAGS) $(OPT_FLAG_2)
- 
- LIBRARIES = -lm -mavx -fopenmp
- 
-@@ -21,7 +21,7 @@
- GLOBAL_DEPS = axml.h globalVariables.h ../versionHeader/version.h
- 
- examl-OMP-AVX : $(objs)
--	$(CC) -o examl-OMP-AVX $(objs) $(LIBRARIES) 
-+	$(CC) -o examl-OMP-AVX $(objs) $(LIBRARIES) $(LDFLAGS)
- 
- avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
- 	$(CC) $(CFLAGS) -mavx -c -o avxLikelihood.o avxLikelihood.c
---- examl.orig/examl/Makefile.OMP.SSE3.gcc
-+++ examl/examl/Makefile.OMP.SSE3.gcc
-@@ -8,7 +8,7 @@
- OPT_FLAG_1 = -O1 
- OPT_FLAG_2 = -O2
- 
--CFLAGS = $(COMMON_FLAGS) $(OPT_FLAG_2)
-+CFLAGS += $(COMMON_FLAGS) $(OPT_FLAG_2)
- 
- LIBRARIES = -lm -fopenmp
- 
-@@ -21,7 +21,7 @@
- GLOBAL_DEPS = axml.h globalVariables.h ../versionHeader/version.h
- 
- examl-OMP : $(objs)
--	$(CC) -o examl-OMP $(objs) $(LIBRARIES) 
-+	$(CC) -o examl-OMP $(objs) $(LIBRARIES) $(LDFLAGS)
- 
- models.o : models.c $(GLOBAL_DEPS)
- 	 $(CC) $(COMMON_FLAGS) $(OPT_FLAG_1) -c -o models.o models.c
---- examl.orig/examl/Makefile.SSE3.gcc
-+++ examl/examl/Makefile.SSE3.gcc
-@@ -9,7 +9,7 @@
- OPT_FLAG_1 = -O1 
- OPT_FLAG_2 = -O2
- 
--CFLAGS = $(COMMON_FLAGS) $(OPT_FLAG_2)
-+CFLAGS += $(COMMON_FLAGS) $(OPT_FLAG_2)
- 
- LIBRARIES = -lm
- 
-@@ -22,7 +22,7 @@
- GLOBAL_DEPS = axml.h globalVariables.h ../versionHeader/version.h
- 
- examl : $(objs)
--	$(CC) -o examl $(objs) $(LIBRARIES) 
-+	$(CC) -o examl $(objs) $(LIBRARIES) $(LDFLAGS)
- 
- models.o : models.c $(GLOBAL_DEPS)
- 	 $(CC) $(COMMON_FLAGS) $(OPT_FLAG_1) -c -o models.o models.c
 --- examl.orig/parser/Makefile.SSE3.gcc
 +++ examl/parser/Makefile.SSE3.gcc
 @@ -2,7 +2,7 @@


=====================================
debian/rules
=====================================
@@ -80,4 +80,4 @@ else
 endif
 
 override_dh_gencontrol:
-	dh_gencontrol -- -Vsimde:Built-Using=$(shell dpkg-query -f '$${source:Package} (= $${source:Version}), ' -W "libsimde-dev")
+	dh_gencontrol -- -Vsimde:Built-Using="$(shell dpkg-query -f '$${source:Package} (= $${source:Version}), ' -W "libsimde-dev")"


=====================================
examl/Makefile.AVX.gcc
=====================================
@@ -8,7 +8,7 @@ COMMON_FLAGS = -D__SIM_SSE3 -D__AVX -D_OPTIMIZED_FUNCTIONS -msse3 -D_GNU_SOURCE
 OPT_FLAG_1 = -O1
 OPT_FLAG_2 = -O2
 
-CFLAGS = $(COMMON_FLAGS) $(OPT_FLAG_2)
+CFLAGS += $(COMMON_FLAGS) $(OPT_FLAG_2)
 
 LIBRARIES = -lm -mavx
 
@@ -21,13 +21,13 @@ all : clean examl-AVX
 GLOBAL_DEPS = axml.h globalVariables.h ../versionHeader/version.h
 
 examl-AVX : $(objs)
-	$(CC) -o examl-AVX $(objs) $(LIBRARIES) 
+	$(CC) -o examl-AVX $(objs) $(LIBRARIES) $(LDFLAGS)
 
 avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
-	$(CC) $(CFLAGS) -mavx -c -o avxLikelihood.o avxLikelihood.c
+	$(CC) $(CFLAGS) $(CPPFLAGS) -mavx -c -o avxLikelihood.o avxLikelihood.c
 
 models.o : models.c $(GLOBAL_DEPS)
-	 $(CC) $(COMMON_FLAGS) $(OPT_FLAG_1) -c -o models.o models.c
+	$(CC) $(CFLAGS) $(COMMON_FLAGS) $(OPT_FLAG_1) $(CPPFLAGS) -c -o models.o models.c
 
 bipartitionList.o : bipartitionList.c $(GLOBAL_DEPS)
 evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)


=====================================
examl/Makefile.OMP.AVX.gcc
=====================================
@@ -8,7 +8,7 @@ COMMON_FLAGS = -D__SIM_SSE3 -D__AVX -D_USE_OMP -fopenmp -D_OPTIMIZED_FUNCTIONS -
 OPT_FLAG_1 = -O1
 OPT_FLAG_2 = -O2
 
-CFLAGS = $(COMMON_FLAGS) $(OPT_FLAG_2)
+CFLAGS += $(COMMON_FLAGS) $(OPT_FLAG_2)
 
 LIBRARIES = -lm -mavx -fopenmp
 
@@ -21,7 +21,7 @@ all : clean examl-OMP-AVX
 GLOBAL_DEPS = axml.h globalVariables.h ../versionHeader/version.h
 
 examl-OMP-AVX : $(objs)
-	$(CC) -o examl-OMP-AVX $(objs) $(LIBRARIES) 
+	$(CC) -o examl-OMP-AVX $(objs) $(LIBRARIES) $(LDFLAGS)
 
 avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
 	$(CC) $(CFLAGS) -mavx -c -o avxLikelihood.o avxLikelihood.c


=====================================
examl/Makefile.OMP.SSE3.gcc
=====================================
@@ -8,7 +8,7 @@ COMMON_FLAGS = -D_USE_OMP -fopenmp -D_GNU_SOURCE -D__SIM_SSE3  -msse3 -fomit-fra
 OPT_FLAG_1 = -O1 
 OPT_FLAG_2 = -O2
 
-CFLAGS = $(COMMON_FLAGS) $(OPT_FLAG_2)
+CFLAGS += $(COMMON_FLAGS) $(OPT_FLAG_2)
 
 LIBRARIES = -lm -fopenmp
 
@@ -21,7 +21,7 @@ all : clean examl-OMP
 GLOBAL_DEPS = axml.h globalVariables.h ../versionHeader/version.h
 
 examl-OMP : $(objs)
-	$(CC) -o examl-OMP $(objs) $(LIBRARIES) 
+	$(CC) -o examl-OMP $(objs) $(LIBRARIES) $(LDFLAGS)
 
 models.o : models.c $(GLOBAL_DEPS)
 	 $(CC) $(COMMON_FLAGS) $(OPT_FLAG_1) -c -o models.o models.c


=====================================
examl/Makefile.SSE3.gcc
=====================================
@@ -9,7 +9,7 @@ COMMON_FLAGS = -D_GNU_SOURCE -D__SIM_SSE3  -msse3 -fomit-frame-pointer -funroll-
 OPT_FLAG_1 = -O1 
 OPT_FLAG_2 = -O2
 
-CFLAGS = $(COMMON_FLAGS) $(OPT_FLAG_2)
+CFLAGS += $(COMMON_FLAGS) $(OPT_FLAG_2)
 
 LIBRARIES = -lm
 
@@ -22,7 +22,7 @@ all : clean examl
 GLOBAL_DEPS = axml.h globalVariables.h ../versionHeader/version.h
 
 examl : $(objs)
-	$(CC) -o examl $(objs) $(LIBRARIES) 
+	$(CC) -o examl $(objs) $(LIBRARIES) $(LDFLAGS)
 
 models.o : models.c $(GLOBAL_DEPS)
 	 $(CC) $(COMMON_FLAGS) $(OPT_FLAG_1) -c -o models.o models.c


=====================================
versionHeader/version.h
=====================================
@@ -1,4 +1,4 @@
 #define programName        "ExaML"
-#define programVersion     "3.0.21"
-#define programVersionInt  3021
-#define programDate        "May 29 2018"
+#define programVersion     "3.0.22"
+#define programVersionInt  3022
+#define programDate        "April 21 2020"



View it on GitLab: https://salsa.debian.org/med-team/examl/-/compare/051767c7890394416cb66604a7bff2d8b1b0e396...bd8acb65b1fb2c7bb8e2292e0ef00f0108718cf4

-- 
View it on GitLab: https://salsa.debian.org/med-team/examl/-/compare/051767c7890394416cb66604a7bff2d8b1b0e396...bd8acb65b1fb2c7bb8e2292e0ef00f0108718cf4
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