[med-svn] [Git][med-team/allelecount][master] 2 commits: hardening.patch: include CPPFLAGS to hardening.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / allelecount


Commits:
04c681cb by Étienne Mollier at 2026-03-05T22:44:36+01:00
hardening.patch: include CPPFLAGS to hardening.

The change is reflected in stabilise-makefiles.patch refresh.

- - - - -
601ce077 by Étienne Mollier at 2026-03-05T22:46:00+01:00
d/changelog: initialise the changelog.

- - - - -


3 changed files:

- debian/changelog
- debian/patches/hardening.patch
- debian/patches/stabilise-makefiles.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+allelecount (4.3.0-5) UNRELEASED; urgency=medium
+
+  * hardening.patch: include CPPFLAGS to hardening.
+    The change is reflected in stabilise-makefiles.patch refresh.
+
+ -- Étienne Mollier <emollier at debian.org>  Thu, 05 Mar 2026 22:45:53 +0100
+
 allelecount (4.3.0-4) unstable; urgency=medium
 
   * stabilise-makefiles.patch: new: fix --shuffle. (Closes: #1105234)


=====================================
debian/patches/hardening.patch
=====================================
@@ -1,10 +1,11 @@
 Author: Andreas Tille <tille at debian.org>
-Last-Update: 2020-05-11
+Reviewed-By: Étienne Mollier <emollier at debian.org>
+Last-Update: 2026-03-05
 Description: Propagate hardening flags
 
---- a/c/Makefile
-+++ b/c/Makefile
-@@ -6,7 +6,7 @@ CC = gcc -O3 -DALLELECOUNTER_VERSION='"$
+--- allelecount.orig/c/Makefile
++++ allelecount/c/Makefile
+@@ -6,7 +6,7 @@
  #compiler flags
  # -g adds debug info to the executable file
  # -Wall turns on most warnings from compiler
@@ -13,12 +14,21 @@ Description: Propagate hardening flags
  
  #Location of samtools/htslib libraries
  HTSLOC?=$(HTSLIB)
-@@ -67,7 +67,7 @@ all: clean make_bin make_htslib_tmp $(CO
+@@ -67,7 +67,7 @@
  	@echo  Binaries have been compiled.
  
  $(COUNTER_TARGET): $(OBJS)
 -	$(CC) $(JOIN_INCLUDES) $(INCLUDES) $(CFLAGS) -o $(COUNTER_TARGET) $(OBJS) $(LFLAGS) $(CAT_LFLAGS) $(LIBS) ./src/alleleCounter.c
-+	$(CC) $(JOIN_INCLUDES) $(INCLUDES) $(CFLAGS) -o $(COUNTER_TARGET) $(OBJS) $(LFLAGS) $(CAT_LFLAGS) $(LIBS) ./src/alleleCounter.c $(LDFLAGS)
++	$(CC) $(CPPFLAGS) $(JOIN_INCLUDES) $(INCLUDES) $(CFLAGS) -o $(COUNTER_TARGET) $(OBJS) $(LFLAGS) $(CAT_LFLAGS) $(LIBS) ./src/alleleCounter.c $(LDFLAGS)
  
  #Unit Tests
  test: $(COUNTER_TARGET)
+@@ -100,7 +100,7 @@
+ # the rule(a .c file) and $@: the name of the target of the rule (a .o file)
+ # (see the gnu make manual section about automatic variables)
+ .c.o:
+-	$(CC) $(CFLAGS) $(JOIN_INCLUDES) $(INCLUDES) -c $<  -o $@
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(JOIN_INCLUDES) $(INCLUDES) -c $<  -o $@
+ 
+ clean:
+ 	$(RM) ./src/*.o *~ $(COUNTER_TARGET) ./bin/* ./tests/tests_log $(TESTS) ./src/*.gcda ./src/*.gcov ./src/*.gcno *.gcda *.gcov *.gcno ./tests/*.gcda ./tests/*.gcov ./tests/*.gcno


=====================================
debian/patches/stabilise-makefiles.patch
=====================================
@@ -23,7 +23,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
  
 -$(COUNTER_TARGET): $(OBJS)
 +$(COUNTER_TARGET): $(OBJS) bin 
- 	$(CC) $(JOIN_INCLUDES) $(INCLUDES) $(CFLAGS) -o $(COUNTER_TARGET) $(OBJS) $(LFLAGS) $(CAT_LFLAGS) $(LIBS) ./src/alleleCounter.c $(LDFLAGS)
+ 	$(CC) $(CPPFLAGS) $(JOIN_INCLUDES) $(INCLUDES) $(CFLAGS) -o $(COUNTER_TARGET) $(OBJS) $(LFLAGS) $(CAT_LFLAGS) $(LIBS) ./src/alleleCounter.c $(LDFLAGS)
  
  #Unit Tests
 @@ -79,7 +79,7 @@



View it on GitLab: https://salsa.debian.org/med-team/allelecount/-/compare/25b2e246e740e9a95feed77b99fed044be1fa316...601ce07782e9c2f2d7f2e6a41f67a32c65525646

-- 
View it on GitLab: https://salsa.debian.org/med-team/allelecount/-/compare/25b2e246e740e9a95feed77b99fed044be1fa316...601ce07782e9c2f2d7f2e6a41f67a32c65525646
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