[med-svn] [Git][med-team/ampliconnoise][master] 3 commits: gcc-14.patch: new: fix functions implicitly typed.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Wed Aug 7 13:05:02 BST 2024
Étienne Mollier pushed to branch master at Debian Med / ampliconnoise
Commits:
f1fae7f6 by Étienne Mollier at 2024-08-07T13:45:18+02:00
gcc-14.patch: new: fix functions implicitly typed.
Closes: #1077153
- - - - -
df7af6aa by Étienne Mollier at 2024-08-07T14:03:10+02:00
hardening.patch: also propagate CPPFLAGS for fortify support.
- - - - -
7704138e by Étienne Mollier at 2024-08-07T14:04:03+02:00
Ready to upload to unstable.
- - - - -
4 changed files:
- debian/changelog
- + debian/patches/gcc-14.patch
- debian/patches/hardening.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+ampliconnoise (1.29-12) unstable; urgency=medium
+
+ * Team upload.
+ * gcc-14.patch: new: fix functions implicitly typed. (Closes: #1077153)
+ * hardening.patch: also propagate CPPFLAGS for fortify support.
+
+ -- Étienne Mollier <emollier at debian.org> Wed, 07 Aug 2024 14:03:47 +0200
+
ampliconnoise (1.29-11) unstable; urgency=medium
* Fix the sequence of function definitions to make sure
=====================================
debian/patches/gcc-14.patch
=====================================
@@ -0,0 +1,36 @@
+Description: declare void functions implicitly typed int.
+ This fixes the following error, now fatal, with gcc-14:
+ .
+ FCluster.c:223:1: error: return type defaults to ‘int’ [-Wimplicit-int]
+ 223 | UpdateMinCacheForRow(struct t_Min* asMin,int i,float** aafDistMatrix)
+ | ^~~~~~~~~~~~~~~~~~~~
+ FCluster.c:244:1: error: return type defaults to ‘int’ [-Wimplicit-int]
+ 244 | UpdateMinCacheForMarkedRows(struct t_Min* asMin,float** aafDistMatrix,int nN)
+ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Author: Étienne Mollier <emollier at emlwks999.eu>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1077153
+Forwarded: no
+Last-Update: 2024-08-07
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- ampliconnoise.orig/FCluster/FCluster.c
++++ ampliconnoise/FCluster/FCluster.c
+@@ -220,7 +220,7 @@
+ };
+
+ // Update the cached data for a row
+-UpdateMinCacheForRow(struct t_Min* asMin,int i,float** aafDistMatrix)
++void UpdateMinCacheForRow(struct t_Min* asMin,int i,float** aafDistMatrix)
+ {
+ // re-calculate the whole row as the old min has been overwritten
+ float fdist = aafDistMatrix[i][0];
+@@ -241,7 +241,7 @@
+ };
+
+ // Recalculate cached data for all rows
+-UpdateMinCacheForMarkedRows(struct t_Min* asMin,float** aafDistMatrix,int nN)
++void UpdateMinCacheForMarkedRows(struct t_Min* asMin,float** aafDistMatrix,int nN)
+ {
+ int i;
+ for (i = 1; i < nN; i++)
=====================================
debian/patches/hardening.patch
=====================================
@@ -1,10 +1,11 @@
Author: Andreas Tille <tille at debian.org>
-LastChanged: Tue, 30 Jul 2013 09:49:02 +0200
Description: Propagate hardening options
Forwarded: No (orphaned upstream)
+Last-Update: 2024-08-07
+Reviewed-By: Étienne Mollier <emollier at debian.org>
---- a/FCluster/makefile
-+++ b/FCluster/makefile
+--- ampliconnoise.orig/FCluster/makefile
++++ ampliconnoise/FCluster/makefile
@@ -1,6 +1,6 @@
CC = cc
-CFLAGS = -O3
@@ -14,19 +15,37 @@ Forwarded: No (orphaned upstream)
EFILE = FCluster
LIBS = -lm
OBJS = FCluster.o
---- a/FastaUnique/makefile
-+++ b/FastaUnique/makefile
+@@ -10,7 +10,7 @@
+ $(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS)
+
+ $(OBJS) : FCluster.c FCluster.h
+- $(CC) $(CFLAGS) -c $*.c
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c
+
+ clean:
+ rm -rf *o FCluster
+--- ampliconnoise.orig/FastaUnique/makefile
++++ ampliconnoise/FastaUnique/makefile
@@ -1,6 +1,6 @@
CC = cc
-CFLAGS = -O3
-EFLAGS =
-+CFLAGS += -O3
++CFLAGS += -O3
+EFLAGS = $(LDFLAGS)
EFILE = FastaUnique
LIBS = -lm
OBJS = FastaUnique.o
---- a/NDist/makefile
-+++ b/NDist/makefile
+@@ -10,7 +10,7 @@
+ $(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS)
+
+ $(OBJS) : FastaUnique.c FastaUnique.h
+- $(CC) $(CFLAGS) -c $*.c
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c
+
+ clean:
+ rm -rf *.o FastaUnique
+--- ampliconnoise.orig/NDist/makefile
++++ ampliconnoise/NDist/makefile
@@ -1,6 +1,6 @@
CC = mpicc
-CFLAGS = -O3
@@ -36,30 +55,57 @@ Forwarded: No (orphaned upstream)
EFILE = NDist
LIBS = -lm
OBJS = NDist.o
---- a/Perseus/makefile
-+++ b/Perseus/makefile
+@@ -10,7 +10,7 @@
+ $(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS)
+
+ $(OBJS) : NDist.h
+- $(CC) $(CFLAGS) -c $*.c
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c
+
+ clean:
+ rm -rf *.o NDist
+--- ampliconnoise.orig/Perseus/makefile
++++ ampliconnoise/Perseus/makefile
@@ -1,6 +1,6 @@
CC = cc
-CFLAGS = -O3
-EFLAGS =
-+CFLAGS += -O3
++CFLAGS += -O3
+EFLAGS = $(LDFLAGS)
EFILE = Perseus
LIBS = -lm -lgsl -lgslcblas
OBJS = Perseus.o
---- a/PerseusD/makefile
-+++ b/PerseusD/makefile
+@@ -10,7 +10,7 @@
+ $(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS)
+
+ $(OBJS) : Perseus.c Perseus.h
+- $(CC) $(CFLAGS) -c $*.c
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c
+
+ clean:
+ rm -rf *.o Perseus
+--- ampliconnoise.orig/PerseusD/makefile
++++ ampliconnoise/PerseusD/makefile
@@ -1,6 +1,6 @@
CC = cc
-CFLAGS = -O3
-EFLAGS =
-+CFLAGS += -O3
++CFLAGS += -O3
+EFLAGS = $(LDFLAGS)
EFILE = PerseusD
LIBS = -lm -lgsl -lgslcblas
OBJS = PerseusD.o
---- a/PyroDist/makefile
-+++ b/PyroDist/makefile
+@@ -10,7 +10,7 @@
+ $(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS)
+
+ $(OBJS) : PerseusD.c PerseusD.h
+- $(CC) $(CFLAGS) -c $*.c
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c
+
+ clean:
+ rm -rf *.o PerseusD
+--- ampliconnoise.orig/PyroDist/makefile
++++ ampliconnoise/PyroDist/makefile
@@ -1,6 +1,6 @@
CC = mpicc
-CFLAGS = -O3
@@ -69,8 +115,17 @@ Forwarded: No (orphaned upstream)
EFILE = PyroDist
LIBS = -lm
OBJS = PyroDist.o
---- a/PyroNoise/makefile
-+++ b/PyroNoise/makefile
+@@ -10,7 +10,7 @@
+ $(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS)
+
+ $(OBJS) : PyroDist.c PyroDist.h
+- $(CC) $(CFLAGS) -c $*.c
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c
+
+ clean:
+ rm -rf *.o PyroDist
+--- ampliconnoise.orig/PyroNoise/makefile
++++ ampliconnoise/PyroNoise/makefile
@@ -1,6 +1,6 @@
CC = mpicc
-CFLAGS = -O3
@@ -80,8 +135,17 @@ Forwarded: No (orphaned upstream)
EFILE = PyroNoise
LIBS = -lm
OBJS = PyroNoise.o
---- a/PyroNoiseM/makefile
-+++ b/PyroNoiseM/makefile
+@@ -10,7 +10,7 @@
+ $(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS)
+
+ $(OBJS) : PyroNoise.c PyroNoise.h
+- $(CC) $(CFLAGS) -c $*.c
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c
+
+ clean:
+ rm -rf *.o PyroNoise
+--- ampliconnoise.orig/PyroNoiseM/makefile
++++ ampliconnoise/PyroNoiseM/makefile
@@ -1,6 +1,6 @@
CC = mpicc
-CFLAGS = -O3
@@ -91,8 +155,17 @@ Forwarded: No (orphaned upstream)
EFILE = PyroNoiseM
LIBS = -lm
OBJS = PyroNoiseM.o
---- a/SeqDist/makefile
-+++ b/SeqDist/makefile
+@@ -10,7 +10,7 @@
+ $(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS)
+
+ $(OBJS) : PyroNoiseM.c PyroNoiseM.h
+- $(CC) $(CFLAGS) -c $*.c
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c
+
+ clean:
+ rm -rf *.o PyroNoiseM
+--- ampliconnoise.orig/SeqDist/makefile
++++ ampliconnoise/SeqDist/makefile
@@ -1,6 +1,6 @@
CC = mpicc
-CFLAGS = -O3
@@ -102,8 +175,17 @@ Forwarded: No (orphaned upstream)
EFILE = SeqDist
LIBS = -lm
OBJS = SeqDist.o
---- a/SeqNoise/makefile
-+++ b/SeqNoise/makefile
+@@ -10,7 +10,7 @@
+ $(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS)
+
+ $(OBJS) : SeqDist.c SeqDist.h
+- $(CC) $(CFLAGS) -c $*.c
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c
+
+ clean:
+ rm -rf *.o SeqDist
+--- ampliconnoise.orig/SeqNoise/makefile
++++ ampliconnoise/SeqNoise/makefile
@@ -1,6 +1,6 @@
CC = mpicc
-CFLAGS = -O3
@@ -113,8 +195,17 @@ Forwarded: No (orphaned upstream)
EFILE = SeqNoise
LIBS = -lm
OBJS = SeqNoise.o
---- a/SplitClusterClust/makefile
-+++ b/SplitClusterClust/makefile
+@@ -10,7 +10,7 @@
+ $(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS)
+
+ $(OBJS) : SeqNoise.c SeqNoise.h
+- $(CC) $(CFLAGS) -c $*.c
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c
+
+ clean:
+ rm -rf *.o SeqNoise
+--- ampliconnoise.orig/SplitClusterClust/makefile
++++ ampliconnoise/SplitClusterClust/makefile
@@ -1,6 +1,6 @@
CC = gcc
-CFLAGS = -O3
@@ -124,8 +215,17 @@ Forwarded: No (orphaned upstream)
EFILE = SplitClusterClust
LIBS = -lm
OBJS = SplitClusterClust.o
---- a/SplitClusterEven/makefile
-+++ b/SplitClusterEven/makefile
+@@ -10,7 +10,7 @@
+ $(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS)
+
+ $(OBJS) : SplitClusterClust.c SplitClusterClust.h
+- $(CC) $(CFLAGS) -c $*.c
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c
+
+ clean:
+ rm -rf *.o SplitClusterClust
+--- ampliconnoise.orig/SplitClusterEven/makefile
++++ ampliconnoise/SplitClusterEven/makefile
@@ -1,6 +1,6 @@
CC = cc
-CFLAGS = -O3
@@ -135,8 +235,17 @@ Forwarded: No (orphaned upstream)
EFILE = SplitClusterEven
LIBS = -lm
OBJS = SplitClusterEven.o
---- a/makefile
-+++ b/makefile
+@@ -10,7 +10,7 @@
+ $(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS)
+
+ $(OBJS) : SplitClusterEven.c SplitClusterEven.h
+- $(CC) $(CFLAGS) -c $*.c
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c
+
+ clean:
+ rm -rf *.o SplitClusterEven
+--- ampliconnoise.orig/makefile
++++ ampliconnoise/makefile
@@ -1,17 +1,17 @@
all:
- (cd FCluster && make)
@@ -162,15 +271,15 @@ Forwarded: No (orphaned upstream)
+ (cd PyroNoiseA && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
+ (cd SeqNoise && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
+ (cd SplitClusterEven && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
-+ (cd SplitClusterClust && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
-+ (cd Perseus && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
-+ (cd PerseusD && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
++ (cd SplitClusterClust && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
++ (cd Perseus && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
++ (cd PerseusD && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
clean:
(cd FCluster && make clean)
(cd FastaUnique && make clean)
---- a/PyroNoiseA/makefile
-+++ b/PyroNoiseA/makefile
-@@ -7,7 +7,7 @@ OBJS = PyroNoiseA.o
+--- ampliconnoise.orig/PyroNoiseA/makefile
++++ ampliconnoise/PyroNoiseA/makefile
+@@ -7,10 +7,10 @@
$(EFILE) : $(OBJS)
@echo "linking..."
@@ -178,4 +287,8 @@ Forwarded: No (orphaned upstream)
+ $(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS) $(LDFLAGS)
$(OBJS) : PyroNoiseA.c PyroNoiseA.h
- $(CC) $(CFLAGS) -c $*.c
+- $(CC) $(CFLAGS) -c $*.c
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c
+
+ clean:
+ rm -rf *.o PyroNoiseA
=====================================
debian/patches/series
=====================================
@@ -5,3 +5,4 @@ clang-ftbfs.patch
mayhem.patch
fix_sequence_of_function_definitions.patch
fix_missing_header.patch
+gcc-14.patch
View it on GitLab: https://salsa.debian.org/med-team/ampliconnoise/-/compare/42b9afe37fcabc749e9a6d07b9e42cbb611ee0b7...7704138ecb4c90b4641f90d82433863c21f9a026
--
View it on GitLab: https://salsa.debian.org/med-team/ampliconnoise/-/compare/42b9afe37fcabc749e9a6d07b9e42cbb611ee0b7...7704138ecb4c90b4641f90d82433863c21f9a026
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