[med-svn] [Git][med-team/mothur][master] 2 commits: merge and simplify patches

[Tomasz Buchert (@tomasz)]

Tomasz Buchert pushed to branch master at Debian Med / mothur


Commits:
2832aeda by Tomasz Buchert at 2026-02-10T22:13:18+01:00
merge and simplify patches

- - - - -
f7394670 by Tomasz Buchert at 2026-02-10T22:20:02+01:00
pending release

- - - - -


4 changed files:

- debian/changelog
- − debian/patches/add-hardening-opts.patch
- debian/patches/c++14.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+mothur (1.48.5-2) UNRELEASED; urgency=medium
+
+  * Fix hardening flags for uchime (fixes blhc salsa pipeline)
+
+ -- Tomasz Buchert <tomasz at debian.org>  Tue, 10 Feb 2026 22:19:17 +0100
+
 mothur (1.48.5-1) unstable; urgency=medium
 
   * New upstream version 1.48.5


=====================================
debian/patches/add-hardening-opts.patch deleted
=====================================
@@ -1,36 +0,0 @@
-From: Debian Med Packaging Team
- <debian-med-packaging at lists.alioth.debian.org>
-Date: Sun, 2 Jun 2024 10:20:18 +0200
-Subject: add-hardening-opts
-
----
- source/uchime_src/makefile | 6 +++---
- 1 file changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/source/uchime_src/makefile b/source/uchime_src/makefile
-index 61f9913..0adfa72 100644
---- a/source/uchime_src/makefile
-+++ b/source/uchime_src/makefile
-@@ -1,6 +1,7 @@
- CXXFLAGS = -O3 -std=c++11 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++11
- LDFLAGS = -g
--
-+CXXFLAGS += -g -fstack-protector-strong -Wformat -Werror=format-security
-+LDFLAGS += -Wl,-z,relro -Wl,-z,now
- #
- # Get the list of all .cpp files, rename to .o files
- #
-@@ -10,7 +11,7 @@ LDFLAGS = -g
-     OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
- 
- uchime : $(OBJECTS)
--	$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
- 
- install : uchime
- 
-@@ -26,4 +27,3 @@ install : uchime
- 
- clean :
- 	@rm -f $(OBJECTS)
--


=====================================
debian/patches/c++14.patch
=====================================
@@ -1,21 +1,40 @@
-From: Andreas Tille <tille at debian.org>
-Date: Mon, 20 Jun 2022 13:56:45 +0200
-Subject: uchime code does not fit c++17 standard
+From: Debian Med Packaging Team
+ <debian-med-packaging at lists.alioth.debian.org>
+Date: Sun, 2 Jun 2024 10:20:18 +0200
+Subject: uchime code does not fit c++17 standard - use c++14
+
+also, make sure the CXXFLAGS are appended, see also
+https://docs-archive.freebsd.org/doc/10.3-RELEASE/usr/local/share/doc/freebsd/en/books/porters-handbook/dads-cflags.html
 
 Bug-Debian: https://bugs.debian.org/984243
 Last-Update: Thu, 21 Oct 2021 11:22:32 +0200
 Origin: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=984243#33
 ---
- source/uchime_src/makefile | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
+ source/uchime_src/makefile | 6 ++----
+ 1 file changed, 2 insertions(+), 4 deletions(-)
 
 diff --git a/source/uchime_src/makefile b/source/uchime_src/makefile
-index 0adfa72..69a4ca0 100644
+index 61f9913..cd1cdd9 100644
 --- a/source/uchime_src/makefile
 +++ b/source/uchime_src/makefile
-@@ -1,4 +1,4 @@
+@@ -1,5 +1,4 @@
 -CXXFLAGS = -O3 -std=c++11 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++11
-+CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14
- LDFLAGS = -g
- CXXFLAGS += -g -fstack-protector-strong -Wformat -Werror=format-security
- LDFLAGS += -Wl,-z,relro -Wl,-z,now
+-LDFLAGS = -g
++CXXFLAGS += -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14
+ 
+ #
+ # Get the list of all .cpp files, rename to .o files
+@@ -10,7 +9,7 @@ LDFLAGS = -g
+     OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
+ 
+ uchime : $(OBJECTS)
+-	$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
+ 
+ install : uchime
+ 
+@@ -26,4 +25,3 @@ install : uchime
+ 
+ clean :
+ 	@rm -f $(OBJECTS)
+-


=====================================
debian/patches/series
=====================================
@@ -1,6 +1,5 @@
-add-hardening-opts.patch
+c++14.patch
 0002-Fix-include.patch
 drop_sys_sysctl.h.patch
 gcc-11.patch
-c++14.patch
 fix_linking.patch



View it on GitLab: https://salsa.debian.org/med-team/mothur/-/compare/01f317c341579b6b29668b904ee6e225308b8f85...f739467080dfee0f9e3c359bb98f7e7242df0659

-- 
View it on GitLab: https://salsa.debian.org/med-team/mothur/-/compare/01f317c341579b6b29668b904ee6e225308b8f85...f739467080dfee0f9e3c359bb98f7e7242df0659
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