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