[med-svn] [Git][med-team/mothur][master] 4 commits: Fix batch file for autopkgtest

[Mohd Bilal (@rmb)]

Mohd  Bilal pushed to branch master at Debian Med / mothur


Commits:
dd6fe90d by Mohammed Bilal at 2022-08-06T13:44:29+00:00
Fix batch file for autopkgtest

- - - - -
aa859c80 by Mohammed Bilal at 2022-08-06T13:47:24+00:00
Add patch to add hardening flags

- - - - -
9ac880d0 by Mohammed Bilal at 2022-08-06T13:49:17+00:00
Refresh patch

- - - - -
cdfaa0bc by Mohammed Bilal at 2022-08-06T14:27:09+00:00
Update changelog

- - - - -


5 changed files:

- debian/changelog
- + debian/patches/add-hardening-opts.patch
- debian/patches/c++14.patch
- debian/patches/series
- debian/tests/test.batch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+mothur (1.48.0-2) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Fix batch file for autopkgtest (Closes: #1014104)
+  * Add patch to add hardening flags
+  * Refresh patch
+
+ -- Mohammed Bilal <mdbilal at disroot.org>  Sat, 06 Aug 2022 14:24:47 +0000
+
 mothur (1.48.0-1) unstable; urgency=medium
 
   * New upstream version 1.48.0


=====================================
debian/patches/add-hardening-opts.patch
=====================================
@@ -0,0 +1,27 @@
+--- a/source/uchime_src/makefile
++++ b/source/uchime_src/makefile
+@@ -1,6 +1,7 @@
+ CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1
+ 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 @@
+     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 +27,4 @@
+ 
+ clean :
+ 	@rm -f $(OBJECTS)
+-	
+\ No newline at end of file
++	


=====================================
debian/patches/c++14.patch
=====================================
@@ -9,20 +9,11 @@ Origin: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=984243#33
  source/uchime_src/makefile | 4 ++--
  1 file changed, 2 insertions(+), 2 deletions(-)
 
-diff --git a/source/uchime_src/makefile b/source/uchime_src/makefile
-index 428babe..87623e7 100644
 --- a/source/uchime_src/makefile
 +++ b/source/uchime_src/makefile
 @@ -1,4 +1,4 @@
 -CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1
 +CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14
  LDFLAGS = -g
- 
- #
-@@ -26,4 +26,4 @@ install : uchime
- 
- clean :
- 	@rm -f $(OBJECTS)
--	
-\ No newline at end of file
-+	
+ CXXFLAGS += -g -fstack-protector-strong -Wformat -Werror=format-security
+ LDFLAGS += -Wl,-z,relro -Wl,-z,now


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
+add-hardening-opts.patch
 0002-Fix-include.patch
 drop_sys_sysctl.h.patch
 gcc-11.patch


=====================================
debian/tests/test.batch
=====================================
@@ -1,6 +1,6 @@
 unique.seqs(fasta=HA.fasta)
 dist.seqs(fasta=HA.unique.fasta, countends=F, cutoff=0.01)
-cluster(method=furthest, column=HA.unique.dist, name=HA.names, cutoff=0.01, precision=1000)
+cluster(method=furthest, column=HA.unique.dist, count=current, cutoff=0.01, precision=1000)
 summary.single(list=HA.unique.fn.list, calc=nseqs-sobs-chao, label=unique-0.001-0.003-0.005-0.008)
 heatmap.bin(scale=linear, label=unique-0.001-0.003)
 rarefaction.single(calc=sobs-chao, label=unique-0.001-0.003, freq=10)



View it on GitLab: https://salsa.debian.org/med-team/mothur/-/compare/6e10a450b5689fcc0fc6b8883495927cb7bc4f83...cdfaa0bc84c70593a01b9a94f56a600989617606

-- 
View it on GitLab: https://salsa.debian.org/med-team/mothur/-/compare/6e10a450b5689fcc0fc6b8883495927cb7bc4f83...cdfaa0bc84c70593a01b9a94f56a600989617606
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