[med-svn] [Git][med-team/gemma][master] 3 commits: Upload to unstable

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / gemma


Commits:
77993006 by Andreas Tille at 2021-07-31T07:19:24+02:00
Upload to unstable

- - - - -
2f656025 by Andreas Tille at 2021-07-31T07:26:55+02:00
Enable hardening

- - - - -
08e18566 by Andreas Tille at 2021-07-31T07:28:49+02:00
Rename autopkgtest script to use a unique name for all our packages

- - - - -


6 changed files:

- debian/changelog
- + debian/patches/hardening.patch
- debian/patches/series
- debian/rules
- debian/tests/control
- debian/tests/run-sample-analysis → debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,4 +1,12 @@
-gemma (0.98.4+dfsg-4) UNRELEASED; urgency=medium
+gemma (0.98.4+dfsg-5) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Enable hardening
+  * Rename autopkgtest script to use a unique name for all our packages
+
+ -- Andreas Tille <tille at debian.org>  Sat, 31 Jul 2021 07:26:49 +0200
+
+gemma (0.98.4+dfsg-4) unstable; urgency=medium
 
   * Team upload.
   * Apply patch from upstream who explained:
@@ -7,7 +15,7 @@ gemma (0.98.4+dfsg-4) UNRELEASED; urgency=medium
     results (mostly SIMD differences).
     Closes: #991652
 
- -- Andreas Tille <tille at debian.org>  Fri, 30 Jul 2021 21:52:30 +0200
+ -- Andreas Tille <tille at debian.org>  Fri, 30 Jul 2021 21:53:57 +0200
 
 gemma (0.98.4+dfsg-3) unstable; urgency=medium
 


=====================================
debian/patches/hardening.patch
=====================================
@@ -0,0 +1,23 @@
+Description: Propagate LDFLAGS to enable hardening
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 22 Mar 2021 14:38:26 +0100
+
+--- a/Makefile
++++ b/Makefile
+@@ -219,14 +219,14 @@ debug: $(OUTPUT)
+ 	$(shell bash $(VGEN) $(GUIX_PROFILE) > src/version.h)
+ 
+ $(OUTPUT): $(OBJS)
+-	$(CPP) $(CPPFLAGS) $(OBJS) $(LIBS) -o $(OUTPUT)
++	$(CPP) $(CPPFLAGS) $(OBJS) $(LIBS) -o $(OUTPUT) $(LDFLAGS)
+ 
+ $(OBJS): $(HDR)
+ 
+ .SUFFIXES : .cpp .c .o $(SUFFIXES)
+ 
+ ./bin/unittests-gemma: $(TEST_SRC_DIR)/unittests-main.o $(TEST_SRC_DIR)/unittests-math.o $(OBJS)
+-	$(CPP) $(CPPFLAGS) $(TEST_SRC_DIR)/unittests-main.o  $(TEST_SRC_DIR)/unittests-math.o $(filter-out src/main.o, $(OBJS)) $(LIBS) -o ./bin/unittests-gemma
++	$(CPP) $(CPPFLAGS) $(TEST_SRC_DIR)/unittests-main.o  $(TEST_SRC_DIR)/unittests-math.o $(filter-out src/main.o, $(OBJS)) $(LIBS) -o ./bin/unittests-gemma $(LDFLAGS)
+ 
+ unittests: all ./bin/unittests-gemma
+ 	./bin/unittests-gemma


=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ exclude_assertions_failing_under_some_circumstances.patch
 Reproducible_builds.patch
 no-lquadmath.patch
 Makefile.patch
+hardening.patch


=====================================
debian/rules
=====================================
@@ -1,7 +1,7 @@
 #!/usr/bin/make -f
 export DH_VERBOSE = 1
 
-#export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 export DEB_CFLAGS_MAINT_APPEND  = -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen
 export DEB_CXXFLAGS_MAINT_APPEND  = -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen


=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
-Tests: run-sample-analysis
+Tests: run-unit-test
 Depends: @
 Restrictions: allow-stderr


=====================================
debian/tests/run-sample-analysis → debian/tests/run-unit-test
=====================================
@@ -4,6 +4,7 @@ pkg=gemma
 
 if [ "$AUTOPKGTEST_TMP" = "" ] ; then
   AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+  trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
 fi
 
 cp -a /usr/share/doc/${pkg}/example/* $AUTOPKGTEST_TMP
@@ -18,7 +19,7 @@ gemma -g mouse_hs1940.geno.txt.gz -p mouse_hs1940.pheno.txt \
 
 hostarch=$(dpkg-architecture -qDEB_HOST_ARCH)
 
-# Ignore single test on armhf and i386 (see bug #972553)
+# Ignore single test on armhf (see bug #972553)
 if [ "$hostarch" = "armhf" ] ; then
   echo "Do only one test for $hostarch to reduce test time (see bug #985004)"
   exit 0



View it on GitLab: https://salsa.debian.org/med-team/gemma/-/compare/7daa7b267b1bc18516dc776461633e00c4487629...08e185663601aed00e23dd8de2de19110083e6f7

-- 
View it on GitLab: https://salsa.debian.org/med-team/gemma/-/compare/7daa7b267b1bc18516dc776461633e00c4487629...08e185663601aed00e23dd8de2de19110083e6f7
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