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 <[email protected]> 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 <[email protected]> Fri, 30 Jul 2021 21:52:30 +0200 + -- Andreas Tille <[email protected]> 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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