Andreas Tille pushed to branch master at Debian Med / gemma
Commits: 9ed0abe4 by Andreas Tille at 2021-04-07T16:47:57+02:00 Merge released changelog entry - - - - - 2d0ce86d by Andreas Tille at 2021-04-07T16:55:03+02:00 Merge branch 'debian/experimental' - - - - - 2c1c2836 by Andreas Tille at 2021-04-07T16:57:43+02:00 Restore changes from debian/experimental branch which somehow were not applied. - - - - - a33b99d4 by Andreas Tille at 2021-04-07T16:58:43+02:00 Remove useless comment - - - - - b0772442 by Andreas Tille at 2021-04-07T17:01:55+02:00 Provide autopkgtest as example in /usr/share/doc/gemma - - - - - 2b70cd94 by Andreas Tille at 2021-04-07T17:18:58+02:00 Example files are not shipped in binary package - rewerting last change - - - - - 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 ===================================== @@ -1,3 +1,10 @@ +gemma (0.98.4+dfsg-4) UNRELEASED; urgency=medium + + * Team upload. + * Enable hardening + + -- Andreas Tille <[email protected]> Wed, 07 Apr 2021 16:31:37 +0200 + gemma (0.98.4+dfsg-3) unstable; urgency=medium * Team upload. ===================================== 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/* $AUTOPKGTEST_TMP @@ -18,7 +19,6 @@ gemma -g mouse_hs1940.geno.txt.gz -p mouse_hs1940.pheno.txt \ hostarch=$(dpkg-architecture -qDEB_HOST_ARCH) -# Ignore single test on armhf and i386 (see bug #972553) 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/e665bff6d93fa88e71353d9bc8f41629758247d7...2b70cd9471612c66868457eebd590c8ca4b61b50 -- View it on GitLab: https://salsa.debian.org/med-team/gemma/-/compare/e665bff6d93fa88e71353d9bc8f41629758247d7...2b70cd9471612c66868457eebd590c8ca4b61b50 You're receiving this email because of your account on salsa.debian.org.
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