[med-svn] [Git][med-team/gemma][master] 6 commits: Merge released changelog entry

[Andreas Tille]

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 <tille at debian.org>  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 <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 +19,6 @@ 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
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