[med-svn] [Git][med-team/t-coffee][master] 2 commits: Force -O0 to avoid crash in test suite

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / t-coffee


Commits:
9e2c3708 by Andreas Tille at 2022-10-12T12:08:26+02:00
Force -O0 to avoid crash in test suite

- - - - -
ac16df38 by Andreas Tille at 2022-10-12T12:13:48+02:00
Upload to unstable

- - - - -


5 changed files:

- debian/changelog
- debian/patches/hardening.patch
- debian/patches/stable-linking-inputs.patch
- debian/rules
- debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -6,14 +6,9 @@ t-coffee (13.45.0.4846264+dfsg-1) unstable; urgency=medium
   * Remove trailing whitespace in debian/changelog (routine-update)
   * Use secure URI in Homepage field.
   * lintian-overrides for html files
+  * Force -O0 to avoid crash in test suite
 
-  TODO: autopkgtest fails with
-  *************************************************************************************************
-  *                        FULL TRACE BACK PID: 305
-  305 -- ERROR: COREDUMP: T-COFFEE Version_13.45.0.4846264 (2020-09-21 17:25:40 - Revision 0818d8a - Build 619)
-  *************************************************************************************************
-
- -- Andreas Tille <tille at debian.org>  Mon, 18 Jul 2022 10:02:47 +0200
+ -- Andreas Tille <tille at debian.org>  Wed, 12 Oct 2022 12:12:17 +0200
 
 t-coffee (13.41.0.28bdc39+dfsg-4) unstable; urgency=medium
 


=====================================
debian/patches/hardening.patch
=====================================
@@ -7,7 +7,7 @@ Description: propagate hardening options
 @@ -1,14 +1,14 @@
  CC=g++
 -CFLAGS=-O3 -Wno-write-strings
-+CFLAGS+=-O3 -Wno-write-strings
++CFLAGS+=-Wno-write-strings
  SOURCES := $(shell find . -type f -name *.c)
  OBJECTS := $(SOURCES:.c=.o)
  DEPS := $(OBJECTS:.o=.deps)


=====================================
debian/patches/stable-linking-inputs.patch
=====================================
@@ -5,7 +5,7 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
 +++ b/t_coffee_source/makefile
 @@ -1,6 +1,6 @@
  CC=g++
- CFLAGS+=-O3 -Wno-write-strings
+ CFLAGS+=-Wno-write-strings
 -SOURCES := $(shell find . -type f -name *.c)
 +SOURCES := $(sort $(shell find . -type f -name *.c))
  OBJECTS := $(SOURCES:.c=.o)


=====================================
debian/rules
=====================================
@@ -7,6 +7,9 @@ sampledir:=$(CURDIR)/debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/examples
 FCC = gfortran $(shell dpkg-buildflags --get FFLAGS)
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
+# Force -O0 to avoid crash in test suite (see debian/tests/run-unit-test)
+export DEB_CFLAGS_MAINT_APPEND+=-O0
+
 %:
 	dh $@ --sourcedirectory=t_coffee_source
 


=====================================
debian/tests/run-unit-test
=====================================
@@ -1,4 +1,16 @@
 #!/bin/bash
+
+# Attention:
+# Hamid Nassiby found if build with -Ox for x>0 a crash
+# occurs and Valgrind can only lead to the same place in this scenario.
+# That is here:
+#  https://github.com/cbcrg/tcoffee/blob/master/lib/util_lib/util.c#L6151
+#  name_array[a][0]='\0';
+# If the program is compiled with -O(1-3), when we reach to this line,
+# the name_array[a][0] is not allocated (or it may has been freed earlier),
+# so the assignment leads to a crash!
+# That's why -O0 is forced in d/rules.
+
 set -e
 
 pkg='t-coffee'



View it on GitLab: https://salsa.debian.org/med-team/t-coffee/-/compare/b8378aec22d395a0bcc586cfa37a5c21115e2371...ac16df38ee38debe05bcae67129c157e41d7dbeb

-- 
View it on GitLab: https://salsa.debian.org/med-team/t-coffee/-/compare/b8378aec22d395a0bcc586cfa37a5c21115e2371...ac16df38ee38debe05bcae67129c157e41d7dbeb
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