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 <[email protected]> Mon, 18 Jul 2022 10:02:47 +0200 + -- Andreas Tille <[email protected]> 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 <[email protected]> +++ 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 You're receiving this email because of your account on salsa.debian.org.
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