debian/bin/NEWS.Debian

+t-coffee (11.00.8cbe486-8) unstable; urgency=medium
+
+  As documented in bug #716373 (https://bugs.debian.org/716373) and
+  #909530 (https://bugs.debian.org/909530) the t_coffee variable trows
+  Segmentation Fault when HOME environment variable is not set.  Since
+  some limited environments like autopkgtest chroot might not set HOME
+  t_coffee is now started via a wrapper shell script which will set
+  HOME to $PWD.
+
+ -- Andreas Tille <tille@debian.org>  Fri, 28 Sep 2018 13:13:33 +0200
+

debian/bin/README

+This wrapper approach was done to always guarantee a HOME dir.
+Unfortunately this approach did not worked well together with the
+test suite.
+Lets live with the "problem" that users really need to set a
+HOME dir and at least make sure that the test suite will set one.

debian/bin/t_coffee

+#!/bin/sh
+# t_coffee really needs $HOME variable set.
+# Since limited environments like autopkgtest chroots do not necessarily
+# set this variable this is set here to $PWD if it is not set.
+export HOME=${HOME:-$PWD}
+real_t_coffee_path=/usr/lib/t-coffee
+real_t_coffee=$real_t_coffee_path/t_coffee
+# set $PATH to find real t_coffee before this wrapper.  Otherwise test suite fails when started via wrapper
+export PATH="$real_t_coffee_path:$PATH"
+if [ -x $real_t_coffee ] ; then
+  t_coffee $@
+else
+  echo "Broken installation.  Wrapper $0 can not find $real_t_coffee ."
+fi

debian/changelog

-t-coffee (11.00.8cbe486-8) UNRELEASED; urgency=medium
+t-coffee (11.00.8cbe486-8) unstable; urgency=medium
 
   * Deal with "Segmentation fault" in exit of mayhem patch
     Closes: #909530
+  * Make sure autopkgtest will set HOME variable to $PWD in case HOME
+    is not set
 
- -- Andreas Tille <tille@debian.org>  Fri, 28 Sep 2018 13:13:33 +0200
+ -- Andreas Tille <tille@debian.org>  Fri, 28 Sep 2018 14:24:07 +0200
 
 t-coffee (11.00.8cbe486-7) unstable; urgency=medium
 

debian/t-coffee.install

-t_coffee_source/t_coffee	/usr/bin
+t_coffee_source/t_coffee	usr/bin

debian/tests/run-unit-test

@@ -12,6 +12,9 @@ cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
 cd $AUTOPKGTEST_TMP
 find . -name "*.gz" -exec gunzip \{\} \;
 
+# Make sure HOME is set in environment (see bug #909530)
+export HOME=${HOME:-$PWD}
+
 t_coffee sample_seq1.fasta    
 t_coffee sample_seq1.fasta -mode quickaln    
 t_coffee sample_seq1.fasta -mode quickaln -ndiag=10