[med-svn] [Git][med-team/t-coffee][master] 6 commits: Add wrapper which sets HOME variable to $PWD in case HOME is not set

[Andreas Tille]

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


Commits:
89cca1bf by Andreas Tille at 2018-09-28T11:49:40Z
Add wrapper which sets HOME variable to $PWD in case HOME is not set

- - - - -
9ad21016 by Andreas Tille at 2018-09-28T11:54:13Z
Add NEWS.Debian to document the usage of a wrapper script

- - - - -
931e227b by Andreas Tille at 2018-09-28T12:09:14Z
Fix wrapper

- - - - -
fa629b58 by Andreas Tille at 2018-09-28T12:17:14Z
Test suite fails when t_coffee is started via wrapper.  Set PATH to find real t_coffee first.

- - - - -
52e126cc by Andreas Tille at 2018-09-28T12:23:31Z
Drop wrapper approach and instead make sure autopkgtest will set HOME variable to $PWD in case HOME is not set

- - - - -
d9cb7de5 by Andreas Tille at 2018-09-28T12:26:11Z
Upload to unstable

- - - - -


6 changed files:

- + debian/bin/NEWS.Debian
- + debian/bin/README
- + debian/bin/t_coffee
- debian/changelog
- debian/t-coffee.install
- debian/tests/run-unit-test


Changes:

=====================================
debian/bin/NEWS.Debian
=====================================
@@ -0,0 +1,11 @@
+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 at debian.org>  Fri, 28 Sep 2018 13:13:33 +0200
+


=====================================
debian/bin/README
=====================================
@@ -0,0 +1,5 @@
+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
=====================================
@@ -0,0 +1,14 @@
+#!/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
=====================================
@@ -1,9 +1,11 @@
-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 at debian.org>  Fri, 28 Sep 2018 13:13:33 +0200
+ -- Andreas Tille <tille at debian.org>  Fri, 28 Sep 2018 14:24:07 +0200
 
 t-coffee (11.00.8cbe486-7) unstable; urgency=medium
 


=====================================
debian/t-coffee.install
=====================================
@@ -1 +1 @@
-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    



View it on GitLab: https://salsa.debian.org/med-team/t-coffee/compare/9cffa995e4603e396054062c6f3dbff1568bf243...d9cb7de5089addc29c1c33538a68a2680a705e76

-- 
View it on GitLab: https://salsa.debian.org/med-team/t-coffee/compare/9cffa995e4603e396054062c6f3dbff1568bf243...d9cb7de5089addc29c1c33538a68a2680a705e76
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