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 <[email protected]> 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 $PWD in case HOME + is not set - -- Andreas Tille <[email protected]> Fri, 28 Sep 2018 13:13:33 +0200 + -- Andreas Tille <[email protected]> Fri, 28 Sep 2018 14:24:07 +0200 t-coffee (11.00.8cbe486-7) unstable; urgency=medium ===================================== debian/t-coffee.install ===================================== @@ -1 +1 @@ -t_coffee_source/t_coffee /usr/bin +t_coffee_source/t_coffee usr/bin ===================================== debian/tests/run-unit-test ===================================== @@ -12,6 +12,9 @@ cp -a /usr/share/doc/${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 You're receiving this email because of your account on salsa.debian.org.
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