debian/changelog

-gff2aplot (2.0-11) UNRELEASED; urgency=medium
+gff2aplot (2.0-11) unstable; urgency=medium
 
   * README files in examples are actually scripts - fix PATH to gff2aplot
   * Add autopkgtest
@@ -7,8 +7,10 @@ gff2aplot (2.0-11) UNRELEASED; urgency=medium
   * Fix definition of CP in upstream makefile
   * Try hard to make sprint buffers have proper size
   * Recommends: graphicsmagick | imagemagick, ghostscript (+ Test-Depends)
+  * Fix README used as shell script for testing
+  * hardening=+all
 
- -- Andreas Tille <tille@debian.org>  Mon, 10 Dec 2018 07:36:57 +0100
+ -- Andreas Tille <tille@debian.org>  Wed, 30 Jan 2019 14:12:34 +0100
 
 gff2aplot (2.0-10) unstable; urgency=medium
 

debian/patches/fix_README_used_for_test.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 10 Dec 2018 07:36:57 +0100
+Description: The README file is used as shell script and one function
+ is broken.  It should return basenames of *.ps files.  This is fixed here
+
+--- a/examples/splice_sites/README
++++ b/examples/splice_sites/README
+@@ -140,8 +140,7 @@ $BIN/gff2aplot.pl -v -t "DONOR + ACCEPTO
+ # Preparing web images
+ #
+ filenames () {
+-  cat << 'EOF';
+-EOF
++       ls *.ps | sed 's/\.ps//'
+ };
+ #
+ # echo "# Using \"ghostscript\" to obtain JPEG images from PS files" ;

debian/patches/non_lexical_loop_iterator.patch

-Description: Make sure that iterator variable is explicitely decalred as
+Description: Make sure that iterator variable is explicitly decalred as
  a lexcical using my keyword. See PBP, page 108.  Add perl shebang.
 From: Alex Mestiashvili <amestia@rsh2.donotuse.de>
 --- gff2aplot.orig/src/gff2aplot.pl

debian/patches/series

@@ -7,3 +7,4 @@ fis-privacy-breach.patch
 perl_5.28.patch
 fix_install_ali2gff.patch
 enhance_sprintf_buffer.patch
+fix_README_used_for_test.patch

debian/rules

@@ -3,6 +3,8 @@
 # Andreas Tille <tille@debian.org>
 # GPL
 
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
 %:
 	dh $@
 

debian/tests/run-unit-test

@@ -19,9 +19,19 @@ ERR=0
 for script in `find . -name README` ; do
    cd $(dirname $script)
    # Suppress verbose output for testing
-   sed -i -e '/^[[:space:]]\+--verbose[[:space:]]\+\\$/d' -e 's/--verbose//' -e 's/MG *-verbose/MG -quiet/' -e 's?$BIN/\([a-z0-9]\+\).pl?\1?' -e 's?^$BIN/??' -e '1i set -x' -e '1i set -e' README
+   sed -i -e '/^[[:space:]]\+--verbose[[:space:]]\+\\$/d' \
+          -e 's/--verbose//' \
+          -e 's/gff2aplot \+-v/gff2aplot /' \
+          -e 's/MG *-verbose/MG -quiet/' \
+          -e 's?$BIN/\([a-z0-9]\+\).pl?\1?' \
+          -e 's?^$BIN/??' \
+          -e '1i set -e' \
+          README
    sh README | grep -v -e '^KCRB.GT.hs-mm.log' -e '^#'
-   if grep -q -v -e '^#' -e '^|' *.log ; then
+   if grep -q -v -e '^#' -e '^|' \
+                 -e '^Redundant argument in sprintf at /usr/bin/gff2aplot line 3676.' \
+                 -e "Can't open taf6.mmhs.genomic.tblastx: No such file or directory at /usr/bin/parseblast line 889." \
+                 *.log ; then
      ERR=1
      echo "Some errors were found in logfiles"
      grep -H -v -e '^#' -e '^|' *.log