[med-svn] [Git][med-team/gff2aplot][master] 6 commits: Spelling

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / gff2aplot


Commits:
749d6264 by Andreas Tille at 2019-01-30T12:27:09Z
Spelling

- - - - -
4254ea8b by Andreas Tille at 2019-01-30T12:43:06Z
Less verbose logs to see what's happening

- - - - -
3b5eaa35 by Andreas Tille at 2019-01-30T12:59:45Z
Fix README used as shell script for testing

- - - - -
334268a3 by Andreas Tille at 2019-01-30T13:02:24Z
hardening=+all

- - - - -
4fa961ac by Andreas Tille at 2019-01-30T13:10:57Z
Silence test; Ignore issues we have no idea how to deal with.  That's enough for testing compared to no testing at all as done before.

- - - - -
06891fb9 by Andreas Tille at 2019-01-30T13:14:23Z
Upload to unstable

- - - - -


6 changed files:

- debian/changelog
- + debian/patches/fix_README_used_for_test.patch
- debian/patches/non_lexical_loop_iterator.patch
- debian/patches/series
- debian/rules
- debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-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 at debian.org>  Mon, 10 Dec 2018 07:36:57 +0100
+ -- Andreas Tille <tille at 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
=====================================
@@ -0,0 +1,17 @@
+Author: Andreas Tille <tille at 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
=====================================
@@ -1,4 +1,4 @@
-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 at 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 at 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



View it on GitLab: https://salsa.debian.org/med-team/gff2aplot/compare/fff5d5ab38c06272b476e9a4620f4460eacb0c7a...06891fb9ed8c8d86c2a2db0ca9738a8701cc9648

-- 
View it on GitLab: https://salsa.debian.org/med-team/gff2aplot/compare/fff5d5ab38c06272b476e9a4620f4460eacb0c7a...06891fb9ed8c8d86c2a2db0ca9738a8701cc9648
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