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 <[email protected]> Mon, 10 Dec 2018 07:36:57 +0100 + -- Andreas Tille <[email protected]> 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 <[email protected]> +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 <[email protected]> --- 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 <[email protected]> # 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 You're receiving this email because of your account on salsa.debian.org.
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