Andreas Tille pushed to branch master at Debian Med / trnascan-se
Commits: 1ea1873a by Andreas Tille at 2018-08-04T13:18:42Z Don't try to start the arch dependant executable in arch all builds - - - - - 3828758d by Andreas Tille at 2018-08-04T13:19:27Z Point Vcs fields to salsa.debian.org - - - - - 84bf5cce by Andreas Tille at 2018-08-04T13:19:27Z Standards-Version: 4.1.5 - - - - - 63ec4da1 by Andreas Tille at 2018-08-04T13:36:23Z Clean up properly - - - - - eaae159a by Andreas Tille at 2018-08-05T00:00:55Z Fix paths in d/copyright - - - - - e33f8fc8 by Andreas Tille at 2018-08-05T00:02:12Z hardening=+all - - - - - cf542bfb by Andreas Tille at 2018-08-05T00:16:38Z Remove unused paragraph - - - - - c797f0a9 by Andreas Tille at 2018-08-05T00:22:49Z Check existence of files before calling chmod on them to fix arch indep builds - - - - - 7c76a100 by Andreas Tille at 2018-08-05T00:27:21Z Upload to unstable - - - - - 7 changed files: - debian/changelog - + debian/clean - debian/control - debian/copyright - + debian/patches/chmod_only_if_exists.patch - debian/patches/series - debian/rules Changes: ===================================== debian/changelog ===================================== --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,17 @@ +trnascan-se (2.0.0-2) unstable; urgency=medium + + * Team upload. + * Check existence of files before calling chmod on them to fix arch indep + builds + Closes: #904444 + * Point Vcs fields to salsa.debian.org + * Standards-Version: 4.1.5 + * Clean up properly + * Fix paths in d/copyright + * hardening=+all + + -- Andreas Tille <[email protected]> Sun, 05 Aug 2018 02:22:58 +0200 + trnascan-se (2.0.0-1) unstable; urgency=medium [ Steffen Moeller ] ===================================== debian/clean ===================================== --- /dev/null +++ b/debian/clean @@ -0,0 +1 @@ +tRNAscan-SE.conf ===================================== debian/control ===================================== --- a/debian/control +++ b/debian/control @@ -1,22 +1,22 @@ Source: trnascan-se -Section: non-free/science -Priority: optional Maintainer: Debian Med Packaging Team <[email protected]> Uploaders: Afif Elghraoui <[email protected]> +Section: non-free/science +XS-Autobuild: no +Priority: optional Build-Depends: debhelper (>= 11) -Standards-Version: 4.1.3 +Standards-Version: 4.1.5 +Vcs-Browser: https://salsa.debian.org/med-team/trnascan-se +Vcs-Git: https://salsa.debian.org/med-team/trnascan-se.git Homepage: http://lowelab.ucsc.edu/tRNAscan-SE -Vcs-Git: https://anonscm.debian.org/git/debian-med/trnascan-se.git -Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/trnascan-se.git Package: trnascan-se Architecture: any -Depends: - ${shlibs:Depends}, - ${misc:Depends}, - ${perl:Depends}, - trnascan-se-common (= ${source:Version}), - infernal (>= 1.0), +Depends: ${shlibs:Depends}, + ${misc:Depends}, + ${perl:Depends}, + trnascan-se-common (= ${source:Version}), + infernal Description: detection of transfer RNA genes in genomic sequence tRNAscan-SE identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Two previously described @@ -30,9 +30,8 @@ Description: detection of transfer RNA genes in genomic sequence Package: trnascan-se-common Architecture: all -Depends: - ${misc:Depends}, - ${perl:Depends} +Depends: ${misc:Depends}, + ${perl:Depends} Description: detection of transfer RNA genes in genomic sequence (common files) tRNAscan-SE identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Two previously described ===================================== debian/copyright ===================================== --- a/debian/copyright +++ b/debian/copyright @@ -11,23 +11,23 @@ Copyright: 2017 Brian Lin License: GPL-3.0+ -Files: dbmalloc.h +Files: src/dbmalloc.h Copyright: 1990-1992 Conor P. Cahill License: Cahill You may copy, distribute, and use this software as long as this copyright statement is not removed. -Files: gnuregex.* +Files: src/gnuregex.* Copyright: 1985, 1989-1993 Free Software Foundation, Inc. License: GPL-2.0+ -Files: sqio.c +Files: src/sqio.c Copyright: 1990 Don Gilbert <[email protected]> 1992-1996 Sean R. Eddy License: GPL-2.0+ -Files: trnascan.c +Files: src/trnascan.c Copyright: 1991 The Regents of the University of California License: UC This software was produced by the Los Alamos National Laboratory, @@ -41,10 +41,6 @@ License: UC express or implied, or assumes any liability or responsibility for the use of this software. -Files: Cove/* -Copyright: 1993-1994 Sean R. Eddy -License: GPL-2.0+ - Files: debian/* Copyright: 2015-2018 Afif Elghraoui <[email protected]> License: GPL-2.0+ ===================================== debian/patches/chmod_only_if_exists.patch ===================================== --- /dev/null +++ b/debian/patches/chmod_only_if_exists.patch @@ -0,0 +1,26 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Sat, 04 Aug 2018 15:15:12 +0200 +Bug-Debian: https://bugs.debian.org/904444 +Description: Check existence of files before calling chmod on them to fix arch indep builds + +--- a/Makefile.am ++++ b/Makefile.am +@@ -52,15 +52,15 @@ tRNAscan-SE.conf: tRNAscan-SE.conf.src M + + bin/sstofa: src/sstofa.in Makefile + $(do_subst) < $(srcdir)/src/sstofa.in > bin/sstofa +- chmod +x bin/sstofa ++ if [ -x bin/sstofa ] ; then chmod +x bin/sstofa ; fi + + bin/fasta2gsi: src/fasta2gsi.in Makefile + $(do_subst) < $(srcdir)/src/fasta2gsi.in > bin/fasta2gsi +- chmod +x bin/fasta2gsi ++ if [ -x bin/fasta2gsi ] ; then chmod +x bin/fasta2gsi ; fi + + bin/EukHighConfidenceFilter: EukHighConfidenceFilter.in Makefile + $(do_subst) < $(srcdir)/EukHighConfidenceFilter.in > bin/EukHighConfidenceFilter +- chmod +x bin/EukHighConfidenceFilter ++ if [ -x bin/EukHighConfidenceFilter ] ; then chmod +x bin/EukHighConfidenceFilter ; fi + + # copy data libraries + install-data-hook: ===================================== debian/patches/series ===================================== --- a/debian/patches/series +++ b/debian/patches/series @@ -1,2 +1,3 @@ pkg-data.patch confdir.patch +chmod_only_if_exists.patch ===================================== debian/rules ===================================== --- a/debian/rules +++ b/debian/rules @@ -1,5 +1,7 @@ #!/usr/bin/make -f +export DEB_BUILD_MAINT_OPTIONS=hardening=+all + %: dh $@ View it on GitLab: https://salsa.debian.org/med-team/trnascan-se/compare/fecf4b04327f309793013f3b5a8070c49995ccb8...7c76a10078b51e0f913f9e11dfcd8c97de25c4ab -- View it on GitLab: https://salsa.debian.org/med-team/trnascan-se/compare/fecf4b04327f309793013f3b5a8070c49995ccb8...7c76a10078b51e0f913f9e11dfcd8c97de25c4ab You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
