[med-svn] [Git][med-team/trnascan-se][master] 9 commits: Don't try to start the arch dependant executable in arch all builds
Andreas Tille
gitlab at salsa.debian.org
Sun Aug 5 01:28:15 BST 2018
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 <tille at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Afif Elghraoui <afif at debian.org>
+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 <gilbertd at bio.indiana.edu>
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 <afif at debian.org>
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 <tille at debian.org>
+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
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