[med-svn] r15844 - in trunk/packages: mrbayes/trunk/debian staden/trunk/debian staden/trunk/debian/icons staden/trunk/debian/patches
Andreas Tille
tille at moszumanska.debian.org
Mon Jan 20 17:51:24 UTC 2014
Author: tille
Date: 2014-01-20 17:51:24 +0000 (Mon, 20 Jan 2014)
New Revision: 15844
Added:
trunk/packages/staden/trunk/debian/patches/1001_fix_zlib_linkage.patch
trunk/packages/staden/trunk/debian/patches/delete_rpath_from_configure.patch
trunk/packages/staden/trunk/debian/patches/fix_awk.patch
trunk/packages/staden/trunk/debian/patches/fix_tcl_path.patch
Removed:
trunk/packages/mrbayes/trunk/debian/README.source
Modified:
trunk/packages/staden/trunk/debian/changelog
trunk/packages/staden/trunk/debian/control
trunk/packages/staden/trunk/debian/copyright
trunk/packages/staden/trunk/debian/icons/staden_gap4.desktop
trunk/packages/staden/trunk/debian/icons/staden_gap5.desktop
trunk/packages/staden/trunk/debian/icons/staden_pregap4.desktop
trunk/packages/staden/trunk/debian/icons/staden_trev.desktop
trunk/packages/staden/trunk/debian/patches/hardening_format-security.patch
trunk/packages/staden/trunk/debian/patches/make_help_menus_work
trunk/packages/staden/trunk/debian/patches/series
trunk/packages/staden/trunk/debian/rules
trunk/packages/staden/trunk/debian/watch
Log:
Mass commit changes for staden done when traveling home from MiniDebConf Paris
Deleted: trunk/packages/mrbayes/trunk/debian/README.source
===================================================================
--- trunk/packages/mrbayes/trunk/debian/README.source 2014-01-20 12:31:26 UTC (rev 15843)
+++ trunk/packages/mrbayes/trunk/debian/README.source 2014-01-20 17:51:24 UTC (rev 15844)
@@ -1,4 +0,0 @@
-This packages uses the quilt patch system. Please read
-/usr/share/doc/quilt/README.source for more information.
-
- -- Andreas Tille <tille at debian.org> Thu, 03 Feb 2011 16:39:19 +0100
Modified: trunk/packages/staden/trunk/debian/changelog
===================================================================
--- trunk/packages/staden/trunk/debian/changelog 2014-01-20 12:31:26 UTC (rev 15843)
+++ trunk/packages/staden/trunk/debian/changelog 2014-01-20 17:51:24 UTC (rev 15844)
@@ -1,12 +1,28 @@
staden (2.0.0b9-1) UNRELEASED; urgency=low
+ FIXME: TODO
+ it seems gap[45], pregap4, spin (not sure about trev) are the main
+ applications of staden what about hiding all those helper tools in
+ /usr/lib/staden/bin
+ and set the PATH appropriately inside the wrapper scripts gap[45],
+ pregap4 and spin?
+ This would make the package way more clean and would silence drastically
+ regarding missing manpages (which are hard to write anyway since even
+ help2man would not be able to do a reasonable job)
+
+ [ Tim Booth ]
* Initial release to Debian (Closes: #710324)
* Fix dependency for Debian after realising io-lib was already packaged
as libstaden-read
- -- Tim Booth <tbooth at ceh.ac.uk> Wed, 12 Jun 2013 17:47:51 +0100
+ [ Andreas Tille ]
+ * Port some changes from other attempt to package staden by
+ Jonas Smedegaard
+ * Fix several lintian issues
+ -- Andreas Tille <tille at debian.org> Mon, 20 Jan 2014 11:21:17 +0100
+
staden (2.0.0b9-0biolinux4) precise; urgency=low
* Add patches to show copyright form Help menu
Modified: trunk/packages/staden/trunk/debian/control
===================================================================
--- trunk/packages/staden/trunk/debian/control 2014-01-20 12:31:26 UTC (rev 15843)
+++ trunk/packages/staden/trunk/debian/control 2014-01-20 17:51:24 UTC (rev 15844)
@@ -18,7 +18,7 @@
libncurses5-dev,
iwidgets4,
libcurl4-openssl-dev
-Standards-Version: 3.9.4
+Standards-Version: 3.9.5
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/staden/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/staden/trunk/
Homepage: https://staden.sf.net
@@ -70,7 +70,8 @@
Package: staden-common
Architecture: all
-Depends: ${misc:Depends}
+Depends: ${misc:Depends},
+ tk8.6 | wish
Recommends: ksh | zsh
Description: Architecture independent files for Staden
Staden is a fully developed set of DNA sequence assembly (Gap4 and
Modified: trunk/packages/staden/trunk/debian/copyright
===================================================================
--- trunk/packages/staden/trunk/debian/copyright 2014-01-20 12:31:26 UTC (rev 15843)
+++ trunk/packages/staden/trunk/debian/copyright 2014-01-20 17:51:24 UTC (rev 15844)
@@ -4,7 +4,8 @@
Source: http://sourceforge.net/projects/staden/files/
Files: *
-Copyright: 2005-2013, James Bonfield
+Copyright: 1995-2001 Medical Research Council, Laboratory of Molecular Biology
+ 2005-2013, James Bonfield
2005-2013, Andrew Whitwham
Rodger Staden
Kathryn Beal
@@ -12,8 +13,77 @@
Yaping Cheng
Simon Dear
Matthew Betts
-License: Modified BSD
+License: BSD-like
+Files: primer3/*
+Copyright: 1996,1997,1998 Whitehead Institute for Biomedical Research. All rights reserved.
+ 2001 James Bonfield
+License: BSD-primer3
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ .
+ 1. Redistributions must reproduce the above copyright notice, this
+ list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution. Redistributions of
+ source code must also reproduce this information in the source code itself.
+ .
+ 2. If the program is modified, redistributions must include a notice
+ (in the same places as above) indicating that the redistributed program is
+ not identical to the version distributed by Whitehead Institute.
+ .
+ 3. All advertising materials mentioning features or use of this
+ software must display the following acknowledgment:
+ This product includes software developed by the
+ Whitehead Institute for Biomedical Research.
+ .
+ 4. The name of the Whitehead Institute may not be used to endorse or
+ promote products derived from this software without specific prior written
+ permission.
+ .
+ We also request that use of this software be cited in publications as
+ .
+ Steve Rozen, Helen J. Skaletsky (1996,1997,1998)
+ Primer3. Code available at
+ http://www-genome.wi.mit.edu/genome_software/other/primer3.html
+ .
+ THIS SOFTWARE IS PROVIDED BY THE WHITEHEAD INSTITUTE ``AS IS'' AND ANY
+ EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE WHITEHEAD INSTITUTE BE LIABLE FOR ANY
+ DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+Files: tk_utils/tclAppInit.c
+Copyright: 1993 The Regents of the University of California.
+ 1994-1997 Sun Microsystems, Inc.
+ 1998-1999 by Scriptics Corporation.
+License: FIXME: seek sources.debian.net for the file "license.terms"
+
+Files: tk_utils/tk_defs.h
+Copyright: 1991-1994 The Regents of the University of California.
+ 1994-1995 Sun Microsystems, Inc
+License: FIXME: seek sources.debian.net for the file "license.terms"
+ See the file "license.terms" for information on usage and redistribution
+ of this file, and for a DISCLAIMER OF ALL WARRANTIES.
+
+Files: tracediff/*
+Copyright: 2001 Medical Research Council
+License: FIXME: non-free_without_fee
+ Permission to use, copy, modify and distribute this software and its
+ documentation for any purpose is hereby granted without fee, provided that
+ this copyright and notice appears in all copies.
+ .
+ This file was written as part of the Staden Package at the MRC Laboratory
+ of Molecular Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ .
+ MRC disclaims all warranties with regard to this software.
+
Files: debian/*
-Copyright: 2013, Tim Booth <tbooth at ceh.ac.uk>
-License: Simplified BSD
+Copyright: 2013 Tim Booth <tbooth at ceh.ac.uk>
+ 2013-2014 Andreas Tille <tille at debian.org>
+License: BSD-like
Modified: trunk/packages/staden/trunk/debian/icons/staden_gap4.desktop
===================================================================
--- trunk/packages/staden/trunk/debian/icons/staden_gap4.desktop 2014-01-20 12:31:26 UTC (rev 15843)
+++ trunk/packages/staden/trunk/debian/icons/staden_gap4.desktop 2014-01-20 17:51:24 UTC (rev 15844)
@@ -2,11 +2,10 @@
Name=gap4
Comment=Staden gap4 assembly editor
Exec=gap4
-Encoding=UTF-8
Icon=/usr/share/staden/icon4bl.svg
Terminal=false
Type=Application
-Categories=Bioinformatics;
+Categories=Biology;Science
#Help out Unity:
#WM_CLASS(STRING) = "gap.tcl", "Gap.tcl"
StartupWMClass=gap.tcl
Modified: trunk/packages/staden/trunk/debian/icons/staden_gap5.desktop
===================================================================
--- trunk/packages/staden/trunk/debian/icons/staden_gap5.desktop 2014-01-20 12:31:26 UTC (rev 15843)
+++ trunk/packages/staden/trunk/debian/icons/staden_gap5.desktop 2014-01-20 17:51:24 UTC (rev 15844)
@@ -2,11 +2,10 @@
Name=gap5
Comment=Staden gap5 assembly editor
Exec=gap5
-Encoding=UTF-8
Icon=/usr/share/staden/icon4bl.svg
Terminal=false
Type=Application
-Categories=Bioinformatics;
+Categories=Biology;Science
#Help out Unity:
#WM_CLASS(STRING) = "Gap5", "Gap5.tcl"
StartupWMClass=Gap5
Modified: trunk/packages/staden/trunk/debian/icons/staden_pregap4.desktop
===================================================================
--- trunk/packages/staden/trunk/debian/icons/staden_pregap4.desktop 2014-01-20 12:31:26 UTC (rev 15843)
+++ trunk/packages/staden/trunk/debian/icons/staden_pregap4.desktop 2014-01-20 17:51:24 UTC (rev 15844)
@@ -2,11 +2,10 @@
Name=pregap4
Comment=Staden pregap4 DNA preprocessor
Exec=pregap4
-Encoding=UTF-8
Icon=/usr/share/staden/icon4bl.svg
Terminal=false
Type=Application
-Categories=Bioinformatics;
+Categories=Biology;Science
#Help out Unity:
#WM_CLASS(STRING) = "pregap4.tcl", "Pregap4.tcl"
StartupWMClass=pregap4.tcl
Modified: trunk/packages/staden/trunk/debian/icons/staden_trev.desktop
===================================================================
--- trunk/packages/staden/trunk/debian/icons/staden_trev.desktop 2014-01-20 12:31:26 UTC (rev 15843)
+++ trunk/packages/staden/trunk/debian/icons/staden_trev.desktop 2014-01-20 17:51:24 UTC (rev 15844)
@@ -2,11 +2,10 @@
Name=trev
Comment=Staden trev program
Exec=trev
-Encoding=UTF-8
Icon=/usr/share/staden/icon4bl.svg
Terminal=false
Type=Application
-Categories=Bioinformatics;
+Categories=Biology;Science
#Help out Unity
#WM_CLASS(STRING) = "trev.tcl", "Trev.tcl"
StartupWMClass=trev.tcl
Added: trunk/packages/staden/trunk/debian/patches/1001_fix_zlib_linkage.patch
===================================================================
--- trunk/packages/staden/trunk/debian/patches/1001_fix_zlib_linkage.patch (rev 0)
+++ trunk/packages/staden/trunk/debian/patches/1001_fix_zlib_linkage.patch 2014-01-20 17:51:24 UTC (rev 15844)
@@ -0,0 +1,15 @@
+Author: Jonas Smedegaard <dr at jones.dk>
+Last-Update: Wed, 29 May 2013 15:22:02 +0200
+Description: Fix usage of zlib
+
+--- a/gap5/zfio.h
++++ b/gap5/zfio.h
+@@ -9,7 +9,7 @@
+ */
+ typedef struct {
+ FILE *fp;
+- gzFile *gz;
++ gzFile gz;
+ } zfp;
+
+ off_t zftello(zfp *zf);
Added: trunk/packages/staden/trunk/debian/patches/delete_rpath_from_configure.patch
===================================================================
--- trunk/packages/staden/trunk/debian/patches/delete_rpath_from_configure.patch (rev 0)
+++ trunk/packages/staden/trunk/debian/patches/delete_rpath_from_configure.patch 2014-01-20 17:51:24 UTC (rev 15844)
@@ -0,0 +1,25 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 20 Jan 2014 11:21:17 +0100
+Description: UNUSED
+ The intention was to fix multi-arch build but this failed
+
+--- a/configure
++++ b/configure
+@@ -11477,15 +11477,8 @@ fi
+
+
+ # Step 0.d: Disable -rpath support?
+-
+- { echo "$as_me:$LINENO: checking if rpath support is requested" >&5
+-echo $ECHO_N "checking if rpath support is requested... $ECHO_C" >&6; }
+- # Check whether --enable-rpath was given.
+-if test "${enable_rpath+set}" = set; then
+- enableval=$enable_rpath; doRpath=$enableval
+-else
+- doRpath=yes
+-fi
++ # Force disabling rpath
++ doRpath=no
+
+ { echo "$as_me:$LINENO: result: $doRpath" >&5
+ echo "${ECHO_T}$doRpath" >&6; }
Added: trunk/packages/staden/trunk/debian/patches/fix_awk.patch
===================================================================
--- trunk/packages/staden/trunk/debian/patches/fix_awk.patch (rev 0)
+++ trunk/packages/staden/trunk/debian/patches/fix_awk.patch 2014-01-20 17:51:24 UTC (rev 15844)
@@ -0,0 +1,12 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 20 Jan 2014 11:21:17 +0100
+Description: Debian usually has /usr/bin/awk
+
+--- a/scripts/fasta-split
++++ b/scripts/fasta-split
+@@ -1,4 +1,4 @@
+-#!/usr/bin/nawk -f
++#!/usr/bin/awk -f
+ BEGIN {
+ file="";
+ }
Added: trunk/packages/staden/trunk/debian/patches/fix_tcl_path.patch
===================================================================
--- trunk/packages/staden/trunk/debian/patches/fix_tcl_path.patch (rev 0)
+++ trunk/packages/staden/trunk/debian/patches/fix_tcl_path.patch 2014-01-20 17:51:24 UTC (rev 15844)
@@ -0,0 +1,36 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 20 Jan 2014 11:21:17 +0100
+Description: Debian has /usr/bin/wish
+
+--- a/tk_utils/help_ext.tcl
++++ b/tk_utils/help_ext.tcl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/wish4.0
++#!/usr/bin/wish
+ #
+ # Copyright (c) 1995 Medical Research Council, Laboratory of Molecular Biology.
+ # All rights reserved.
+--- a/tk_utils/help_galeon.tcl
++++ b/tk_utils/help_galeon.tcl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/wish4.0
++#!/usr/bin/wish
+ #
+ # Copyright (c) 1995 Medical Research Council, Laboratory of Molecular Biology.
+ # All rights reserved.
+--- a/tk_utils/help_int.tcl
++++ b/tk_utils/help_int.tcl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/wish4.0
++#!/usr/bin/wish
+ #
+ # Copyright (c) 1995 Medical Research Council, Laboratory of Molecular Biology.
+ # All rights reserved.
+--- a/tk_utils/help_netscape.tcl
++++ b/tk_utils/help_netscape.tcl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/wish4.0
++#!/usr/bin/wish
+ #
+ # Copyright (c) 1995 Medical Research Council, Laboratory of Molecular Biology.
+ # All rights reserved.
Modified: trunk/packages/staden/trunk/debian/patches/hardening_format-security.patch
===================================================================
--- trunk/packages/staden/trunk/debian/patches/hardening_format-security.patch 2014-01-20 12:31:26 UTC (rev 15843)
+++ trunk/packages/staden/trunk/debian/patches/hardening_format-security.patch 2014-01-20 17:51:24 UTC (rev 15844)
@@ -59,3 +59,26 @@
}
static int db_version = DB_VERSION;
+--- a/gap5/gap-error.c
++++ b/gap5/gap-error.c
+@@ -89,7 +89,7 @@ void error_sig(int sig) {
+ }
+
+ static void xperror_out_func(char *name, char *str) {
+- verror(ERR_FATAL, name, str);
++ verror(ERR_FATAL, name, "%s", str);
+ }
+
+ /* NOT FATAL */
+--- a/gap5/tk-io-reg.c
++++ b/gap5/tk-io-reg.c
+@@ -1169,7 +1169,8 @@ int str2reg_data(Tcl_Interp *interp, Gap
+ break;
+
+ default:
+- verror(ERR_WARN, "str2reg_data: unsupported event type '%s'", type);
++ /* Debian fix might be not reasonable */
++ verror(ERR_WARN, "str2reg_data", "str2reg_data: unsupported event type '%s'", type);
+ return -1;
+ }
+
Modified: trunk/packages/staden/trunk/debian/patches/make_help_menus_work
===================================================================
--- trunk/packages/staden/trunk/debian/patches/make_help_menus_work 2014-01-20 12:31:26 UTC (rev 15843)
+++ trunk/packages/staden/trunk/debian/patches/make_help_menus_work 2014-01-20 17:51:24 UTC (rev 15844)
@@ -1,3 +1,7 @@
+Author: Tim Booth <tbooth at ceh.ac.uk>
+Last-Update: Wed, 12 Jun 2013 17:47:51 +0100
+Description: Fix help menus
+
--- a/gap5/gap5rc_menu_full
+++ b/gap5/gap5rc_menu_full
@@ -196,12 +196,12 @@
Modified: trunk/packages/staden/trunk/debian/patches/series
===================================================================
--- trunk/packages/staden/trunk/debian/patches/series 2014-01-20 12:31:26 UTC (rev 15843)
+++ trunk/packages/staden/trunk/debian/patches/series 2014-01-20 17:51:24 UTC (rev 15844)
@@ -1,3 +1,7 @@
+1001_fix_zlib_linkage.patch
remove_svnversion_dep
make_help_menus_work
hardening_format-security.patch
+fix_tcl_path.patch
+fix_awk.patch
+# delete_rpath_from_configure.patch
Modified: trunk/packages/staden/trunk/debian/rules
===================================================================
--- trunk/packages/staden/trunk/debian/rules 2014-01-20 12:31:26 UTC (rev 15843)
+++ trunk/packages/staden/trunk/debian/rules 2014-01-20 17:51:24 UTC (rev 15844)
@@ -1,19 +1,43 @@
#!/usr/bin/make -f
+
%:
dh $@
-override_dh_auto_build:
- env LD_LIBRARY_PATH="`pwd`/lib" dh_auto_build
+## Try to deal with multi-arch libraries ... this does not help
+# override_dh_auto_build:
+# env LD_LIBRARY_PATH="$(CURDIR)/lib/$(DEB_HOST_MULTIARCH)" dh_auto_build
+## Try to deal with multi-arch libraries by disabling rpath ... which does not work as expected
+#override_dh_auto_configure:
+# dh_auto_configure -- --disable-rpath
+
override_dh_auto_install:
dh_auto_install
#These are identical to the files without the extension.
#If I really need them I'll symlink them, or better patch the
#code to not need them.
rm -f debian/*/usr/bin/*.bin
+ # Remove file causing lintian errors that is targeting at windows
+ find debian -name help_windows.tcl -delete
+ # Remove some empty directories
+ find debian -type d -empty -name acdtcl -delete
+ find debian -type d -empty -name templates -delete
+ # Build system is not prepared for multi-arch
+ mv $(CURDIR)/debian/tmp/usr/lib/$(DEB_HOST_MULTIARCH)/* $(CURDIR)/debian/tmp/usr/lib
+ rmdir $(CURDIR)/debian/tmp/usr/lib/$(DEB_HOST_MULTIARCH)
override_dh_auto_clean:
make spotless || true
rm -f config.log config.status
rm -f Makefile shlib.conf staden_config.h system.mk
find -name debian -prune -o -name .dir -exec rm '{}' ';'
+
+override_dh_fixperms:
+ dh_fixperms
+ # scripts should be executable
+ chmod a+x debian/*/usr/share/staden/tcl/prefinish/add_stops.tcl
+ chmod a+x debian/*/usr/share/staden/tcl/prefinish/finish_sanger.tcl
+ chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_ext.tcl
+ chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_galeon.tcl
+ chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_int.tcl
+ chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_netscape.tcl
Modified: trunk/packages/staden/trunk/debian/watch
===================================================================
--- trunk/packages/staden/trunk/debian/watch 2014-01-20 12:31:26 UTC (rev 15843)
+++ trunk/packages/staden/trunk/debian/watch 2014-01-20 17:51:24 UTC (rev 15844)
@@ -1,2 +1,3 @@
version=3
-http://sf.net/staden/staden-([0-9ab.]*).tar.(?:bz2|gz)
+opts=dversionmangle=s/~b/b/ \
+ http://sf.net/staden/staden-([0-9ab.]*).tar.(?:bz2|gz)
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