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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> -License: Simplified BSD +Copyright: 2013 Tim Booth <[email protected]> + 2013-2014 Andreas Tille <[email protected]> +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 <[email protected]> +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 <[email protected]> +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 <[email protected]> +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 <[email protected]> +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 <[email protected]> +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) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
