[med-svn] r3185 - in trunk/packages/seaview/trunk/debian: . patches
plessy at alioth.debian.org
plessy at alioth.debian.org
Mon Mar 16 11:25:29 UTC 2009
Author: plessy
Date: 2009-03-16 11:25:29 +0000 (Mon, 16 Mar 2009)
New Revision: 3185
Removed:
trunk/packages/seaview/trunk/debian/patches/20-no-PDF-in-help.patch
trunk/packages/seaview/trunk/debian/patches/21-location-of-seaview.help.patch
trunk/packages/seaview/trunk/debian/patches/40-seaview_align.sh-newline.patch
trunk/packages/seaview/trunk/debian/patches/seaview_align-full_path.patch
trunk/packages/seaview/trunk/debian/patches/series
Modified:
trunk/packages/seaview/trunk/debian/changelog
trunk/packages/seaview/trunk/debian/control
trunk/packages/seaview/trunk/debian/copyright
trunk/packages/seaview/trunk/debian/install
trunk/packages/seaview/trunk/debian/rules
Log:
New upstream release.
TODO: add new debtags (download, phylogeny, ?\226?\128?\166)
rewrite description.
Debdiff, update manpage if necessary, document changes.
* New upstream version.
* debian/control:
- Recommends Phyml.
- checked package conformance with Policy 3.8.1.
- Removed reference from description.
- Dropped build dependency on quilt.
* debian/patches removed:
- 20-no-PDF-in-help.patch: upstream wording became true for Debian as well.
- 21-location-of-seaview.help.patch: passing -DHELPFILENAME through
debian/rules instead.
- 40-seaview_align.sh-newline.patch, seaview_align-full_path.patch:
seaview_align.sh was removed upstream.
* debian/rules:
- Makes `seaview' instead of `seaviewps' as (non-free) PDF support is not
default anymore.
- Indicate the location of the help file with:
-DHELPFILENAME=\\\"/usr/share/njplot/njplot.help\\\"
- Uses `dh clean' and $(RM) macro in the clean target.
- Removed protein.mase from examples (removed upstream).
- Removed patching facilities (no patches to apply anymore).
* Removed `seaview_align.sh' from debian/install, as it was removed upstream.
* debian/copyright:
- Incremented year and version.
- Link to the precise versions of the GNU GPL and LGPL
Modified: trunk/packages/seaview/trunk/debian/changelog
===================================================================
--- trunk/packages/seaview/trunk/debian/changelog 2009-03-15 06:25:55 UTC (rev 3184)
+++ trunk/packages/seaview/trunk/debian/changelog 2009-03-16 11:25:29 UTC (rev 3185)
@@ -1,3 +1,36 @@
+seaview (1:4.0-1) UNRELEASED; urgency=low
+
+ TODO: add new debtags (download, phylogeny, …)
+ rewrite description.
+ Debdiff, update manpage if necessary, document changes.
+
+ * New upstream version.
+ * debian/control:
+ - Recommends Phyml.
+ - checked package conformance with Policy 3.8.1.
+ - Removed reference from description.
+ - Dropped build dependency on quilt.
+ * debian/patches removed:
+ - 20-no-PDF-in-help.patch: upstream wording became true for Debian as well.
+ - 21-location-of-seaview.help.patch: passing -DHELPFILENAME through
+ debian/rules instead.
+ - 40-seaview_align.sh-newline.patch, seaview_align-full_path.patch:
+ seaview_align.sh was removed upstream.
+ * debian/rules:
+ - Makes `seaview' instead of `seaviewps' as (non-free) PDF support is not
+ default anymore.
+ - Indicate the location of the help file with:
+ -DHELPFILENAME=\\\"/usr/share/njplot/njplot.help\\\"
+ - Uses `dh clean' and $(RM) macro in the clean target.
+ - Removed protein.mase from examples (removed upstream).
+ - Removed patching facilities (no patches to apply anymore).
+ * Removed `seaview_align.sh' from debian/install, as it was removed upstream.
+ * debian/copyright:
+ - Incremented year and version.
+ - Link to the precise versions of the GNU GPL and LGPL.
+
+ -- Charles Plessy <plessy at debian.org> Mon, 16 Mar 2009 13:18:29 +0900
+
seaview (1:3.2-1) unstable; urgency=low
* New upstream version:
Modified: trunk/packages/seaview/trunk/debian/control
===================================================================
--- trunk/packages/seaview/trunk/debian/control 2009-03-15 06:25:55 UTC (rev 3184)
+++ trunk/packages/seaview/trunk/debian/control 2009-03-16 11:25:29 UTC (rev 3185)
@@ -4,8 +4,8 @@
Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Charles Plessy <plessy at debian.org>
-Build-Depends: debhelper ( >= 7 ), libfltk1.1-dev, libjpeg62-dev, libpng12-dev, zlib1g-dev, quilt
-Standards-Version: 3.8.0
+Build-Depends: debhelper ( >= 7 ), libfltk1.1-dev, libjpeg62-dev, libpng12-dev, zlib1g-dev
+Standards-Version: 3.8.1
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/seaview/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/seaview/trunk/
Homepage: http://pbil.univ-lyon1.fr/software/seaview.html
@@ -13,7 +13,7 @@
Package: seaview
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
-Recommends: xterm
+Recommends: xterm, phyml
Suggests: muscle, clustalw
Description: Multiple sequence alignment editor
SeaView is a graphical multiple sequence alignment editor developed by Manolo
@@ -21,10 +21,3 @@
are supported for reading and writing. Alignments can be manually edited.
The user is further supported by an integration of external programs,
i.e., to run DOT-PLOT or MUSCLE, to locally improve the alignment.
- .
- When using SeaView for investigations that lead to a publication, please
- cite the following reference:
- .
- Galtier, N., Gouy, M. and Gautier, C. (1996) "SeaView and
- Phylo_win, two graphic tools for sequence alignment and molecular
- phylogeny." Comput. Applic. Biosci. 12:543-548.
Modified: trunk/packages/seaview/trunk/debian/copyright
===================================================================
--- trunk/packages/seaview/trunk/debian/copyright 2009-03-15 06:25:55 UTC (rev 3184)
+++ trunk/packages/seaview/trunk/debian/copyright 2009-03-16 11:25:29 UTC (rev 3185)
@@ -1,12 +1,12 @@
Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=402
Upstream-Name: SeaView
Upstream-Maintainer: Manolo Gouy <mgouy at biomserv.univ-lyon1.fr>
-Upstream-Source: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_3.2.tar.gz
+Upstream-Source: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.0.tar.gz
X-Packaged-By: Stephane Bortzmeyer <bortzmeyer at debian.org>
X-Packaged-Date: Mon, 1 Mar 1999 16:41:51 +0100
Files: *
-Copyright: © 1996-2008 Manolo Gouy <mgouy at biomserv.univ-lyon1.fr>
+Copyright: © 1996-2009 Manolo Gouy <mgouy at biomserv.univ-lyon1.fr>
X-Comment: If you use SeaView in a published work, please cite the following reference:
Galtier, N., Gouy, M. and Gautier, C. (1996) SeaView and Phylo_win, two graphic
tools for sequence alignment and molecular phylogeny. Comput. Applic. Biosci.,
@@ -26,7 +26,7 @@
along with this package; if not, write to the Free Software
Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
X-Comment: On Debian systems, the complete text of the GNU General
- Public License can be found in `/usr/share/common-licenses/GPL'.
+ Public License version 2 can be found in `/usr/share/common-licenses/GPL-2'.
Files: FL/*
Copyright: © 2004 Greg Ercolano
@@ -46,7 +46,7 @@
License along with this library; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston MA 02110-1301 USA
X-Comment: On Debian systems, the complete text of the GNU Lesser General
- Public License can be found in `/usr/share/common-licenses/LGPL'.
+ Public License version 2 can be found in `/usr/share/common-licenses/LGPL-2'.
Files: debian/*
Copyright: © 1999 Stephane Bortzmeyer <bortzmeyer at debian.org>
@@ -59,6 +59,6 @@
© 2003 Brian R Furry <bfurry at nac.net>
© 2005 Steve Langasek <vorlon at debian.org>
© 2007 Nelson A. de Oliveira <naoliv at debian.org>
- © 2006-2008 Charles Plessy <charles-debian-nospam at plessy.org>
+ © 2006-2009 Charles Plessy <charles-debian-nospam at plessy.org>
License: unknown
Please treat the contributions of Charles Plessy as if they were in the public domain.
Modified: trunk/packages/seaview/trunk/debian/install
===================================================================
--- trunk/packages/seaview/trunk/debian/install 2009-03-15 06:25:55 UTC (rev 3184)
+++ trunk/packages/seaview/trunk/debian/install 2009-03-16 11:25:29 UTC (rev 3185)
@@ -1,5 +1,4 @@
seaview usr/bin
-seaview_align.sh usr/share/seaview
seaview.help usr/share/seaview
seaview.xpm usr/share/pixmaps
debian/seaview.desktop usr/share/applications
Deleted: trunk/packages/seaview/trunk/debian/patches/20-no-PDF-in-help.patch
===================================================================
--- trunk/packages/seaview/trunk/debian/patches/20-no-PDF-in-help.patch 2009-03-15 06:25:55 UTC (rev 3184)
+++ trunk/packages/seaview/trunk/debian/patches/20-no-PDF-in-help.patch 2009-03-16 11:25:29 UTC (rev 3185)
@@ -1,19 +0,0 @@
-Author: Charles Plessy
-Description: As PDF support is disabled in Debian's SeaView, mention of it is
- removed in the help file.
-Forwarded: no
-
-Index: seaview-2.2/seaview.help
-===================================================================
---- seaview-2.2.orig/seaview.help
-+++ seaview-2.2/seaview.help
-@@ -17,9 +17,6 @@
-
- Seaview uses the FLTK project (http://www.fltk.org) for its user interface.
-
--Seaview uses the PDFlib Lite library (http://www.pdflib.com) for pdf output
--under the "Open Source Developer Exemption" of the PDFlib Lite License Agreement.
--
- >>>Alignment panel
- Mouse Use:
-
Deleted: trunk/packages/seaview/trunk/debian/patches/21-location-of-seaview.help.patch
===================================================================
--- trunk/packages/seaview/trunk/debian/patches/21-location-of-seaview.help.patch 2009-03-15 06:25:55 UTC (rev 3184)
+++ trunk/packages/seaview/trunk/debian/patches/21-location-of-seaview.help.patch 2009-03-16 11:25:29 UTC (rev 3185)
@@ -1,16 +0,0 @@
-Author: Charles Plessy
-Description: To store the help file in a FHS-compliant directory.
-Forwarded: no
-Index: seaview-2.2/Makefile
-===================================================================
---- seaview-2.2.orig/Makefile
-+++ seaview-2.2/Makefile
-@@ -8,7 +8,7 @@
- X11 = /usr/X11R6
-
- #comment out and customize next line to set helpfile name at compile-time
--#HELP_NOT_IN_PATH = -DDEFAULT_HELPFILE=\"/bge/mgouy/seaview/seaview.help\"
-+HELP_NOT_IN_PATH = -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.help\"
-
- CXX = g++
- CC = gcc
Deleted: trunk/packages/seaview/trunk/debian/patches/40-seaview_align.sh-newline.patch
===================================================================
--- trunk/packages/seaview/trunk/debian/patches/40-seaview_align.sh-newline.patch 2009-03-15 06:25:55 UTC (rev 3184)
+++ trunk/packages/seaview/trunk/debian/patches/40-seaview_align.sh-newline.patch 2009-03-16 11:25:29 UTC (rev 3185)
@@ -1,13 +0,0 @@
-Index: seaview_2.2/seaview_align.sh
-===================================================================
---- seaview_2.2.orig/seaview_align.sh
-+++ seaview_2.2/seaview_align.sh
-@@ -14,7 +14,7 @@
- echo ' '
- echo ' '
- echo 'Program' $algo 'terminated.'
--echo 'Load new alignment? [(y)/n] \c'
-+echo -n 'Load new alignment? [(y)/n]'
- read rep
- if [ "$rep" = "n" ]; then
- echo aborted > $arg1.status
Deleted: trunk/packages/seaview/trunk/debian/patches/seaview_align-full_path.patch
===================================================================
--- trunk/packages/seaview/trunk/debian/patches/seaview_align-full_path.patch 2009-03-15 06:25:55 UTC (rev 3184)
+++ trunk/packages/seaview/trunk/debian/patches/seaview_align-full_path.patch 2009-03-16 11:25:29 UTC (rev 3185)
@@ -1,34 +0,0 @@
-Author: Charles Plessy
-Description: since seaview_align.sh is always there, do not mention that it
- could be absent in the error message. Location of seaview_align.sh is hardcoded.
-Forwarded: no
-diff --git a/align.cxx b/align.cxx
-index 349470c..f4b3a17 100644
---- a/align.cxx
-+++ b/align.cxx
-@@ -139,9 +139,9 @@ FILE *in;
- status = get_full_path("seaview_align.sh") == NULL;
- }
- if(status != 0) {
-- fl_message("Alignment operation is impossible because\n"
-- "one of the programs xterm, seaview_align.sh\n"
-- "is missing from PATH or seaview's directory");
-+ fl_message("Alignment operation is impossible\n"
-+ "because the program xterm is missing\n"
-+ "from PATH or seaview's directory");
- ((Fl_Menu_ *)view->menu_edit)->mode(ALIGN_ALL_SEQS, FL_MENU_INACTIVE);
- ((Fl_Menu_ *)view->menu_edit)->mode(ALIGN_SELECTION, FL_MENU_INACTIVE);
- return;
-@@ -597,9 +597,10 @@ if((p=strchr(local, '>')) != NULL) {
- memmove(p+3, p+1, strlen(p+1) + 1);
- memcpy(p, "'>'", 3);
- }
--p = strdup(get_full_path("seaview_align.sh"));
-+/* Hardcoded in Debian
-+ p = strdup(get_full_path("seaview_align.sh")); */
- sprintf(command, "xterm -T \"%s alignment\" -n %s -sb -sl 2000 -e %s %s %s %s ",
-- algo_name, algo_name, p, get_full_path(algo_name), base_fname, local);
-+ algo_name, algo_name, "/usr/share/seaview/seaview_align.sh", get_full_path(algo_name), base_fname, local);
- free(p);
- #endif
- return 0;
Deleted: trunk/packages/seaview/trunk/debian/patches/series
===================================================================
--- trunk/packages/seaview/trunk/debian/patches/series 2009-03-15 06:25:55 UTC (rev 3184)
+++ trunk/packages/seaview/trunk/debian/patches/series 2009-03-16 11:25:29 UTC (rev 3185)
@@ -1,4 +0,0 @@
-20-no-PDF-in-help.patch
-21-location-of-seaview.help.patch
-40-seaview_align.sh-newline.patch
-seaview_align-full_path.patch
Modified: trunk/packages/seaview/trunk/debian/rules
===================================================================
--- trunk/packages/seaview/trunk/debian/rules 2009-03-15 06:25:55 UTC (rev 3184)
+++ trunk/packages/seaview/trunk/debian/rules 2009-03-16 11:25:29 UTC (rev 3185)
@@ -21,29 +21,23 @@
CFLAGS += -g
endif
-include /usr/share/quilt/quilt.make
-
-build: patch build-stamp
+build: build-stamp
build-stamp:
dh_testdir
- $(MAKE) OPT="$(CFLAGS)" seaviewps PNGJPEGLIBS='-lpng -ljpeg' FLTKLIBS='-lfltk -lfltk_images'
- mv seaviewps seaview
+ $(MAKE) OPT="$(CFLAGS) \
+ -DPHYMLNAME=\\\"phyml\\\" \
+ -DDEFAULT_HELPFILE=\\\"/usr/share/seaview/seaview.help\\\"" \
+ $(PROGRAM_NAME) \
+ PNGJPEGLIBS='-lpng -ljpeg' FLTKLIBS='-lfltk -lfltk_images'
touch build-stamp
-clean: clean-patched unpatch
-
+clean: clean-patched
clean-patched:
- dh_testdir
- dh_testroot
- rm -f build-stamp
- rm -f *.o seaview seaviewps
+ dh clean
+ $(RM) *.o seaview seaviewps
install: build
- dh_testdir
- dh_testroot
- dh_clean -k
- dh_installdirs
- dh_install
+ dh install
# Build architecture-dependent files here.
binary-arch: build install
@@ -51,7 +45,7 @@
dh_testroot
dh_installchangelogs
dh_installdocs debian/references
- dh_installexamples debian/examples/* protein.mase
+ dh_installexamples debian/examples/*
dh_installmenu
dh_desktop
dh_installmime
More information about the debian-med-commit
mailing list