[med-svn] r3921 - in trunk/packages/arb/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Tue Sep 8 07:44:10 UTC 2009
Author: tille
Date: 2009-09-08 07:44:09 +0000 (Tue, 08 Sep 2009)
New Revision: 3921
Modified:
trunk/packages/arb/trunk/debian/arb-common.dirs
trunk/packages/arb/trunk/debian/arb-common.install
trunk/packages/arb/trunk/debian/arb.README.debian
trunk/packages/arb/trunk/debian/changelog
trunk/packages/arb/trunk/debian/control
trunk/packages/arb/trunk/debian/patches/30_phyml
trunk/packages/arb/trunk/debian/rules
Log:
CLeanup some leftovers, deal with lintian problems, updated docs
Modified: trunk/packages/arb/trunk/debian/arb-common.dirs
===================================================================
--- trunk/packages/arb/trunk/debian/arb-common.dirs 2009-09-08 06:53:34 UTC (rev 3920)
+++ trunk/packages/arb/trunk/debian/arb-common.dirs 2009-09-08 07:44:09 UTC (rev 3921)
@@ -1,2 +1,3 @@
usr/share/lintian/overrides
usr/bin
+usr/share/doc/arb/
Modified: trunk/packages/arb/trunk/debian/arb-common.install
===================================================================
--- trunk/packages/arb/trunk/debian/arb-common.install 2009-09-08 06:53:34 UTC (rev 3920)
+++ trunk/packages/arb/trunk/debian/arb-common.install 2009-09-08 07:44:09 UTC (rev 3921)
@@ -1,7 +1,7 @@
GDEHELP/DATA_FILES usr/lib/arb/GDEHELP
GDEHELP/ARB_GDEmenus etc/arb
PERL_SCRIPTS usr/lib/arb
-SH usr/lib/arb
+SH/[a-z]* usr/lib/arb
HELP_SOURCE/oldhelp/*.hlp usr/lib/arb/HELP_SOURCE/oldhelp
HELP_SOURCE/oldhelp/prompt usr/lib/arb/HELP_SOURCE/oldhelp
lib/[d-gi-kmoqt-z]* usr/lib/arb/lib
Modified: trunk/packages/arb/trunk/debian/arb.README.debian
===================================================================
--- trunk/packages/arb/trunk/debian/arb.README.debian 2009-09-08 06:53:34 UTC (rev 3920)
+++ trunk/packages/arb/trunk/debian/arb.README.debian 2009-09-08 07:44:09 UTC (rev 3921)
@@ -4,40 +4,6 @@
Known bugs of arb are listed in the bug-tracker at
http://bugs.arb-home.de/
-
-The FTP archive where this version was downloaded from says:
-
-+---------------------------------------------------------------------------------+
-| |
-| IMPORTANT - Please read: |
-| |
-| The version in this directory is the latest build from our development team. |
-| Regard this version as 'NOT RELEASED'. |
-| |
-| You are DISALLOWED to supply copies of the files from this directory. |
-| As well you are DISALLOWED to make direct links to the files in this directory. |
-| |
-| Please do not encourage normal ARB users to download version from here. |
-| |
-| This version is completely untested and/or experimental - so it may easily |
-| VAPORIZE all your data, your machine or even yourself. |
-| |
-| |
-| *** Use at your own risk! *** |
-| |
-| |
-| The versions in the subdirectories below this directory are/have been used |
-| by several people at our institute, so they can be regarded as less dangerous |
-| than the latest build. |
-| |
-| Known bugs: |
-| |
-| - Many refresh problems in EDIT4 (2005_03_15 + 2005_03_31) |
-| - Secondary structure editor has problems with base positions |
-| (2005_03_15 + 2005_03_31 + 2005_05_06) |
-| |
-+---------------------------------------------------------------------------------+
-
Dependencies
------------
@@ -59,6 +25,10 @@
As the maintainer of the molphy package which is orphaned
upstream I included the patches from Arb and thus I expect
the Debian packaged version to run with the symlinks from Arb.
+ - Arb contains a patched version of phyml which is lagging behind
+ upstream releases of phyml. The latest version of phyml is
+ available as Debian package as well and it is in the list of
+ Suggested packages of Arb to enable you to compare the results.
- The nameserver data are build in a separat package. The reason
is that there are perhaps more recent packages available from
http://download.arb-home.de/xtra/
Modified: trunk/packages/arb/trunk/debian/changelog
===================================================================
--- trunk/packages/arb/trunk/debian/changelog 2009-09-08 06:53:34 UTC (rev 3920)
+++ trunk/packages/arb/trunk/debian/changelog 2009-09-08 07:44:09 UTC (rev 3921)
@@ -9,12 +9,16 @@
- Build-Depends: dpkg-dev (>= 1.15.4) to make use of
`dpkg-architecture -qDEB_BUILD_ARCH_BITS` in Makefile
- Build-Depends: xutils-dev
- - debian/control: arb Recommends: bioperl
+ - arb Recommends: bioperl
+ - arb Suggests: phyml
* Removed / changed patches which were applied upstream
- debian/patches/ARB_release200712_gcc4.3.1.patch removed
- debian/patches/20_replace_rxp_by_xmllint.patch removed
- debian/patches/tmpfile_CVE-2008-5378.patch removed applied part
* debian/{rules,*.install}: Cleanup regarding changes in new upstream version
+ * debian/arb.README.debian:
+ - Removed useless warning about prereleases
+ - Added hint about different phyml versions
[ David Paleino ]
* Removed myself from Uploaders
Modified: trunk/packages/arb/trunk/debian/control
===================================================================
--- trunk/packages/arb/trunk/debian/control 2009-09-08 06:53:34 UTC (rev 3920)
+++ trunk/packages/arb/trunk/debian/control 2009-09-08 07:44:09 UTC (rev 3921)
@@ -20,7 +20,7 @@
phylip (>= 3.6b), fastdnaml (>= 1.2.2-4), readseq (>= 1-1), tree-puzzle (>=5.0-3), molphy,
ssh, transfig, ${misc:Depends}
Recommends: xfig, bioperl
-Suggests: arb-database, gnuplot, gv
+Suggests: arb-database, gnuplot, gv, phyml
Description: Integrated package for sequence database handling and analysis
The ARB software is a graphically oriented package comprising various tools
for sequence database handling and data analysis. A central database of
Modified: trunk/packages/arb/trunk/debian/patches/30_phyml
===================================================================
--- trunk/packages/arb/trunk/debian/patches/30_phyml 2009-09-08 06:53:34 UTC (rev 3920)
+++ trunk/packages/arb/trunk/debian/patches/30_phyml 2009-09-08 07:44:09 UTC (rev 3921)
@@ -10,3 +10,12 @@
# CFLAGS = -Wall
# CFLAGS = -g -Wall
# CFLAGS = -pg -Wall -fprofile-arcs -static
+@@ -30,8 +31,6 @@
+
+ ifdef DARWIN
+ CFLAGS += -fPIC
+-else
+-CFLAGS += -static
+ endif
+
+ # ARBs standard target
Modified: trunk/packages/arb/trunk/debian/rules
===================================================================
--- trunk/packages/arb/trunk/debian/rules 2009-09-08 06:53:34 UTC (rev 3920)
+++ trunk/packages/arb/trunk/debian/rules 2009-09-08 07:44:09 UTC (rev 3921)
@@ -96,9 +96,8 @@
done ; \
fi
- # Fix permissions
- chmod 755 debian/arb-common/usr/lib/arb/SH/*
- chmod 644 debian/arb-common/usr/lib/arb/lib/pixmaps/*.xpm
+ # Move SH/README to docs
+ cp -a SH/README debian/arb-common/usr/share/doc/arb/README_SH
# Build architecture-independent files here.
binary-indep: build install
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