[med-svn] r17823 - in trunk/packages/arb/trunk/debian: . conf patches source
Elmar Pruesse
epruesse-guest at moszumanska.debian.org
Fri Aug 22 14:12:16 UTC 2014
Author: epruesse-guest
Date: 2014-08-22 14:12:16 +0000 (Fri, 22 Aug 2014)
New Revision: 17823
Added:
trunk/packages/arb/trunk/debian/application-x-arb.png
trunk/packages/arb/trunk/debian/arb-common.docs
trunk/packages/arb/trunk/debian/arb-common.examples
trunk/packages/arb/trunk/debian/libarb-dev.install
trunk/packages/arb/trunk/debian/libarb-dev.links
trunk/packages/arb/trunk/debian/libarb-dev/
trunk/packages/arb/trunk/debian/source/include-binaries
trunk/packages/arb/trunk/debian/source/options
Removed:
trunk/packages/arb/trunk/debian/arb-common.lintian-overrides
trunk/packages/arb/trunk/debian/patches/10_config.makefiles.patch
trunk/packages/arb/trunk/debian/patches/20_Makefile_main.patch
trunk/packages/arb/trunk/debian/patches/30_tmpfile_CVE-2008-5378.patch
trunk/packages/arb/trunk/debian/patches/50_fix_gcc-4.8.patch
trunk/packages/arb/trunk/debian/patches/60_use_debian_packaged_raxml.patch
Modified:
trunk/packages/arb/trunk/debian/arb-common.dirs
trunk/packages/arb/trunk/debian/arb-common.install
trunk/packages/arb/trunk/debian/arb-common.links
trunk/packages/arb/trunk/debian/arb-doc.install
trunk/packages/arb/trunk/debian/arb.install
trunk/packages/arb/trunk/debian/arb.links
trunk/packages/arb/trunk/debian/changelog
trunk/packages/arb/trunk/debian/conf/arb.conf
trunk/packages/arb/trunk/debian/control
trunk/packages/arb/trunk/debian/libarb.dirs
trunk/packages/arb/trunk/debian/libarb.install
trunk/packages/arb/trunk/debian/patches/series
trunk/packages/arb/trunk/debian/rules
Log:
Reworked package for ARB 6.0
- added icons and descriptions for desktop integration
- removed globbing from .install files
- using ARB "install" equivalent now instead of picking from build dir
- removed arb-add-pt server in favor of preconfigured per-user slots
- added libarb-dev with include files and static libs
- replaced "config.makefile" patch with sed script as configure target
- removed patches merged upstream
TODO:
- check custom scripts, they may no longer be necessary/valid
- remove old PT servers (incompatible change to format)
- add splash screen to indicate that ARB is loading the database
(load times can exceed minutes, in the shell this was obvious, when
launching from a file manager the "nothing happens" will cause
users to launch multiple instances. will be a backport from
upstream)
Added: trunk/packages/arb/trunk/debian/application-x-arb.png
===================================================================
(Binary files differ)
Property changes on: trunk/packages/arb/trunk/debian/application-x-arb.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Modified: trunk/packages/arb/trunk/debian/arb-common.dirs
===================================================================
--- trunk/packages/arb/trunk/debian/arb-common.dirs 2014-08-22 13:47:15 UTC (rev 17822)
+++ trunk/packages/arb/trunk/debian/arb-common.dirs 2014-08-22 14:12:16 UTC (rev 17823)
@@ -1,3 +1,2 @@
usr/share/lintian/overrides
-usr/bin
-usr/share/doc/arb/
+var/lib/arb/pts
Added: trunk/packages/arb/trunk/debian/arb-common.docs
===================================================================
--- trunk/packages/arb/trunk/debian/arb-common.docs (rev 0)
+++ trunk/packages/arb/trunk/debian/arb-common.docs 2014-08-22 14:12:16 UTC (rev 17823)
@@ -0,0 +1,3 @@
+debian/About
+arb_*.txt
+lib/submit
Added: trunk/packages/arb/trunk/debian/arb-common.examples
===================================================================
--- trunk/packages/arb/trunk/debian/arb-common.examples (rev 0)
+++ trunk/packages/arb/trunk/debian/arb-common.examples 2014-08-22 14:12:16 UTC (rev 17823)
@@ -0,0 +1 @@
+demo.arb
Modified: trunk/packages/arb/trunk/debian/arb-common.install
===================================================================
--- trunk/packages/arb/trunk/debian/arb-common.install 2014-08-22 13:47:15 UTC (rev 17822)
+++ trunk/packages/arb/trunk/debian/arb-common.install 2014-08-22 14:12:16 UTC (rev 17823)
@@ -1,17 +1,34 @@
-HELP_SOURCE/oldhelp/*.hlp usr/lib/arb/HELP_SOURCE/oldhelp
-HELP_SOURCE/oldhelp/prompt usr/lib/arb/HELP_SOURCE/oldhelp
-PERL2ARB/ARB.pm usr/lib/arb/lib
-PERL_SCRIPTS usr/lib/arb
-SH/[a-z]* usr/lib/arb/SH
-debian/About usr/share/doc/arb/
-debian/bin/arb_create_debian_conffile usr/lib/arb/SH
-demo.arb usr/share/doc/arb/examples
-lib/[d-gi-kmoqt-z]* usr/lib/arb/lib
-lib/arb_default/* usr/lib/arb/lib/arb_default
-lib/help usr/lib/arb/lib
-lib/nas/names.dat* var/lib/arb/nas
-lib/pi* usr/share/arb/lib
-lib/pts var/lib/arb
-lib/rna3d usr/share/arb/lib
-lib/s[a-tv-z]* usr/lib/arb/lib
-lib/submit usr/share/doc/arb
+debian/tmp/demo.arb usr/share/doc/arb/examples
+debian/tmp/arb_*.txt usr/share/doc/arb
+debian/tmp/lib/BUGS usr/share/doc/arb
+debian/tmp/lib/dtd usr/share/doc/arb
+debian/tmp/lib/LoVPBN.* usr/share/doc/arb
+
+debian/tmp/lib/pictures usr/share/arb
+debian/tmp/lib/pixmaps usr/share/arb
+debian/tmp/lib/motifHack usr/share/arb
+debian/tmp/lib/rna3d usr/share/arb
+
+debian/tmp/lib/import etc/arb
+debian/tmp/lib/export etc/arb
+debian/tmp/lib/arb_default etc/arb
+debian/tmp/lib/sellists etc/arb
+debian/tmp/lib/gde etc/arb
+debian/tmp/lib/macros etc/arb
+debian/tmp/lib/inputMasks etc/arb
+debian/tmp/lib/submit etc/arb
+
+debian/tmp/lib/nas var/lib/arb
+
+debian/tmp/lib/desktop/arb.png usr/share/pixmaps
+debian/tmp/lib/desktop/arb.mime usr/lib/mime/packages/arb
+debian/tmp/lib/desktop/arb.xml usr/share/mime/packages
+
+debian/tmp/lib/help usr/lib/arb/lib
+
+debian/tmp/PERL_SCRIPTS usr/lib/arb
+debian/tmp/SH usr/lib/arb
+debian/tmp/lib/ARB.pm usr/lib/arb/lib
+debian/tmp/lib/macro.head usr/lib/arb/lib
+
+debian/application-x-arb.png usr/share/icons/hicolor/256x256
Modified: trunk/packages/arb/trunk/debian/arb-common.links
===================================================================
--- trunk/packages/arb/trunk/debian/arb-common.links 2014-08-22 13:47:15 UTC (rev 17822)
+++ trunk/packages/arb/trunk/debian/arb-common.links 2014-08-22 14:12:16 UTC (rev 17823)
@@ -1,9 +1,17 @@
-etc/arb/ARB_GDEmenus usr/lib/arb/GDEHELP/ARB_GDEmenus
+usr/share/arb/pictures usr/lib/arb/lib/pictures
+usr/share/arb/pixmaps usr/lib/arb/lib/pixmaps
+usr/share/arb/motifHack usr/lib/arb/lib/motifHack
+usr/share/arb/rna3d usr/lib/arb/lib/rna3d
+
+etc/arb/import usr/lib/arb/lib/import
+etc/arb/export usr/lib/arb/lib/export
+etc/arb/arb_default usr/lib/arb/lib/arb_default
+etc/arb/sellists usr/lib/arb/lib/sellists
+etc/arb/gde usr/lib/arb/lib/gde
+etc/arb/macros usr/lib/arb/lib/macros
+etc/arb/inputMasks usr/lib/arb/lib/inputMasks
+etc/arb/submit usr/lib/arb/lib/submit
+
+var/lib/arb/nas usr/lib/arb/lib/nas
var/lib/arb/pts usr/lib/arb/lib/pts
-var/lib/arb/nas usr/lib/arb/lib/nas
-usr/lib/arb/SH/arb_clean usr/bin/arb_clean
-usr/share/doc/arb/html usr/lib/arb/lib/help_html
-usr/share/doc/arb/submit usr/lib/arb/lib/submit
-usr/share/arb/lib/pictures usr/lib/arb/lib/pictures
-usr/share/arb/lib/pixmaps usr/lib/arb/lib/pixmaps
-usr/share/arb/lib/rna3d usr/lib/arb/lib/rna3d
+
Deleted: trunk/packages/arb/trunk/debian/arb-common.lintian-overrides
===================================================================
--- trunk/packages/arb/trunk/debian/arb-common.lintian-overrides 2014-08-22 13:47:15 UTC (rev 17822)
+++ trunk/packages/arb/trunk/debian/arb-common.lintian-overrides 2014-08-22 14:12:16 UTC (rev 17823)
@@ -1,3 +0,0 @@
-# This script is not intended to be run by itself. Instead
-# it is used to construct a script at runtime
-arb-common: script-not-executable ./usr/lib/arb/lib/macro.head
Modified: trunk/packages/arb/trunk/debian/arb-doc.install
===================================================================
--- trunk/packages/arb/trunk/debian/arb-doc.install 2014-08-22 13:47:15 UTC (rev 17822)
+++ trunk/packages/arb/trunk/debian/arb-doc.install 2014-08-22 14:12:16 UTC (rev 17823)
@@ -1,2 +1 @@
-HELP_SOURCE/oldhelp/arb.pdf.gz usr/share/doc/arb/help
-lib/help_html/* usr/share/doc/arb/html
+debian/tmp/lib/help_html/* usr/share/doc/arb/html
Modified: trunk/packages/arb/trunk/debian/arb.install
===================================================================
--- trunk/packages/arb/trunk/debian/arb.install 2014-08-22 13:47:15 UTC (rev 17822)
+++ trunk/packages/arb/trunk/debian/arb.install 2014-08-22 14:12:16 UTC (rev 17823)
@@ -1,7 +1,9 @@
-bin/[A-LN-Zabcd-z]* usr/lib/arb/bin
debian/arb.xpm usr/share/arb
debian/bin/arb usr/bin
-debian/bin/arb-add-pt-server usr/bin
debian/bin/arb-kill usr/bin
debian/conf/arb.conf etc/arb
debian/conf/arb_tcp.dat etc/arb
+
+debian/tmp/bin usr/lib/arb
+
+debian/tmp/lib/desktop/arb.desktop usr/share/applications
Modified: trunk/packages/arb/trunk/debian/arb.links
===================================================================
--- trunk/packages/arb/trunk/debian/arb.links 2014-08-22 13:47:15 UTC (rev 17822)
+++ trunk/packages/arb/trunk/debian/arb.links 2014-08-22 14:12:16 UTC (rev 17823)
@@ -1,6 +1,7 @@
usr/bin/readseq usr/lib/arb/bin/arb_readseq
+usr/bin/tree-puzzle usr/lib/arb/bin/puzzle
+usr/bin/fastDNAml usr/lib/arb/bin/fastdnaml
usr/lib/phylip/bin/clique usr/lib/arb/bin/clique
-usr/bin/clustalw usr/lib/arb/bin/clustalw
usr/lib/phylip/bin/consense usr/lib/arb/bin/consense
usr/lib/phylip/bin/contml usr/lib/arb/bin/contml
usr/lib/phylip/bin/contrast usr/lib/arb/bin/contrast
@@ -30,11 +31,8 @@
usr/lib/phylip/bin/promlk usr/lib/arb/bin/promlk
usr/lib/phylip/bin/protdist usr/lib/arb/bin/protdist
usr/lib/phylip/bin/protpars usr/lib/arb/bin/protpars
-usr/bin/tree-puzzle usr/lib/arb/bin/puzzle
usr/lib/phylip/bin/restdist usr/lib/arb/bin/restdist
usr/lib/phylip/bin/restml usr/lib/arb/bin/restml
usr/lib/phylip/bin/retree usr/lib/arb/bin/retree
usr/lib/phylip/bin/seqboot usr/lib/arb/bin/seqboot
usr/lib/phylip/bin/treedist usr/lib/arb/bin/treedist
-usr/bin/fastDNAml usr/lib/arb/bin/fastdnaml
-usr/bin/protml usr/lib/arb/bin/protml
Modified: trunk/packages/arb/trunk/debian/changelog
===================================================================
--- trunk/packages/arb/trunk/debian/changelog 2014-08-22 13:47:15 UTC (rev 17822)
+++ trunk/packages/arb/trunk/debian/changelog 2014-08-22 14:12:16 UTC (rev 17823)
@@ -1,4 +1,4 @@
-arb (6.0.1-1) UNRELEASED; urgency=medium
+arb (6.0.2-1) UNRELEASED; urgency=medium
* New upstream version
* debian/upstream -> debian/upstream/metadata
Modified: trunk/packages/arb/trunk/debian/conf/arb.conf
===================================================================
--- trunk/packages/arb/trunk/debian/conf/arb.conf 2014-08-22 13:47:15 UTC (rev 17822)
+++ trunk/packages/arb/trunk/debian/conf/arb.conf 2014-08-22 14:12:16 UTC (rev 17823)
@@ -12,7 +12,11 @@
# ARB_XCMD -- prefix to run command-line tools
# upstream default: "$ARB_XTERM -e"
-#ARB_XCMD=x-terminal-emulator -e
+# IMPORTANT::this command must block until its subprocess as finished
+# konsole does not do this, gnome-terminal requires the
+# --disable-factory command
+#ARB_XCMD=gnome-terminal --disable-factory -e
+ARB_XCMD=xterm -sl 1000 -sb -geometry 120x50 -e
# ARB_TEXTEDIT -- command to use for editing ASCII files
# upstream default: <unset>
Modified: trunk/packages/arb/trunk/debian/control
===================================================================
--- trunk/packages/arb/trunk/debian/control 2014-08-22 13:47:15 UTC (rev 17822)
+++ trunk/packages/arb/trunk/debian/control 2014-08-22 14:12:16 UTC (rev 17823)
@@ -23,7 +23,7 @@
perl-doc,
xsltproc,
xutils-dev
-Standards-Version: 3.9.5
+Standards-Version: 3.9.4
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/arb/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/arb/trunk/
Homepage: http://www.arb-home.de/
@@ -42,14 +42,14 @@
readseq,
transfig,
tree-puzzle,
+ xdg-utils,
${misc:Depends},
${shlibs:Depends}
Recommends: bioperl,
xfig
Suggests: arb-database,
gnuplot,
- gv,
- phyml
+ gv
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
@@ -83,6 +83,26 @@
.
This package contains the dynamic libraries which are used by arb.
+Package: libarb-dev
+Section: non-free/libdevel
+Architecture: amd64 i386 kfreebsd-i386 kfreebsd-amd64
+Depends: libarb (= ${binary:Version}),
+ ${misc:Depends}
+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
+ processed (aligned) sequences and any type of additional data linked to the
+ respective sequence entries is structured according to phylogeny or other
+ user defined criteria.
+ .
+ The ARB project (latin, "arbor"=tree) is a joint initiative of the Lehrstuhl
+ fuer Mikrobiologie http://www.mikro.biologie.tu-muenchen.de/ and the
+ Lehrstuhl fuer Rechnertechnik und Rechnerorganisation
+ http://wwwbode.informatik.tu-muenchen.de/ of the Technical University
+ of Munich.
+ .
+ This package contains headers and static libs needed to link against libARBDB.
+
Package: arb-common
Architecture: all
Depends: adduser,
Added: trunk/packages/arb/trunk/debian/libarb-dev.install
===================================================================
--- trunk/packages/arb/trunk/debian/libarb-dev.install (rev 0)
+++ trunk/packages/arb/trunk/debian/libarb-dev.install 2014-08-22 14:12:16 UTC (rev 17823)
@@ -0,0 +1,4 @@
+debian/tmp-dev/INCLUDE/* usr/include/arb
+debian/tmp-dev/*_COM usr/lib/arb
+debian/tmp-dev/SL usr/lib/arb
+
Added: trunk/packages/arb/trunk/debian/libarb-dev.links
===================================================================
--- trunk/packages/arb/trunk/debian/libarb-dev.links (rev 0)
+++ trunk/packages/arb/trunk/debian/libarb-dev.links 2014-08-22 14:12:16 UTC (rev 17823)
@@ -0,0 +1 @@
+usr/include/arb usr/lib/arb/INCLUDE
Modified: trunk/packages/arb/trunk/debian/libarb.dirs
===================================================================
--- trunk/packages/arb/trunk/debian/libarb.dirs 2014-08-22 13:47:15 UTC (rev 17822)
+++ trunk/packages/arb/trunk/debian/libarb.dirs 2014-08-22 14:12:16 UTC (rev 17823)
@@ -1 +0,0 @@
-usr/share/lintian/overrides
Modified: trunk/packages/arb/trunk/debian/libarb.install
===================================================================
--- trunk/packages/arb/trunk/debian/libarb.install 2014-08-22 13:47:15 UTC (rev 17822)
+++ trunk/packages/arb/trunk/debian/libarb.install 2014-08-22 14:12:16 UTC (rev 17823)
@@ -1 +1 @@
-lib/*.so usr/lib/arb/lib
+debian/tmp/lib/*.so usr/lib/arb/lib
Deleted: trunk/packages/arb/trunk/debian/patches/10_config.makefiles.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/10_config.makefiles.patch 2014-08-22 13:47:15 UTC (rev 17822)
+++ trunk/packages/arb/trunk/debian/patches/10_config.makefiles.patch 2014-08-22 14:12:16 UTC (rev 17823)
@@ -1,35 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Description: Set basic makefile configuration variables
-
-Index: arbsrc_12565/config.makefile
-===================================================================
---- /dev/null 1970-01-01 00:00:00.000000000 +0000
-+++ arbsrc_12565/config.makefile 2014-08-01 10:37:21.788971144 +0200
-@@ -0,0 +1,27 @@
-+# --------------------------------------------------------------------------------
-+# If this file is named config.makefile.template then copy it to config.makefile
-+# DO NOT EDIT config.makefile.template
-+# --------------------------------------------------------------------------------
-+
-+# Enter your name (upper case, no spaces) here, to enable '#ifdef DEVEL_YOURNAME #endif' sections
-+DEVELOPER=ANY
-+
-+DEBUG=0# build with debug information
-+DEBUG_GRAPHICS = 0# force instant graphic update
-+# SEER = 1
-+OPENGL=0
-+# ARB_64=0# compile on 64 bit machine (has no effect yet)
-+ARB_64 := $(shell if [ `dpkg-architecture -qDEB_BUILD_ARCH_BITS` -eq 64 ] ; then echo 1 ; else echo 0 ; fi)
-+
-+# --------------------------------------------------------------------------------
-+# target machine section
-+# [Note: Uncomment one section, depending on your machine type and compiler options]
-+
-+# ********* LINUX / gcc g++ / static ********
-+MACH = LINUX# Linux g++ and gcc
-+LINUX = 1
-+ECGS = 1# use GCC? (always 1 for LINUX)
-+
-+# ******** Debian GNU/Linux and (K)Ubuntu system ********
-+DEBIAN = 1
-+
Deleted: trunk/packages/arb/trunk/debian/patches/20_Makefile_main.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/20_Makefile_main.patch 2014-08-22 13:47:15 UTC (rev 17822)
+++ trunk/packages/arb/trunk/debian/patches/20_Makefile_main.patch 2014-08-22 14:12:16 UTC (rev 17823)
@@ -1,16 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Date: Thu, 26 Jul 2012 12:15:21 +0200
-Description: Some adaptations to Debian
- * Enable building with Debian default compiler
-
---- a/Makefile
-+++ b/Makefile
-@@ -96,7 +96,7 @@ ALLOWED_gcc_VERSIONS=\
- 4.6.1 4.6.2 4.6.3 \
- 4.7.1 4.7.2 4.7.3 \
- 4.8.0 4.8.1 4.8.2 4.8.3 \
-- 4.9.0 \
-+ 4.9.0 4.9.1 \
-
- # supported clang versions:
- ALLOWED_clang_VERSIONS=\
Deleted: trunk/packages/arb/trunk/debian/patches/30_tmpfile_CVE-2008-5378.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/30_tmpfile_CVE-2008-5378.patch 2014-08-22 13:47:15 UTC (rev 17822)
+++ trunk/packages/arb/trunk/debian/patches/30_tmpfile_CVE-2008-5378.patch 2014-08-22 14:12:16 UTC (rev 17823)
@@ -1,18 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-BugClosed: http://bugs.debian.org/508942
-Last-Update: Mon, 28 Jul 2014 15:31:20 +0200
-Description: This patch fixes tmpfile issues reported in CVE-2008-5378
-
---- a/SH/arb_panic
-+++ b/SH/arb_panic
-@@ -22,7 +22,9 @@ echo " There may be more than one datab
- echo " --------------------------------"
-
- for i in $chooser ; do
-- /bin/echo " - >" `ls $i` "<";
-+ if [ ! -L "$i" ] ; then
-+ /bin/echo " - >" `ls $i` "<";
-+ fi
- done
- echo " --------------------------------"
-
Deleted: trunk/packages/arb/trunk/debian/patches/50_fix_gcc-4.8.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/50_fix_gcc-4.8.patch 2014-08-22 13:47:15 UTC (rev 17822)
+++ trunk/packages/arb/trunk/debian/patches/50_fix_gcc-4.8.patch 2014-08-22 14:12:16 UTC (rev 17823)
@@ -1,15 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 28 Jul 2014 15:42:56 +0200
-Description: Propagate hardening options
-
---- a/GDE/AxML/Makefile
-+++ b/GDE/AxML/Makefile
-@@ -31,7 +31,7 @@ endif
- all : $(TARGET)
-
- $(TARGET) : $(OBJECTS)
-- $(CC) $(CFLAGS) -o $@ $< -lm
-+ $(CC) $(CFLAGS) -o $@ $< -lm $(LDFLAGS)
-
- .c.o:
- $(CC) $(CFLAGS) -c -o $@ $<
Deleted: trunk/packages/arb/trunk/debian/patches/60_use_debian_packaged_raxml.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/60_use_debian_packaged_raxml.patch 2014-08-22 13:47:15 UTC (rev 17822)
+++ trunk/packages/arb/trunk/debian/patches/60_use_debian_packaged_raxml.patch 2014-08-22 14:12:16 UTC (rev 17823)
@@ -1,39 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Description: Do not build raxml because we use Debian packaged version
-
---- a/GDE/Makefile
-+++ b/GDE/Makefile
-@@ -3,16 +3,9 @@ ARCHS_COMMON = \
- CLUSTAL/CLUSTAL.dummy \
- SUPPORT/SUPPORT.dummy \
- AxML/AxML.dummy \
-- RAxML/RAxML.dummy \
-- PHYML/PHYML.dummy \
-- MrBAYES/MrBAYES.dummy \
-
- ARCHS_NO_DEPENDS = \
- PHYML20130708/PHYML20130708.dummy \
-- MAFFT/MAFFT.dummy \
-- MUSCLE/MUSCLE.dummy \
-- PROBCONS/PROBCONS.dummy \
-- FASTTREE/FASTTREE.dummy \
-
- # --------------------------------------------------------------------------------
- # If a package is available as debian package it should go here
-@@ -22,9 +15,16 @@ ARCHS_NO_DEPENDS = \
-
- ARCHS_NON_DEBIAN = \
- CLUSTALW/CLUSTALW.dummy \
-+ FASTTREE/FASTTREE.dummy \
-+ MAFFT/MAFFT.dummy \
-+ MrBAYES/MrBAYES.dummy \
-+ MUSCLE/MUSCLE.dummy \
- PHYLIP/PHYLIP.dummy \
-+ PROBCONS/PROBCONS.dummy \
-+ RAxML/RAxML.dummy \
- TREEPUZZLE/TREEPUZZLE.dummy \
- FASTDNAML/FASTDNAML.dummy \
-+ PHYML/PHYML.dummy \
-
- # --------------------------------------------------------------------------------
-
Modified: trunk/packages/arb/trunk/debian/patches/series
===================================================================
--- trunk/packages/arb/trunk/debian/patches/series 2014-08-22 13:47:15 UTC (rev 17822)
+++ trunk/packages/arb/trunk/debian/patches/series 2014-08-22 14:12:16 UTC (rev 17823)
@@ -1,7 +0,0 @@
-10_config.makefiles.patch
-20_Makefile_main.patch
-21_Makefiles.patch
-30_tmpfile_CVE-2008-5378.patch
-50_fix_gcc-4.8.patch
-60_use_debian_packaged_raxml.patch
-70_hardening.patch
Modified: trunk/packages/arb/trunk/debian/rules
===================================================================
--- trunk/packages/arb/trunk/debian/rules 2014-08-22 13:47:15 UTC (rev 17822)
+++ trunk/packages/arb/trunk/debian/rules 2014-08-22 14:12:16 UTC (rev 17823)
@@ -18,96 +18,69 @@
ARB_64:=0
endif
+LD_LIBRARY_PATH := $(ARBHOME)/lib:$(LD_LIBRARY_PATH)
+PATH := $(ARBHOME)/bin:$(PATH)
+LC_ALL := C
+
+export ARBHOME LD_LIBRARY_PATH PATH LC_ALL
+
%:
- dh $@
+ dh $@ --parallel
+config.makefile: config.makefile.template
+ # ARB's build system is configured with config.makefile. This file is
+ # created on the first run of make from config.makefile.template. We
+ # just use sed here to set the desired parameters:
+ sed -e 's/DEVELOPER := ANY/DEVELOPER := RELEASE/;'\
+ -e 's/ARB_64 := 1/ARB_64 := $(ARB_64)/;'\
+ -e 's/# DEBIAN := 1/DEBIAN := 1/;' \
+ config.makefile.template > config.makefile
+
override_dh_auto_build:
- mkdir -p LIBLINK MAKEBIN lib/help
- export LC_ALL=C ; \
- export PATH=$(ARBHOME)/bin:$${PATH} ; \
- export LD_LIBRARY_PATH=$(ARBHOME)/lib:$${LD_LIBRARY_PATH} && \
- $(MAKE) DEBIAN=1 ARBHOME=$(ARBHOME) ARB_64=$(ARB_64) \
- CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" CXXFLAGS="$(CXXFLAGS)" LDFLAGS="$(LDFLAGS)" -lm \
- all && \
- export LD_LIBRARY_PATH=$(ARBHOME)/lib:$${LD_LIBRARY_PATH}; \
- cd HELP_SOURCE; $(MAKE) ARBHOME=$(ARBHOME) html
- #Ensure arb_edit4 was actually built
- ls bin/arb_edit4
+ $(MAKE) all
-# Remove links inside these directories because Makefile does not really clean
-# these directories
-DIRSTOREMOVELINKS=AWT ARBDBS ARBDB2 EDIT4 LIBLINK MAKEBIN NALIGNER NAMES_COM ORS_COM PROBE PROBE_COM PROBE_SERVER TOOLS bin lib/inputMasks lib/help
-# The following subdirectorys where created at compile time in some directories
-# but will not be removed by clean target
-SUBDIRSTOREMOVE=GENC GENH O
-# Sometimes clean target does not work as expected. Try to clean some dirs manually
-DIRSTOCLEAN=AISC AISC_MKPTPS SOURCE_TOOLS
+override_dh_auto_configure: config.makefile
-RemoveFromSourceAndBuild=PERL2ARB/Makefile PERL2ARB/ARB.c HELP_SOURCE/date.xsl \
- lib/arb_tcp.dat lib/ARB.pm \
- *.last_gcc TEMPLATES/arb_build.h \
- GDE/MOLPHY/prot_tml.h \
- PERL2ARB/perlmain.c \
- PERL2ARB/ARB.bs PERL_SCRIPTS/test/test.stamp PERL2ARB/MYMETA.yml
-FILESTOREMOVE=libXm.so.3 NALIGNER/NALIGNER.com lib/nas/names.dat $(RemoveFromSourceAndBuild) \
- GDE/PHYML20130708/phyml/config.h.in GDE/PHYML20130708/phyml/configure
-DIRSTOREMOVE=INCLUDE HELP_SOURCE/Xml lib/help lib/help_html PERL5 lib/perl5 PROBE_SERVER/bin PERL2ARB/blib/man3 PROBE_SET/bin NAMES_COM/DUMP PROBE_COM/DUMP
-DirsToKeepOnlyMAKEFILE=bin
-
-override_dh_auto_clean:
- # Make does only work if config.makefile exists which is only the
- # case when quilt has installed the patches. So there is neither
- # a need nor the expection of success if config.makefile is missing
- [ ! -f config.makefile ] || $(MAKE) DEBIAN=1 ARBHOME=$(ARBHOME) clean
-
- # fix broken clean process
- find . -type f -name "*.a" -delete
- find . -type f -name "*.o" -delete
- find . -type f -name "*.so" -delete
- rm -f `find bin -name "arb*" | grep -v ".pl$$"`
- rm -f `find $(DIRSTOREMOVELINKS) -type l`
- rm -f `find . -type f -name ".depends"`
- for dir in $(SUBDIRSTOREMOVE) ; do \
- rm -rf `find . -name $${dir} -type d` ; \
- done
- rm -f `find $(DirsToKeepOnlyMAKEFILE) -maxdepth 1 -type f | grep -v Makefile`
- rm -f `find PROBE_WEB/CLIENT -name \*.class -type f`
- rm -f `find PROBE_WEB/CLIENT -name \*.jar -type f`
- rm -f $(FILESTOREMOVE)
- rm -fr $(DIRSTOREMOVE)
- for dtc in $(DIRSTOCLEAN); do if [ -d $${dtc} ] ; then cd $${dtc}; make clean ; fi; done
- find . -name "*.stamp" -o -name "*.bs" -o -name ".exists" -delete
+override_dh_auto_clean: config.makefile
+ # config.makefile is required to run make clean, hence the dependency
+ # on ..._auto_configure.
+ $(MAKE) clean
+ rm config.makefile
+ # ARB does not have "distclean" or "realclean". Remove some leftovers:
rm -f UNIT_TESTER/Makefile.setup.local
+ find -name \*.log -a ! -name phyml-manual.log -print0 | xargs -0 rm -f
+ rm -f TEMPLATES/arb_build.h
override_dh_install:
- dh_install
- # remove files from arb package which are in arb-nas
- if [ -s debian/arb-nas.install ] ; then \
- for arbfile in `sed 's?^bin/\([^[:space:]]\+\)[[:space:]]\+\(.\+\)?debian/$(pkg)/\2/\1?' debian/arb-nas.install | grep debian/$(arb)` ; do \
- rm -f $${arbfile} ; \
- done ; \
- fi
+ # ARB has no "install" target. It has "tarfile_quick", though, which
+ # creates a tarball for distribution. We build this and unpack it
+ # into debian/tmp so that dh_install can pick up the files.
+ make tarfile_quick
+ rm -rf debian/tmp
+ mkdir debian/tmp
+ tar -C debian/tmp -xzf arb.tgz
+ rm -rf debian/tmp-dev
+ mkdir debian/tmp-dev
+ tar -C debian/tmp-dev -xzf arb-dev.tgz
+ rm arb.tgz arb-dev.tgz
+ dh_install --list-missing
# the check is needed to make sure it will not fail when doing binary-arch only builds
if [ -e debian/$(pkgcom)/usr/lib/arb/SH/arb_create_debian_conffile ] ; then \
- # Move SH/README to docs \
+ # Move SH/README :to docs \
cp -a SH/README debian/$(pkgcom)/usr/share/doc/arb/README_SH ; \
# Fix permission of scripts \
chmod a+x debian/$(pkgcom)/usr/lib/arb/SH/arb_create_debian_conffile ; \
chmod a+x debian/$(pkgcom)/usr/lib/arb/lib/macro.head ; \
fi
- # Man page is not really needed and throws just a lintian warning
- # mkdir `pwd`/debian/$(pkg)/usr/share/man/man3
- # perldoc PERL2ARB/ARB.pm > `pwd`/debian/$(pkg)/usr/share/man/man3/ARB.3pm
-
-
override_dh_strip:
# Fix rpath issue (once libarb is installed)
if [ -e debian/libarb/usr/lib/arb/lib/ARB.so ] ; then \
chrpath --delete debian/libarb/usr/lib/arb/lib/ARB.so ; \
fi
- dh_strip
+ dh_strip
+ find debian/libarb-dev -name \*.a -print0 | xargs -0 -n 1 strip
override_dh_shlibdeps:
dh_shlibdeps -a -l debian/libarb/usr/lib
@@ -115,6 +88,12 @@
override_dh_builddeb:
dh_builddeb -- -Z xz
+override_dh_fixperms:
+ dh_fixperms
+ -chmod 0644 debian/arb-common/etc/arb/submit/*
+ -chmod 0644 debian/libarb-dev/usr/include/arb/xml.hxx
+ -chmod 0755 debian/arb-common/usr/lib/arb/lib/macro.head
+
# To update po files as recommended in po-debconf(7)
debian/po/templates.pot: debian/arb-common.templates
@debconf-updatepo
Added: trunk/packages/arb/trunk/debian/source/include-binaries
===================================================================
--- trunk/packages/arb/trunk/debian/source/include-binaries (rev 0)
+++ trunk/packages/arb/trunk/debian/source/include-binaries 2014-08-22 14:12:16 UTC (rev 17823)
@@ -0,0 +1 @@
+debian/application-x-arb.png
Added: trunk/packages/arb/trunk/debian/source/options
===================================================================
--- trunk/packages/arb/trunk/debian/source/options (rev 0)
+++ trunk/packages/arb/trunk/debian/source/options 2014-08-22 14:12:16 UTC (rev 17823)
@@ -0,0 +1 @@
+extend-diff-ignore=PERL_SCRIPTS/test/test.stamp
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