--- arb-0.0.20071207.1.orig/debian/About +++ arb-0.0.20071207.1/debian/About @@ -0,0 +1,40 @@ +Initially, ARB was developed for rRNA data, however, the package also +supports handling and analysis of protein coding genes. + +Currently, the ARB software is under further development for genome +sequence database management. + +Highlighted features: + + - Any database entry can be visualised in the main window along with + a phylogenetic tree. Database access and navigation is possible via + mouse click in the displayed tree or by using a search tool. + + - Sequence and additional data can be im- and exported in a variety + of commonly used flat file formates. + + - A powerfull editor for real or virtual primary structures includes + versatile tools for string searching, automated alignment of + primary structures, local alignment optimisation, automated + secondary structure check as well as secondary structure + visualisation. + + - Conservation profiles and column filters can be established + according to user defined criteria applying different procedures. + + - Distance matrix, maximum parsimony and maximum likelihood based + phylogenetic treeing can be performed applying the respective + integrated tools. A special maximum parsimony approach allows + reconstruction and optimisation of comprehensive trees representing + the full sequence data set (currently more than 20.000 entries). + + - Publication ready trees can be generated and exported in various + formates. + + - The ARB PT server (positional tree) provides the basis for rapid + searching closest relatives or specific sequence signatures. Such + signatures can be evaluated as taxon specific probes against the + background of the full database. + + - The ARB project maintains processed databases for ribosomal RNAs + and selected evolutionary conserved genes. --- arb-0.0.20071207.1.orig/debian/arb-common.README.debian +++ arb-0.0.20071207.1/debian/arb-common.README.debian @@ -0,0 +1 @@ +Please read the docs in /usr/share/doc/arb. --- arb-0.0.20071207.1.orig/debian/arb-common.config +++ arb-0.0.20071207.1/debian/arb-common.config @@ -0,0 +1,77 @@ +#!/bin/sh +set -e + +PROG=arb +GROUP=${PROG} +PROGUSERS="" + +DEBCONF_DEBUG=developer + +. /usr/share/debconf/confmodule +db_version 2.0 + +## Add group ${PROG} if not existent + +## This returns the group including the members of the group which are needed later +TESTGROUP=`getent group ${GROUP}` || true +if [ -z "${TESTGROUP}" ] ; then + /usr/sbin/addgroup --system "${GROUP}" >/dev/null + # if the group was just created it can not have any users ... + PROGUSERS="none" +fi + +# store user info in TMPFILE +TMPFILE=`tempfile` + +[ -s /etc/adduser.conf ] && . /etc/adduser.conf +if [ _"$FIRST_UID" = _"" ] ; then + FIRST_UID=1000 +fi + +(IFS=":" + while read user pass uid gid name rest ; do + if [ "$uid" != "" ] ; then + # in case NIS is used on the machine $uid remains + # empty and breaks the following condition. + if [ $uid -ge $FIRST_UID -a "$user" != "" ] ; then + name=`echo $name | sed "s/,.*//"` + echo "$user ($name)" >> ${TMPFILE} + fi + fi + done < /etc/passwd +) + +# Login names of all users of the system as comma separated list +USERS=`sort -u "${TMPFILE}" | tr '\n' ',' | sed 's/,/&\ /g' | sed 's/, *$//g'` + +# "login (Real Name)" of group "${PROG}" as comma separated list +if [ "$PROGUSERS" != "none" ] ; then + PROGUSERS=`echo "${TESTGROUP}" | sed "s/.*:\([^:]*\)/\1/" | tr ',' '\n'` + # check whether the TESTGROUP contains any user or is just empty + if [ _"$PROGUSERS" != _"" ] ; then + TMPFILE2=`tempfile` + for user in "${PROGUSERS}" ; do + # add "|| true" because of -e option which would cause an exit otherwise + grep -w "$user" "$TMPFILE" >> "$TMPFILE2" || true + done + mv "$TMPFILE2" "$TMPFILE" + PROGUSERS=`sort -u "${TMPFILE}" | tr '\n' ',' | sed 's/,/&\ /g' | sed 's/, *$//g'` + fi +else + PROGUSERS="" +fi +rm -rf "${TMPFILE}" + +# Check for system users who just belong to group ${PROG} +if [ ! _"$PROGUSERS" = _"" ] ; then + db_set ${GROUP}/group "$PROGUSERS" || true +fi + +# Initialize List of Systemusers for debconf question +db_subst ${GROUP}/group users "$USERS" || true + +db_get ${GROUP}/group || true + +db_input high ${GROUP}/group || true + +db_go || true --- arb-0.0.20071207.1.orig/debian/arb-common.dirs +++ arb-0.0.20071207.1/debian/arb-common.dirs @@ -0,0 +1,2 @@ +usr/share/lintian/overrides +usr/bin --- arb-0.0.20071207.1.orig/debian/arb-common.install +++ arb-0.0.20071207.1/debian/arb-common.install @@ -0,0 +1,22 @@ +GDEHELP/DATA_FILES usr/lib/arb/GDEHELP +GDEHELP/ARB_GDEmenus etc/arb +PERL_SCRIPTS usr/lib/arb +SH usr/lib/arb +HELP_SOURCE/oldhelp/*.hlp usr/lib/arb/HELP_SOURCE/oldhelp +HELP_SOURCE/oldhelp/prompt usr/lib/arb/HELP_SOURCE/oldhelp +HELP_SOURCE/oldhelp/seer usr/lib/arb/HELP_SOURCE/oldhelp +lib/[d-gi-kmoqt-z]* usr/lib/arb/lib +lib/pi* usr/share/arb/lib +lib/rna3d usr/share/arb/lib +lib/s[a-tv-z]* usr/lib/arb/lib +lib/pts var/lib/arb +lib/arb_default/* usr/lib/arb/lib/arb_default +lib/help usr/lib/arb/lib +lib/ARB.pm usr/lib/arb/lib +GDEHELP/HELP_GEN/* usr/lib/arb/GDEHELP +lib/config.Linux usr/lib/arb/lib +debian/bin/arb_create_debian_conffile usr/lib/arb/SH +lib/nas/names.dat* var/lib/arb/nas +debian/About usr/share/doc/arb/ +lib/submit usr/share/doc/arb +demo.arb usr/share/doc/arb/examples --- arb-0.0.20071207.1.orig/debian/arb-common.links +++ arb-0.0.20071207.1/debian/arb-common.links @@ -0,0 +1,9 @@ +etc/arb/ARB_GDEmenus usr/lib/arb/GDEHELP/ARB_GDEmenus +var/lib/arb/pts usr/lib/arb/lib/pts +var/lib/arb/nas usr/lib/arb/lib/nas +usr/lib/arb/SH/arb_clean usr/bin/arb_clean +usr/share/doc/arb/html usr/lib/arb/lib/help_html +usr/share/doc/arb/submit usr/lib/arb/lib/submit +usr/share/arb/lib/pictures usr/lib/arb/lib/pictures +usr/share/arb/lib/pixmaps usr/lib/arb/lib/pixmaps +usr/share/arb/lib/rna3d usr/lib/arb/lib/rna3d --- arb-0.0.20071207.1.orig/debian/arb-common.manpages +++ arb-0.0.20071207.1/debian/arb-common.manpages @@ -0,0 +1 @@ +debian/bin/arb_clean.1 --- arb-0.0.20071207.1.orig/debian/arb-common.postinst +++ arb-0.0.20071207.1/debian/arb-common.postinst @@ -0,0 +1,53 @@ +#!/bin/sh +set -e + +PROG=arb +GROUP=${PROG} + +DEBCONF_DEBUG=developer +. /usr/share/debconf/confmodule +db_version 2.0 + +db_get ${PROG}/group +retusers=${RET} + +db_go || true + +CURRENTGROUPUSERS=`getent group ${GROUP} | sed "s/.*:\([^:]*\)/\1/" | tr ',' '\n'` + +# Add those users which were selected but are not yet in the group +for user in `echo "$retusers" | sed "s/([^)]*)//g" | sed "s/ //g" | tr ',' '\n'` ; do + if ! `echo "${CURRENTGROUPUSERS}" | grep -q -w "$user"` ; then + adduser $user $GROUP + fi +done + +# Del those users which were obviousely removed from list of ${PROG} users +for user in ${CURRENTGROUPUSERS} ; do + if ! `echo "$retusers" | grep -q -w "$user"` && \ + `getent group "$GROUP" | grep -q -w $user` ; then + deluser $user $GROUP + fi +done + +ptsdir=/var/lib/${PROG}/pts + +# Make sure that demo pts-server file can be accesed by members of group arb +[ -d ${ptsdir} ] || mkdir -p ${ptsdir} +ptsdemo=${ptsdir}/demo.arb +# Create empty pts-server demo file +touch $ptsdemo +chgrp ${GROUP} $ptsdemo +chmod 664 $ptsdemo + +# Make sure that users in group arb are able to write to pts-server dir +chgrp ${GROUP} $ptsdir +chmod 775 $ptsdir + +nasdir=/var/lib/${PROG}/nas +# Make sure that nameserver can be accesed by members of group arb +[ -d ${nasdir} ] || mkdir -p ${nasdir} +chgrp ${GROUP} $nasdir +chmod 775 $nasdir + +#DEBHELPER# --- arb-0.0.20071207.1.orig/debian/arb-common.preinst +++ arb-0.0.20071207.1/debian/arb-common.preinst @@ -0,0 +1,23 @@ +#!/bin/sh +set -e + +# Reason: When upgrading from a pre-0.0.20050526-4 version a directory +# /usr/share/arb/lib/nas exists and prevents setting the symlink from +# the package correctly. Thus this directory has to be removed first + +dirtoremove=/usr/share/arb/lib/nas + +case "$1" in + upgrade) + if [ ! -L $dirtoremove ] ; then + if [ -d $dirtoremove ] ; then + # Just rmdir the directory, if there should be some user + # files the user get's the information to clean the + # directory by the error message + rmdir $dirtoremove + fi + fi + ;; +esac + +#DEBHELPER# --- arb-0.0.20071207.1.orig/debian/arb-common.templates +++ arb-0.0.20071207.1/debian/arb-common.templates @@ -0,0 +1,6 @@ +Template: arb/group +Type: multiselect +Choices: ${users} +_Description: Arb users: + Please choose, among the list of all unprivileged users of the system, + those who will be allowed running ${pkg}. --- arb-0.0.20071207.1.orig/debian/arb-doc.doc-base +++ arb-0.0.20071207.1/debian/arb-doc.doc-base @@ -0,0 +1,14 @@ +Document: arb +Title: ARB Manuals +Author: Wolfgang Ludwig and Oliver Strunk +Abstract: Integrated package for data 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. +Section: Science/Biology + +Format: html +Index: /usr/share/doc/arb/html/index.html +Files: /usr/share/doc/arb/html/* --- arb-0.0.20071207.1.orig/debian/arb-doc.install +++ arb-0.0.20071207.1/debian/arb-doc.install @@ -0,0 +1,2 @@ +lib/help_html/* usr/share/doc/arb/html +HELP_SOURCE/oldhelp/arb.ps.gz usr/share/doc/arb/help --- arb-0.0.20071207.1.orig/debian/arb-doc.links +++ arb-0.0.20071207.1/debian/arb-doc.links @@ -0,0 +1 @@ +usr/share/doc/arb/html/manual.html usr/share/doc/arb/html/index.html --- arb-0.0.20071207.1.orig/debian/arb.README.debian +++ arb-0.0.20071207.1/debian/arb.README.debian @@ -0,0 +1,110 @@ +Arb for DEBIAN +-------------- + +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 +------------ + + - Arb comes with its own version of Phylip. Because Phylip has + its Debian package this is not build into arb package. Instead + I replaced links to the apropriate locations. + - Arb has its own version of FastDNAml which has also a separate + Debian package. Here also symlinks to the Debian packaged + version are used. + - Arb makes also use of a patched Version of ReadSeq. The Arb + version is identical with the latest C version (ReadSeq 2 is + written from scratch in Java). The Arb-Verion is missing some + patches, but has additional patches which make it incompatible + with the Debian packaged version. I try to clarify this issue. + - Arb has its own Version of tree-puzzle 5.0 which is completely + identical with the Debian version. Just not compile it and + set the apropriate links. + - I applied the arb patches of molphy to the upstream molphy. + 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. + - 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/ + So this package can be overriden by a separat package if + necessary. + - libmotif: I tried to compile Arb against liblesstif. The + package builds fine but when running the program some controls + are just missing or not usable. I will try future versions + of lesstif and Arb. + + +Comments regarding the packaging +-------------------------------- + +Config file: + + Under Debian GNU/Linux all configuration file have to be stored under /etc. + Thus the config file is symlinked from /usr/lib/arb/lib/arb_tcp.dat to + /etc/arb/arb_tcp.dat. + +User group arb: + + It has shown that arb users need to add their own PT_SERVER databases. + To enable users to create such database files and insert this file into + the config file a script arb-add-pt-server was written (see + "man arb-add-pt-server"). + +Dynamic libraries: + + The dynamic libraries which are builded by the upstream Arb Makefile + are moved from ${ARBHOME} to /usr/lib. Strangely enough these libraries + issue a warninig of + + dpkg-shlibdeps: warning: format of libA*.so not recognized + + which results in a lintian error + + E: libarb: sharedobject-in-library-directory-not-actually-a-shlib usr/lib/libA*.so + + This was reportet upstream and is topic of further investigations. + +Potentially separate package + + Formerly arb_ntree was separated in an extra package which makes no + real sense because it is the main Arb application. The only target + for splitting would be PT-Server (binary bin/arb_pt_server - needs + libraries+(arb_)gene_probe) + +Andreas Tille , Sat, 20 Oct 2001 08:09:48 +0200 --- arb-0.0.20071207.1.orig/debian/arb.install +++ arb-0.0.20071207.1/debian/arb.install @@ -0,0 +1,7 @@ +bin/[A-LN-Zabcd-z]* usr/lib/arb/bin +debian/bin/arb usr/bin +debian/bin/arb-add-pt-server usr/bin +debian/bin/arb-kill usr/bin +debian/arb.xpm usr/share/arb +debian/conf/arb_tcp.dat etc/arb +debian/conf/arb.conf etc/arb --- arb-0.0.20071207.1.orig/debian/arb.links +++ arb-0.0.20071207.1/debian/arb.links @@ -0,0 +1,40 @@ +usr/bin/readseq usr/lib/arb/bin/arb_readseq +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 +usr/lib/phylip/bin/dnacomp usr/lib/arb/bin/dnacomp +usr/lib/phylip/bin/dnadist usr/lib/arb/bin/dnadist +usr/lib/phylip/bin/dnainvar usr/lib/arb/bin/dnainvar +usr/lib/phylip/bin/dnaml usr/lib/arb/bin/dnaml +usr/lib/phylip/bin/dnamlk usr/lib/arb/bin/dnamlk +usr/lib/phylip/bin/dnamove usr/lib/arb/bin/dnamove +usr/lib/phylip/bin/dnapars usr/lib/arb/bin/dnapars +usr/lib/phylip/bin/dnapenny usr/lib/arb/bin/dnapenny +usr/lib/phylip/bin/dollop usr/lib/arb/bin/dollop +usr/lib/phylip/bin/dolmove usr/lib/arb/bin/dolmove +usr/lib/phylip/bin/dolpenny usr/lib/arb/bin/dolpenny +usr/lib/phylip/bin/drawgram usr/lib/arb/bin/drawgram +usr/lib/phylip/bin/drawtree usr/lib/arb/bin/drawtree +usr/lib/phylip/bin/factor usr/lib/arb/bin/factor +usr/lib/phylip/bin/fitch usr/lib/arb/bin/fitch +usr/lib/phylip/bin/gendist usr/lib/arb/bin/gendist +usr/lib/phylip/bin/kitsch usr/lib/arb/bin/kitsch +usr/lib/phylip/bin/mix usr/lib/arb/bin/mix +usr/lib/phylip/bin/move usr/lib/arb/bin/move +usr/lib/phylip/bin/neighbor usr/lib/arb/bin/neighbor +usr/lib/phylip/bin/pars usr/lib/arb/bin/pars +usr/lib/phylip/bin/penny usr/lib/arb/bin/penny +usr/lib/phylip/bin/proml usr/lib/arb/bin/proml +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 --- arb-0.0.20071207.1.orig/debian/arb.manpages +++ arb-0.0.20071207.1/debian/arb.manpages @@ -0,0 +1,3 @@ +debian/bin/arb.1 +debian/bin/arb-kill.1 +debian/bin/arb-add-pt-server.1 --- arb-0.0.20071207.1.orig/debian/arb.menu +++ arb-0.0.20071207.1/debian/arb.menu @@ -0,0 +1,2 @@ +?package(arb):needs="X11" section="Applications/Science/Biology" \ + title="Arb" icon="/usr/share/arb/arb.xpm" command="/usr/bin/arb" --- arb-0.0.20071207.1.orig/debian/arb.postinst +++ arb-0.0.20071207.1/debian/arb.postinst @@ -0,0 +1,26 @@ +#!/bin/sh +set -e + +PROG=arb +GROUP=${PROG} +CONFFILE=/etc/${PROG}/${PROG}_tcp.dat + +## Add group ${PROG} if not existent +TESTGROUP="`getent group ${GROUP}`" || true +if [ -z "${TESTGROUP}" ] ; then + /usr/sbin/addgroup --system "${GROUP}" >/dev/null +fi + +if [ -e /usr/share/${PROG}/SH/arb_create_debian_conffile ] ; then + /usr/share/${PROG}/SH/arb_create_debian_conffile +fi + +ARBLIBDIR=/usr/lib/${PROG}/lib/ +if [ ! -d ${ARBLIBDIR} ] ; then + mkdir -p ${ARBLIBDIR} +fi +if [ ! -L ${ARBLIBDIR}/`basename ${CONFFILE}` ] ; then + ln -s ${CONFFILE} ${ARBLIBDIR}/`basename ${CONFFILE}` +fi + +#DEBHELPER# --- arb-0.0.20071207.1.orig/debian/arb.xpm +++ arb-0.0.20071207.1/debian/arb.xpm @@ -0,0 +1,18 @@ +/* XPM */ +static char * arb_xpm[] = { +"31 13 2 1", +" c None", +". c #000000", +" .. ", +" ... .. ", +" .... .. ", +" ..... .. ", +" ...... ... ... ", +" ... .. .... ..... ", +" ... .. ...... ..... ", +" ... .. .. ..", +" ... .. .. ..", +" ... .. ... ..", +" ... .. .. ...", +" ... .. .. ........ ", +"... .. .. ...... "}; --- arb-0.0.20071207.1.orig/debian/changelog +++ arb-0.0.20071207.1/debian/changelog @@ -0,0 +1,297 @@ +arb (0.0.20071207.1-5) unstable; urgency=low + + * Fix tempfile issues in upstream scripts + Closes: #496396 + * Fix arb name server location in config file (Thanks to + Felipe Figueiredo ) + Closes: #495650 + * arb-common.config: Make sure that config file will not fail + when NIS is used + + -- Andreas Tille Tue, 23 Sep 2008 13:32:05 +0200 + +arb (0.0.20071207.1-4) unstable; urgency=low + + * debian/arb-common.postrm: Remove stuff arb leaves behind in + /var/lib in case the package is purged + Closes: #463010 + * More precise copyright / license statements in debian/copyright + * debian/arb-doc.lintian-overrides: Explain why arb-doc should + not be in section doc + * Moved debian/*.lintian.overrides to *.lintian-overrides and + make use of dh_lintian (includes increasing versioned depends + of debhelper to >= 6.0.7) + * Strip rpath from ARB.so using chrpath + * Better short description which was to generic after [Biology] + marker was removed. + + -- Andreas Tille Wed, 23 Jul 2008 08:10:46 +0200 + +arb (0.0.20071207.1-3) unstable; urgency=low + + [ Charles Plessy ] + * Changed the doc-base section according to the new policy. + + [ Andreas Tille ] + * Updated dependency from libglew (Build-Depends: libglew-dev -> + libglew1.5-dev) + Closes: #489330 + * Standards-Version: 3.8.0 (no changes needed) + * debian/patches/30_Makefile_main: Enable gcc-4.3 + * Applied upstream patches to compile with gcc-4.3 (thanks to + Ralf Westram ) + + -- Andreas Tille Mon, 07 Jul 2008 09:11:40 +0200 + +arb (0.0.20071207.1-2) unstable; urgency=low + + * Added XS-Autobuild: yes to enable autobuilding + * Slightly enhanced description + + -- Andreas Tille Thu, 06 Mar 2008 23:23:07 +0100 + +arb (0.0.20071207.1-1) unstable; urgency=low + + [ David Paleino ] + * debian/control: + - Standards-Version 3.7.3 + - long lines wrapped + - architecture set to "any" for architecture-dependent packages + - fixed some typos in long descriptions + - removed [Biology] pseudo-tag from short descriptions -- why not + using DebTags? + - updated Vcs-* fields + - added myself to Uploaders + - removing XS- from DM-Upload-Allowed + * debian/watch added + * debian/po/it.po added + * debian/rules updated + + [ Andreas Tille ] + * New upstream source + debian/get-orig-source: Obtain official release. + Remark: The originally downloaded source from 2007_12_07 was + different from the currently available one. This is expressed + in the additional ".1" in the version number. + * Removed warning from long description because this is now an + official release + * debian/rules: + - removed get-orig-source.old target + - added missing '-' in clean target + * Switched to quilt (dpatch was not able to apply patches + from previous version) + + -- Andreas Tille Mon, 25 Feb 2008 09:34:30 +0100 + +arb (0.0.20071207-1) unstable; urgency=low + + * New upstream version + Closes: #446666 + * Added Build-Depends libglew-dev which is needed for 3D version + * Added Build-Depends libxpm4-dev according to the advise of + Charles Plessy in bug #364908 + * Added x11proto-print-dev, libxpm-dev, libxp-dev, + libgl1-mesa-swx11-dev (> 6.5.1-0.4) + to build dependencies + * Added to Build-Depends: libtiff4-dev, libxaw7-dev + * Standards-Version: 3.7.2 (no changes necessary) + * debhelper 5 + * use dpatch + * Added license of new component RAxML to debian/copyright + * Substituded ${Source-Version} by ${source:Version} resp. + ${binary:Version} + * debian/arb.menu: Applications/Science/Biology + * move files from lib/* directly to /usr/lib/arb/lib instead of + /usr/share/arb/lib and a bunch of symlinks + * Set maintainer to Maintainer: Debian-Med Packaging Team + + * Added Portugese debconf translations (thanks to Miguel Figueiredo + + Closes: #341558 + * Updated Czech debconf translations (thanks to Jakub Kasparec + ) + Closes: #356713, #392683 + * Do not build molphy and symlink to molphy executables instead + * New configuration file format for arb_tcp.dat + * Added Vcs-Browser, Vcs-Svn + * Moved Homepage from long description to tags field + + -- Andreas Tille Mon, 05 Nov 2007 18:17:32 +0100 + +arb (0.0.20050526-7) unstable; urgency=low + + * arb-common recommends arb + * Added Build-Depends: g++ + * Because there is no sign that this version shows the behaviour + reported in #325640 against the former version and the bug reporter + did not respond to any request I decide to close this bug. Feel + free to reopen if it seems necessary. + Clsoes: #325640 + + -- Andreas Tille Mon, 21 Nov 2005 14:09:01 +0100 + +arb (0.0.20050526-6) unstable; urgency=low + + * Added transfig to depends + * Removed "Depends: arb" from arb-common to avoid circular dependencies + Closes: #339861 + * Added gcc 4.0.3 to supported compilers in Makefile + + -- Andreas Tille Wed, 9 Nov 2005 13:17:52 +0100 + +arb (0.0.20050526-5) unstable; urgency=low + + * Enable writing of large amounts of sequence files. (Thanks for + the patch to Elmar Pruesse ) + Closes: #333391 + * Updated Swedish debconf template (Thanks to Daniel Nylander + ) + Closes: #332788 + * Updated French debconf template (Thanks to Jean-Luc Coulon + ) + Closes: #333108 + + -- Andreas Tille Wed, 12 Oct 2005 09:25:15 +0200 + +arb (0.0.20050526-4) unstable; urgency=low + + * Included names.dat.template in arb-common:/var/lib/nas + actually not only the file is missing but the directory of the file + is also not found because a link to /var/lib/arb/nas is needed + To enable a clean installation of the link the old empty directory + has to be removed in a preinst script + * Fixed location of arb nameserver in debian/conf/{arb_tcp,arb_ntree}.dat + Closes: #332436 + * Make sure that nameserver directory is accessible by members of group + arb in postinst file + * Changed debconf template to ask for arb users + * Added warning to arb wrapper script if the user who starts arb is not + yet member of group arb and thus not allowed to write to /var/lib/arb + + -- Andreas Tille Thu, 6 Oct 2005 21:38:12 +0200 + +arb (0.0.20050526-3) unstable; urgency=low + + * Added Swedish debconf templates translation (thanks to + Daniel Nylander + Closes: #330428 + * Added ssh to dependencies because it is used in some scripts + * Dropped last version number in Standards-Version (now: 3.6.2) + + -- Andreas Tille Wed, 28 Sep 2005 11:18:17 +0200 + +arb (0.0.20050526-2) unstable; urgency=low + + * Added explicite permission to distribute with Debian to + debian/copyright + * Fixed debian/rules + WINDOW/Makefile to ensure that libARB can be found + in the build process (Many thanks to Petr Salinger ) + * Reduced number of architectures to the set that features xviewg-dev + + -- Andreas Tille Thu, 8 Sep 2005 14:08:07 +0200 + +arb (0.0.20050526-1) unstable; urgency=low + + * New upstream version. + * Added disclaimer from FTP-download directory to debian/arb.README.Debian + and debian/copyright + * Added parts of the disclaimer from FTP-download directory to + debian/control + * Patch for NAMES/names.cxx (Thanks to Petr Salinger ) + + -- Andreas Tille Tue, 30 Aug 2005 09:49:01 +0200 + +arb (0.0.20050506-3) unstable; urgency=low + + * Recommend: xfig + * solved debconf | debconf-2.0 issue by ${misc:Depends} + * debian/control: Homepage: http://www.arb-home.de/ + * Renamed debian/po/cz.po to cs.po (Thanks to Denis Barbier ) + Closes: #325062 + * Depends: freeglut3-dev | libglu-dev + * Build-Depends: libpng12-dev (Thanks to Petr Salinger ) + * Some patches that where necessary for building with gcc 4.0.x + (Thanks to Petr Salinger ) + * arb-common: Depends: adduser + * arb-common.config: Removed bashism + + -- Andreas Tille Fri, 26 Aug 2005 12:58:01 +0200 + +arb (0.0.20050506-2) unstable; urgency=low + + * Enable killing all arb processes in arb-kill + * Standards-Version: 3.6.2.1 + * menu items moved (no changes in packaging, just use new debhelper) + * Czech debconf translation, thanks to Igor Jasa + Closes: #318442 + + -- Andreas Tille Wed, 1 Jun 2005 13:15:04 +0200 + +arb (0.0.20050506-1) unstable; urgency=low + + * New upstream version + * Adapted get-orig-source target to new directory layout + * Added French debconf template + Closes: #309222 + + -- Andreas Tille Mon, 30 May 2005 15:17:44 +0200 + +arb (0.0.20050318-1) unstable; urgency=low + + * New upstream snapshot + * Added freeglut3-dev and libglew-dev Build-dependency + * First official package uploaded to Debian + Closes: #282037 + + -- Andreas Tille Thu, 10 Mar 2005 11:23:28 +0100 + +arb (0.0.20041206-1) unstable; urgency=low + + * New upstream snapshot + * Reintegrate also arb-nas package because it is the main + Arb application according to the author. It makes no sense + to separate it in an extra package. + + -- Andreas Tille Mon, 06 Dec 2004 10:48:01 +0100 + +arb (0.0.20041112-4) unstable; urgency=low + + * Group arb which has rw-permissions to arb databases + * Split configuration file into several pieces and megre them in + postinst. This enables splitting into several independent packages + because upstream uses a single config file + * Script arb-add-pt-server enables users of group arb to add + PT_SERVER entries to configuration files + * Manage users of group arb via debconf + + -- Andreas Tille Tue, 23 Nov 2004 12:50:22 +0100 + +arb (0.0.20041112-3) unstable; urgency=low + + * Dropped package arb-extra and abr-server after discussing with the + authors because it does not really make sense to split this from + main package. + * Enhanced package arb-nas + * New package libarb with dynamic libraries + + -- Andreas Tille Fri, 19 Nov 2004 15:56:53 +0100 + +arb (0.0.20041112-2) unstable; urgency=low + + * Compile with libmotif-dev because liblesstif has trouble with + some controls in the search inteface. + * Moved some files to the server package. + * Exclude arb/lib/BUGS from package because its irrelevant + * Move arb/lib/help_html to doc package + * Wrote placeholder manpage + * Added lintian.overrides + * Moved arb_tcp.dat to /etc/arb and set symlink + + -- Andreas Tille Tue, 16 Nov 2004 18:23:59 +0100 + +arb (0.0.20041112-1) unstable; urgency=low + + * Inoffcial test release. + + -- Andreas Tille Fri, 12 Nov 2004 13:15:16 +0100 + --- arb-0.0.20071207.1.orig/debian/compat +++ arb-0.0.20071207.1/debian/compat @@ -0,0 +1 @@ +6 --- arb-0.0.20071207.1.orig/debian/control +++ arb-0.0.20071207.1/debian/control @@ -0,0 +1,83 @@ +Source: arb +Section: non-free/science +Priority: extra +Maintainer: Debian-Med Packaging Team +DM-Upload-Allowed: yes +Uploaders: Andreas Tille , + David Paleino +Build-Depends: debhelper (>= 6.0.7), quilt, libmotif-dev, xviewg-dev, + rxp, lynx, sablotron, libtiff4-dev, libxaw7-dev, kaffe | free-java-sdk, + freeglut3-dev | libglu-dev, libglew1.5-dev, libpng12-dev, x11proto-print-dev, + libxpm-dev, libxp-dev, libglw1-mesa-dev, perl-doc, chrpath +Standards-Version: 3.8.0 +Homepage: http://www.arb-home.de/ +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/arb/trunk/?rev=0&sc=0 +Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/arb/trunk/ +XS-Autobuild: yes + +Package: arb +Architecture: any +Depends: ${shlibs:Depends}, libarb (= ${binary:Version}), arb-common (= ${source:Version}), + phylip (>= 3.6b), fastdnaml (>= 1.2.2-4), readseq (>= 1-1), tree-puzzle (>=5.0-3), molphy, + ssh, transfig +Recommends: xfig +Suggests: arb-database, gnuplot, 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 + 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. + +Package: libarb +Architecture: any +Depends: ${shlibs:Depends} +Recommends: arb +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 the dynamic libraries which are used by arb. + +Package: arb-common +Architecture: all +Depends: arb-doc (= ${source:Version}), adduser, ghostscript | postscript-preview, gv | postscript-viewer, + perl-modules, ${perl:Depends}, ${misc:Depends} +Recommends: arb +Suggests: xview-clients +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. + . + Architecture independent scripts of Arb. + +Package: arb-doc +Architecture: all +Depends: ghostscript | postscript-preview, gv | postscript-viewer +Suggests: arb +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. + . + Documentation for ARB. --- arb-0.0.20071207.1.orig/debian/copyright +++ arb-0.0.20071207.1/debian/copyright @@ -0,0 +1,204 @@ +Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat +Upstream-Author: Arb development team , + Ralf Westram +Packaged-By: Andreas Tille +Packaged-Date: Thu, 03 Jun 2004 11:17:55 +0200 +Upstream-Source: http://download.arb-home.de/src/ + +Files: debian/* +Copyright: (C) 2008 Andreas Tille +License: GPL +X-Comment: On Debian systems, the complete text of the GNU Public + License can be found in `/usr/share/common-licenses/GPL'. + +Files: * +License: ARB copyright and license information + * The ARB software and documentation are not in the public domain. + * External programs distributed together with ARB are copyrighted + by and are the property of their respective authors unless otherwise stated. + * All other copyrights are owned by Lehrstuhl fuer Mikrobiologie, TU Muenchen. + . + USAGE LICENSE + . + You have the right to use this version of ARB for free. Please read as well the + attached copyright notices below whether you may or may not install this package. + . + REDISTRIBUTION LICENSE + . + * This release of the ARB program and documentation may not be sold or + incorporated into a commercial product, in whole or in part, without + the expressed written consent of the Technical University of Munich and + of its supervisors Oliver Strunk, Ralf Westram & Wolfgang Ludwig. + * All interested parties may redistribute and modify ARB as long as all + copies are accompanied by this license information and all copyright + notices remain intact. Parties redistributing ARB must do so on a non-profit + basis, charging only for cost of media. + * If you modify parts of ARB and redistribute these changes the + 'Lehrstuhl fuer Mikrobiologie' gains the right to incorporate these changes + into ARB and to redistribute them with future versions of ARB. + . + Disclaimer + . + THE TU MUENCHEN AND THE VARIOUS AUTHORS OF ARB GIVE NO WARRANTIES, EXPRESSED + OR IMPLIED FOR THE SOFTWARE AND DOCUMENTATION PROVIDED, INCLUDING, BUT NOT + LIMITED TO WARRANTY OF MERCHANTABILITY AND WARRANTY OF FITNESS FOR A PARTICULAR + PURPOSE. + User understands the software is a research tool for which no warranties as to + capabilities or accuracy are made, and user accepts the software "as is." + User assumes the entire risk as to the results and performance of the software + and documentation. The above parties cannot be held liable for any direct, + indirect, consequential or incidental damages with respect to any claim by user + or any third party on account of, or arising from the use of software and + associated materials. This disclaimer covers both the ARB core applications and + all external programs used by ARB. + . + Additional not for Debian packaging: + . + Hereby anybody is granted the right to build debian-pakets of the ARB + software package (http:://www.arb-home.de/) and publish them on debian + mirrors (or any other way of debian-distribution). + . + This includes any debian derivates like ubuntu. + . + The ARB developers may (but most likely wont ever) revoke this + granting. If really done so, it'll only affect ARB versions released + after such a revocation. + . + 9. July 2008 + Ralf Westram +Copyright: (C) 1994-2008 + Department of Microbiology: + - Dr. Wolfgang Ludwig (Biologist) + Task: Group Leader; Inventor of ARB, knows everything about it + - Ralf Westram (Computer scientist) + Task: General ARB development + - Dr. Lothar Richter (Biologist) + Task: ARB Database Curation and Automatization + - Arno Buchner (Biologist) + Task: ARB Database Curation and Genomics + . + Department of Computer Science: + - Prof. Dr. Thomas Ludwig + Task: Computer Science Supervisor + - Dr. Harald Meier (Biologist) + Task: ARB GENOME programming + - Gangolf Jobb (Biologist) + Task: Development and integration of alignment- and tree-generation-software + +X-Comment: Copyright notices for programs distributes together with ARB + +Files: GDE/* +License: + * The Genetic Data Environment (GDE) software and documentation are not in the + public domain. Portions of this code are owned and copyrighted by the + The Board of Trustees of the University of Illinois and by Steven Smith. + External functions used by GDE are the property of their authors. + This release of the GDE program and documentation may not be sold, or + incorporated into a commercial product, in whole or in part without the + expressed written consent of the University of Illinois and of its author, + Steven Smith. + * All interested parties may redistribute the GDE as long as all copies are + accompanied by this documentation, and all copyright notices remain intact. + Parties interested in redistribution must do so on a non-profit basis, + charging only for cost of media. Modifications to the GDE core editor + should be forwarded to the author Steven Smith. External programs used + by the GDE are copyrighted by, and are the property of their respective + authors unless otherwise stated. + + +Files: GDE/PHYLIP/* +Copyright: (c) Copyright 1986-1993 by Joseph Felsenstein and the University + of Washington. +License: Permission is granted to copy this document provided that + no fee is charged for it and that this copyright notice is not removed. +X-Comment: Remark from the Debian package maintainer Andreas Tille + Phylp is not used in the binary package because the Debian + package is used which is in the non-free part of Debian. + Remark: After heavy discussion with the author of Phylip it + was not possible to convince him to use a free license. + +Files: GDE/SUPPORT/CAP2.c +Copyright: (C) 1991 Xiaoqiu Huang +License: The distribution of the program is granted provided no charge + is made and the copyright notice is included. +X-Comment: Remark from the Debian package maintainer Andreas Tille + I was unable to find a source URL where this program which is + claimed as external can be downloaded. + +Files: CONVERTALN/* +Copyright: (C) 1992 Wen-Min Kuan +License: The files in this directory do not contain an explicite license + statement. It has to be assumed that the license is the same as the + general usage and redistribution license for Arb and the authors of + Arb got a permission to distribute this code in their product. + . + This paragraph was just added to the copyright file to mention that + there is some copyrighted work which was not mentioned above. +X-Comment: convert_aln -- an alignment(or sequence) converter written + by Wen-Min Kuan for the Ribsomal Database Project(RDP), April 28, 1992. + . + Remark from the Debian package maintainer Andreas Tille: + I was unable to find a source URL where this program which is + claimed as external can be downloaded. + +Files: GDE/FASTDNAML/* +Copyright: (C) 1998, 1999, 2000 by Gary J. Olsen, + 1986 - 1990 by the University of Washington and Joseph Felsenstein. +License: GPL +X-Comment: On Debian systems, the complete text of the GNU Public + License can be found in `/usr/share/common-licenses/GPL'. + . + Remark from the Debian package maintainer Andreas Tille: + This is not used in the binary package because it is available as + official Debian package and has a free license (see this package). + +Files: GDE/RAxML/[a]* +Copyright: (C) 2004-2008 Alexandros Stamatakis, Michael Ott, Thomas Ludwig +License: GPL +Comment: There is also a file GDE/RAxML/softwaredisclaimer in this directory + which contains some license text which might be provided in a private + mail or whatever from the RAxML authors to the Arb authors. The relevance + of this file is completely unclear because RAxML as it can be obtained from + http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm is GPLed and the + remaining files in this directory are neither copyrighted by the RAxML + authors nor do they feature a similar license statement. This file is + subject for clarification by the Arb authors. + +Files: GDE/RAxML/[cdp]* +Copyright: (C) 1993-2002 by the University of Washington. + Written by Joseph Felsenstein, Hisashi Horino, and others +License: Permission is granted to copy and use this program provided no + fee is charged for it and provided that this copyright notice is not + removed. + +Files: GDE/RAxML/[g]* +Copyright: (C) 1987, 1993, 1994 + The Regents of the University of California. All rights reserved. +License: BSD + +Files: GDE/TREEPUZZLE/* +Copyright: (C) 1995-1999 Korbinian Strimmer and Arndt von Haeseler + (C) 1999-2001 Heiko A. Schmidt, Korbinian Strimmer,Martin Vingron, + Arndt von Haeseler +License: GPL +X-Comment: On Debian systems, the complete text of the GNU Public + License can be found in `/usr/share/common-licenses/GPL'. + . + This code is not used in the binary package because it is available as + official Debian package and has a free license (see this package). + +Files: READSEQ/* +Copyright: 1990-1993 D. Gilbert +License: Public Domain +X-Comment: This code is not used in the binary package because it is + available as official Debian package and has a free license (see this + package). + +Files: GDE/MOLPHY/* +Copyright: (c) 1992-1996, Jun Adachi & Masami Hasegawa +License: MOLPHY is a free software, and you can use and redistribute it. +X-Comment: I wrote an e-mail to the authors if they could fix this license + because it conflicts with DFSG #3 (Derived works) but I got no response yet. + . + This code is also not used in the binary package because the Debian + package is used which is in the non-free part of Debian. --- arb-0.0.20071207.1.orig/debian/get-orig-source +++ arb-0.0.20071207.1/debian/get-orig-source @@ -0,0 +1,55 @@ +#!/bin/sh -e +set -e +#set -x +NAME=arb +UVERSION=2007_12_07 +UTARBALL=${NAME}src_${UVERSION}.tgz +downloadurl=http://download.arb-home.de/src/ + +RemoveFilesFromSource="GDEHELP/HELP_DOC_GEN/* GDEHELP/HELP_GEN/* GDEHELP/ARB_GDEmenus GDEHELP/helpfiles.lst HELP_SOURCE/_index.html NTREE/nt_date.h lib/ARB.pm" + +TMPDIR=../tarballs +mkdir -p "$TMPDIR" +cd "$TMPDIR" + +if [ -e ${UTARBALL} ] ; then + echo "Using existing tarball ${UTARBALL}" +else + wget --quiet ${downloadurl}/${UTARBALL} +fi + +if [ "$UVERSION" != "" ] ; then + VERSION=0.0.`echo $UVERSION | sed -e 's/_//g'`.1 +else + # Several releases do not contain a version in the tarball name, so + # use versioning according to newest file inside tarball + VERSION=`ls -lt "$UTARBALL" | grep '^[^d]rw.r' | sed -e '2,$d' -e 's/^.[-rwxr]\{9\} \+[0-9] \w\+ \w\+[[:space:]]\+[0-9]\+ \([0-9]\{4\}\)-\([0-9]\{2\}\)-\([0-9]\{2\}\).*/0.0.\1\2\3/'` +fi +mkdir -p arbdir +cd arbdir +tar -xzf ../"$UTARBALL" + +cd .. +mv arbdir "$NAME"-"$VERSION" +cd "$NAME"-"$VERSION" + +rm -rf `find . -type d -name CVS` +rm -rf `find . -type f -name ".#*"` +rm -rf ${RemoveFilesFromSource} +find . -name .cvsignore -exec rm -f \{\} \; +rm -f HELP_SOURCE/oldhelp/help.tar +find lib ! -newer lib/config.HP-UX -exec touch -r lib/config.HP-UX \{\} \; +find SH ! -newer SH/arb_ale -exec touch -r SH/arb_ale \{\} \; +find PERL_SCRIPTS ! -newer SH/arb_ale -exec touch -r SH/arb_ale \{\} \; +find HELP_SOURCE ! -newer SH/arb_ale -exec touch -r SH/arb_ale \{\} \; +rm -f SH/arb_oneach +# remove binary that should be installed on modern systems anyway +rm -f zcat + +chmod 644 lib/submit/* + +cd .. + +GZIP=-9 tar -czf "$NAME"_"$VERSION".orig.tar.gz "$NAME"-"$VERSION" + +rm -rf "$NAME"-"$VERSION" --- arb-0.0.20071207.1.orig/debian/libarb.install +++ arb-0.0.20071207.1/debian/libarb.install @@ -0,0 +1 @@ +lib/*.so usr/lib/arb/lib --- arb-0.0.20071207.1.orig/debian/libarb.dirs +++ arb-0.0.20071207.1/debian/libarb.dirs @@ -0,0 +1 @@ +usr/share/lintian/overrides --- arb-0.0.20071207.1.orig/debian/rules +++ arb-0.0.20071207.1/debian/rules @@ -0,0 +1,178 @@ +#!/usr/bin/make -f +# debian/rules for arp using quilt + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +pkg=arb +pkgcom=$(pkg)-common +pkgdoc=$(pkg)-doc +### pkgnas=$(pkg)-nas +### do not build server-package any more +### pkgserv=$(pkg)-server +common=debian/$(pkgcom) + +include /usr/share/quilt/quilt.make + +build: build-stamp debian/po/templates.pot +build-stamp: patch + dh_testdir + + mkdir -p LIBLINK MAKEBIN lib/help + export ARBHOME=`pwd` ; \ + export LC_ALL=C ; \ + export PATH=$${ARBHOME}/bin:$${PATH} ; \ + export LD_LIBRARY_PATH=$${ARBHOME}/lib:$${LD_LIBRARY_PATH}; \ + $(MAKE) DEBIAN=1 all + export ARBHOME=`pwd` ; \ + export LC_ALL=C ; \ + export PATH=$${ARBHOME}/bin:$${PATH} ; \ + export LD_LIBRARY_PATH=$${ARBHOME}/lib:$${LD_LIBRARY_PATH}; \ + $(MAKE) DEBIAN=1 arbxtras + + touch $@ + +# 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 + +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 +FILESTOREMOVE=libXm.so.3 NALIGNER/NALIGNER.com lib/nas/names.dat $(RemoveFromSourceAndBuild) +DIRSTOREMOVE=INCLUDE HELP_SOURCE/Xml lib/help lib/help_html PERL5 lib/perl5 PROBE_SERVER/bin PERL2ARB/blib/man3 PROBE_SET/bin +DirsToKeepOnlyMAKEFILE=bin + +clean: realclean unpatch +realclean: + dh_testdir + dh_testroot + + # 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) clean + + # fix broken clean process + find . -type f -name "*.a" -exec rm -f \{\} \; + find . -type f -name "*.o" -exec rm -f \{\} \; + find . -type f -name "*.so" -exec rm -f \{\} \; + 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 + + dh_clean build-stamp + +install: +install: build + dh_testdir + dh_testroot + dh_clean -k + dh_installdirs + + dh_install + dh_link + + # 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/arb/\2/\1?' debian/arb-nas.install | grep debian/arb` ; do \ + rm -f $${arbfile} ; \ + done ; \ + fi + + # Fix permissions + chmod 755 debian/arb-common/usr/lib/arb/SH/* + chmod 755 debian/arb-common/usr/lib/arb/PERL_SCRIPTS/IFTHELP/* + chmod 644 debian/arb-common/usr/lib/arb/lib/pixmaps/*.xpm + # Remove thumbnail dir + rm -rf debian/arb-common/usr/lib/arb/lib/pixmaps/.xvpics + +# Build architecture-independent files here. +binary-indep: build install + dh_testdir -i + dh_testroot -i + dh_installdebconf -i + dh_installdocs -i + dh_installexamples -i + dh_installmenu -i +# dh_installlogrotate -i +# dh_installpam -i +# dh_installmime -i +# dh_installinit -i + dh_installcron -i + dh_installman -i + dh_installinfo -i + dh_installchangelogs -i + dh_lintian -i + dh_link -i + dh_compress -i + dh_fixperms -i + dh_installdeb -i + dh_perl -i + dh_gencontrol -i + dh_md5sums -i + dh_builddeb -i + +# Build architecture-dependent files here. +binary-arch: build install + dh_testdir -a + dh_testroot -a + dh_installdebconf -a + dh_installdocs -a + dh_installexamples -a + dh_installmenu -a +# dh_installlogrotate -a +# dh_installpam -a +# dh_installmime -a +# dh_installinit -a + dh_installcron -a + dh_installman -a + # Man page is not really needed and throwas just a lintian warning + # mkdir `pwd`/debian/arb/usr/share/man/man3 + # perldoc PERL2ARB/ARB.pm > `pwd`/debian/arb/usr/share/man/man3/ARB.3pm + dh_installinfo -a + dh_installchangelogs -a + dh_lintian -a + # Fix rpath issue + chrpath --delete debian/libarb/usr/lib/arb/lib/ARB.so + dh_strip -a + dh_link -a + dh_compress -a + dh_fixperms -a + dh_makeshlibs -a + dh_installdeb -a +# dh_perl -a + dh_shlibdeps -a -l debian/libarb/usr/lib + dh_gencontrol -a + dh_md5sums -a + dh_builddeb -a + +RemoveFilesFromSource=GDEHELP/HELP_DOC_GEN/* GDEHELP/HELP_GEN/* GDEHELP/ARB_GDEmenus GDEHELP/helpfiles.lst \ + HELP_SOURCE/_index.html NTREE/nt_date.h \ + lib/ARB.pm \ + $(RemoveFromSourceAndBuild) + +# To update po files as recommended in po-debconf(7) +debian/po/templates.pot: debian/arb-common.templates + @debconf-updatepo + +get-orig-source: + sh debian/get-orig-source + +binary: binary-indep binary-arch +.PHONY: build clean binary-indep binary-arch binary install --- arb-0.0.20071207.1.orig/debian/libarb.lintian-overrides +++ arb-0.0.20071207.1/debian/libarb.lintian-overrides @@ -0,0 +1,3 @@ +# rpath is set intentionally to make use of private dynamic +# libraries +libarb: binary-or-shlib-defines-rpath ./usr/lib/arb/lib/ARB.so --- arb-0.0.20071207.1.orig/debian/watch +++ arb-0.0.20071207.1/debian/watch @@ -0,0 +1,3 @@ +version=3 +opts="uversionmangle=s/_//g;s/^/0.0./" \ + http://download.arb-home.de/src/arbsrc_([[:digit:]].*)\.(?:tar\.gz|tar|tgz)$ --- arb-0.0.20071207.1.orig/debian/arb-common.postrm +++ arb-0.0.20071207.1/debian/arb-common.postrm @@ -0,0 +1,12 @@ +#!/bin/sh + +set -e + +# In case arb should be purged remove all stuff it might have dropped +# in /var/lib + +if [ "$1" = "purge" ] && [ -d /var/lib/arb ]; then + rm -rf /var/lib/arb +fi + +#DEBHELPER# --- arb-0.0.20071207.1.orig/debian/arb-common.lintian-overrides +++ arb-0.0.20071207.1/debian/arb-common.lintian-overrides @@ -0,0 +1,3 @@ +# 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 --- arb-0.0.20071207.1.orig/debian/arb-doc.lintian-overrides +++ arb-0.0.20071207.1/debian/arb-doc.lintian-overrides @@ -0,0 +1,6 @@ +# While the arb-doc package in fact contains documentation +# that can be read by itself it is a basic component of the +# help system binary programm arb and needs to be installed +# in any case if arb should be running. So the decision +# to move arb-doc not into the doc section was done intentionally +arb-doc: doc-package-should-be-section-doc arb-doc --- arb-0.0.20071207.1.orig/debian/patches/20_config.makefiles +++ arb-0.0.20071207.1/debian/patches/20_config.makefiles @@ -0,0 +1,29 @@ +--- /dev/null ++++ arb-0.0.20071207.1/config.makefile +@@ -0,0 +1,26 @@ ++# -------------------------------------------------------------------------------- ++# 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=1 ++ARB_64=0# compile on 64 bit machine (has no effect yet) ++ ++# -------------------------------------------------------------------------------- ++# 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 ++ --- arb-0.0.20071207.1.orig/debian/patches/30_Makefile_main +++ arb-0.0.20071207.1/debian/patches/30_Makefile_main @@ -0,0 +1,28 @@ +--- arb-0.0.20071207.1.orig/Makefile ++++ arb-0.0.20071207.1/Makefile +@@ -76,7 +76,7 @@ + # cflags = -O2 $(dflag1) $(dflags) $(DEVEL_DEF) + # cflags = -O4 $(dflag1) $(dflags) $(DEVEL_DEF) + +- lflags = $(dflag1) ++ lflags = $(dflag1) $(lflags) + fflags = $(dflag1) -C + extended_warnings = -Wwrite-strings -Wunused -Wno-aggregate-return -Wshadow + extended_cpp_warnings = -Wnon-virtual-dtor -Wreorder -Wpointer-arith +@@ -109,7 +109,7 @@ + + ALLOWED_GCC_295_VERSIONS=2.95.3 + ALLOWED_GCC_3xx_VERSIONS=3.2 3.3.1 3.3.3 3.3.4 3.3.5 3.3.6 3.4.0 3.4.2 3.4.3 +-ALLOWED_GCC_4xx_VERSIONS=4.0.0 4.0.2 4.0.3 4.1.1 4.1.2 4.1.3 4.2.0 4.2.1 4.2.3 ++ALLOWED_GCC_4xx_VERSIONS=4.0.0 4.0.2 4.0.3 4.1.1 4.1.2 4.1.3 4.2.0 4.2.1 4.2.3 4.3.1 4.3.2 4.3.3 + ALLOWED_GCC_VERSIONS=$(ALLOWED_GCC_295_VERSIONS) $(ALLOWED_GCC_3xx_VERSIONS) $(ALLOWED_GCC_4xx_VERSIONS) + + GCC_VERSION_FOUND=$(shell $(GCC) -dumpversion) +@@ -133,6 +133,7 @@ + + ifdef DEBIAN + XHOME = /usr/X11R6 ++ lflags = -Wl,-rpath,/usr/lib/arb/lib + else + XHOME = /usr/X11 + endif --- arb-0.0.20071207.1.orig/debian/patches/20_Makefiles +++ arb-0.0.20071207.1/debian/patches/20_Makefiles @@ -0,0 +1,63 @@ +--- arb-0.0.20071207.1.orig/ARBDB2/Makefile ++++ arb-0.0.20071207.1/ARBDB2/Makefile +@@ -1,7 +1,11 @@ + # INCLUDE und GLOBALS MAIN CC cflags werden von aussen uebergeben + .SUFFIXES: .o .c .depend + +-include AD_MOBJECTS.h ++HeaderFile = AD_MOBJECTS.h ++CheckHEADER := $(shell if [ -e $(HeaderFile) ] ; then echo 1 ; else echo 0 ; fi) ++ifeq ($(CheckHEADER),1) ++ include $(HeaderFile) ++endif + + ACC_OBJECTS = $(GB_O) $(GB_T) $(GB_X) + +--- arb-0.0.20071207.1.orig/ARBDBS/Makefile ++++ arb-0.0.20071207.1/ARBDBS/Makefile +@@ -1,7 +1,11 @@ + # INCLUDE und GLOBALS MAIN CC cflags werden von aussen uebergeben + .SUFFIXES: .o .c .cxx .depend + +-include AD_MOBJECTS.h ++HeaderFile = AD_MOBJECTS.h ++CheckHEADER := $(shell if [ -e $(HeaderFile) ] ; then echo 1 ; else echo 0 ; fi) ++ifeq ($(CheckHEADER),1) ++ include $(HeaderFile) ++endif + + + OBJECTS = $(GB_O) $(GB_T) $(GB_PP) $(GB_X) +--- arb-0.0.20071207.1.orig/NAMES_COM/Makefile ++++ arb-0.0.20071207.1/NAMES_COM/Makefile +@@ -27,7 +27,7 @@ + # $(MAKE) -r -f AISC/Makefile depends + + clean: +- $(MAKE) $(makeflags) -f AISC/Makefile clean ++ $(MAKE) $(makeflags) -f ../AISC/Makefile clean + + # DO NOT DELETE + +--- arb-0.0.20071207.1.orig/ORS_COM/Makefile ++++ arb-0.0.20071207.1/ORS_COM/Makefile +@@ -28,7 +28,7 @@ + # @echo "no automatic dependencies for ORS_COM - skipped" + + clean: +- $(MAKE) $(makeflags) -f AISC/Makefile clean ++ $(MAKE) $(makeflags) -f ../AISC/Makefile clean + + # DO NOT DELETE + +--- arb-0.0.20071207.1.orig/PROBE_COM/Makefile ++++ arb-0.0.20071207.1/PROBE_COM/Makefile +@@ -30,7 +30,7 @@ + # @echo "no automatic dependencies for PROBE_COM - skipped" + + clean: +- $(MAKE) $(makeflags) -f AISC/Makefile clean ++ $(MAKE) $(makeflags) -f ../AISC/Makefile clean + + # DO NOT DELETE + --- arb-0.0.20071207.1.orig/debian/patches/series +++ arb-0.0.20071207.1/debian/patches/series @@ -0,0 +1,7 @@ +20_perlscripts +30_phyml +20_config.makefiles +30_Makefile_main +20_Makefiles +ARB_release200712_gcc4.3.1.patch +20_tmpfile_issue.patch --- arb-0.0.20071207.1.orig/debian/patches/20_perlscripts +++ arb-0.0.20071207.1/debian/patches/20_perlscripts @@ -0,0 +1,7 @@ +--- arb-0.0.20071207.1.orig/PERL_SCRIPTS/IFTHELP/genbank_gen_long_features.pl ++++ arb-0.0.20071207.1/PERL_SCRIPTS/IFTHELP/genbank_gen_long_features.pl +@@ -1,4 +1,3 @@ +- + #!/usr/bin/perl + # ================================================================ # + # # --- arb-0.0.20071207.1.orig/debian/patches/30_phyml +++ arb-0.0.20071207.1/debian/patches/30_phyml @@ -0,0 +1,22 @@ +--- arb-0.0.20071207.1.orig/GDE/PHYML/Makefile ++++ arb-0.0.20071207.1/GDE/PHYML/Makefile +@@ -13,7 +13,8 @@ + # original compilation + + CC = gcc #cc +-CFLAGS = -O4 -fomit-frame-pointer -Wall -static ++CFLAGS = -O4 -fomit-frame-pointer -Wall ++# -static + # CFLAGS = -Wall + # CFLAGS = -g -Wall + # CFLAGS = -pg -Wall -fprofile-arcs -static +@@ -25,7 +26,8 @@ + # compilation together with ARB + + CC = $(ACC) +-CFLAGS = $(cflags) -fomit-frame-pointer -static ++CFLAGS = $(cflags) -fomit-frame-pointer ++# -static + EXEC = $(ARBHOME)/bin/phyml + + # ARBs standard target --- arb-0.0.20071207.1.orig/debian/patches/ARB_release200712_gcc4.3.1.patch +++ arb-0.0.20071207.1/debian/patches/ARB_release200712_gcc4.3.1.patch @@ -0,0 +1,726 @@ +--- arb-0.0.20071207.1.orig/AISC_MKPTPS/mkptypes.c ++++ arb-0.0.20071207.1/AISC_MKPTPS/mkptypes.c +@@ -899,6 +899,7 @@ static Word *getparamlist(FILE *f){ + dummy_name[DUMMY_COUNTER_POS] = (dummy_counter/10)+'0'; + dummy_name[DUMMY_COUNTER_POS] = (dummy_counter%10)+'0'; + addword(tlist, dummy_name); ++ dummy_counter++; + } + #endif + +--- arb-0.0.20071207.1.orig/AWT/AWT_config_manager.cxx ++++ arb-0.0.20071207.1/AWT/AWT_config_manager.cxx +@@ -2,7 +2,7 @@ + // // + // File : AWT_config_manager.cxx // + // Purpose : // +-// Time-stamp: // ++// Time-stamp: // + // // + // // + // Coded by Ralf Westram (coder@reallysoft.de) in January 2002 // +@@ -18,6 +18,8 @@ + + #include + #include ++#include ++#include + + using namespace std; + +--- arb-0.0.20071207.1.orig/AWT/AWT_db_browser.cxx ++++ arb-0.0.20071207.1/AWT/AWT_db_browser.cxx +@@ -2,7 +2,7 @@ + // // + // File : AWT_db_browser.cxx // + // Purpose : Simple database viewer // +-// Time-stamp: // ++// Time-stamp: // + // // + // // + // Coded by Ralf Westram (coder@reallysoft.de) in May 2004 // +@@ -13,13 +13,14 @@ + // ==================================================================== // + + #include "awt.hxx" ++#include + + #include + #include + #include + #include +-#include +-// #include ++ ++#include + + using namespace std; + +--- arb-0.0.20071207.1.orig/AWT/AWT_input_mask.cxx ++++ arb-0.0.20071207.1/AWT/AWT_input_mask.cxx +@@ -2,7 +2,7 @@ + // // + // File : AWT_input_mask.cxx // + // Purpose : General input masks // +-// Time-stamp: // ++// Time-stamp: // + // // + // // + // Coded by Ralf Westram (coder@reallysoft.de) in August 2001 // +@@ -13,13 +13,13 @@ + // // + // ==================================================================== // + +-#include +-#include +- + #include + #include + #include + ++#include "awt_input_mask.hxx" ++#include "awt_changekey.hxx" ++ + #ifndef __MAP__ + #include + #endif +@@ -31,8 +31,11 @@ + #include + #include + +-#include "awt_input_mask.hxx" +-#include "awt_changekey.hxx" ++#include ++#include ++#include ++#include ++#include + + using namespace std; + +--- arb-0.0.20071207.1.orig/AWT/AWT_tree_cmp.cxx ++++ arb-0.0.20071207.1/AWT/AWT_tree_cmp.cxx +@@ -1,7 +1,3 @@ +-#include +-// #include +-#include +-#include + #include + #include + #include +@@ -11,6 +7,9 @@ + + #include + ++#include ++#include ++#include + #include + + using namespace std; +--- arb-0.0.20071207.1.orig/GENOM/EXP_main.cxx ++++ arb-0.0.20071207.1/GENOM/EXP_main.cxx +@@ -2,7 +2,7 @@ + // // + // File : EXP_main.cxx // + // Purpose : // +-// Time-stamp: // ++// Time-stamp: // + // // + // // + // Coded by Ralf Westram (coder@reallysoft.de) in September 2001 // +@@ -25,6 +25,8 @@ class AWT_canvas; + #include "EXP.hxx" + #include "EXP_local.hxx" + #include "EXP_interface.hxx" ++ ++#include + + using namespace std; + +--- arb-0.0.20071207.1.orig/GENOM/GEN_graphic.cxx ++++ arb-0.0.20071207.1/GENOM/GEN_graphic.cxx +@@ -4,13 +4,6 @@ + * http://www.mikro.biologie.tu-muenchen.de/ * + *********************************************************************************/ + +-#include +-#include +-#include +-#include +- +-#include +- + #include + #include + #include +@@ -25,6 +18,15 @@ + #include "GEN_local.hxx" + #include "GEN_gene.hxx" + #include "GEN_graphic.hxx" ++ ++#include ++#include ++#include ++#include ++#include ++ ++#include ++ + + using namespace std; + +--- arb-0.0.20071207.1.orig/HELP_SOURCE/arb_help2xml.cxx ++++ arb-0.0.20071207.1/HELP_SOURCE/arb_help2xml.cxx +@@ -2,7 +2,7 @@ + // // + // File : arb_help2xml.cxx // + // Purpose : Converts old ARB help format to XML // +-// Time-stamp: // ++// Time-stamp: // + // // + // // + // Coded by Ralf Westram (coder@reallysoft.de) in October 2001 // +@@ -20,13 +20,18 @@ + #endif + #define h2x_assert(bed) arb_assert(bed) + +-#include +-#include + #include + #include + #include + #include + #include ++ ++#include ++#include ++#include ++#include ++#include ++ + #include + + #include +--- arb-0.0.20071207.1.orig/MERGE/MG_preserves.cxx ++++ arb-0.0.20071207.1/MERGE/MG_preserves.cxx +@@ -2,7 +2,7 @@ + // // + // File : MG_preserves.cxx // + // Purpose : find candidates for alignment preservation // +-// Time-stamp: // ++// Time-stamp: // + // // + // // + // Coded by Ralf Westram (coder@reallysoft.de) in July 2003 // +@@ -162,7 +162,7 @@ public: + + long src_bases = count_bases(gb_src_data); + long dst_bases = count_bases(gb_dst_data); +- base_count_diff = abs(src_bases-dst_bases); ++ base_count_diff = labs(src_bases-dst_bases); + + if (GB_get_error()) valid = false; + +--- arb-0.0.20071207.1.orig/NTREE/nt_cb.hxx ++++ arb-0.0.20071207.1/NTREE/nt_cb.hxx +@@ -52,9 +52,9 @@ void NT_fix_database(AW_window *); + void NT_pseudo_species_to_organism(AW_window *, AW_CL ntwcl); + void NT_test_input_mask(AW_root *root); + void NT_update_marked_counter(AW_window *aww, long count); +-void NT_popup_species_window(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_1x); ++void NT_popup_species_window(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_2x); + void NT_rename_test(AW_window *, AW_CL cl_gb_main, AW_CL dummy_1x); + void NT_test_AWT(AW_window *aww); +-void NT_dump_gcs(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_1x); ++void NT_dump_gcs(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_2x); + void NT_alltree_remove_leafs(AW_window *, AW_CL cl_mode, AW_CL cl_gb_main); + AW_window *create_nt_main_window(AW_root *awr, AW_CL clone); +--- arb-0.0.20071207.1.orig/NTREE/nt_internal.h ++++ arb-0.0.20071207.1/NTREE/nt_internal.h +@@ -66,16 +66,16 @@ void NT_fix_database(AW_window *); + void NT_pseudo_species_to_organism(AW_window *, AW_CL ntwcl); + void NT_test_input_mask(AW_root *root); + void NT_update_marked_counter(AW_window *aww, long count); +-void NT_popup_species_window(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_1x); ++void NT_popup_species_window(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_2x); + void NT_rename_test(AW_window *, AW_CL cl_gb_main, AW_CL dummy_1x); + void NT_test_AWT(AW_window *aww); +-void NT_dump_gcs(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_1x); ++void NT_dump_gcs(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_2x); + void NT_alltree_remove_leafs(AW_window *, AW_CL cl_mode, AW_CL cl_gb_main); + + /* NT_validNames.cxx */ +-void NT_deleteValidNames(AW_window *, AW_CL dummy_1x, AW_CL dummy_1x); +-void NT_importValidNames(AW_window *, AW_CL dummy_1x, AW_CL dummy_1x); +-void NT_suggestValidNames(AW_window *, AW_CL dummy_1x, AW_CL dummy_1x); ++void NT_deleteValidNames(AW_window *, AW_CL dummy_1x, AW_CL dummy_2x); ++void NT_importValidNames(AW_window *, AW_CL dummy_1x, AW_CL dummy_2x); ++void NT_suggestValidNames(AW_window *, AW_CL dummy_1x, AW_CL dummy_2x); + + /* NT_validNameParser.cxx */ + +@@ -90,7 +90,7 @@ AW_window *NT_create_MAUS_window(AW_root + /* NT_ins_col.cxx */ + + /* NT_import.cxx */ +-void NT_import_sequences(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_1x); ++void NT_import_sequences(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_2x); + + /* NT_concatenate.cxx */ + void NT_createConcatenationAwars(AW_root *aw_root, AW_default aw_def); +--- arb-0.0.20071207.1.orig/PRIMER_DESIGN/PRD_Design.cxx ++++ arb-0.0.20071207.1/PRIMER_DESIGN/PRD_Design.cxx +@@ -6,8 +6,10 @@ + #include "PRD_SequenceIterator.hxx" + #include "PRD_SearchFIFO.hxx" + +-#include + #include ++ ++#include ++#include + #include + + // using namespace std; (does not work well with Solaris CC) +--- arb-0.0.20071207.1.orig/PRIMER_DESIGN/primer_design.cxx ++++ arb-0.0.20071207.1/PRIMER_DESIGN/primer_design.cxx +@@ -1,7 +1,3 @@ +-#include +-#include +-#include +- + #include + #include + #include +@@ -15,6 +11,12 @@ + #include "primer_design.hxx" + #include "PRD_Design.hxx" + #include "PRD_SequenceIterator.hxx" ++ ++#include ++#include ++#include ++#include ++#include + + extern GBDATA *gb_main; + +--- arb-0.0.20071207.1.orig/PROBE/PT_new_design.cxx ++++ arb-0.0.20071207.1/PROBE/PT_new_design.cxx +@@ -1,7 +1,7 @@ +-#include +-#include +-#include +-// #include ++#include ++#include ++#include ++#include + + #include + #include +--- arb-0.0.20071207.1.orig/PROBE/pt_prototypes.h ++++ arb-0.0.20071207.1/PROBE/pt_prototypes.h +@@ -26,7 +26,7 @@ extern "C" int PT_start_design P_((PT_pd + void ptnd_new_match P_((PT_local *locs, char *probestring)); + + /* PT_family.cxx */ +-int mark_all_matches_chain_handle P_((int name, int dummy_1x, int dummy_1x, long dummy_1x)); ++int mark_all_matches_chain_handle P_((int name, int dummy_1x, int dummy_2x, long dummy_3x)); + int mark_all_matches P_((PT_local *locs, POS_TREE *pt, char *probe, int length, int mismatches, int height, int max_mismatches)); + void clear_statistic P_((void)); + void make_match_statistic P_((int probe_len)); +--- arb-0.0.20071207.1.orig/PROBE_SERVER/common.h ++++ arb-0.0.20071207.1/PROBE_SERVER/common.h +@@ -3,7 +3,7 @@ + // File : common.h // + // Purpose : Common code for all tools // + // Note : include only once in each executable!!! // +-// Time-stamp: // ++// Time-stamp: // + // // + // // + // Coded by Ralf Westram (coder@reallysoft.de) in September 2003 // +@@ -16,6 +16,14 @@ + + #ifndef COMMON_H + #define COMMON_H ++ ++#ifndef _CPP_CSTRING ++#include ++#endif ++#ifndef _CPP_CSTDLIB ++#include ++#endif ++ + + #ifdef NEED_setDatabaseState + static GB_ERROR setDatabaseState(GBDATA *gb_main, const char *type, const char *state) { +--- arb-0.0.20071207.1.orig/PROBE_SERVER/PROBE_GROUP/pg_db.cxx ++++ arb-0.0.20071207.1/PROBE_SERVER/PROBE_GROUP/pg_db.cxx +@@ -1,17 +1,13 @@ +-#include ++#include "pg_db.hxx" ++#include "pg_def.hxx" + +-#ifndef __MAP__ +-#include +-#endif ++#include + +-#ifndef __PG_DB_HXX__ +-#include +-#endif +-#ifndef __PG_DEF_HXX__ +-#include +-#endif ++#include + +-#include ++#include ++#include ++#include + + + using namespace std; +--- arb-0.0.20071207.1.orig/PROBE_SERVER/PROBE_GROUP/pg_main.cxx ++++ arb-0.0.20071207.1/PROBE_SERVER/PROBE_GROUP/pg_main.cxx +@@ -1,7 +1,7 @@ + // ==================================================================== // + // // + // File : pg_main.cxx // +-// Time-stamp: // ++// Time-stamp: // + // // + // // + // Coded by Tina Lai & Ralf Westram (coder@reallysoft.de) 2001-2004 // +@@ -15,20 +15,20 @@ + // #define DUMP_SMART_PTRS + // #define DUMP_COVERAGE_SEARCH + +-#ifndef PG_SEARCH_HXX + #include "pg_search.hxx" +-#endif ++ ++#include ++#include ++ ++#include + + #include + #include + #include + #include +-#include +- +-#include +-#include + +-#include ++#include ++#include + + #define NEED_encodeTreeNode + #define NEED_saveProbeContainerToString +--- arb-0.0.20071207.1.orig/PROBE_SERVER/PROBE_GROUP/pg_search.cxx ++++ arb-0.0.20071207.1/PROBE_SERVER/PROBE_GROUP/pg_search.cxx +@@ -4,14 +4,7 @@ + * http://www.mikro.biologie.tu-muenchen.de/ * + *********************************************************************************/ + +-#include +-#include +- +-#include +-#include +-#include +- +-#include ++#include "pg_search.hxx" + + #include + #include +@@ -19,9 +12,14 @@ + #include + #include + +-#ifndef PG_SEARCH_HXX +-#include "pg_search.hxx" +-#endif ++#include ++#include ++ ++#include ++#include ++#include ++#include ++ + + #define MAX_SPECIES 999999 // max species returned by pt-server (probe match) + +--- arb-0.0.20071207.1.orig/PROBE_SET/ps_bitmap.hxx ++++ arb-0.0.20071207.1/PROBE_SET/ps_bitmap.hxx +@@ -217,7 +217,7 @@ long PS_BitMap::getTrueIndicesFor( const + data[ _index ]->getTrueIndices( _index_set, _index ); + // scan column _index in the remaining rows + for (long row = _index+1; row <= max_row; ++row) { +- if (data[ row ]->get( _index )) _index_set.insert( row ); ++ if (data[ row ]->Get( _index )) _index_set.insert( row ); + } + return _index_set.size(); + } +@@ -231,7 +231,7 @@ long PS_BitMap::getFalseIndicesFor( cons + data[ _index ]->getFalseIndices( _index_set, _index ); + // scan column _index in the remaining rows + for (long row = _index+1; row <= max_row; ++row) { +- if (!(data[ row ]->get( _index ))) _index_set.insert( row ); ++ if (!(data[ row ]->Get( _index ))) _index_set.insert( row ); + } + return _index_set.size(); + } +@@ -256,7 +256,7 @@ long PS_BitMap::getCountOfTrues() { + bool PS_BitMap::set( const long _row, const long _col, const bool _value ) { + reserve( _row+1 ); + if (_row > max_row) max_row = _row; +- return data[_row]->set( _col, _value ); ++ return data[_row]->Set( _col, _value ); + } + + +@@ -265,7 +265,7 @@ bool PS_BitMap::set( const long _row, co + // ************************************************************ + bool PS_BitMap::get( const long _row, const long _col ) { + reserve( _row+1 ); +- return data[_row]->get( _col ); ++ return data[_row]->Get( _col ); + } + + +@@ -441,7 +441,7 @@ bool PS_BitMap::load( PS_FileBuffer *_fi + // ************************************************************ + inline bool PS_BitMap_Fast::set( const long _row, const long _col, const bool _value ) { + if (_row > max_row) max_row = _row; +- return data[_row]->set( _col, _value ); ++ return data[_row]->Set( _col, _value ); + } + + +@@ -450,7 +450,7 @@ inline bool PS_BitMap_Fast::set( const l + // ************************************************************ + inline bool PS_BitMap_Fast::get( const long _row, const long _col ) { + if (_row > max_row) max_row = _row; +- return data[_row]->get( _col ); ++ return data[_row]->Get( _col ); + } + + +@@ -548,7 +548,7 @@ long PS_BitMap_Counted::getTrueIndicesFo + for (long row = _index+1; + ((row <= max_row) && (_index_set.size() < total_count_trues)); + ++row) { +- if (data[ row ]->get( _index )) _index_set.insert( row ); ++ if (data[ row ]->Get( _index )) _index_set.insert( row ); + } + return _index_set.size(); + } +@@ -566,7 +566,7 @@ long PS_BitMap_Counted::getFalseIndicesF + for (long row = _index+1; + ((row <= max_row) && (_index_set.size() < total_count_falses)); + ++row) { +- if (!(data[ row ]->get( _index ))) _index_set.insert( row ); ++ if (!(data[ row ]->Get( _index ))) _index_set.insert( row ); + } + return _index_set.size(); + } +@@ -611,7 +611,7 @@ long PS_BitMap_Counted::getCountOfTrues( + bool PS_BitMap_Counted::set( const long _row, const long _col, const bool _value ) { + if (_col > _row) printf( "PS_BitMap_Counted::set( %li,%li,%1i ) not allowed\n", _row, _col, _value ); + if (_row > max_row) max_row = _row; +- bool previous_value = data[_row]->set( _col, _value ); ++ bool previous_value = data[_row]->Set( _col, _value ); + if (_value && !previous_value) { + ++count_true_per_index[ _row ]; + ++count_true_per_index[ _col ]; +@@ -629,7 +629,7 @@ bool PS_BitMap_Counted::set( const long + inline bool PS_BitMap_Counted::get( const long _row, const long _col ) { + if (_col > _row) printf( "PS_BitMap_Counted::get( %li,%li ) not allowed\n", _row, _col ); + if (_row > max_row) max_row = _row; +- return data[_row]->get( _col ); ++ return data[_row]->Get( _col ); + } + + +@@ -824,7 +824,7 @@ void PS_BitMap_Counted::recalcCounters() + PS_BitSet *row_data = data[row]; + if (row_data->getMaxUsedIndex() > row) printf( "row %4li 0..%li ??\n", row, row_data->getMaxUsedIndex() ); + for (long col = 0; col <= row_data->getMaxUsedIndex(); ++col) { +- if (row_data->get(col)) { ++ if (row_data->Get(col)) { + ++count_true_per_index[ col ]; + if (row != col) ++count_true_per_index[ row ]; // dont count diagonal trues twice + } +--- arb-0.0.20071207.1.orig/PROBE_SET/ps_bitset.hxx ++++ arb-0.0.20071207.1/PROBE_SET/ps_bitset.hxx +@@ -47,8 +47,8 @@ public: + virtual long getCountOfTrues( const long _fill_index = -1 ); + long getMaxUsedIndex() { return max_index; } + +- virtual bool get( const long _index ); +- virtual bool set( const long _index, const bool _value ); ++ virtual bool Get( const long _index ); ++ virtual bool Set( const long _index, const bool _value ); + virtual void setTrue( const long _index ); + virtual void setFalse( const long _index ); + +@@ -201,10 +201,7 @@ long PS_BitSet::getCountOfTrues( const l + } + + +-// ************************************************************ +-// * PS_BitSet::set( _index, _value ) +-// ************************************************************ +-bool PS_BitSet::set( const long _index, const bool _value ) { ++bool PS_BitSet::Set( const long _index, const bool _value ) { + bs_assert( _index >= 0 ); + reserve( _index ); + // unsigned char byte = data[_index / 8]; +@@ -267,10 +264,7 @@ void PS_BitSet::setFalse( const long _in + } + + +-// ************************************************************ +-// * PS_BitSet::get( _index ) +-// ************************************************************ +-bool PS_BitSet::get( const long _index ) { ++bool PS_BitSet::Get( const long _index ) { + bs_assert( _index >= 0 ); + reserve( _index ); + // unsigned char byte = data[_index / 8]; +@@ -342,7 +336,7 @@ void PS_BitSet::x_or( const PS_BitSet *_ + void PS_BitSet::print( const bool _header = true, const long _fill_index = -1 ) { + if (_header) printf( "PS_BitSet: bias(%1i) max_index(%6li) capacity(%6li) ", bias, max_index, capacity ); + for (long i = 0; i <= max_index; ++i) { +- printf( get(i) ? "+" : "_" ); ++ printf( Get(i) ? "+" : "_" ); + } + for (long i = max_index+1; i <= _fill_index; ++i) { + printf( "." ); +--- arb-0.0.20071207.1.orig/PROBE_SET/ps_candidate.hxx ++++ arb-0.0.20071207.1/PROBE_SET/ps_candidate.hxx +@@ -11,6 +11,10 @@ + #include "ps_filebuffer.hxx" + #endif + ++#ifndef _CPP_CLIMITS ++#include ++#endif ++ + using namespace std; + + class PS_Candidate; +--- arb-0.0.20071207.1.orig/PROBE_SET/ps_detect_weak_differences.cxx ++++ arb-0.0.20071207.1/PROBE_SET/ps_detect_weak_differences.cxx +@@ -1,15 +1,13 @@ +-#include +-#include +-#include +-#include +- +-#ifndef PS_DATABASE_HXX + #include "ps_database.hxx" +-#endif +-#ifndef PS_BITMAP_HXX + #include "ps_bitmap.hxx" +-#endif + #include "ps_tools.hxx" ++ ++#include ++#include ++#include ++#include ++ ++#include + + // common globals + SpeciesID __MAX_ID; +--- arb-0.0.20071207.1.orig/RNA3D/RNA3D_Textures.cxx ++++ arb-0.0.20071207.1/RNA3D/RNA3D_Textures.cxx +@@ -5,6 +5,7 @@ + + #include + #include ++#include + + #include + +--- arb-0.0.20071207.1.orig/SL/FILE_BUFFER/FileBuffer.cxx ++++ arb-0.0.20071207.1/SL/FILE_BUFFER/FileBuffer.cxx +@@ -2,7 +2,7 @@ + // // + // File : FileBuffer.cxx // + // Purpose : // +-// Time-stamp: // ++// Time-stamp: // + // // + // Coded by Ralf Westram (coder@reallysoft.de) in December 2006 // + // Institute of Microbiology (Technical University Munich) // +@@ -10,7 +10,8 @@ + // // + // ================================================================ // + #include "FileBuffer.h" +- ++#include ++#include + + using namespace std; + +--- arb-0.0.20071207.1.orig/TOOLS/arb_gene_probe.cxx ++++ arb-0.0.20071207.1/TOOLS/arb_gene_probe.cxx +@@ -1,14 +1,17 @@ +-#include +-#include +-#include +-#include ++#include ++#include ++#include ++ + #include + #include + #include + +-#include +-#include +-#include ++#include ++#include ++#include ++ ++#include ++#include + + #define gp_assert(cond) arb_assert(cond) + +--- arb-0.0.20071207.1.orig/bin/Makefile ++++ arb-0.0.20071207.1/bin/Makefile +@@ -7,10 +7,10 @@ help: + @echo ' cleanlinks: remove all links' + + all: cleanlinks +- /bin/ln -s `find ../SH ../PERL_SCRIPTS -perm -100 ! -type d ! -name 'config*' -print` . ++ /bin/ln -s -f `find ../SH ../PERL_SCRIPTS -perm -100 ! -type d ! -name 'config*' -print` . + + develall: all +- /bin/ln -s `find ../SOURCE_TOOLS -name "arb_*" -perm -100 ! -type d -print` . ++ /bin/ln -s -f `find ../SOURCE_TOOLS -name "arb_*" -perm -100 ! -type d -print` . + + + clean: realclean +@@ -21,5 +21,4 @@ realclean: + + + cleanlinks: +- ln -s dummy dummy +- rm -f dummy `find . -type l -print` ++ find . -type l -exec rm {} \; --- arb-0.0.20071207.1.orig/debian/patches/20_tmpfile_issue.patch +++ arb-0.0.20071207.1/debian/patches/20_tmpfile_issue.patch @@ -0,0 +1,66 @@ +--- arb-0.0.20071207.1.orig/SH/arb_fastdnaml ++++ arb-0.0.20071207.1/SH/arb_fastdnaml +@@ -1,5 +1,5 @@ + #!/bin/sh +-tmp=/tmp/arb_fdnaml_${USER}_$$ ++tmp=`mktemp -t arb_fdnaml_XXXXXXXXXX` + mv infile $tmp + nice -19 $1 < $tmp & + sig=$! +--- arb-0.0.20071207.1.orig/SH/dszmconnect.pl ++++ arb-0.0.20071207.1/SH/dszmconnect.pl +@@ -20,7 +20,7 @@ + use HTTP::Request::Common qw(POST); + use LWP::UserAgent; + +- ++use File::Temp qw/ tempfile tempdir /; + + + +@@ -51,9 +51,12 @@ + + "; + ++my $TMPOUT; ++my $template = 'arbdsmz_XXXXXX'; ++(undef, $TMPOUT) = tempfile($template, OPEN => 0); ++$TMPOUT = $TMPOUT . ".html"; + +- +-open (OUTPUT , "> /tmp/arbdsmz.html") or die "cannot open input file /tmp/arbdsmz.html"; ++open (OUTPUT , "> $TMPOUT") or die "cannot open temporary input file $TMPOUT"; + + if (scalar(@ARGV) == 0) + {print OUTPUT $errordocument; +@@ -86,7 +89,10 @@ + $req_selection->content($selection_content); + + # Pass request to the user agent and get a response back +- my $res_selection = $ua_selection -> request($req_selection, '/tmp/arbdsmz.htm'); ++ my $TMPUSEROUT; ++ (undef, $TMPUSEROUT) = tempfile($template, OPEN => 0); ++ $TMPUSEROUT = $TMPUSEROUT . ".htm"; ++ my $res_selection = $ua_selection -> request($req_selection, $TMPUSEROUT); + + + +@@ -95,7 +101,7 @@ + else {die "Bad luck this time, request failed\n";}; + + +-open (INPUT , "< /tmp/arbdsmz.htm") or die "cannot open input file /tmp/arbdsmz.htm"; ++open (INPUT , "< $TMPUSEROUT") or die "cannot open input file $TMPUSEROUT"; + + + my $htmlcontent; +@@ -111,7 +117,7 @@ + + print OUTPUT $htmlcontent ; + +-#exec ('netscape', '/tmp/arbdsmz.html'); +-print "file:///tmp/arbdsmz.html"; ++#exec ('netscape', $TMPOUT); ++print "file://" . $TMPOUT; + + ##print "$htmlcontent\n"; --- arb-0.0.20071207.1.orig/debian/conf/arb.conf +++ arb-0.0.20071207.1/debian/conf/arb.conf @@ -0,0 +1,19 @@ +# ARB_TEXTEDIT='xedit' +ARB_TEXTEDIT=$EDITOR +export ARB_TEXTEDIT +ARB_XTERM='xterm -sl 1000 -sb' +export ARB_XTERM +ARB_XCMD='xterm -sl 1000 -sb -e' +export ARB_XCMD +# ARB_GS=ghostview +ARB_GS=gv +export ARB_GS + +############################################################### +## Additional options for Debian GNU/Linux +############################################################### + +## Navigation after firing up arb might be a little bit clumsy +## Thus you are able to set a directory for all users as default +## starting directory +# ARBUSERDATA=${HOME}/arb --- arb-0.0.20071207.1.orig/debian/conf/arb_ntree.dat +++ arb-0.0.20071207.1/debian/conf/arb_ntree.dat @@ -0,0 +1,4 @@ +#*********** Nameserver The server should run on the nfs server ****************** + +## This is the Debian location for ARB name server +ARB_NAME_SERVER localhost:3029 arb_name_server -d/var/lib/arb/nas/names.dat --- arb-0.0.20071207.1.orig/debian/conf/arb_pt_server.dat +++ arb-0.0.20071207.1/debian/conf/arb_pt_server.dat @@ -0,0 +1,27 @@ +#*********** PT_SERVERS The server should run on the nfs server ****************** +#******* You may add new pt_servers here: (numbers must be continues) ********* + +# FORMAT: +# ARB_PT_SERVER localhost:303 arb_pt_server -D +# where is a integer number increased by one according to the entry before +# path_to_arb_database is the location of the database file +# +# The Debian packages contain a script arb-add-pt-server which enables each user +# in group arb to add further PT_SERVERS. +# +# Under Debian we store the files under /var/lib/arb/pts but $(ARBHOME)/lib/pts +# should work as well because it is symlinked +# +# The following database is shipped with the package arb-database +# Further versions will add this in the postinst script but this is left +# here for the process of beta testing. +ARB_PT_SERVER0 localhost:3030 arb_pt_server -D/var/lib/arb/pts/demo.arb + +# Examples: +#ARB_PT_SERVER1 localhost:3031 arb_pt_server -D$(ARBHOME)/lib/pts/6rrns_sept99.arb +#ARB_PT_SERVER2 localhost:3032 arb_pt_server -D$(ARBHOME)/lib/pts/user1.arb +#ARB_PT_SERVER3 localhost:3033 arb_pt_server -D$(ARBHOME)/lib/pts/user2.arb +#ARB_PT_SERVER4 localhost:3034 arb_pt_server -D$(ARBHOME)/lib/pts/16s_mw300WL_camp.arb +#ARB_PT_SERVER5 localhost:3035 arb_pt_server -D$(ARBHOME)/lib/pts/3rrna_old.arb +#ARB_PT_SERVER6 localhost:3036 arb_pt_server -D$(ARBHOME)/lib/pts/neu_08august5.arb +#ARB_PT_SERVER7 localhost:3037 arb_pt_server -D$(ARBHOME)/lib/pts/3apr501.arb --- arb-0.0.20071207.1.orig/debian/conf/arb_tcp.dat +++ arb-0.0.20071207.1/debian/conf/arb_tcp.dat @@ -0,0 +1,89 @@ +#******************* Syntax *********************************** +# +# [USER:]SERVER_ID HOST:IP_NR [programm args] +# [USER:]SERVER_ID :SOCKETPATH [programm args] +# [xxx] means optional field +# all $(enviroment_variable) are replaced by the value of the 'enviroment_variable'. +# if host is localhost then it is replaced by the result of `hostname`. +# +# Specifying an username before the SERVER_ID makes the server user specific. +# +# This file is searched at several locations: +# - in the current directory +# - in the $(HOME) (=home directory of the current user) +# - in $(ARBHOME)/lib +# The first occurrance found is taken. +# +# Existing SERVER_IDs: +# +# ARB_DB_SERVER Your private database server. It is automatically started +# ARB_PT_SERVER Default PT_SERVER for PB_RETRIEVE (privat TU_Munich server) +# ARB_PT_SERVERn Global PT_SERVERs. Needed for fast database search (align seq, probe des.) +# n starts from 0 to max, no number can be excluded !!! +# ARB_NAME_SERVER Generates short names for species (using 'acc') +# ARB_NAME_SERVER_field Generates short names for species (using 'acc' and 'field') +# +#***************************************************************** + +# version of arb_tcp.dat +ARB_TCP_DAT_VERSION 2 + +#*********** Private Servers (for each user) ****************** +# +# This is a local server, running on one machine. Each user has his own socket: +# ARB_PID is an Enviroment Variable which is set by the command 'arb' to its own process id +# see programm $ARBHOME/SH/arb_clean to remove the sockets + +ARB_DB_SERVER :/tmp/arb_db_$(USER)_$(ARB_PID) + +# If you want to run programs on a workstation cluster, you have to assign your arbdb server +# and one ip-id for each user. To choose an ip_id choose any number between 1000 and 4000 and +# examine /etc/services whether this ip-id has not yet been allocated by another programm +# smith:ARB_DB_SERVER myhost:4011 // socket for smith ('arb' has to be started on 'myhost') +# ludwig:ARB_DB_SERVER myhost:4012 // socket for ludwig +# ARB_DB_SERVER :/tmp/arb_db_$(USER)_$(ARB_PID) // and sockets for all others + +#*********** Global Servers (for all users) ****************** +# +#*********** Nameserver The server should run on the nfs server ****************** +# The primary nameserver (ARB_NAME_SERVER) uses the field 'acc' for species identification +# +# You may define additional nameservers, using one additional field for identification. +# The defined nameserver 'ARB_NAME_SERVER_START' uses the fields 'acc' and 'start'. + +ARB_NAME_SERVER localhost:3020 arb_name_server -d/var/lib/arb/nas/names.dat +ARB_NAME_SERVER_START localhost:3021 arb_name_server -d/var/lib/arb/nas/names_start.dat -fstart + +#*********** PT_SERVERS The server should run on the nfs server ****************** +#******* You may add new pt_servers here: (numbers must be continued) ********* +# Note: If the database name is '!ASSUME_RUNNING' (i.e. -D!ASSUME_RUNNING), ARB will not +# try to start/stop/update/... the server and will not check DB for existance. +# To use such a PT-Server you'll have to start it manually on the remote host +# +# FORMAT: +# ARB_PT_SERVER localhost:303 arb_pt_server -D +# where is a integer number increased by one according to the entry before +# path_to_arb_database is the location of the database file +# +# The Debian packages contain a script arb-add-pt-server which enables each user +# in group arb to add further PT_SERVERS. +# +# Under Debian we store the files under /var/lib/arb/pts but $(ARBHOME)/lib/pts +# should work as well because it is symlinked +# +# The following database is shipped with the package arb-database +# Further versions will add this in the postinst script but this is left +# here for the process of beta testing. +ARB_PT_SERVER0 localhost:3030 arb_pt_server -D/var/lib/arb/pts/demo.arb + +# Examples +#ARB_PT_SERVER1 localhost:3031 arb_pt_server -D$(ARBHOME)/lib/pts/LSU_rRNA.arb +#ARB_PT_SERVER2 localhost:3032 arb_pt_server -D$(ARBHOME)/lib/pts/SSU_rRNA.arb +#ARB_PT_SERVER3 localhost:3033 arb_pt_server -D$(ARBHOME)/lib/pts/user1.arb +#ARB_PT_SERVER4 localhost:3034 arb_pt_server -D$(ARBHOME)/lib/pts/user2.arb +#ARB_PT_SERVER5 localhost:3035 arb_pt_server -D$(ARBHOME)/lib/pts/user3.arb +#ARB_PT_SERVER6 localhost:3036 arb_pt_server -D$(ARBHOME)/lib/pts/user4.arb +#ARB_PT_SERVER7 localhost:3037 arb_pt_server -D$(ARBHOME)/lib/pts/user5.arb +#ARB_PT_SERVER8 localhost:3038 arb_pt_server -D$(ARBHOME)/lib/pts/user6.arb +#ARB_PT_SERVER9 localhost:3039 arb_pt_server -D$(ARBHOME)/lib/pts/user7.arb +#ARB_PT_SERVER10 localhost:3040 arb_pt_server -D$(ARBHOME)/lib/pts/user8.arb --- arb-0.0.20071207.1.orig/debian/conf/arb_tcp_template.dat +++ arb-0.0.20071207.1/debian/conf/arb_tcp_template.dat @@ -0,0 +1,36 @@ +#******************* Syntax *********************************** +# +# [USER:]SERVER_ID HOST:IP_NR [programm args] +# [USER:]SERVER_ID :SOCKETPATH [programm args] +# [xxx] means optional field +# all $(enviroment_variable) are replaced by the value of the 'enviroment_variable' +# if host is localhost than it replaces by `hostname` +# +# Existing SERVER_IDs: +# +# ARB_DB_SERVER Your private database server. It is automatically started +# ARB_PT_SERVER Default PT_SERVER for PB_RETRIEVE (privat TU_Munich server) +# ARB_PT_SERVERn Global PT_SERVERs. Needed for fast database search (align seq, probe des.) +# n starts from 0 to max, no number can be excluded !!! +# ARB_NAME_SERVER Generates short names for species +# +#***************************************************************** + + +#*********** Private Servers (for each user) ****************** +# +# This is a local server, running on one machine. Each user has his own socket: +# ARB_PID is an Enviroment Variable which is set by the command 'arb' to its own process id +# see programm $ARBHOME/SH/arb_clean to remove the sockets + +ARB_DB_SERVER :/tmp/arb_db_$(USER)_$(ARB_PID) + +# If you want to run programs on a workstation cluster, you have to assign your arbdb server +# and one ip-id for each user. To choose an ip_id choose any number between 1000 and 4000 and +# examine /etc/services whether this ip-id has not yet been allocated by another programm +# smith:ARB_DB_SERVER myhost:4011 // socket for smith ('arb' have to be started on 'myhost') +# ludwig:ARB_DB_SERVER myhost:4012 // socket for ludwig +# ARB_DB_SERVER :/tmp/arb_db_$(USER)_$(ARB_PID) // and sockets for all others + +#*********** Global Servers (for all users) ****************** +# --- arb-0.0.20071207.1.orig/debian/bin/arb +++ arb-0.0.20071207.1/debian/bin/arb @@ -0,0 +1,56 @@ +#!/bin/sh +CONF=/etc/arb/arb.conf +USERCONF=${HOME}/.arb.conf +USERPROP=${HOME}/.arb_prop + +[ -s $CONF ] && . $CONF +# override general settings with user specific settings +[ -s $USERCONF ] && . $USERCONF + +# Try to make user working directory for arb data +if [ _"$ARBUSERDATA" != _"" ] ; then + if [ ! -d $ARBUSERDATA ] ; then + mkdir -p $ARBUSERDATA || ARBUSERDATA="" + fi +fi +if [ _"$ARBUSERDATA" != _"" ] ; then + cd $ARBUSERDATA + if [ ! -s demo.arb ] ; then + if [ -s /usr/share/doc/arb/examples/demo.arb.gz ] ; then + cp -a /usr/share/doc/arb/examples/demo.arb.gz . + gunzip demo.arb.gz + fi + fi +fi + +# if user has no arb input masks just symlink to the sample masks +[ -d "$USERPROP/inputMasks" ] || mkdir -p "$USERPROP/inputMasks" +MASKS=`ls "$USERPROP/inputMasks" | wc -l` +if [ $MASKS -eq 0 ] ; then + cd "$USERPROP/inputMasks" + for mask in `ls /usr/lib/arb/lib/inputMasks/*.mask` ; do + ln -s $mask . + done +fi + +# Save files as group readable +umask 002 + +# Warn if the user is not member of group arb and thus not allowed to write +# to /var/lib/arb subdirectories +if ! groups | grep -q -w arb ; then + cat < +# License: GPL + +use warnings; +use strict; +use POSIX; + +my $group2seek = "arb" ; +my $seekgroup = getgrnam($group2seek) ; +my @PTServerLines = () ; +my %PTEntry; +my $PTServerDir = "/var/lib/arb/pts" ; +my @ptservers; +my $user = getpwuid($<) ; + +if ( ! $seekgroup ) { + print STDERR "Group $group2seek does not exist.\n" ; + exit -1 ; +} +$_ = $( ; + +if ( ! /\b$seekgroup\b/ ) { + print STDERR "User $user is not member of group $group2seek.\n" ; + exit(-1) ; +} + +my $cfgfile = "/etc/arb/arb_tcp.dat" ; +# my $cfgfile = "/etc/arb/arb_pt_server.dat" ; +my $tmpfile = tmpnam(); +open ( CFG, $cfgfile ) || die ( "Unable to open Arb config file $cfgfile." ) ; +open ( TMP, ">$tmpfile" ) || die ( "Unable to open temporary file $tmpfile for writing." ) ; + +my ( $i, $port, $path, $i_max, $port_max ) ; +$i_max = $port_max = 0; + +while ( ) { + if ( ! /^[^#]*\bARB_PT_SERVER/ ) { + print TMP ; + next ; + } + chomp ; + s/\s*#.*// ; + if ( /ARB_PT_SERVER([0-9]+)\s+localhost:([0-9]{4})\s+arb_pt_server\s+-D(.+)$/ ) { + $i = $1; + $port = $2; + $path = $3; + print "$i: $port, $path\n" ; + if ( $i > $i_max ) { $i_max = $i ; } + if ( $port > $port_max ) { $port_max = $port ; } + } else { + print "Canot parse PT_SERVER entry: $_\n" ; + } + @PTServerLines = (@PTServerLines, $_) ; +} + +my $pts ; +foreach $pts ( @PTServerLines ) { + print TMP "$pts\n" ; +} + +print STDERR "Verify existing Servers in $PTServerDir.\n" ; +if ( ! opendir(DIR, $PTServerDir) ) { + print STDERR "PT-Server directory $PTServerDir does not exist.\n" ; + exit -1 ; +} +@ptservers = grep { /^$user[0-9]+\.arb$/ } readdir(DIR); +closedir DIR; + +my $pts_usermax = 0; +foreach $pts ( @ptservers ) { + if ( $pts =~ /$user([0-9]+)\.arb/ ) { + if ( $1 > $pts_usermax ) { $pts_usermax = $1 ; } + } +} +$pts_usermax += 1 ; +system ("touch $PTServerDir/$user$pts_usermax.arb"); + +close TMP ; + +print "$i_max, $port_max\n" ; +system ("mv $tmpfile tempfile.dat"); --- arb-0.0.20071207.1.orig/debian/bin/arb-add-pt-server.1 +++ arb-0.0.20071207.1/debian/bin/arb-add-pt-server.1 @@ -0,0 +1,30 @@ +'\" t +.\" ** The above line should force tbl to be a preprocessor ** +.\" Copyright (C), 2001, Andreas Tille +.\" +.\" You may distribute under the terms of the GNU General Public +.\" License as specified in the file COPYING that comes with the +.\" man_db distribution. +.\" +.\" +.TH arb-add-pt-server 1 "November 17, 2004" "Arb add PT_Server" +.SH NAME +.B arb-add-pt-server +\- enable users to maintain their arb PT_Server databases + + +.SH SYNOPSIS +.B arb-add-pt-server + +.SH DESCRIPTION +On Debian GNU/Linux systems this script adds a new (empty) +PT_Server database to the arb PT_Server repository and adds +an entry to the relevant config file provided that the user +belongs to the group arb. + +.SH SEE ALSO +arb(1), arb_clean(1), arb-kill(1) + +.SH AUTHOR +This manual page was written by Andreas Tille , +for the Debian GNU/Linux system (but may be used by others). --- arb-0.0.20071207.1.orig/debian/bin/arb-kill +++ arb-0.0.20071207.1/debian/bin/arb-kill @@ -0,0 +1,18 @@ +#!/bin/sh +arb_clean + +if [ _"$1" != _"--all" ] ; then + # grep only the processes owned by $USER + kill -9 `ps aux | grep -w "^${USER}" | grep -v "0:0[0-9] grep " | grep -v "0:0[0-9] ps " | \ + grep -w -e arb -e arb_ntree | \ + grep -v nxagent | \ + sed "s/^${USER}[[:space:]]\+\([0-9]\+\)[[:space:]]\+.*/\1/"` + rm -f /tmp/arb_pids_${USER}_* +else + # # if option --all was given kill all processes trying sudo + sudo kill -9 `ps aux | grep -v "0:0[0-9] grep " | grep -v "0:0[0-9] ps " | \ + grep -w -e arb -e arb_ntree | \ + grep -v nxagent | \ + sed "s/^[a-z0-9]\+[[:space:]]\+\([0-9]\+\)[[:space:]]\+.*/\1/"` + rm -f /tmp/arb_pids_*_* +fi --- arb-0.0.20071207.1.orig/debian/bin/arb-kill.1 +++ arb-0.0.20071207.1/debian/bin/arb-kill.1 @@ -0,0 +1,29 @@ +'\" t +.\" ** The above line should force tbl to be a preprocessor ** +.\" Copyright (C), 2001, Andreas Tille +.\" +.\" You may distribute under the terms of the GNU General Public +.\" License as specified in the file COPYING that comes with the +.\" man_db distribution. +.\" +.\" +.TH arb-kill 1 "November 17, 2004" "Kill arb processes" +.SH NAME +arb-kill \- definitely kill all processes started by arb that are started by the user + +If option --all is given try sudo to kill all processes even if they are owned +by other users. + +.SH SYNOPSIS +.B arb-kill [--all] + +.SH DESCRIPTION +Sometimes arb leaves some processes running. All processes that +belong to the user who is calling arb-kill will be killed. + +.SH SEE ALSO +arb_clean(), arb(1), kill(1), sudo(1) + +.SH AUTHOR +This manual page was written by Andreas Tille , +for the Debian GNU/Linux system (but may be used by others). --- arb-0.0.20071207.1.orig/debian/bin/arb.1 +++ arb-0.0.20071207.1/debian/bin/arb.1 @@ -0,0 +1,36 @@ +'\" t +.\" ** The above line should force tbl to be a preprocessor ** +.\" Copyright (C), 2001, Andreas Tille +.\" +.\" You may distribute under the terms of the GNU General Public +.\" License as specified in the file COPYING that comes with the +.\" man_db distribution. +.\" +.\" +.TH Arb 1 "November 17, 2004" "ARB" +.SH NAME +.B arb +\- various tools for sequence database handling and data analysis + + +.SH SYNOPSIS +.B arb + +.SH DESCRIPTION +This is the Debian GNU/Linux version of Arb. + +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. + +For a more detailed description see the Arb homepage +http://rtfm.arb-home.de/ + +.SH SEE ALSO +arb-add-pt-server(), arb_clean(), arb-kill(1), arb_ntree(1) + +.SH AUTHOR +This manual page was written by Andreas Tille , +for the Debian GNU/Linux system (but may be used by others). --- arb-0.0.20071207.1.orig/debian/bin/arb_clean.1 +++ arb-0.0.20071207.1/debian/bin/arb_clean.1 @@ -0,0 +1,28 @@ +'\" t +.\" ** The above line should force tbl to be a preprocessor ** +.\" Copyright (C), 2001, Andreas Tille +.\" +.\" You may distribute under the terms of the GNU General Public +.\" License as specified in the file COPYING that comes with the +.\" man_db distribution. +.\" +.\" +.TH arb_clean 1 "November 17, 2004" "Clean arb processes" +.SH NAME +.B arb_clean +\- clean processes started by arb that are started by the user + + +.SH SYNOPSIS +.B arb_clean + +.SH DESCRIPTION +Sometimes arb leaves some processes running. All processes +which are cleanly registered by arb will be killed. + +.SH SEE ALSO +arb-kill(), arb(1) + +.SH AUTHOR +This manual page was written by Andreas Tille , +for the Debian GNU/Linux system (but may be used by others). --- arb-0.0.20071207.1.orig/debian/bin/arb_create_debian_conffile +++ arb-0.0.20071207.1/debian/bin/arb_create_debian_conffile @@ -0,0 +1,20 @@ +#!/bin/sh +exit 0 + +# Do nothing for the moment ... +set -e + +PROG=arb +GROUP=${PROG} +CONFFILE=/etc/${PROG}/${PROG}_tcp.dat + +CATTEMPLATES="/etc/${PROG}/${PROG}_tcp_template.dat + /etc/${PROG}/${PROG}_ntree.dat + /etc/${PROG}/${PROG}_pt_server.dat" +CATFILES="" +for catfile in ${CATTEMPLATES} ; do + if [ -e $catfile ] ; then CATFILES="$CATFILES $catfile" ; fi +done +cat ${CATFILES} > ${CONFFILE} +chgrp ${GROUP} /etc/${PROG}/${PROG}_*.dat +chmod 664 /etc/${PROG}/${PROG}_*.dat --- arb-0.0.20071207.1.orig/debian/po/POTFILES.in +++ arb-0.0.20071207.1/debian/po/POTFILES.in @@ -0,0 +1 @@ +[type: gettext/rfc822deb] arb-common.templates --- arb-0.0.20071207.1.orig/debian/po/cs.po +++ arb-0.0.20071207.1/debian/po/cs.po @@ -0,0 +1,42 @@ +# translation of arb_0.0.20050526-7_cs.po to czech +# +# Translators, if you are not familiar with the PO format, gettext +# documentation is worth reading, especially sections dedicated to +# this format, e.g. by running: +# info -n '(gettext)PO Files' +# info -n '(gettext)Header Entry' +# +# Some information specific to po-debconf are available at +# /usr/share/doc/po-debconf/README-trans +# or http://www.debian.org/intl/l10n/po-debconf/README-trans +# +# Developers do not need to manually edit POT or PO files. +# +# Jakub Kasparec , 2006. +msgid "" +msgstr "" +"Project-Id-Version: arb_0.0.20050526-7_cs\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2006-09-09 14:14-0600\n" +"PO-Revision-Date: 2006-10-12 21:23+0200\n" +"Last-Translator: Jakub Kasparec \n" +"Language-Team: czech \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" +"X-Generator: KBabel 1.11.4\n" + +#. Type: multiselect +#. Description +#: ../arb-common.templates:1001 +msgid "Arb users:" +msgstr "Uživatelé Arbu:" + +#. Type: multiselect +#. Description +#: ../arb-common.templates:1001 +msgid "" +"Please choose, among the list of all unprivileged users of the system, those " +"who will be allowed running ${pkg}." +msgstr "Prosím, zvolte, kteří z neprivilegovaných uživatelů systému budou moci spuÅ¡tÄ›t ${pkg}." + --- arb-0.0.20071207.1.orig/debian/po/de.po +++ arb-0.0.20071207.1/debian/po/de.po @@ -0,0 +1,41 @@ +# +# Translators, if you are not familiar with the PO format, gettext +# documentation is worth reading, especially sections dedicated to +# this format, e.g. by running: +# info -n '(gettext)PO Files' +# info -n '(gettext)Header Entry' +# +# Some information specific to po-debconf are available at +# /usr/share/doc/po-debconf/README-trans +# or http://www.debian.org/intl/l10n/po-debconf/README-trans +# +# Developers do not need to manually edit POT or PO files. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Arb\n" +"Report-Msgid-Bugs-To: tille@debian.org\n" +"POT-Creation-Date: 2005-10-07 07:35+0200\n" +"PO-Revision-Date: 2005-10-07 08:18+0100\n" +"Last-Translator: Andreas Tille \n" +"Language-Team: German \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=iso-8859-15\n" +"Content-Transfer-Encoding: 8bit\n" + +#. Type: multiselect +#. Description +#: ../arb-common.templates:4 +msgid "Arb users:" +msgstr "Arb Nutzer:" + +#. Type: multiselect +#. Description +#: ../arb-common.templates:4 +msgid "" +"Please choose, among the list of all unprivileged users of the system, those " +"who will be allowed running ${pkg}." +msgstr "" +"Bitte wählen Sie aus der Liste aller nichtprivilegierten Nutzer des Systems " +"all diejenigen aus, die ${pkg} nutzen dürfen." --- arb-0.0.20071207.1.orig/debian/po/fr.po +++ arb-0.0.20071207.1/debian/po/fr.po @@ -0,0 +1,38 @@ +# Translators, if you are not familiar with the PO format, gettext +# documentation is worth reading, especially sections dedicated to +# this format, e.g. by running: +# info -n '(gettext)PO Files' +# info -n '(gettext)Header Entry' +# Some information specific to po-debconf are available at +# /usr/share/doc/po-debconf/README-trans +# or http://www.debian.org/intl/l10n/po-debconf/README-trans +# Developers do not need to manually edit POT or PO files. +# +# +msgid "" +msgstr "" +"Project-Id-Version: arb\n" +"Report-Msgid-Bugs-To: tille@debian.org\n" +"POT-Creation-Date: 2005-10-07 07:35+0200\n" +"PO-Revision-Date: 2005-10-08 22:31+0200\n" +"Last-Translator: Jean-Luc Coulon (f5ibh) \n" +"Language-Team: French \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=iso-8859-15\n" +"Content-Transfer-Encoding: 8bit\n" + +#. Type: multiselect +#. Description +#: ../arb-common.templates:4 +msgid "Arb users:" +msgstr "Liste des utilisateurs d'Arb :" + +#. Type: multiselect +#. Description +#: ../arb-common.templates:4 +msgid "" +"Please choose, among the list of all unprivileged users of the system, those " +"who will be allowed running ${pkg}." +msgstr "" +"Veuillez choisir, parmi la liste des utilisateurs non privilégiés du système, " +"ceux qui seront autorisés à utiliser ${pkg}." --- arb-0.0.20071207.1.orig/debian/po/sv.po +++ arb-0.0.20071207.1/debian/po/sv.po @@ -0,0 +1,38 @@ +# Translators, if you are not familiar with the PO format, gettext +# documentation is worth reading, especially sections dedicated to +# this format, e.g. by running: +# info -n '(gettext)PO Files' +# info -n '(gettext)Header Entry' +# Some information specific to po-debconf are available at +# /usr/share/doc/po-debconf/README-trans +# or http://www.debian.org/intl/l10n/po-debconf/README-trans +# Developers do not need to manually edit POT or PO files. +# , fuzzy +# +# +msgid "" +msgstr "" +"Project-Id-Version: arb 0.0.20050526-2\n" +"Report-Msgid-Bugs-To: tille@debian.org\n" +"POT-Creation-Date: 2005-10-07 07:35+0200\n" +"PO-Revision-Date: 2005-10-09 18:16+0200\n" +"Last-Translator: Daniel Nylander \n" +"Language-Team: Swedish \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=iso-8859-1\n" +"Content-Transfer-Encoding: 8bit" + +#. Type: multiselect +#. Description +#: ../arb-common.templates:4 +msgid "Arb users:" +msgstr "Arb användare:" + +#. Type: multiselect +#. Description +#: ../arb-common.templates:4 +msgid "" +"Please choose, among the list of all unprivileged users of the system, those " +"who will be allowed running ${pkg}." +msgstr "" +"Välj i listan av opriviligerade användare på systemet, de som ska tillåtas att köra ${pkg}." --- arb-0.0.20071207.1.orig/debian/po/templates.pot +++ arb-0.0.20071207.1/debian/po/templates.pot @@ -0,0 +1,31 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) YEAR THE PACKAGE'S COPYRIGHT HOLDER +# This file is distributed under the same license as the PACKAGE package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: PACKAGE VERSION\n" +"Report-Msgid-Bugs-To: tille@debian.org\n" +"POT-Creation-Date: 2005-10-07 07:35+0200\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=CHARSET\n" +"Content-Transfer-Encoding: 8bit\n" + +#. Type: multiselect +#. Description +#: ../arb-common.templates:4 +msgid "Arb users:" +msgstr "" + +#. Type: multiselect +#. Description +#: ../arb-common.templates:4 +msgid "" +"Please choose, among the list of all unprivileged users of the system, those " +"who will be allowed running ${pkg}." +msgstr "" --- arb-0.0.20071207.1.orig/debian/po/pt.po +++ arb-0.0.20071207.1/debian/po/pt.po @@ -0,0 +1,29 @@ +# 2005-11-13 - Marco Ferra (initial translation) +# +msgid "" +msgstr "" +"Project-Id-Version: arb 0.0.20050526-5\n" +"Report-Msgid-Bugs-To: tille@debian.org\n" +"POT-Creation-Date: 2003-08-04 20:03+0200\n" +"PO-Revision-Date: 2005-11-13 22:10+0100\n" +"Last-Translator: Marco Ferra \n" +"Language-Team: Portuguese \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#. Type: multiselect +#. Description +#: ../arb-common.templates:4 +msgid "Arb users:" +msgstr "Utilizadores Arb:" + +#. Type: multiselect +#. Description +#: ../arb-common.templates:4 +msgid "" +"Please choose, among the list of all unprivileged users of the system, those " +"who will be allowed running ${pkg}." +msgstr "" +"Por favor escolha da lista de utilizadores não-privilegiados do sistema, " +"aqueles que poderão correr o ${pkg}." --- arb-0.0.20071207.1.orig/debian/po/it.po +++ arb-0.0.20071207.1/debian/po/it.po @@ -0,0 +1,42 @@ +# translation of arb_0.0.20050526-7_cs.po to czech +# +# Translators, if you are not familiar with the PO format, gettext +# documentation is worth reading, especially sections dedicated to +# this format, e.g. by running: +# info -n '(gettext)PO Files' +# info -n '(gettext)Header Entry' +# +# Some information specific to po-debconf are available at +# /usr/share/doc/po-debconf/README-trans +# or http://www.debian.org/intl/l10n/po-debconf/README-trans +# +# Developers do not need to manually edit POT or PO files. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: PACKAGE VERSION\n" +"Report-Msgid-Bugs-To: tille@debian.org\n" +"POT-Creation-Date: 2005-10-07 07:35+0200\n" +"PO-Revision-Date: 2008-01-27 19:58+0100\n" +"Last-Translator: David Paleino \n" +"Language-Team: Italian \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#. Type: multiselect +#. Description +#: ../arb-common.templates:4 +msgid "Arb users:" +msgstr "Utente Arb:" + +#. Type: multiselect +#. Description +#: ../arb-common.templates:4 +msgid "" +"Please choose, among the list of all unprivileged users of the system, those " +"who will be allowed running ${pkg}." +msgstr "" +"Per favore scegli, tra l'elenco di tutti gli utenti non privilegiati del sistema, " +"quelli che avranno diritto ad eseguire ${pkg}."