|Last updated on 02.Sep 2021|
|A detailed list is available from the ARB online help.|
They are saved in ~/.arb_prop.
If you want share your ARB settings with another user or copy them to your second home directory simply copy ~/.arb_prop.
System error occured while running ´fig2dev -L ps -M -m 1.0000 /tmp/arb print user 4626.xfig /tmp/arb :print user 4626.ps´
|Reason:||You´ve updated from an older ARB version and there´s a leftover fig2dev binary in /usr/arb/bin which is called instead of the one installed globally on your machine.|
|Solution:||Delete fig2dev from /usr/arb/bin|
|Reason:||You don´t have fig2dev installed or your version is outdated.|
|Solution:||Install (a newer) fig2dev.|
arb_ntree: error while loading shared libraries: libstdc++-libc6.2-2.so.3: cannot open shared object file : No such file or directory
On your system another version of libstdc++ is installed than on our system.
If anybody knows a general solution to solve this library problem, please mail it to . Thanks.
Create a link in /usr/lib to the version existing on your system (preferrable a newer version) using
For Debian-Linux you need to install the following packages: libc5, xpm4.7, xlib6
To install them run 'apt-get install libc5 xpm4.7 xlib6'
|Solution:||ARB uses Redhat 6.2 libraries. To use ARB you have to install ld.so-1.05-13.i386.rpm and libc-5.3.12-31.i386.rpm (use http://www.rpmfind.net to find them)|
|Solution:||On Fedora Core 2 systems you need to install the compat-libstdc++-7.3-2.96.126.i386.rpm from Disk #3 of FC2. Symlink to /usr/lib/libstdc++-3-libc6.2-2-2.10.0.so or similar.|
For Ubuntu 5.10 the following solution has been reported to us:
I used the synaptic package manager to install the libstdc++2.10-dev library (to eliminated the usually libstdc++-libc6.2-2.so.3 error) and transfig and xfig.
(I think the symlinking like above was necessary as well -Ralf)
|Reason:||You have a Linux-Distribution based on the new shared C-libraries (i.e. SuSE 6.4 or higher) and use one of our last-century ARB-versions.|
|Solution:||Start your Linux installation tool (i.e. yast) and install the ShlibS5 library(SuSE).|
|Solution:||Reported by users: For RedHat7.1: ld.so-1.9.5-13.i386.rpm and libc-5.3.12-31.i386.rpm (these packages are not included in the 7.1 distribution, but they are included in the 6.2 distribution so it should work if you´ve updated from 6.2; these RPMs are also available from http://mirrors.kernel.org/redhat/redhat/redhat-6.2-en/os/i386/RedHat/RPMS/ )|
Reported by Gregory Devulder:
With Mandrake 8.0, three libraries are missing (ld.so, libdl.so.1 and ld-linux.so.1)
So, after installing the RPM libc-5.3.12-35mdk.i586.rpm you copy this three
libraries into /lib. Then you do
ARB:Loading '/data/arb/lib/arb_default/ntree.arb' done
Error: Can´t open display: ...
|Reason:||Your enviroment variable DISPLAY is not set correctly.|
Start a xterm, type ...
|Reason:||This directory is protected from saving databases to, in order to avoid inconsistencies with the PT-Server-databases.|
|Solution:||Save your databases somewhere else.|
|Reason:||This is a bug in ARB. It uses wrong ports for communication.|
Edit /usr/arb/lib/arb_tcp.dat and change the port numbers to different
values. Ports 3152 and following worked fine for other people.
If not - try other port numbers.
Goto ARB_NTREE/Etc/Probe functions/PTserver admin/template to edit /usr/arb/lib/arb_tcp.dat
|Reason:||You forgot to create the index file for the pt_server.|
|Solution:||Load your database, open the ETC/Probe/PT_SERVER admin window, choose your server and press update. Than wait for the process to finish (this may take several hours).|
|Reason:||The link /usr/arb/lib/pts points to no valid directory.|
|Solution:||Goto the directory where arb_install is located. Enter 'sh ./arb_install', do not update the old package but enter the correct location for the pt_server files when asked.|
|Solution:||Consult the section "PT_SERVER What Why and How" in ARB-help|
|Reason:||You have an old version of ARB.|
|Solution:||Please download the latest release from the ARB download site and install it.|
|Solution:||Load your data and update the pt_server (only your private data will be accessible).|
|Solution:||Merge your data with Wolfgang Ludwigs database and update the pt_server afterwards.|
|Reason:||You have updated ARB from an older installation and your /usr/arb/lib/arb_tcp.dat is outdated.|
|Solution:||Edit the file /usr/arb/lib/arb_tcp.dat and fix the nameserver definition for ARB_NAME_SERVER_START: the parameter at the end of the line has to be ´-fstart=1´. Take a look at the default arb_tcp.dat showing a correct definition.|
alert : arb_naligner
out of logical swap space during brk/sbrk
see swap (im)
|Solution:||Check your swap ( try the command 'swap -s', or 'free' or 'top' or 'swapon -v', or if failed read the manual pages ( 'man -k swap' or man swap ); There should be at least 150 mbytes swap. It is not to difficult to add new swap to your system, normally it just means creating a file and telling the system that that file should be added as swap. Consult the man pages for more details.|
|Solution:||Sometimes the aligner V2 needs an extreme amount of memory. If so switch to the new FastAligner in the new ARB_EDIT4 sequence editor, of which a prototype is available since Mai 97.|
|Reason:||The labels at the tips of the tree have to match the 'name' field in the database. Otherwise you have a tree consisting of 'zombies'.|
|Solution:||All you can do is to change all the names in the newick file, which is a lot of work for a big tree.|
|Reason:||The problem with printing multiple pages is, that we use a public domain postscript generator. It sends all pages at once to the printer and let's the printer split the document into multiple pages. Because of limited printer memory, many printers refuse to print more than x pages.|
|Solution:||Try to reduce the size of the tree being printed. Start with a fully collapsed tree and print it. Open group by group and print to find out the size of the tree your printer can handle (Note: folded groups are not send to the printer). To print the entire tree fold the groups at the bottom and print, than fold all group except some inner groups, ..., finally fold everything except the last groups.|
|Solution:||Try to install a non postscript printer ( for Linux users only ). ( Use your native printer driver instead ). Linux can do the postscript precessing itself and your PC has much more memory than the printer|