ImageJ can't be updated on Ubuntu

[panovr]

Hi,
  I installed ImageJ through "sudo apt-get" on Ubuntu 9.10. Then I clicked
"Help->Update ImageJ..." menu, but an dialog shows : "No write access:
/usr/share/java/ij.jar".
  It seems that I use the root privilege to install ImageJ by "sudo", and the
file "ij.jar" belongs root. So when I start ImageJ by non root user, it can't
write to file "ij.jar".
  How to solve this problem?
  Thanks!

[Colin Rickman-3]

Hi

You should be able to fix this by checking the permissions of ij.jar and
changing them using the chmod command.

Colin

Dr Colin Rickman
Department of Chemistry (WP 2.03)
School of Engineering and Physical Sciences
Heriot-Watt University
Edinburgh
EH14 4AS

Tel: [phone] (Office)
Tel: [phone]
Fax: [phone]


On 23/02/2010 08:58, Yili Zhao wrote:

> Hi,
>    I installed ImageJ through "sudo apt-get" on Ubuntu 9.10. Then I clicked
> "Help->Update ImageJ..." menu, but an dialog shows : "No write access:
> /usr/share/java/ij.jar".
>    It seems that I use the root privilege to install ImageJ by "sudo", and the
> file "ij.jar" belongs root. So when I start ImageJ by non root user, it can't
> write to file "ij.jar".
>    How to solve this problem?
>    Thanks!
>    

[Johan Henriksson-2]

On Tue, 2010-02-23 at 09:03 +0000, Colin Rickman wrote:
> Hi
>
> You should be able to fix this by checking the permissions of ij.jar and
> changing them using the chmod command.

run imagej with sudo to get write access. it's essentially a clash
between built-in program updates and the linux package system. one
shouldn't have both but unfortunately the debian-med team cannot keep up
with the updates.

/Johan

>
> Colin
>
> Dr Colin Rickman
> Department of Chemistry (WP 2.03)
> School of Engineering and Physical Sciences
> Heriot-Watt University
> Edinburgh
> EH14 4AS
>
> Tel: [phone] (Office)
> Tel: [phone]
> Fax: [phone]
>
>
> On 23/02/2010 08:58, Yili Zhao wrote:
> > Hi,
> >    I installed ImageJ through "sudo apt-get" on Ubuntu 9.10. Then I clicked
> > "Help->Update ImageJ..." menu, but an dialog shows : "No write access:
> > /usr/share/java/ij.jar".
> >    It seems that I use the root privilege to install ImageJ by "sudo", and the
> > file "ij.jar" belongs root. So when I start ImageJ by non root user, it can't
> > write to file "ij.jar".
> >    How to solve this problem?
> >    Thanks!
> >    

[Ruszkai Ákos]

Hello,

I'm using ImageJ on Debian testing, and I can further confirm the advice:
remove ImageJ from the ubuntu repository, and choose a manual install of
ImageJ from the website.
In that case, you should put ImageJ in /opt. That's where "optional"
software shoould be installed on Linux. Beware, you should come familiar
with the chown and chmod commands there too, as a regular user has no write
permissions for /opt.

Slight threadjack: I also suffer from the "cannot update ImageJ" problem.
But for me, it's not a permission issue: it seems ImageJ can't use network
for me. My investigations shows that it's something to do with IPV4 and
IPV6. Has anybody else experienced this problem before?

Regards,

Ákos

[Roger Koot]

Hi,

the simple solution is: do not install imagej system-wide, but let the
users maintain their own copy.
you really do not want to update a system-wide
installed-from-repositories version.
just download the imagej package from imagej's main site, unpack it in
your homedirectory and run it from there. then you can update imagej
whenever you want without being bothered by permission problems.

roger


On 02/23/2010 09:58 AM, Yili Zhao wrote:
> Hi,
>   I installed ImageJ through "sudo apt-get" on Ubuntu 9.10. Then I clicked
> "Help->Update ImageJ..." menu, but an dialog shows : "No write access:
> /usr/share/java/ij.jar".
>   It seems that I use the root privilege to install ImageJ by "sudo", and the
> file "ij.jar" belongs root. So when I start ImageJ by non root user, it can't
> write to file "ij.jar".
>   How to solve this problem?
>   Thanks!

[dscho]

Hi,

On Tue, 23 Feb 2010, Ákos Ruszkai wrote:

> Slight threadjack: I also suffer from the "cannot update ImageJ"
> problem. But for me, it's not a permission issue: it seems ImageJ can't
> use network for me. My investigations shows that it's something to do
> with IPV4 and IPV6. Has anybody else experienced this problem before?

No, I did not. However, it would be interesting to know how
"File>Import>URL..." fails, if it does. If it does not fail, it is not an
IPv4 vs IPv6 problem :-)

Ciao,
Dscho

[Ruszkai Ákos]

On 23 February 2010 16:33, Johannes Schindelin
<[hidden email]>wrote:

>
> No, I did not. However, it would be interesting to know how
> "File>Import>URL..." fails, if it does. If it does not fail, it is not an
> IPv4 vs IPv6 problem :-)
>

Hello,

Yes, it fails. -debug gives me this log:

runPlugin: ij.plugin.DragAndDrop
actionPerformed: time=1266940789402,
java.awt.event.ActionEvent[ACTION_PERFORMED,cmd=URL...,when=1266940789401,modifiers=]
on menuitem0
runPlugin: ij.plugin.URLOpener
setKeyUp: -1

I don't know what setKeyUp: -1 is, but I don't think it has anything to do
with the fact that IJ can't use network.

Browsing debian bugreports, I've found this:

http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=560142#5

Reading through that, following:

http://pvaneynd.livejournal.com/132635.html

and doing the suggested:

echo 0 > /proc/sys/net/ipv6/bindv6only

fixes my problems. But as we know, /proc is not even a real directory, this
is only a temporary solution. The permanent solution would be editing
/etc/sysctl.d/bindv6only.conf and change it there. As I've read from the
debian bugreports, this comes form the "netbase" package.

Regards,

Ákos

[Jim Passmore]

ImageJ Interest Group <[hidden email]> wrote on 02/23/2010 09:36:48
AM:

> Hi,
>
> the simple solution is: do not install imagej system-wide, but let the
> users maintain their own copy.
> you really do not want to update a system-wide
> installed-from-repositories version.
> just download the imagej package from imagej's main site, unpack it in
> your homedirectory and run it from there. then you can update imagej
> whenever you want without being bothered by permission problems.
>
> roger
>
>
> On 02/23/2010 09:58 AM, Yili Zhao wrote:
> > Hi,
> >   I installed ImageJ through "sudo apt-get" on Ubuntu 9.10. Then I

clicked
> > "Help->Update ImageJ..." menu, but an dialog shows : "No write access:

> > /usr/share/java/ij.jar".
> >   It seems that I use the root privilege to install ImageJ by
> "sudo", and the
> > file "ij.jar" belongs root. So when I start ImageJ by non root
> user, it can't
> > write to file "ij.jar".
> >   How to solve this problem?
> >   Thanks!


No new ideas here, but perhaps some explanation:

This is definitely the best solution, and not just to enable ImageJ's
update feature.  Let's say you installed via apt-get and then changed
permissions so ImageJ could update itself.  You've set up the following
scenario:
1.  Let's say apt-get installs version 1.40 (don't know what version is
actually in the repository).
2.  You run the ImageJ update and get the latest 1.43q
3.  In the mean time, say 1.43a finds it's way into the repository.
4.  You update your whole Ubuntu system via standard apt method.  Your
system is unaware of your ImageJ update, and installs the latest version
it is aware of--1.43a.
5.  ------> You have now REGRESSED from 1.43q to 1.43a!

This illustrates why, as Johan said, you shouldn't have 2 competing
methods for updating software.  Go for the local install.

Jim

----------------------------------------------
Jim Passmore
Research Associate
Sealed Air Corporation
[hidden email]
864-433-2927 voice
864-433-2205 fax
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