Linux Fiji doesn't work after update

[Ilan]

 This morning I just did an update after which Fiji no longer worked. I
erased the file mentioned in the critical fix to no avail. After this I
reinstalled Fiji according to the here link in the critical fix. I can get
it to work by pressing on ImageJ-linux32 but it won't work from the
launcher. I even locked the Microscope icon to the launcher and that too
fails.
As executable files I see only 4 files: ImageJ-linux32, 64 and
ImageJ-win32,64 - nothing with the name Fiji. It sounds like the here link
needs to point to something better.

Thanks,
Ilan

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[Aryeh Weiss]

On 11/4/12 8:49 AM, Ilan Tal wrote:

>   This morning I just did an update after which Fiji no longer worked. I
> erased the file mentioned in the critical fix to no avail. After this I
> reinstalled Fiji according to the here link in the critical fix. I can get
> it to work by pressing on ImageJ-linux32 but it won't work from the
> launcher. I even locked the Microscope icon to the launcher and that too
> fails.
> As executable files I see only 4 files: ImageJ-linux32, 64 and
> ImageJ-win32,64 - nothing with the name Fiji. It sounds like the here link
> needs to point to something better.
>

I had a similar problem after a recent update. I did not report it to
the Fiji bug mechanism because I could not characterize it accurately,
beyond saying that I updated and it did not launch.

In any case, I solved the problem  by reinstalling Fiji and then copying
my plugins and macro folder to the new installation.

There was one oddity -- the startup icon changed from the Fiji logo to a
microscope, and the taskbar icon changed form the Fiji logo to a java icon.

My system is a mac running OSX 10.6.8
with Java 1.6.0_37 (64 bit)

--aryeh
--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

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[Ilan]

Hi Aryeh,
In my case even a complete reinstall didn't help. It looks suspicious that
there are no Fiji files, but rather only ImageJ files. It looks, at a
minimum, that the here link is wrong.

In any case, I did the same thing that you did but the launcher still
doesn't work.

Ilan

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[Robert Baer]

On 11/4/2012 1:49 AM, Ilan Tal wrote:

>   This morning I just did an update after which Fiji no longer worked. I
> erased the file mentioned in the critical fix to no avail. After this I
> reinstalled Fiji according to the here link in the critical fix. I can get
> it to work by pressing on ImageJ-linux32 but it won't work from the
> launcher. I even locked the Microscope icon to the launcher and that too
> fails.
> As executable files I see only 4 files: ImageJ-linux32, 64 and
> ImageJ-win32,64 - nothing with the name Fiji. It sounds like the here link
> needs to point to something better.
>
> Thanks,
> Ilan
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

I had a non-working install under Windows.Something seems to have gone
wrong with the build process.  I am happy to report that regular ImageJ
is working just fine.

Rob

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__________________
Robert W Baer, Ph.D.
Professor of Physiology
Kirksville College of Osteopathic Medicine
A. T. Still University of Health Sciences
Kirksville, MO 63501 US

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[dscho]

Hi Ilan,

On Sun, 4 Nov 2012, Ilan Tal wrote:

>  This morning I just did an update after which Fiji no longer worked.

The problem was that the Fiji launcher was a little bit too old. I forgot
to upload a newer version to the updater.

For the moment, you should be able to start the launcher with

        ./fiji-linux --ij1

in the Fiji.app/ directory.

> I erased the file mentioned in the critical fix to no avail. After this
> I reinstalled Fiji according to the here link in the critical fix. I can
> get it to work by pressing on ImageJ-linux32 but it won't work from the
> launcher. I even locked the Microscope icon to the launcher and that too
> fails.
>
> As executable files I see only 4 files: ImageJ-linux32, 64 and
> ImageJ-win32,64 - nothing with the name Fiji. It sounds like the here
> link needs to point to something better.

In the next official Fiji release, there will be no Fiji launcher anymore.
It has moved to be the official launcher for ImageJ2 and it can still
launch Fiji (via the --ij1 option should the auto-detection fail).

Ciao,
Johannes

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[dscho]

Hi Aryeh,

On Sun, 4 Nov 2012, Aryeh Weiss wrote:

> the startup icon changed from the Fiji logo to a microscope, and the
> taskbar icon changed form the Fiji logo to a java icon.

My original idea was to replace the Fiji logo by the ImageJ2 logo to
demonstrate that it is the ImageJ2 launcher now, no longer the Fiji one.

The rationale was two-fold: too many people got confused by Fiji being
named differently from ImageJ and they thought that Fiji is competing with
ImageJ when it is everything but.

The other part of the rationale was that our hope is that the
infrastructure in Fiji that is independent of life sciences (and was put
into Fiji only because there was nowhere else to put it) will be put
completely into ImageJ2, which has a more reliable and robust development
style than Fiji and caters to a larger audience.

As you saw at the ImageJ conference, the script editor is already in the
process of being moved, and the scripting infrastructure was completely
redesigned in ImageJ2 and will be reused by Fiji.

So to answer your concerns: the startup icon was changed back for now, and
I hope to get around to fixing the taskbar icon tomorrow.

Thanks,
Dscho

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[Ilan]

Hi Johannes,
I just did another update of Fiji from the official site. I let it
overwrite what I already had - rather than deleting the Fiji.app directory.
I ran it by double clicking on ImageJ-linux32. It updated itself and
prompted me to remove 3 old duplicate packages which I did.

I locked the icon to the launcher bar but pressing on the icon fails. This
doesn't really bother me since I can double click on ImageJ-linux32 but it
is surprising that it doesn't set itself properly. Even more surprising is
that there are only 4 executable files on the path: ImageJ-linux32, 64 and
ugly ImageJ-win32.exe (and 64). There is no sign of fiji-linux. Where is
fiji-linux and why do I need the ugly windows files if I asked for Linux?

Thanks,
Ilan

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[Ilan]

Hi Johannes,
It could be that the ImageJ-win files were left over from the previous
installation. I deleted them and it works fine. Still where is fiji-linux?
Apparently I don't need it as the Fiji logo comes up if I double click on
ImageJ-linux32.

Ilan

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[dscho]

Hi,

On Sun, 4 Nov 2012, Johannes Schindelin wrote:

> the startup icon {of Fiji} was changed back for now, and I hope to get
> around to fixing the taskbar icon tomorrow.

The icon should also be fixed. It is in the directory
Fiji.app/Contents/Resources/ which is now also updated by the ImageJ2
updater.

Ciao,
Dscho

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[Richard Fetter]

Johannes,

I just updated my Fiji on Windows 64 bit, and the icon is not fixed.
Trying to change the icon by navigating to
Fiji.app/Contents/Resources/ does not show any files available as
icons.

Rick

On Tue, Nov 6, 2012 at 7:21 PM, Johannes Schindelin
<[hidden email]> wrote:

> Hi,
>
> On Sun, 4 Nov 2012, Johannes Schindelin wrote:
>
>> the startup icon {of Fiji} was changed back for now, and I hope to get
>> around to fixing the taskbar icon tomorrow.
>
> The icon should also be fixed. It is in the directory
> Fiji.app/Contents/Resources/ which is now also updated by the ImageJ2
> updater.
>
> Ciao,
> Dscho
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[dscho]

Hi Richard,

On Wed, 7 Nov 2012, Richard Fetter wrote:

> I just updated my Fiji on Windows 64 bit, and the icon is not fixed.
> Trying to change the icon by navigating to
> Fiji.app/Contents/Resources/ does not show any files available as
> icons.

Could you please use Help>Report a Bug which automatically provides more
information about your setup?

Thanks,
Johannes

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[dscho]

Hi Ilan,

On Mon, 5 Nov 2012, Ilan Tal wrote:

> I locked the icon to the launcher bar but pressing on the icon fails.

This is on Linux, right? If so, could you have a look at the file
.xsession-errors in your home directory whether there is an error message?

> This doesn't really bother me since I can double click on ImageJ-linux32
> but it is surprising that it doesn't set itself properly. Even more
> surprising is that there are only 4 executable files on the path:
> ImageJ-linux32, 64 and ugly ImageJ-win32.exe (and 64). There is no sign
> of fiji-linux. Where is fiji-linux

Since Fiji Is Just ImageJ, the next official Fiji release will no longer
sport the Fiji launchers but only ImageJ launchers.

The continuous releases already reflect that plan. If you insist on having
the Fiji launchers (which are really just the ImageJ launchers, on Windows
with an embedded Fiji logo), you can still get them via the advanced mode
of the updater. But please note that they will go away.

> and why do I need the ugly windows files if I asked for Linux?

There seems to be a bug in the updater that makes at least the win64
launcher to be installed always. I did not yet have time to investigate
that issue.

Ciao,
Johannes

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[Ilan]

Hi Johannes,
I have Ubuntu Linux. What I did was something a simple user would do: I
double clicked ImageJ-linux32 and up came the program with the Fiji logo on
the splash screen. Linux allows you to lock a logo to the launcher bar
which I did.

Then I exited Fiji and pressed the launcher on the bar. It flickered 5
times, supposedly trying to do something, but nothing happened. There was
no point to leaving it locked to the bar, so I released it. Then I double
clicked on ImageJ-linux32 and up came the splash screen with Fiji, etc.

Again, this isn't a big deal if it is going to be fixed. I just wanted to
let you know that Linux has a problem. I don't insist on Fiji launchers,
and I don't have any direct users who use Linux. If I did, I would have a
problem if they knew only the very basic stuff.

I found .xsession-errors and it was a big file. I searched for ImageJ and
it found a number of repeating error messages. I had no idea of date-times
and they could all be very old. I simply deleted the file and started
again. Clicking on the Fiji logo on the launch bar doesn't generate any
error messages. BTW, I didn't really understand what the messages were
trying to tell me, but they didn't look connected to the problem, so I
killed them.

The win64 is just an annoyance for a Linux user, not something which
seriously bothers me. When you find it, kill it, but it is FAR from urgent.

Please let me know if there is anything I can do from here to help with
anything.

Thanks,
Ilan

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[dscho]

Hi Ilan,

On Thu, 8 Nov 2012, Ilan Tal wrote:

> I have Ubuntu Linux. What I did was something a simple user would do: I
> double clicked ImageJ-linux32 and up came the program with the Fiji logo
> on the splash screen. Linux allows you to lock a logo to the launcher
> bar which I did.

I still try to reproduce this. In my clean virtual machine with Ubuntu and
Unity in it, I failed to be able to lock the icon to the launcher.

> The win64 is just an annoyance for a Linux user, not something which
> seriously bothers me. When you find it, kill it, but it is FAR from urgent.

This should be fixed now. I labeled ImageJ-win64.exe as dependency of
fiji-scripting.jar by mistake (already in January, my apologies for not
catching this earlier).

Ciao,
Dscho

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[dscho]

Hi Ilan,

On Thu, 8 Nov 2012, Ilan Tal wrote:

> Linux allows you to lock a logo to the launcher bar

Sorry, I was not able to do that. Ubuntu never offered me to "Lock to
Launcher", so for now I give up; I saw other programs could be pinned that
way, though.

Ciao,
Johannes

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[Ilan]

Hi Johannes,
Thanks for your efforts. I'll try to give you a few more clues. I'll send
you a screen shot in a private communication (so as not to flood the
server). I don't really understand how the pinning to the launcher could
work without the previous file called fiji-linux or some such thing. My
fiji.app root has a single executable (especially after I deleted the win64
file - thanks for that!).

Ilan

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[Volker Baecker]

Hello,
I think this is the case when you use ubuntu with unity (which is the
standard). I don't know how to use the lock to launcher with java
applications, but I can nevertheless create an icon that runs it from
the launcher.

You can do this the following way:
- click on the dash
- type menu
- click on main menu
- create a new item under the menu you want and call it FIJI
- choose application as type
- In my case the command is
    /home/baecker/programs/Fiji.app/fiji-linux64
- click on the logo and select the icon.png from Fiji.app/images
- close the menu editor
- click on the dash again and type FIJI
- drag the FIJI icon from the dash to the launcher
- the icon will now remain in the launcher and you can run FIJI from it

It behaves still a bit different from native applications. The running
application is not connected to the original icon but has a second icon
in the launcher while it is running.

Volker


On 08/11/12 23:18, Johannes Schindelin wrote:

> Hi Ilan,
>
> On Thu, 8 Nov 2012, Ilan Tal wrote:
>
>> Linux allows you to lock a logo to the launcher bar
> Sorry, I was not able to do that. Ubuntu never offered me to "Lock to
> Launcher", so for now I give up; I saw other programs could be pinned that
> way, though.
>
> Ciao,
> Johannes
>
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[dscho]

Hi Ilan,

On Thu, 15 Nov 2012, Ilan Tal wrote:

> I just switched on Fiji and you have a Catch-22 situation. It asked for an
> update and of course I agreed. In the list of things it needs to do are an
> uninstall of jars/loci-common-4.4-SNAPSHOT.jar. Then pops up another window
> for Resolve dependencies which want me to install exactly the same file. OK
> is grayed out so I can't install the file which will then be removed.
> Catch-22.

As I indicated in a reply to Leon Espinosa's mail about the same bug: I
fixed it yesterday.

Ciao,
Johannes

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[dscho]

Hi Ilan,

On Thu, 8 Nov 2012, Ilan Tal wrote:

> I have Ubuntu Linux. What I did was something a simple user would do: I
> double clicked ImageJ-linux32 and up came the program with the Fiji logo
> on the splash screen. Linux allows you to lock a logo to the launcher
> bar which I did.

Good news. I finally managed to solve this problem, however, some user
interaction is required. Update your Fiji and call

        Plugins>Utilities>Create Desktop Icon

This will add a Fiji.desktop icon to your Desktop. Most likely, this will
already be enough for Unity to let you lock the Fiji icon to the launcher,
i.e. not even a restart of Fiji is required.

Ciao,
Dscho

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[Ilan]

Hi Johannes,
I have the launcher made from Plugins>Utilities>Create Desktop Icon running
already some months here.
I can drag it to the launcher bar and it will lock to it but it is more
confusing than helpful.
In practice I find it far better to just have the icon on the desktop and
not on the launcher bar.

The problem with dragging it to the launcher bar is that when you press on
it, up comes an identical icon from the running Fiji. As with any running
program you can lock this to the launcher bar as well. Clicking on this
when Fiji is running will do the expected thing: transfer the focus to the
running Fiji program. After you close the program, since you locked it to
the launcher bar it will remain there, but if you press on it nothing will
happen, i.e. it won't launch Fiji.

On the other hand if you press on the shortcut you dragged to the launcher
bar, it will start another instance of Fiji, which is not the expected
action of other programs on the launcher bar.

Since the 2 identical icons is confusing once Fiji starts to run, I prefer
KISS (keep it simple, stupid) and leave a single Create Desktop Icon on the
desktop and not on the launcher bar.

Ilan


On Thu, Feb 14, 2013 at 1:09 AM, Johannes Schindelin <
[hidden email]> wrote:

> Hi Ilan,
>
> On Thu, 8 Nov 2012, Ilan Tal wrote:
>
> > I have Ubuntu Linux. What I did was something a simple user would do: I
> > double clicked ImageJ-linux32 and up came the program with the Fiji logo
> > on the splash screen. Linux allows you to lock a logo to the launcher
> > bar which I did.
>
> Good news. I finally managed to solve this problem, however, some user
> interaction is required. Update your Fiji and call
>
>         Plugins>Utilities>Create Desktop Icon
>
> This will add a Fiji.desktop icon to your Desktop. Most likely, this will
> already be enough for Unity to let you lock the Fiji icon to the launcher,
> i.e. not even a restart of Fiji is required.
>
> Ciao,
> Dscho
>

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