problem with find command and new fiji install on macos

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problem with find command and new fiji install on macos

Aryeh Weiss
This started with a problem using the search bar in fiji. When entering
some string, eg skeleton, I would get back all of the commands that
include skeleton in their name, including skeleton1, skeleton2, etc that
appear in plugins/Morphology (Gabriel Landini's macros).
Also, those macros used ot appear in the Plugins>Morphology menu, but no
longer.

That stopped happening  - the search bar, and find command, and the
plugins menu all no longer see the macros in that subdirectory of plugins.
The search bar seems to lose other commands also.

On a xubuntu system I have, this problem does not occur.

So the natural thing to try was to download a fresh Fiji, unzip it on my
Desktop or in Downloads, select the appropriate sites (eg Morphology),
and see if the problem is present there. However, when I try, that, I
that the updater does not work , and it pops up a long window with a lot
of files that it thinks are read only (but my  computer does not list
them as read only). I cannot copy that window, but the list starts with
jars/miglayou-3.7.4-swing.jar, and goes on and on. If I try to add an
update site, it says the installer failed.

java.io.FileNotFoundException:
/private/var/folders/z5/zp1ywtqso3q4...../T/AppTranslocation/1FA0...../Fiji.app/update/plugins/Bar_-1.5.2-SNAPSHOT.jar
(Read-only file system)

The ... means that there is a long apparently randomly generated name
with lots of digits and characters.

This is new and worries me, because it means I cannot install Fiji on my
system.

I rebooted the system, thinking that maybe the OS messed up some temp
file system, but this did not help.

Now here is something interesting -- if I launch the new fiji by going
into the MacOS sub-directory and directly clicking on  imagej-macosx, it
will launch, and successfully update. Launching again from Fiji.app
reproduces the updater problem.

And BTW, the search bar problem remains even in the new installation, so
at least there I think that there is some problem introduced in a recent
update. I have not had a chance to pull up my backups, I will do that
tomorrow if the problem is not identified by then.

The search bar problem is an annoyance, but the install problem is a big
deal.

Any ideas will be greatly appreciated.

Thanks in advance
--aryeh

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

Ph:  972-3-5317638
FAX: 972-3-7384051

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: problem with find command and new fiji install on macos

Nick George
This sounds like it *might* be related to a problem (I have had)
mentioned on the Forum here
http://forum.imagej.net/t/missing-plugins-menu-item/11888 and here

http://forum.imagej.net/t/plugin-scripts-no-longer-appear-in-plugin-menu-on-mac-osx/11924 
. I think it is specific to Mac OSX-- Jan Eglinger suggested a quick fix
for specific plugins on the forum, but it doesn't look like this has
been resolved yet.Not sure what the status of this is.

Nick


On 7/17/18 1:10 PM, Aryeh Weiss wrote:

> This started with a problem using the search bar in fiji. When
> entering some string, eg skeleton, I would get back all of the
> commands that include skeleton in their name, including skeleton1,
> skeleton2, etc that appear in plugins/Morphology (Gabriel Landini's
> macros).
> Also, those macros used ot appear in the Plugins>Morphology menu, but
> no longer.
>
> That stopped happening  - the search bar, and find command, and the
> plugins menu all no longer see the macros in that subdirectory of
> plugins.
> The search bar seems to lose other commands also.
>
> On a xubuntu system I have, this problem does not occur.
>
> So the natural thing to try was to download a fresh Fiji, unzip it on
> my Desktop or in Downloads, select the appropriate sites (eg
> Morphology), and see if the problem is present there. However, when I
> try, that, I that the updater does not work , and it pops up a long
> window with a lot of files that it thinks are read only (but my 
> computer does not list them as read only). I cannot copy that window,
> but the list starts with jars/miglayou-3.7.4-swing.jar, and goes on
> and on. If I try to add an update site, it says the installer failed.
>
> java.io.FileNotFoundException:
> /private/var/folders/z5/zp1ywtqso3q4...../T/AppTranslocation/1FA0...../Fiji.app/update/plugins/Bar_-1.5.2-SNAPSHOT.jar
> (Read-only file system)
>
> The ... means that there is a long apparently randomly generated name
> with lots of digits and characters.
>
> This is new and worries me, because it means I cannot install Fiji on
> my system.
>
> I rebooted the system, thinking that maybe the OS messed up some temp
> file system, but this did not help.
>
> Now here is something interesting -- if I launch the new fiji by going
> into the MacOS sub-directory and directly clicking on imagej-macosx,
> it will launch, and successfully update. Launching again from Fiji.app
> reproduces the updater problem.
>
> And BTW, the search bar problem remains even in the new installation,
> so at least there I think that there is some problem introduced in a
> recent update. I have not had a chance to pull up my backups, I will
> do that tomorrow if the problem is not identified by then.
>
> The search bar problem is an annoyance, but the install problem is a
> big deal.
>
> Any ideas will be greatly appreciated.
>
> Thanks in advance
> --aryeh
>


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Re: problem with find command and new fiji install on macos

Aryeh Weiss
Thank you for your reply, and pointing me to the forum discussion.
This is probably related. If I put the Morphology directory in scripts,
teh search bar finds the scripts,
but Plugins>Utilities>Command Finder does not. On the other hand,
command finder finds things in plugins, and  the search bar misses much
of that.
I thought that maybe the search bar does not find anything in plugins,
but then I saw that it found a .py file that is in plugins.

Is there a way to list the update history of Fiji? That would allow us
to trace back and see which update introduced the problem.

The new fiji install still has the strange behavior  that the updater
works correctly when I launch it from imagej-macos, but I get the
various permissions errors when I launch from Fiji.app. Time to learn
what macos does when it launches programs from the .app directory...

--aryeh


On 17/07/2018 22:37, Nicholas George wrote:

>
> This sounds like it *might* be related to a problem (I have had)
> mentioned on the Forum here
> http://forum.imagej.net/t/missing-plugins-menu-item/11888 and here
>
> http://forum.imagej.net/t/plugin-scripts-no-longer-appear-in-plugin-menu-on-mac-osx/11924 
> . I think it is specific to Mac OSX-- Jan Eglinger suggested a quick
> fix for specific plugins on the forum, but it doesn't look like this
> has been resolved yet.Not sure what the status of this is.
>
> Nick
>
>
> On 7/17/18 1:10 PM, Aryeh Weiss wrote:
>> This started with a problem using the search bar in fiji. When
>> entering some string, eg skeleton, I would get back all of the
>> commands that include skeleton in their name, including skeleton1,
>> skeleton2, etc that appear in plugins/Morphology (Gabriel Landini's
>> macros).
>> Also, those macros used ot appear in the Plugins>Morphology menu, but
>> no longer.
>>
>> That stopped happening  - the search bar, and find command, and the
>> plugins menu all no longer see the macros in that subdirectory of
>> plugins.
>> The search bar seems to lose other commands also.
>>
>> On a xubuntu system I have, this problem does not occur.
>>
>> So the natural thing to try was to download a fresh Fiji, unzip it on
>> my Desktop or in Downloads, select the appropriate sites (eg
>> Morphology), and see if the problem is present there. However, when I
>> try, that, I that the updater does not work , and it pops up a long
>> window with a lot of files that it thinks are read only (but my 
>> computer does not list them as read only). I cannot copy that window,
>> but the list starts with jars/miglayou-3.7.4-swing.jar, and goes on
>> and on. If I try to add an update site, it says the installer failed.
>>
>> java.io.FileNotFoundException:
>> /private/var/folders/z5/zp1ywtqso3q4...../T/AppTranslocation/1FA0...../Fiji.app/update/plugins/Bar_-1.5.2-SNAPSHOT.jar
>> (Read-only file system)
>>
>> The ... means that there is a long apparently randomly generated name
>> with lots of digits and characters.
>>
>> This is new and worries me, because it means I cannot install Fiji on
>> my system.
>>
>> I rebooted the system, thinking that maybe the OS messed up some temp
>> file system, but this did not help.
>>
>> Now here is something interesting -- if I launch the new fiji by
>> going into the MacOS sub-directory and directly clicking on
>> imagej-macosx, it will launch, and successfully update. Launching
>> again from Fiji.app reproduces the updater problem.
>>
>> And BTW, the search bar problem remains even in the new installation,
>> so at least there I think that there is some problem introduced in a
>> recent update. I have not had a chance to pull up my backups, I will
>> do that tomorrow if the problem is not identified by then.
>>
>> The search bar problem is an annoyance, but the install problem is a
>> big deal.
>>
>> Any ideas will be greatly appreciated.
>>
>> Thanks in advance
>> --aryeh
>>
>

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

Ph:  972-3-5317638
FAX: 972-3-7384051


--
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Re: problem with find command and new fiji install on macos

Pascal Lorentz-2
Has that problem been solved now? I have the same on several Macs in our
institute.
I saw on the forum discussion that there should be a fix. Shouldn't that
be delivered with a FIJI update? I just updated but still have the
problem that my installed macros don't appear in the menu.

Best regards

Pascal


Am 18.07.2018 um 06:04 schrieb Aryeh Weiss:

> Thank you for your reply, and pointing me to the forum discussion.
> This is probably related. If I put the Morphology directory in
> scripts, teh search bar finds the scripts,
> but Plugins>Utilities>Command Finder does not. On the other hand,
> command finder finds things in plugins, and  the search bar misses
> much of that.
> I thought that maybe the search bar does not find anything in plugins,
> but then I saw that it found a .py file that is in plugins.
>
> Is there a way to list the update history of Fiji? That would allow us
> to trace back and see which update introduced the problem.
>
> The new fiji install still has the strange behavior  that the updater
> works correctly when I launch it from imagej-macos, but I get the
> various permissions errors when I launch from Fiji.app. Time to learn
> what macos does when it launches programs from the .app directory...
>
> --aryeh
>
>
> On 17/07/2018 22:37, Nicholas George wrote:
>>
>> This sounds like it *might* be related to a problem (I have had)
>> mentioned on the Forum here
>> http://forum.imagej.net/t/missing-plugins-menu-item/11888 and here
>>
>> http://forum.imagej.net/t/plugin-scripts-no-longer-appear-in-plugin-menu-on-mac-osx/11924 
>> . I think it is specific to Mac OSX-- Jan Eglinger suggested a quick
>> fix for specific plugins on the forum, but it doesn't look like this
>> has been resolved yet.Not sure what the status of this is.
>>
>> Nick
>>
>>
>> On 7/17/18 1:10 PM, Aryeh Weiss wrote:
>>> This started with a problem using the search bar in fiji. When
>>> entering some string, eg skeleton, I would get back all of the
>>> commands that include skeleton in their name, including skeleton1,
>>> skeleton2, etc that appear in plugins/Morphology (Gabriel Landini's
>>> macros).
>>> Also, those macros used ot appear in the Plugins>Morphology menu,
>>> but no longer.
>>>
>>> That stopped happening  - the search bar, and find command, and the
>>> plugins menu all no longer see the macros in that subdirectory of
>>> plugins.
>>> The search bar seems to lose other commands also.
>>>
>>> On a xubuntu system I have, this problem does not occur.
>>>
>>> So the natural thing to try was to download a fresh Fiji, unzip it
>>> on my Desktop or in Downloads, select the appropriate sites (eg
>>> Morphology), and see if the problem is present there. However, when
>>> I try, that, I that the updater does not work , and it pops up a
>>> long window with a lot of files that it thinks are read only (but
>>> my  computer does not list them as read only). I cannot copy that
>>> window, but the list starts with jars/miglayou-3.7.4-swing.jar, and
>>> goes on and on. If I try to add an update site, it says the
>>> installer failed.
>>>
>>> java.io.FileNotFoundException:
>>> /private/var/folders/z5/zp1ywtqso3q4...../T/AppTranslocation/1FA0...../Fiji.app/update/plugins/Bar_-1.5.2-SNAPSHOT.jar
>>> (Read-only file system)
>>>
>>> The ... means that there is a long apparently randomly generated
>>> name with lots of digits and characters.
>>>
>>> This is new and worries me, because it means I cannot install Fiji
>>> on my system.
>>>
>>> I rebooted the system, thinking that maybe the OS messed up some
>>> temp file system, but this did not help.
>>>
>>> Now here is something interesting -- if I launch the new fiji by
>>> going into the MacOS sub-directory and directly clicking on
>>> imagej-macosx, it will launch, and successfully update. Launching
>>> again from Fiji.app reproduces the updater problem.
>>>
>>> And BTW, the search bar problem remains even in the new
>>> installation, so at least there I think that there is some problem
>>> introduced in a recent update. I have not had a chance to pull up my
>>> backups, I will do that tomorrow if the problem is not identified by
>>> then.
>>>
>>> The search bar problem is an annoyance, but the install problem is a
>>> big deal.
>>>
>>> Any ideas will be greatly appreciated.
>>>
>>> Thanks in advance
>>> --aryeh
>>>
>>
>

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Re: problem with find command and new fiji install on macos

Jan Eglinger
Hi Pascal,

as far as I can tell, the fix for this issue [1] hasn't been uploaded to
the Java-8 update site yet, but will be with the next round of Fiji
component updates.

In the meantime, you can still work around the issue by moving your
scripts from
     ./plugins/<Your>/<Scripts>

into the canonical scripts location:
     ./scripts/Plugins/<Your>/<Scripts>

Jan



[1]:
https://github.com/scijava/scijava-common/commit/c4de618d958510e3ecfd20ff54001216e8a51f43


On 02.08.2018 14:02, Pascal Lorentz wrote:

> Has that problem been solved now? I have the same on several Macs in our
> institute.
> I saw on the forum discussion that there should be a fix. Shouldn't that
> be delivered with a FIJI update? I just updated but still have the
> problem that my installed macros don't appear in the menu.
>
> Best regards
>
> Pascal
>
>
> Am 18.07.2018 um 06:04 schrieb Aryeh Weiss:
>> Thank you for your reply, and pointing me to the forum discussion.
>> This is probably related. If I put the Morphology directory in
>> scripts, teh search bar finds the scripts,
>> but Plugins>Utilities>Command Finder does not. On the other hand,
>> command finder finds things in plugins, and  the search bar misses
>> much of that.
>> I thought that maybe the search bar does not find anything in plugins,
>> but then I saw that it found a .py file that is in plugins.
>>
>> Is there a way to list the update history of Fiji? That would allow us
>> to trace back and see which update introduced the problem.
>>
>> The new fiji install still has the strange behavior  that the updater
>> works correctly when I launch it from imagej-macos, but I get the
>> various permissions errors when I launch from Fiji.app. Time to learn
>> what macos does when it launches programs from the .app directory...
>>
>> --aryeh
>>
>>
>> On 17/07/2018 22:37, Nicholas George wrote:
>>>
>>> This sounds like it *might* be related to a problem (I have had)
>>> mentioned on the Forum here
>>> http://forum.imagej.net/t/missing-plugins-menu-item/11888 and here
>>>
>>> http://forum.imagej.net/t/plugin-scripts-no-longer-appear-in-plugin-menu-on-mac-osx/11924 
>>> . I think it is specific to Mac OSX-- Jan Eglinger suggested a quick
>>> fix for specific plugins on the forum, but it doesn't look like this
>>> has been resolved yet.Not sure what the status of this is.
>>>
>>> Nick
>>>
>>>
>>> On 7/17/18 1:10 PM, Aryeh Weiss wrote:
>>>> This started with a problem using the search bar in fiji. When
>>>> entering some string, eg skeleton, I would get back all of the
>>>> commands that include skeleton in their name, including skeleton1,
>>>> skeleton2, etc that appear in plugins/Morphology (Gabriel Landini's
>>>> macros).
>>>> Also, those macros used ot appear in the Plugins>Morphology menu,
>>>> but no longer.
>>>>
>>>> That stopped happening  - the search bar, and find command, and the
>>>> plugins menu all no longer see the macros in that subdirectory of
>>>> plugins.
>>>> The search bar seems to lose other commands also.
>>>>
>>>> On a xubuntu system I have, this problem does not occur.
>>>>
>>>> So the natural thing to try was to download a fresh Fiji, unzip it
>>>> on my Desktop or in Downloads, select the appropriate sites (eg
>>>> Morphology), and see if the problem is present there. However, when
>>>> I try, that, I that the updater does not work , and it pops up a
>>>> long window with a lot of files that it thinks are read only (but
>>>> my  computer does not list them as read only). I cannot copy that
>>>> window, but the list starts with jars/miglayou-3.7.4-swing.jar, and
>>>> goes on and on. If I try to add an update site, it says the
>>>> installer failed.
>>>>
>>>> java.io.FileNotFoundException:
>>>> /private/var/folders/z5/zp1ywtqso3q4...../T/AppTranslocation/1FA0...../Fiji.app/update/plugins/Bar_-1.5.2-SNAPSHOT.jar
>>>> (Read-only file system)
>>>>
>>>> The ... means that there is a long apparently randomly generated
>>>> name with lots of digits and characters.
>>>>
>>>> This is new and worries me, because it means I cannot install Fiji
>>>> on my system.
>>>>
>>>> I rebooted the system, thinking that maybe the OS messed up some
>>>> temp file system, but this did not help.
>>>>
>>>> Now here is something interesting -- if I launch the new fiji by
>>>> going into the MacOS sub-directory and directly clicking on
>>>> imagej-macosx, it will launch, and successfully update. Launching
>>>> again from Fiji.app reproduces the updater problem.
>>>>
>>>> And BTW, the search bar problem remains even in the new
>>>> installation, so at least there I think that there is some problem
>>>> introduced in a recent update. I have not had a chance to pull up my
>>>> backups, I will do that tomorrow if the problem is not identified by
>>>> then.
>>>>
>>>> The search bar problem is an annoyance, but the install problem is a
>>>> big deal.
>>>>
>>>> Any ideas will be greatly appreciated.
>>>>
>>>> Thanks in advance
>>>> --aryeh
>>>>
>>>
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Re: problem with find command and new fiji install on macos

Nick George
In reply to this post by Pascal Lorentz-2
Yes Pascal it was resolved for me, and as far as I know it was delivered
with the last Fiji update. Have you tried updating today? I'd point you
at the forum for the specific discussions but there is a big migration
going on as ImageJ/CellProfilerand other forums are merged. Try updating
now and ensuring that your scripts/macros have an underscore in the names.

Nick


On 8/2/18 6:02 AM, Pascal Lorentz wrote:

> Has that problem been solved now? I have the same on several Macs in
> our institute.
> I saw on the forum discussion that there should be a fix. Shouldn't
> that be delivered with a FIJI update? I just updated but still have
> the problem that my installed macros don't appear in the menu.
>
> Best regards
>
> Pascal
>
>
> Am 18.07.2018 um 06:04 schrieb Aryeh Weiss:
>> Thank you for your reply, and pointing me to the forum discussion.
>> This is probably related. If I put the Morphology directory in
>> scripts, teh search bar finds the scripts,
>> but Plugins>Utilities>Command Finder does not. On the other hand,
>> command finder finds things in plugins, and  the search bar misses
>> much of that.
>> I thought that maybe the search bar does not find anything in
>> plugins, but then I saw that it found a .py file that is in plugins.
>>
>> Is there a way to list the update history of Fiji? That would allow
>> us to trace back and see which update introduced the problem.
>>
>> The new fiji install still has the strange behavior  that the updater
>> works correctly when I launch it from imagej-macos, but I get the
>> various permissions errors when I launch from Fiji.app. Time to learn
>> what macos does when it launches programs from the .app directory...
>>
>> --aryeh
>>
>>
>> On 17/07/2018 22:37, Nicholas George wrote:
>>>
>>> This sounds like it *might* be related to a problem (I have had)
>>> mentioned on the Forum here
>>> http://forum.imagej.net/t/missing-plugins-menu-item/11888 and here
>>>
>>> http://forum.imagej.net/t/plugin-scripts-no-longer-appear-in-plugin-menu-on-mac-osx/11924 
>>> . I think it is specific to Mac OSX-- Jan Eglinger suggested a quick
>>> fix for specific plugins on the forum, but it doesn't look like this
>>> has been resolved yet.Not sure what the status of this is.
>>>
>>> Nick
>>>
>>>
>>> On 7/17/18 1:10 PM, Aryeh Weiss wrote:
>>>> This started with a problem using the search bar in fiji. When
>>>> entering some string, eg skeleton, I would get back all of the
>>>> commands that include skeleton in their name, including skeleton1,
>>>> skeleton2, etc that appear in plugins/Morphology (Gabriel Landini's
>>>> macros).
>>>> Also, those macros used ot appear in the Plugins>Morphology menu,
>>>> but no longer.
>>>>
>>>> That stopped happening  - the search bar, and find command, and the
>>>> plugins menu all no longer see the macros in that subdirectory of
>>>> plugins.
>>>> The search bar seems to lose other commands also.
>>>>
>>>> On a xubuntu system I have, this problem does not occur.
>>>>
>>>> So the natural thing to try was to download a fresh Fiji, unzip it
>>>> on my Desktop or in Downloads, select the appropriate sites (eg
>>>> Morphology), and see if the problem is present there. However, when
>>>> I try, that, I that the updater does not work , and it pops up a
>>>> long window with a lot of files that it thinks are read only (but
>>>> my  computer does not list them as read only). I cannot copy that
>>>> window, but the list starts with jars/miglayou-3.7.4-swing.jar, and
>>>> goes on and on. If I try to add an update site, it says the
>>>> installer failed.
>>>>
>>>> java.io.FileNotFoundException:
>>>> /private/var/folders/z5/zp1ywtqso3q4...../T/AppTranslocation/1FA0...../Fiji.app/update/plugins/Bar_-1.5.2-SNAPSHOT.jar
>>>> (Read-only file system)
>>>>
>>>> The ... means that there is a long apparently randomly generated
>>>> name with lots of digits and characters.
>>>>
>>>> This is new and worries me, because it means I cannot install Fiji
>>>> on my system.
>>>>
>>>> I rebooted the system, thinking that maybe the OS messed up some
>>>> temp file system, but this did not help.
>>>>
>>>> Now here is something interesting -- if I launch the new fiji by
>>>> going into the MacOS sub-directory and directly clicking on
>>>> imagej-macosx, it will launch, and successfully update. Launching
>>>> again from Fiji.app reproduces the updater problem.
>>>>
>>>> And BTW, the search bar problem remains even in the new
>>>> installation, so at least there I think that there is some problem
>>>> introduced in a recent update. I have not had a chance to pull up
>>>> my backups, I will do that tomorrow if the problem is not
>>>> identified by then.
>>>>
>>>> The search bar problem is an annoyance, but the install problem is
>>>> a big deal.
>>>>
>>>> Any ideas will be greatly appreciated.
>>>>
>>>> Thanks in advance
>>>> --aryeh
>>>>
>>>
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html


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Re: problem with find command and new fiji install on macos

Curtis Rueden
In reply to this post by Pascal Lorentz-2
Hi all,

Sorry for my silence. Very busy with the forum.image.sc merge at the moment.

I did release and upload a new scijava-common.jar this morning though,
which includes the critical bug-fix relating to the script discovery. So
update your Fiji and you should receive the fix.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden


On Thu, Aug 2, 2018 at 11:25 AM, Nicholas George <
[hidden email]> wrote:

> Yes Pascal it was resolved for me, and as far as I know it was delivered
> with the last Fiji update. Have you tried updating today? I'd point you at
> the forum for the specific discussions but there is a big migration going
> on as ImageJ/CellProfilerand other forums are merged. Try updating now and
> ensuring that your scripts/macros have an underscore in the names.
>
> Nick
>
>
>
> On 8/2/18 6:02 AM, Pascal Lorentz wrote:
>
>> Has that problem been solved now? I have the same on several Macs in our
>> institute.
>> I saw on the forum discussion that there should be a fix. Shouldn't that
>> be delivered with a FIJI update? I just updated but still have the problem
>> that my installed macros don't appear in the menu.
>>
>> Best regards
>>
>> Pascal
>>
>>
>> Am 18.07.2018 um 06:04 schrieb Aryeh Weiss:
>>
>>> Thank you for your reply, and pointing me to the forum discussion.
>>> This is probably related. If I put the Morphology directory in scripts,
>>> teh search bar finds the scripts,
>>> but Plugins>Utilities>Command Finder does not. On the other hand,
>>> command finder finds things in plugins, and  the search bar misses much of
>>> that.
>>> I thought that maybe the search bar does not find anything in plugins,
>>> but then I saw that it found a .py file that is in plugins.
>>>
>>> Is there a way to list the update history of Fiji? That would allow us
>>> to trace back and see which update introduced the problem.
>>>
>>> The new fiji install still has the strange behavior  that the updater
>>> works correctly when I launch it from imagej-macos, but I get the various
>>> permissions errors when I launch from Fiji.app. Time to learn what macos
>>> does when it launches programs from the .app directory...
>>>
>>> --aryeh
>>>
>>>
>>> On 17/07/2018 22:37, Nicholas George wrote:
>>>
>>>>
>>>> This sounds like it *might* be related to a problem (I have had)
>>>> mentioned on the Forum here http://forum.imagej.net/t/miss
>>>> ing-plugins-menu-item/11888 and here
>>>>
>>>> http://forum.imagej.net/t/plugin-scripts-no-longer-appear-
>>>> in-plugin-menu-on-mac-osx/11924 . I think it is specific to Mac OSX--
>>>> Jan Eglinger suggested a quick fix for specific plugins on the forum, but
>>>> it doesn't look like this has been resolved yet.Not sure what the status of
>>>> this is.
>>>>
>>>> Nick
>>>>
>>>>
>>>> On 7/17/18 1:10 PM, Aryeh Weiss wrote:
>>>>
>>>>> This started with a problem using the search bar in fiji. When
>>>>> entering some string, eg skeleton, I would get back all of the commands
>>>>> that include skeleton in their name, including skeleton1, skeleton2, etc
>>>>> that appear in plugins/Morphology (Gabriel Landini's macros).
>>>>> Also, those macros used ot appear in the Plugins>Morphology menu, but
>>>>> no longer.
>>>>>
>>>>> That stopped happening  - the search bar, and find command, and the
>>>>> plugins menu all no longer see the macros in that subdirectory of plugins.
>>>>> The search bar seems to lose other commands also.
>>>>>
>>>>> On a xubuntu system I have, this problem does not occur.
>>>>>
>>>>> So the natural thing to try was to download a fresh Fiji, unzip it on
>>>>> my Desktop or in Downloads, select the appropriate sites (eg Morphology),
>>>>> and see if the problem is present there. However, when I try, that, I that
>>>>> the updater does not work , and it pops up a long window with a lot of
>>>>> files that it thinks are read only (but my  computer does not list them as
>>>>> read only). I cannot copy that window, but the list starts with
>>>>> jars/miglayou-3.7.4-swing.jar, and goes on and on. If I try to add an
>>>>> update site, it says the installer failed.
>>>>>
>>>>> java.io.FileNotFoundException: /private/var/folders/z5/zp1ywt
>>>>> qso3q4...../T/AppTranslocation/1FA0...../Fiji.app/update/
>>>>> plugins/Bar_-1.5.2-SNAPSHOT.jar (Read-only file system)
>>>>>
>>>>> The ... means that there is a long apparently randomly generated name
>>>>> with lots of digits and characters.
>>>>>
>>>>> This is new and worries me, because it means I cannot install Fiji on
>>>>> my system.
>>>>>
>>>>> I rebooted the system, thinking that maybe the OS messed up some temp
>>>>> file system, but this did not help.
>>>>>
>>>>> Now here is something interesting -- if I launch the new fiji by going
>>>>> into the MacOS sub-directory and directly clicking on imagej-macosx, it
>>>>> will launch, and successfully update. Launching again from Fiji.app
>>>>> reproduces the updater problem.
>>>>>
>>>>> And BTW, the search bar problem remains even in the new installation,
>>>>> so at least there I think that there is some problem introduced in a recent
>>>>> update. I have not had a chance to pull up my backups, I will do that
>>>>> tomorrow if the problem is not identified by then.
>>>>>
>>>>> The search bar problem is an annoyance, but the install problem is a
>>>>> big deal.
>>>>>
>>>>> Any ideas will be greatly appreciated.
>>>>>
>>>>> Thanks in advance
>>>>> --aryeh
>>>>>
>>>>>
>>>>
>>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: problem with find command and new fiji install on macos

Aryeh Weiss
Hi Curtis

On Thu, Aug 2, 2018 at 1:26 PM, Curtis Rueden <000003f604b8695e-dmarc-
[hidden email]> wrote:

> Hi all,
>
> Sorry for my silence. Very busy with the forum.image.sc merge at the
> moment.
>
> I did release and upload a new scijava-common.jar this morning though,
> which includes the critical bug-fix relating to the script discovery. So
> update your Fiji and you should receive the fix.
>
>
I just installed the update, and have the following behavior.

The search bar in the main Fiji window finds things in the scripts
directory, but misses some things in the plugins directory (or maybe
subdirectories. ShapeSmoothing is one that it misses, but I have not
figured out a pattern to be able to say what it misses and what not.

The command finder finds everything that I have looked for under plugins,
but does not find things that arein scripts 9eg, teh Landini-morphology
macros that I put there when this issue first arose).

Between the two search tools, I am covered, so it is not a big deal, but I
thought it would be useful for you to know.
Additional info - my system is  MacOs 10.13.6, and the java version is
1.8.0_144.

Best regards
--aryeh


Regards,

> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
>
>
> On Thu, Aug 2, 2018 at 11:25 AM, Nicholas George <
> [hidden email]> wrote:
>
> > Yes Pascal it was resolved for me, and as far as I know it was delivered
> > with the last Fiji update. Have you tried updating today? I'd point you
> at
> > the forum for the specific discussions but there is a big migration going
> > on as ImageJ/CellProfilerand other forums are merged. Try updating now
> and
> > ensuring that your scripts/macros have an underscore in the names.
> >
> > Nick
> >
> >
> >
> > On 8/2/18 6:02 AM, Pascal Lorentz wrote:
> >
> >> Has that problem been solved now? I have the same on several Macs in our
> >> institute.
> >> I saw on the forum discussion that there should be a fix. Shouldn't that
> >> be delivered with a FIJI update? I just updated but still have the
> problem
> >> that my installed macros don't appear in the menu.
> >>
> >> Best regards
> >>
> >> Pascal
> >>
> >>
> >> Am 18.07.2018 um 06:04 schrieb Aryeh Weiss:
> >>
> >>> Thank you for your reply, and pointing me to the forum discussion.
> >>> This is probably related. If I put the Morphology directory in scripts,
> >>> teh search bar finds the scripts,
> >>> but Plugins>Utilities>Command Finder does not. On the other hand,
> >>> command finder finds things in plugins, and  the search bar misses
> much of
> >>> that.
> >>> I thought that maybe the search bar does not find anything in plugins,
> >>> but then I saw that it found a .py file that is in plugins.
> >>>
> >>> Is there a way to list the update history of Fiji? That would allow us
> >>> to trace back and see which update introduced the problem.
> >>>
> >>> The new fiji install still has the strange behavior  that the updater
> >>> works correctly when I launch it from imagej-macos, but I get the
> various
> >>> permissions errors when I launch from Fiji.app. Time to learn what
> macos
> >>> does when it launches programs from the .app directory...
> >>>
> >>> --aryeh
> >>>
> >>>
> >>> On 17/07/2018 22:37, Nicholas George wrote:
> >>>
> >>>>
> >>>> This sounds like it *might* be related to a problem (I have had)
> >>>> mentioned on the Forum here http://forum.imagej.net/t/miss
> >>>> ing-plugins-menu-item/11888 and here
> >>>>
> >>>> http://forum.imagej.net/t/plugin-scripts-no-longer-appear-
> >>>> in-plugin-menu-on-mac-osx/11924 . I think it is specific to Mac OSX--
> >>>> Jan Eglinger suggested a quick fix for specific plugins on the forum,
> but
> >>>> it doesn't look like this has been resolved yet.Not sure what the
> status of
> >>>> this is.
> >>>>
> >>>> Nick
> >>>>
> >>>>
> >>>> On 7/17/18 1:10 PM, Aryeh Weiss wrote:
> >>>>
> >>>>> This started with a problem using the search bar in fiji. When
> >>>>> entering some string, eg skeleton, I would get back all of the
> commands
> >>>>> that include skeleton in their name, including skeleton1, skeleton2,
> etc
> >>>>> that appear in plugins/Morphology (Gabriel Landini's macros).
> >>>>> Also, those macros used ot appear in the Plugins>Morphology menu, but
> >>>>> no longer.
> >>>>>
> >>>>> That stopped happening  - the search bar, and find command, and the
> >>>>> plugins menu all no longer see the macros in that subdirectory of
> plugins.
> >>>>> The search bar seems to lose other commands also.
> >>>>>
> >>>>> On a xubuntu system I have, this problem does not occur.
> >>>>>
> >>>>> So the natural thing to try was to download a fresh Fiji, unzip it on
> >>>>> my Desktop or in Downloads, select the appropriate sites (eg
> Morphology),
> >>>>> and see if the problem is present there. However, when I try, that,
> I that
> >>>>> the updater does not work , and it pops up a long window with a lot
> of
> >>>>> files that it thinks are read only (but my  computer does not list
> them as
> >>>>> read only). I cannot copy that window, but the list starts with
> >>>>> jars/miglayou-3.7.4-swing.jar, and goes on and on. If I try to add an
> >>>>> update site, it says the installer failed.
> >>>>>
> >>>>> java.io.FileNotFoundException: /private/var/folders/z5/zp1ywt
> >>>>> qso3q4...../T/AppTranslocation/1FA0...../Fiji.app/update/
> >>>>> plugins/Bar_-1.5.2-SNAPSHOT.jar (Read-only file system)
> >>>>>
> >>>>> The ... means that there is a long apparently randomly generated name
> >>>>> with lots of digits and characters.
> >>>>>
> >>>>> This is new and worries me, because it means I cannot install Fiji on
> >>>>> my system.
> >>>>>
> >>>>> I rebooted the system, thinking that maybe the OS messed up some temp
> >>>>> file system, but this did not help.
> >>>>>
> >>>>> Now here is something interesting -- if I launch the new fiji by
> going
> >>>>> into the MacOS sub-directory and directly clicking on imagej-macosx,
> it
> >>>>> will launch, and successfully update. Launching again from Fiji.app
> >>>>> reproduces the updater problem.
> >>>>>
> >>>>> And BTW, the search bar problem remains even in the new installation,
> >>>>> so at least there I think that there is some problem introduced in a
> recent
> >>>>> update. I have not had a chance to pull up my backups, I will do that
> >>>>> tomorrow if the problem is not identified by then.
> >>>>>
> >>>>> The search bar problem is an annoyance, but the install problem is a
> >>>>> big deal.
> >>>>>
> >>>>> Any ideas will be greatly appreciated.
> >>>>>
> >>>>> Thanks in advance
> >>>>> --aryeh
> >>>>>
> >>>>>
> >>>>
> >>>
> >> --
> >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>
> >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: problem with find command and new fiji install on macos

Pascal Lorentz-2
In reply to this post by Curtis Rueden
Hi Curtis

Thanks a lot.
I updated Fiji yesterday before I wrote my email and did not receive the
fix. I just tried it again now and finally got it. So in my case the
macro shows again in the plugins menu and can also be found through the
search bar.

Thanks again.

Pascal

Am 02.08.18 um 19:26 schrieb Curtis Rueden:

> Hi all,
>
> Sorry for my silence. Very busy with the forum.image.sc merge at the moment.
>
> I did release and upload a new scijava-common.jar this morning though,
> which includes the critical bug-fix relating to the script discovery. So
> update your Fiji and you should receive the fix.
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
>
>
> On Thu, Aug 2, 2018 at 11:25 AM, Nicholas George <
> [hidden email]> wrote:
>
>> Yes Pascal it was resolved for me, and as far as I know it was delivered
>> with the last Fiji update. Have you tried updating today? I'd point you at
>> the forum for the specific discussions but there is a big migration going
>> on as ImageJ/CellProfilerand other forums are merged. Try updating now and
>> ensuring that your scripts/macros have an underscore in the names.
>>
>> Nick
>>
>>
>>
>> On 8/2/18 6:02 AM, Pascal Lorentz wrote:
>>
>>> Has that problem been solved now? I have the same on several Macs in our
>>> institute.
>>> I saw on the forum discussion that there should be a fix. Shouldn't that
>>> be delivered with a FIJI update? I just updated but still have the problem
>>> that my installed macros don't appear in the menu.
>>>
>>> Best regards
>>>
>>> Pascal
>>>
>>>
>>> Am 18.07.2018 um 06:04 schrieb Aryeh Weiss:
>>>
>>>> Thank you for your reply, and pointing me to the forum discussion.
>>>> This is probably related. If I put the Morphology directory in scripts,
>>>> teh search bar finds the scripts,
>>>> but Plugins>Utilities>Command Finder does not. On the other hand,
>>>> command finder finds things in plugins, and  the search bar misses much of
>>>> that.
>>>> I thought that maybe the search bar does not find anything in plugins,
>>>> but then I saw that it found a .py file that is in plugins.
>>>>
>>>> Is there a way to list the update history of Fiji? That would allow us
>>>> to trace back and see which update introduced the problem.
>>>>
>>>> The new fiji install still has the strange behavior  that the updater
>>>> works correctly when I launch it from imagej-macos, but I get the various
>>>> permissions errors when I launch from Fiji.app. Time to learn what macos
>>>> does when it launches programs from the .app directory...
>>>>
>>>> --aryeh
>>>>
>>>>
>>>> On 17/07/2018 22:37, Nicholas George wrote:
>>>>
>>>>> This sounds like it *might* be related to a problem (I have had)
>>>>> mentioned on the Forum here http://forum.imagej.net/t/miss
>>>>> ing-plugins-menu-item/11888 and here
>>>>>
>>>>> http://forum.imagej.net/t/plugin-scripts-no-longer-appear-
>>>>> in-plugin-menu-on-mac-osx/11924 . I think it is specific to Mac OSX--
>>>>> Jan Eglinger suggested a quick fix for specific plugins on the forum, but
>>>>> it doesn't look like this has been resolved yet.Not sure what the status of
>>>>> this is.
>>>>>
>>>>> Nick
>>>>>
>>>>>
>>>>> On 7/17/18 1:10 PM, Aryeh Weiss wrote:
>>>>>
>>>>>> This started with a problem using the search bar in fiji. When
>>>>>> entering some string, eg skeleton, I would get back all of the commands
>>>>>> that include skeleton in their name, including skeleton1, skeleton2, etc
>>>>>> that appear in plugins/Morphology (Gabriel Landini's macros).
>>>>>> Also, those macros used ot appear in the Plugins>Morphology menu, but
>>>>>> no longer.
>>>>>>
>>>>>> That stopped happening  - the search bar, and find command, and the
>>>>>> plugins menu all no longer see the macros in that subdirectory of plugins.
>>>>>> The search bar seems to lose other commands also.
>>>>>>
>>>>>> On a xubuntu system I have, this problem does not occur.
>>>>>>
>>>>>> So the natural thing to try was to download a fresh Fiji, unzip it on
>>>>>> my Desktop or in Downloads, select the appropriate sites (eg Morphology),
>>>>>> and see if the problem is present there. However, when I try, that, I that
>>>>>> the updater does not work , and it pops up a long window with a lot of
>>>>>> files that it thinks are read only (but my  computer does not list them as
>>>>>> read only). I cannot copy that window, but the list starts with
>>>>>> jars/miglayou-3.7.4-swing.jar, and goes on and on. If I try to add an
>>>>>> update site, it says the installer failed.
>>>>>>
>>>>>> java.io.FileNotFoundException: /private/var/folders/z5/zp1ywt
>>>>>> qso3q4...../T/AppTranslocation/1FA0...../Fiji.app/update/
>>>>>> plugins/Bar_-1.5.2-SNAPSHOT.jar (Read-only file system)
>>>>>>
>>>>>> The ... means that there is a long apparently randomly generated name
>>>>>> with lots of digits and characters.
>>>>>>
>>>>>> This is new and worries me, because it means I cannot install Fiji on
>>>>>> my system.
>>>>>>
>>>>>> I rebooted the system, thinking that maybe the OS messed up some temp
>>>>>> file system, but this did not help.
>>>>>>
>>>>>> Now here is something interesting -- if I launch the new fiji by going
>>>>>> into the MacOS sub-directory and directly clicking on imagej-macosx, it
>>>>>> will launch, and successfully update. Launching again from Fiji.app
>>>>>> reproduces the updater problem.
>>>>>>
>>>>>> And BTW, the search bar problem remains even in the new installation,
>>>>>> so at least there I think that there is some problem introduced in a recent
>>>>>> update. I have not had a chance to pull up my backups, I will do that
>>>>>> tomorrow if the problem is not identified by then.
>>>>>>
>>>>>> The search bar problem is an annoyance, but the install problem is a
>>>>>> big deal.
>>>>>>
>>>>>> Any ideas will be greatly appreciated.
>>>>>>
>>>>>> Thanks in advance
>>>>>> --aryeh
>>>>>>
>>>>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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