Problem with JRE

[Eric Griffis]

Hi All,

I am running a Mac OS 10.10.5. I’ve updated my java to the newest JDK. When I run java -version on Terminal, I see:

java version "1.8.0_66"
Java(TM) SE Runtime Environment (build 1.8.0_66-b17)
Java HotSpot(TM) 64-Bit Server VM (build 25.66-b17, mixed mode)

I’ve run into a problem trying to use the OMERO plugin in Fiji. When I try to open it I get the message "This plugin requires Java 1.7 or later”. My Fiji is "ImageJ 2.0.0-rc43/1.50e; Java 1.6.0_65 [64-bit]”. I tried downloading the JRE-free version of Fiji, but it is still using the 1.6 JRE. Is there a way that I can have Fiji find the newer JRE?

Also, I can’t run
sudo rm -fr /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin
sudo rm -fr /Library/PreferencePanes/JavaControlPanel.prefpane
to strip out the older version of java since I don’t have the access that I need to run these commands from Terminal. Any suggestions would be greatly appreciated.

Best regards,

Eric



Centre for Gene Regulation and Expression
College of Life Sciences
University of Dundee
MSI/WTB/JBC Complex
Dow Street
Dundee DD1 5EH
United KIngdom

[phone]
[hidden email]<mailto:[hidden email]>
http://www.lifesci.dundee.ac.uk/groups/eric_griffis/GriffisLab/index.html




The University of Dundee is a registered Scottish Charity, No: SC015096

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Jean-Marie Burel (Staff)]

Hi All

I forgot to mention that an answer was posted on
https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=7955

Regards

Jmarie



On 17/12/2015 17:13, "ImageJ Interest Group on behalf of Eric Griffis
(Staff)" <[hidden email] on behalf of [hidden email]> wrote:

>Hi All,
>
>I am running a Mac OS 10.10.5. I¹ve updated my java to the newest JDK.
>When I run java -version on Terminal, I see:
>
>java version "1.8.0_66"
>Java(TM) SE Runtime Environment (build 1.8.0_66-b17)
>Java HotSpot(TM) 64-Bit Server VM (build 25.66-b17, mixed mode)
>
>I¹ve run into a problem trying to use the OMERO plugin in Fiji. When I
>try to open it I get the message "This plugin requires Java 1.7 or
>later². My Fiji is "ImageJ 2.0.0-rc43/1.50e; Java 1.6.0_65 [64-bit]². I
>tried downloading the JRE-free version of Fiji, but it is still using the
>1.6 JRE. Is there a way that I can have Fiji find the newer JRE?
>
>Also, I can¹t run
>sudo rm -fr /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin
>sudo rm -fr /Library/PreferencePanes/JavaControlPanel.prefpane
>to strip out the older version of java since I don¹t have the access that
>I need to run these commands from Terminal. Any suggestions would be
>greatly appreciated.
>
>Best regards,
>
>Eric
>
>
>
>Centre for Gene Regulation and Expression
>College of Life Sciences
>University of Dundee
>MSI/WTB/JBC Complex
>Dow Street
>Dundee DD1 5EH
>United KIngdom
>
>[phone]
>[hidden email]<mailto:[hidden email]>
>http://www.lifesci.dundee.ac.uk/groups/eric_griffis/GriffisLab/index.html
>
>
>
>
>The University of Dundee is a registered Scottish Charity, No: SC015096
>
>--
>ImageJ mailing list: http://imagej.nih.gov/ij/list.html

The University of Dundee is a registered Scottish Charity, No: SC015096

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Eric,

Sorry for the delay in reply; somehow this message ended up in my spam
folder.

> Is there a way that I can have Fiji find the newer JRE?

I know you also asked this question on the OME forums [1], and got some
good answers there, but I just want to reiterate that you can control which
version of Java is used by ImageJ according to this guide:

http://imagej.net/FAQ#How_do_I_launch_ImageJ_with_a_different_version_of_Java.3F

Since you are on Windows, the easiest way to switch to Java 8 is rename the
"java" folder inside your Fiji.app folder to "java6". Then the launcher
will ignore it, and use your system-wide Java 8 installation instead.

Regards,
Curtis

[1] https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=7955

On Thu, Dec 17, 2015 at 11:13 AM, Eric Griffis (Staff) <
[hidden email]> wrote:

> Hi All,
>
> I am running a Mac OS 10.10.5. I’ve updated my java to the newest JDK.
> When I run java -version on Terminal, I see:
>
> java version "1.8.0_66"
> Java(TM) SE Runtime Environment (build 1.8.0_66-b17)
> Java HotSpot(TM) 64-Bit Server VM (build 25.66-b17, mixed mode)
>
> I’ve run into a problem trying to use the OMERO plugin in Fiji. When I try
> to open it I get the message "This plugin requires Java 1.7 or later”. My
> Fiji is "ImageJ 2.0.0-rc43/1.50e; Java 1.6.0_65 [64-bit]”. I tried
> downloading the JRE-free version of Fiji, but it is still using the 1.6
> JRE. Is there a way that I can have Fiji find the newer JRE?
>
> Also, I can’t run
> sudo rm -fr /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin
> sudo rm -fr /Library/PreferencePanes/JavaControlPanel.prefpane
> to strip out the older version of java since I don’t have the access that
> I need to run these commands from Terminal. Any suggestions would be
> greatly appreciated.
>
> Best regards,
>
> Eric
>
>
>
> Centre for Gene Regulation and Expression
> College of Life Sciences
> University of Dundee
> MSI/WTB/JBC Complex
> Dow Street
> Dundee DD1 5EH
> United KIngdom
>
> [phone]
> [hidden email]<mailto:[hidden email]>
> http://www.lifesci.dundee.ac.uk/groups/eric_griffis/GriffisLab/index.html
>
>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi again,

> Since you are on Windows

Ahem! Let me try this again. :-)

Since you are on OS X... this behavior is actually a bit mysterious. You
have installed the Java 8 JDK. Are you using the latest download of Fiji?
If you are using one of the older Life-Line versions, its launcher might be
too old, and be ignoring your Java 8—we only taught the launcher to prefer
Java 7 or 8 last year.

If all else fails, you can try uninstalling Apple Java 6:
http://apple.stackexchange.com/a/83153/137617

Regards,
Curtis


On Sun, Jan 3, 2016 at 8:30 AM, Curtis Rueden <[hidden email]> wrote:

> Hi Eric,
>
> Sorry for the delay in reply; somehow this message ended up in my spam
> folder.
>
> > Is there a way that I can have Fiji find the newer JRE?
>
> I know you also asked this question on the OME forums [1], and got some
> good answers there, but I just want to reiterate that you can control which
> version of Java is used by ImageJ according to this guide:
>
>
> http://imagej.net/FAQ#How_do_I_launch_ImageJ_with_a_different_version_of_Java.3F
>
> Since you are on Windows, the easiest way to switch to Java 8 is rename
> the "java" folder inside your Fiji.app folder to "java6". Then the launcher
> will ignore it, and use your system-wide Java 8 installation instead.
>
> Regards,
> Curtis
>
> [1] https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=7955
>
> On Thu, Dec 17, 2015 at 11:13 AM, Eric Griffis (Staff) <
> [hidden email]> wrote:
>
>> Hi All,
>>
>> I am running a Mac OS 10.10.5. I’ve updated my java to the newest JDK.
>> When I run java -version on Terminal, I see:
>>
>> java version "1.8.0_66"
>> Java(TM) SE Runtime Environment (build 1.8.0_66-b17)
>> Java HotSpot(TM) 64-Bit Server VM (build 25.66-b17, mixed mode)
>>
>> I’ve run into a problem trying to use the OMERO plugin in Fiji. When I
>> try to open it I get the message "This plugin requires Java 1.7 or later”.
>> My Fiji is "ImageJ 2.0.0-rc43/1.50e; Java 1.6.0_65 [64-bit]”. I tried
>> downloading the JRE-free version of Fiji, but it is still using the 1.6
>> JRE. Is there a way that I can have Fiji find the newer JRE?
>>
>> Also, I can’t run
>> sudo rm -fr /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin
>> sudo rm -fr /Library/PreferencePanes/JavaControlPanel.prefpane
>> to strip out the older version of java since I don’t have the access that
>> I need to run these commands from Terminal. Any suggestions would be
>> greatly appreciated.
>>
>> Best regards,
>>
>> Eric
>>
>>
>>
>> Centre for Gene Regulation and Expression
>> College of Life Sciences
>> University of Dundee
>> MSI/WTB/JBC Complex
>> Dow Street
>> Dundee DD1 5EH
>> United KIngdom
>>
>> [phone]
>> [hidden email]<mailto:[hidden email]>
>> http://www.lifesci.dundee.ac.uk/groups/eric_griffis/GriffisLab/index.html
>>
>>
>>
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Eric,

> I’ve looked at my Fiji folder and under Contents -> MacOs I have
> ImageJ-macosx (I had one from August, which I replaced with a freshly
> downloaded version that says it was last modified on 21 November
> 2015), ImageJ-macosx.old (which shows a modification date of 30 June),
> and ImageJ-tiger. Would it be possible to just delete .old and -tiger
> versions?

First, try to get a freshly downloaded Fiji working. Once that works, you
can try with your existing (potentially modified and/or out-of-date)
version. Then, if your existing version does not work, you can compare the
differences between the freshly downloaded one, and the non-working one.

See also:
http://imagej.net/FAQ#How_can_I_verify_that_my_ImageJ_is_really_100.25_up_to_date.3F

Regards,
Curtis


On Mon, Jan 4, 2016 at 10:17 AM, Eric Griffis (Staff) <
[hidden email]> wrote:

> Hi Curtis,
>
> Thanks for taking some time to look into this.
>
> I’ve looked at my Fiji folder and under Contents -> MacOs I have
> ImageJ-macosx (I had one from August, which I replaced with a freshly
> downloaded version that says it was last modified on 21 November 2015),
> ImageJ-macosx.old (which shows a modification date of 30 June), and
> ImageJ-tiger. Would it be possible to just delete .old and -tiger versions?
>
> If this doesn’t fix things, I’ll try to get the IT people here to
> uninstall the older versions of Java. Unfortunately, I don’t have the right
> level of admin control to run sudo commands to do this.
>
> Thanks,
>
> Eric
>
>
>
> Centre for Gene Regulation and Expression
> College of Life Sciences
> University of Dundee
> MSI/WTB/JBC Complex
> Dow Street
> Dundee DD1 5EH
> United KIngdom
>
> [phone]
> [hidden email]
> http://www.lifesci.dundee.ac.uk/groups/eric_griffis/GriffisLab/index.html
>
>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>

On Sun, Jan 3, 2016 at 8:33 AM, Curtis Rueden <[hidden email]> wrote:

> Hi again,
>
> > Since you are on Windows
>
> Ahem! Let me try this again. :-)
>
> Since you are on OS X... this behavior is actually a bit mysterious. You
> have installed the Java 8 JDK. Are you using the latest download of Fiji?
> If you are using one of the older Life-Line versions, its launcher might be
> too old, and be ignoring your Java 8—we only taught the launcher to prefer
> Java 7 or 8 last year.
>
> If all else fails, you can try uninstalling Apple Java 6:
> http://apple.stackexchange.com/a/83153/137617
>
> Regards,
> Curtis
>
>
> On Sun, Jan 3, 2016 at 8:30 AM, Curtis Rueden <[hidden email]> wrote:
>
>> Hi Eric,
>>
>> Sorry for the delay in reply; somehow this message ended up in my spam
>> folder.
>>
>> > Is there a way that I can have Fiji find the newer JRE?
>>
>> I know you also asked this question on the OME forums [1], and got some
>> good answers there, but I just want to reiterate that you can control which
>> version of Java is used by ImageJ according to this guide:
>>
>>
>> http://imagej.net/FAQ#How_do_I_launch_ImageJ_with_a_different_version_of_Java.3F
>>
>> Since you are on Windows, the easiest way to switch to Java 8 is rename
>> the "java" folder inside your Fiji.app folder to "java6". Then the launcher
>> will ignore it, and use your system-wide Java 8 installation instead.
>>
>> Regards,
>> Curtis
>>
>> [1] https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=7955
>>
>> On Thu, Dec 17, 2015 at 11:13 AM, Eric Griffis (Staff) <
>> [hidden email]> wrote:
>>
>>> Hi All,
>>>
>>> I am running a Mac OS 10.10.5. I’ve updated my java to the newest JDK.
>>> When I run java -version on Terminal, I see:
>>>
>>> java version "1.8.0_66"
>>> Java(TM) SE Runtime Environment (build 1.8.0_66-b17)
>>> Java HotSpot(TM) 64-Bit Server VM (build 25.66-b17, mixed mode)
>>>
>>> I’ve run into a problem trying to use the OMERO plugin in Fiji. When I
>>> try to open it I get the message "This plugin requires Java 1.7 or later”.
>>> My Fiji is "ImageJ 2.0.0-rc43/1.50e; Java 1.6.0_65 [64-bit]”. I tried
>>> downloading the JRE-free version of Fiji, but it is still using the 1.6
>>> JRE. Is there a way that I can have Fiji find the newer JRE?
>>>
>>> Also, I can’t run
>>> sudo rm -fr /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin
>>> sudo rm -fr /Library/PreferencePanes/JavaControlPanel.prefpane
>>> to strip out the older version of java since I don’t have the access
>>> that I need to run these commands from Terminal. Any suggestions would be
>>> greatly appreciated.
>>>
>>> Best regards,
>>>
>>> Eric
>>>
>>>
>>>
>>> Centre for Gene Regulation and Expression
>>> College of Life Sciences
>>> University of Dundee
>>> MSI/WTB/JBC Complex
>>> Dow Street
>>> Dundee DD1 5EH
>>> United KIngdom
>>>
>>> [phone]
>>> [hidden email]<mailto:[hidden email]>
>>> http://www.lifesci.dundee.ac.uk/groups/eric_griffis/GriffisLab/index.html
>>>
>>>
>>>
>>>
>>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>
>>
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html