macos sierra

[Aryeh Weiss]

Has anyone on list running FIji upgraded to macos sierra? If so, what
(if any) problems were encountered?

--aryeh

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

Ph:  972-3-5317638
FAX: [phone]


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

[Brandon Hurr]

Aryeh,

I've been running Sierra since about right after it was released and I've
not had any major issues with Fiji/ImageJ not working. I will say that it
seems to take a long time to load now. Way more than it used to, but I'm
unsure if this is a Sierra thing, Java thing or FIJI thing.

If you are interested in upgrading, I can't see anything that would prevent
you from doing so on my two Macs.

Brandon

On Sun, Oct 9, 2016 at 9:57 AM, Aryeh Weiss <[hidden email]> wrote:

> Has anyone on list running FIji upgraded to macos sierra? If so, what (if
> any) problems were encountered?
>
> --aryeh
>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: [phone]
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Aryeh Weiss]

On 10/10/2016 12:52 AM, Brandon Hurr wrote:

> Aryeh,
>
> I've been running Sierra since about right after it was released and
> I've not had any major issues with Fiji/ImageJ not working. I will say
> that it seems to take a long time to load now. Way more than it used
> to, but I'm unsure if this is a Sierra thing, Java thing or FIJI thing.
>
> If you are interested in upgrading, I can't see anything that would
> prevent you from doing so on my two Macs.
> Brandon

Thanks for the quick replies.
Looks like Fiji is ok, but the bigger hassle will be macports, where
some ports are not yet working in sierra.

--aryeh

>
> On Sun, Oct 9, 2016 at 9:57 AM, Aryeh Weiss <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Has anyone on list running FIji upgraded to macos sierra? If so,
>     what (if any) problems were encountered?
>
>     --aryeh
>
>     --
>     Aryeh Weiss
>     Faculty of Engineering
>     Bar Ilan University
>     Ramat Gan 52900 Israel
>
>     Ph:  972-3-5317638
>     FAX: [phone]
>
>
>     --
>     ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>     <http://imagej.nih.gov/ij/list.html>
>
>

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

Ph:  972-3-5317638
FAX: [phone]


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

[Aryeh Weiss]

On 09/10/2016 22:11, James Harris wrote:

> Hello Aryeh,
>
> I run Fiji on an iMac running macOS sierra, and only had one problem.
> After updating to sierra I tried to run Fiji from its desktop icon and
> kept getting the message that I had to install Java, which was already
> on my system. So I went to the oracle site downloaded
> jre-8u101-macosx-x64.dmg, and ran it. But still got the same error
> message until I tried executing Fiji directly from my applications
> folder this worked, so I copied the Fiji app from this folder to my
> desktop, and it runs perfectly.. Since then I have not encountered any
> problems.
>
> Jim.
>

Thanks for this information. I also encountered this problem, and
running Fiji from the Applications folder did not help. Running the
ImageJ-macosx file from Contents/MacOS did work, but this is not how I
wanted to run it.

I downloaded a fresh copy of Fiji, and it worked correctly. I did not
want to replace my installation, so I found that if I replaced the
Contents directory  ( Fiji.app/Contents ), it solved the problem.
Someone who knows the MacOS launcher better than I might be able to
explain this, and suggest a more elegant fix.
I did not proceed to replace the individual files, so I do not know if
info.plist or ImageJ-macosx (or both) are responsible.

--aryeh

>
>> On 9 Oct 2016, at 17:57, Aryeh Weiss <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>> Has anyone on list running FIji upgraded to macos sierra? If so, what
>> (if any) problems were encountered?
>>
>> --aryeh
>>
>> --
>> Aryeh Weiss
>> Faculty of Engineering
>> Bar Ilan University
>> Ramat Gan 52900 Israel
>>
>> Ph:  972-3-5317638
>> FAX: [phone]
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

Ph:  972-3-5317638
FAX: [phone]


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

[ctrueden]

Hi Aryeh,

> Has anyone on list running FIji upgraded to macos sierra? If so, what
> (if any) problems were encountered?

I upgraded to Sierra as soon as was released, expecting something or other
to go wrong with ImageJ because of it. I was pleasantly surprised that it
all seems fine.

Actually, I think Apple fixed at least one memory leak:
http://forum.imagej.net/t/memory-not-clearing-over-time/2137/15?u=ctrueden

However, it does not fix everything -- the horrible Mac speed issues are
not resolved:
http://forum.imagej.net/t/mac-java-speed-issues/304

Fortunately, Wayne's workaround of not setting the menu bar on new windows
avoids the worst of it, for the time being.

> I downloaded a fresh copy of Fiji, and it worked correctly. I did not
> want to replace my installation, so I found that if I replaced the
> Contents directory  ( Fiji.app/Contents ), it solved the problem.

That is certainly safe and reasonable. It is not supposed to be necessary
-- the ImageJ Updater is supposed to update the launcher in the Contents
folder -- but perhaps it did not for some reason. See also
http://imagej.net/Frequently_Asked_Questions#How_can_I_verify_that_my_ImageJ_is_really_100.25_up_to_date.3F

> the bigger hassle will be macports, where some ports are not yet
> working in sierra.

Have you tried Homebrew (http://brew.sh/)? I like it better than MacPorts
and all seems to be working for me on Sierra so far.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Mon, Oct 10, 2016 at 4:40 AM, Aryeh Weiss <[hidden email]> wrote:

> On 09/10/2016 22:11, James Harris wrote:
>
>> Hello Aryeh,
>>
>> I run Fiji on an iMac running macOS sierra, and only had one problem.
>> After updating to sierra I tried to run Fiji from its desktop icon and kept
>> getting the message that I had to install Java, which was already on my
>> system. So I went to the oracle site downloaded jre-8u101-macosx-x64.dmg,
>> and ran it. But still got the same error message until I tried executing
>> Fiji directly from my applications folder this worked, so I copied the Fiji
>> app from this folder to my desktop, and it runs perfectly.. Since then I
>> have not encountered any problems.
>>
>> Jim.
>>
>> Thanks for this information. I also encountered this problem, and running
> Fiji from the Applications folder did not help. Running the ImageJ-macosx
> file from Contents/MacOS did work, but this is not how I wanted to run it.
>
> I downloaded a fresh copy of Fiji, and it worked correctly. I did not want
> to replace my installation, so I found that if I replaced the Contents
> directory  ( Fiji.app/Contents ), it solved the problem. Someone who knows
> the MacOS launcher better than I might be able to explain this, and suggest
> a more elegant fix.
> I did not proceed to replace the individual files, so I do not know if
> info.plist or ImageJ-macosx (or both) are responsible.
>
> --aryeh
>
>
>
>> On 9 Oct 2016, at 17:57, Aryeh Weiss <[hidden email] <mailto:
>>> [hidden email]>> wrote:
>>>
>>> Has anyone on list running FIji upgraded to macos sierra? If so, what
>>> (if any) problems were encountered?
>>>
>>> --aryeh
>>>
>>> --
>>> Aryeh Weiss
>>> Faculty of Engineering
>>> Bar Ilan University
>>> Ramat Gan 52900 Israel
>>>
>>> Ph:  972-3-5317638
>>> FAX: [phone]
>>>
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>
>>
>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: [phone]
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Aryeh Weiss]

Hi Curtis

Thanks for your reply.

On 10/10/2016 22:34, Curtis Rueden wrote:

> Hi Aryeh,
>
> > Has anyone on list running FIji upgraded to macos sierra? If so, what
> > (if any) problems were encountered?
>
> I upgraded to Sierra as soon as was released, expecting something or
> other to go wrong with ImageJ because of it. I was pleasantly
> surprised that it all seems fine.
>
> Actually, I think Apple fixed at least one memory leak:
> http://forum.imagej.net/t/memory-not-clearing-over-time/2137/15?u=ctrueden
>
> However, it does not fix everything -- the horrible Mac speed issues
> are not resolved:
> http://forum.imagej.net/t/mac-java-speed-issues/304
>
> Fortunately, Wayne's workaround of not setting the menu bar on new
> windows avoids the worst of it, for the time being.
>
> > I downloaded a fresh copy of Fiji, and it worked correctly. I did not
> > want to replace my installation, so I found that if I replaced the
> > Contents directory  ( Fiji.app/Contents ), it solved the problem.
>
> That is certainly safe and reasonable. It is not supposed to be
> necessary -- the ImageJ Updater is supposed to update the launcher in
> the Contents folder -- but perhaps it did not for some reason. See
> also
> http://imagej.net/Frequently_Asked_Questions#How_can_I_verify_that_my_ImageJ_is_really_100.25_up_to_date.3F
>

Following these instructions, I found that it reported fiji-macosx and
fiji-tiger as uninstalled. I dont know if this caused a problem, but
following the recommendation in this link I set them to be installed. At
least I can say that doing so did not break anything.

> > the bigger hassle will be macports, where some ports are not yet
> > working in sierra.
>
> Have you tried Homebrew (http://brew.sh/)? I like it better than
> MacPorts and all seems to be working for me on Sierra so far.
>

I have played with Homebrew, but I am fairly heavily set up with
macports, and having two package managers causes confusion. If I was
starting over, I might have started with Homebrew.

Anyway, the transition went ok, using these instructions:
https://trac.macports.org/wiki/Migration

Best regards
--aryeh

> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - http://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Mon, Oct 10, 2016 at 4:40 AM, Aryeh Weiss <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     On 09/10/2016 22:11, James Harris wrote:
>
>         Hello Aryeh,
>
>         I run Fiji on an iMac running macOS sierra, and only had one
>         problem. After updating to sierra I tried to run Fiji from its
>         desktop icon and kept getting the message that I had to
>         install Java, which was already on my system. So I went to the
>         oracle site downloaded jre-8u101-macosx-x64.dmg, and ran it.
>         But still got the same error message until I tried executing
>         Fiji directly from my applications folder this worked, so I
>         copied the Fiji app from this folder to my desktop, and it
>         runs perfectly.. Since then I have not encountered any problems.
>
>         Jim.
>
>     Thanks for this information. I also encountered this problem, and
>     running Fiji from the Applications folder did not help. Running
>     the ImageJ-macosx file from Contents/MacOS did work, but this is
>     not how I wanted to run it.
>
>     I downloaded a fresh copy of Fiji, and it worked correctly. I did
>     not want to replace my installation, so I found that if I replaced
>     the Contents directory  ( Fiji.app/Contents ), it solved the
>     problem. Someone who knows the MacOS launcher better than I might
>     be able to explain this, and suggest a more elegant fix.
>     I did not proceed to replace the individual files, so I do not
>     know if info.plist or ImageJ-macosx (or both) are responsible.
>
>     --aryeh
>
>
>
>             On 9 Oct 2016, at 17:57, Aryeh Weiss <[hidden email]
>             <mailto:[hidden email]> <mailto:[hidden email]
>             <mailto:[hidden email]>>> wrote:
>
>             Has anyone on list running FIji upgraded to macos sierra?
>             If so, what (if any) problems were encountered?
>
>             --aryeh
>

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

Ph:  972-3-5317638
FAX: [phone]


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