http://imagej.273.s1.nabble.com/bio-formats-importer-broken-tp5021107p5021135.html
That fixed it. The update site was MPICBG changing it to Java8 and
> Hi Jeff,
>
> > I do not have BIo-formats checked in my update manager, but I still
> > get this same error. Anything else I can try ?
>
> - Launch Help > Update...
> - When the ImageJ Updater window appears, click "Advanced mode" button
> - Type "formats" (without quotes) into the Search box.
>
> You should see an entry "jars/bio-formats/formats-bsd.jar" with
> Status/Action of "Up-to-date" and "Update Site" of "Java-8".
>
> If the Update Site is not "Java-8" then some other update site is shadowing
> the JAR, which is causing the conflict here. You can disable that update
> site to work around the problem. It would be good to notify the maintainer
> of that update site that they are serving an out-of-date shadowed version
> of Bio-Formats, and they should stop doing that.
>
> If the Update Site is "Java-8" but the Status/Action is not "Up-to-date",
> then right-click the entry and it set the status to "Update it". Then click
> "Apply changes" to download the latest formats-bsd.jar (version 5.9.1 as of
> this writing) and install it.
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect -
https://loci.wisc.edu/software> ImageJ2 lead, Fiji maintainer -
https://imagej.net/User:Rueden> Did you know ImageJ has a forum?
http://forum.imagej.net/>
>
>
> On Tue, Aug 28, 2018 at 1:15 PM Jeff Spector <
[hidden email]> wrote:
>
> > I do not have BIo-formats checked in my update manager, but I still get
> > this same error. Anything else I can try ?
> > -Jeff
> >
> >
> > On Thu, Aug 23, 2018 at 10:33 PM Curtis Rueden <
> >
[hidden email]> wrote:
> >
> > > Hi Jeff,
> > >
> > > Do you have the Bio-Formats update site enabled? If so, try disabling
> it.
> > >
> > > Regards,
> > > Curtis
> > >
> > >
> > > On Thu, Aug 23, 2018, 16:41 Jeff Spector <
[hidden email]> wrote:
> > >
> > > > Hi,
> > > > I've tried this but after the update if I look in advanced mode it
> > syas
> > > > this is jars/bio-formats/formats-bsd-5..7.3.jar not 5.9.1.
> > > > It seems like the update isn't up to date? Can I just download that
> > .jar
> > > > file and replace the one I have with the new one?
> > > >
> > > > -Jeff
> > > >
> > > >
> > > > On Thu, Aug 23, 2018 at 7:49 AM David Gault (Staff) <
> > >
[hidden email]>
> > > > wrote:
> > > >
> > > > > Thanks Jeff,
> > > > >
> > > > > In this case the formats-bad jar is out of sync with the latest
> > > version.
> > > > > If you run the updater and ensure that the Java 8 update site (
> > > > >
http://sites.imagej.net/Java-8/) is included, then in Advanced
> mode
> > > > > search for formats-bsd, this should return the 5.9.1 version from
> > 14th
> > > > > August which can be installed. Hopefully that should resolve your
> > > issue.
> > > > >
> > > > > With Thanks,
> > > > > David Gault
> > > > >
> > > > > On 23 Aug 2018, at 12:11, Jeff Spector <
[hidden email]
> <mailto:
> > > > >
[hidden email]>> wrote:
> > > > >
> > > > > Hi,
> > > > > According to what you asked I am using
> > > > > Bio-formats Release 5.9.1-SNAPSHOT Build Date 10 August 2018
> > > > > formats-api-5.9.1-20180810.111715-4.jar
> > > > > formats-bsd-5.7.3.jar
> > > > > formats-gpl-5.9.1-20180810.111724-4.jar
> > > > >
> > > > > I recently updated. Bio-Formats worked fine before the update. I'm
> > > > running
> > > > > IJ 1.52e on a Mac if that helps.
> > > > >
> > > > > -Jeff
> > > > >
> > > > >
> > > > >
> > > > > On Thu, Aug 23, 2018 at 6:38 AM David Gault (Staff) <
> > > >
[hidden email]
> > > > > <mailto:
[hidden email]>>
> > > > > wrote:
> > > > >
> > > > > Hi,
> > > > >
> > > > > This sounds like you have mismatched versions of some of of the
> > > > > Bio-Formats jars. Can you tell me which version you currently are
> > > using:
> > > > > Help > About Plugins > Bio-Formats Plugins
> > > > >
> > > > > Also if you go to the folder Fiji/jars/bio-formats can you tell me
> > > which
> > > > > versions of the below jars you have:
> > > > > formats-api
> > > > > formats-bsd
> > > > > formats-gpl
> > > > >
> > > > > With Thanks,
> > > > > David Gault
> > > > >
> > > > > On 22 Aug 2018, at 17:07, Glen MacDonald <
[hidden email]<mailto:
> > > > >
[hidden email]><mailto:
> > > > >
[hidden email]<mailto:
[hidden email]>>> wrote:
> > > > >
> > > > > I started getting same behavior and message last week attempting to
> > > open
> > > > > several formats.
> > > > > OS 10.11.6, Java 1.8.0_162 [64-bit]
> > > > > Re-installing Bio-Formats did not resolve thie behavior.
> > > > > Glen
> > > > >
> > > > >
> > > > > On Aug 22, 2018, at 8:42 AM, Jeff Spector <
[hidden email]
> > <mailto:
> > > > >
[hidden email]><mailto:
> > > > >
[hidden email]<mailto:
[hidden email]>>> wrote:
> > > > >
> > > > > Greetings,
> > > > > I updated my FIJI installation today and now Bio-Formats crashed
> > when I
> > > > > try to import an image. I get the following error :
> > > > >
> > > > > (Fiji Is Just) ImageJ 2.0.0-rc-68/1.52e; Java 1.8.0_66 [64-bit];
> Mac
> > > OS X
> > > > > 10.11.6; 267MB of 17778MB (1%)
> > > > >
> > > > > java.lang.NoSuchFieldError: mergeSubIFDs
> > > > > at loci.formats.in.NikonReader.<init>(NikonReader.java:119)
> > > > > at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
> > > Method)
> > > > > at
> > > > >
> > > > >
> > > > >
> > > >
> > >
> >
> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
> > > > > at
> > > > >
> > > > >
> > > > >
> > > >
> > >
> >
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
> > > > > at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
> > > > > at java.lang.Class.newInstance(Class.java:442)
> > > > > at loci.formats.ImageReader.<init>(ImageReader.java:129)
> > > > > at loci.formats.in
> > .FilePatternReader.<init>(FilePatternReader.java:77)
> > > > > at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
> > > Method)
> > > > > at
> > > > >
> > > > >
> > > > >
> > > >
> > >
> >
> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
> > > > > at
> > > > >
> > > > >
> > > > >
> > > >
> > >
> >
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
> > > > > at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
> > > > > at java.lang.Class.newInstance(Class.java:442)
> > > > > at loci.formats.ImageReader.<init>(ImageReader.java:129)
> > > > > at loci.plugins.util.LociPrefs.makeImageReader(LociPrefs.java:100)
> > > > > at
> > > loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:619)
> > > > > at
> > > loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:485)
> > > > > at loci.plugins.in.ImportProcess.execute(ImportProcess.java:138)
> > > > > at loci.plugins.in.Importer.showDialogs(Importer.java:140)
> > > > > at loci.plugins.in.Importer.run(Importer.java:76)
> > > > > at loci.plugins.LociImporter.run(LociImporter.java:78)
> > > > > at ij.IJ.runUserPlugIn(IJ.java:228)
> > > > > at ij.IJ.runPlugIn(IJ.java:192)
> > > > > at ij.Executer.runCommand(Executer.java:137)
> > > > > at ij.Executer.run(Executer.java:66)
> > > > > at java.lang.Thread.run(Thread.java:745)
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > can someone please help? I've tried uninstalling and re-installing
> > > > > bio-formats but get the same result.
> > > > > Thanks!
> > > > > -Jeff
> > > > >
> > > > > --
> > > > > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> > > > >
> > > > > --
> > > > > 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> > > > >
> > > > >
> > > > > --
> > > > > 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> > > > >
> > > >
> > > > --
> > > > 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> >
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>