http://imagej.273.s1.nabble.com/bio-formats-importer-broken-tp5021107p5021140.html
> Thanks!
> That fixed it. The update site was MPICBG changing it to Java8 and
> updating has corrected the issue.
> -Jeff
>
>
> On Tue, Aug 28, 2018 at 2:36 PM Curtis Rueden <
>
[hidden email]> wrote:
>
>> 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 of that update site that they are serving an out-of-date shadowed version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>>
>
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> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>