bio-formats importer broken

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bio-formats importer broken

Jeff Spector-2
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

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Re: bio-formats importer broken

Glen MacDonald-3
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]> 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

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Re: bio-formats importer broken

David Gault (Staff)
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]>> 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]>> 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

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Re: bio-formats importer broken

Jeff Spector-2
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]>
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]>> 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]>> 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
>

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Re: bio-formats importer broken

David Gault (Staff)
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

--
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Re: bio-formats importer broken

Jeff Spector-2
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
>

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Re: bio-formats importer broken

Curtis Rueden
In reply to this post by David Gault (Staff)
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
>

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Re: bio-formats importer broken

Jeff Spector-2
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
>

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Re: bio-formats importer broken

Curtis Rueden
In reply to this post by Curtis Rueden
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
>

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Re: bio-formats importer broken

Jeff Spector-2
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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Re: bio-formats importer broken

Jan Eglinger
Hi Jeff,

you likely meant MPIBPC, not MPICBG, right? (There is no site MPICBG
listed on https://imagej.net/List_of_update_sites, but there is an
MPIBPC site that serves the outdated jar.)

As suggested by Curtis, it would be helpful if you contacted the
maintainers (as stated on the page linked above) so that they can fix
the issue.

Cheers
Jan


On 28.08.2018 23:14, Jeff Spector wrote:

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

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