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why does bioformats give this error on a mac and not on windows

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dksamuel
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why does bioformats give this error on a mac and not on windows

dksamuel
Respected Imagej researchers, why does Bioformats give this error on Mac
and not on windows 10, what should I do to convert czi files, thanks
Dr.D.K.Samuel, Ind Int of Hort Research, Bangalore India
-----------------
(Fiji Is Just) ImageJ 2.0.0-rc-68/1.52g; Java 1.8.0_172 [64-bit]; Mac OS X
10.14; 289MB of 23012MB (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:423)
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:423)
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:748)

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David Gault (Staff)
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Re: why does bioformats give this error on a mac and not on windows

David Gault (Staff)
Hi Duleep,

This error is caused by a version mismatch in some of the Bio-Formats jars suggesting that only some of the files have been updated.
To correct it you should first ensure that the correct update site is being used. To modify the update sites used go to:

Help > Update > Manage update sites

For the latest Bio-Formats release jars you should have the Java-8 site selected,  you can unselect the Bio-Formats site

Once the update site is correctly selected you can select Advanced mode and search for Bio-Formats to list all of the Bio-Formats jars which can be updated.
In particular you want to make sure that formats-api, formats-bsd and formats-gpl are all updated to the same version (this should be the most recent release 5.9.2).

With Thanks,
David Gault

> On 18 Sep 2018, at 11:13, Duleep Samuel <[hidden email]> wrote:
>
> Respected Imagej researchers, why does Bioformats give this error on Mac
> and not on windows 10, what should I do to convert czi files, thanks
> Dr.D.K.Samuel, Ind Int of Hort Research, Bangalore India
> -----------------
> (Fiji Is Just) ImageJ 2.0.0-rc-68/1.52g; Java 1.8.0_172 [64-bit]; Mac OS X
> 10.14; 289MB of 23012MB (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:423)
> 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:423)
> 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:748)
>
> --
> 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
dksamuel
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Re: why does bioformats give this error on a mac and not on windows

dksamuel
Sir, I thank you so much for your response, but still bioformats cannot
find the formats to import, thanks Samuel

Could not generate list of supported formats:

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:423)
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:423)
at java.lang.Class.newInstance(Class.java:442)
at loci.formats.ImageReader.<init>(ImageReader.java:129)
at loci.formats.ImageReader.<init>(ImageReader.java:116)
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:423)
at java.lang.Class.newInstance(Class.java:442)
at loci.plugins.config.ConfigWindow.run(ConfigWindow.java:353)
at java.lang.Thread.run(Thread.java:748)

On Tue, Sep 18, 2018 at 5:19 PM David Gault (Staff) <[hidden email]>
wrote:

> Hi Duleep,
>
> This error is caused by a version mismatch in some of the Bio-Formats jars
> suggesting that only some of the files have been updated.
> To correct it you should first ensure that the correct update site is
> being used. To modify the update sites used go to:
>
> Help > Update > Manage update sites
>
> For the latest Bio-Formats release jars you should have the Java-8 site
> selected,  you can unselect the Bio-Formats site
>
> Once the update site is correctly selected you can select Advanced mode
> and search for Bio-Formats to list all of the Bio-Formats jars which can be
> updated.
> In particular you want to make sure that formats-api, formats-bsd and
> formats-gpl are all updated to the same version (this should be the most
> recent release 5.9.2).
>
> With Thanks,
> David Gault
>
> > On 18 Sep 2018, at 11:13, Duleep Samuel <[hidden email]> wrote:
> >
> > Respected Imagej researchers, why does Bioformats give this error on Mac
> > and not on windows 10, what should I do to convert czi files, thanks
> > Dr.D.K.Samuel, Ind Int of Hort Research, Bangalore India
> > -----------------
> > (Fiji Is Just) ImageJ 2.0.0-rc-68/1.52g; Java 1.8.0_172 [64-bit]; Mac OS
> X
> > 10.14; 289MB of 23012MB (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:423)
> > 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:423)
> > 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:748)
> >
> > --
> > 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
David Gault (Staff)
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Re: why does bioformats give this error on a mac and not on windows

David Gault (Staff)
Hi,

Can you check which version of the following jars are currently installed: formats-gpl, formats-bad and formats-api
Within your FIJI install you can find these in the folder: jars > Bio-Formats

The version number should appear as part of the filename.

With Thanks,
David Gault

> On 19 Sep 2018, at 07:47, Duleep Samuel <[hidden email]> wrote:
>
> Sir, I thank you so much for your response, but still bioformats cannot
> find the formats to import, thanks Samuel
>
> Could not generate list of supported formats:
>
> 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:423)
> 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:423)
> at java.lang.Class.newInstance(Class.java:442)
> at loci.formats.ImageReader.<init>(ImageReader.java:129)
> at loci.formats.ImageReader.<init>(ImageReader.java:116)
> 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:423)
> at java.lang.Class.newInstance(Class.java:442)
> at loci.plugins.config.ConfigWindow.run(ConfigWindow.java:353)
> at java.lang.Thread.run(Thread.java:748)
>
> On Tue, Sep 18, 2018 at 5:19 PM David Gault (Staff) <[hidden email]>
> wrote:
>
>> Hi Duleep,
>>
>> This error is caused by a version mismatch in some of the Bio-Formats jars
>> suggesting that only some of the files have been updated.
>> To correct it you should first ensure that the correct update site is
>> being used. To modify the update sites used go to:
>>
>> Help > Update > Manage update sites
>>
>> For the latest Bio-Formats release jars you should have the Java-8 site
>> selected,  you can unselect the Bio-Formats site
>>
>> Once the update site is correctly selected you can select Advanced mode
>> and search for Bio-Formats to list all of the Bio-Formats jars which can be
>> updated.
>> In particular you want to make sure that formats-api, formats-bsd and
>> formats-gpl are all updated to the same version (this should be the most
>> recent release 5.9.2).
>>
>> With Thanks,
>> David Gault
>>
>>> On 18 Sep 2018, at 11:13, Duleep Samuel <[hidden email]> wrote:
>>>
>>> Respected Imagej researchers, why does Bioformats give this error on Mac
>>> and not on windows 10, what should I do to convert czi files, thanks
>>> Dr.D.K.Samuel, Ind Int of Hort Research, Bangalore India
>>> -----------------
>>> (Fiji Is Just) ImageJ 2.0.0-rc-68/1.52g; Java 1.8.0_172 [64-bit]; Mac OS
>> X
>>> 10.14; 289MB of 23012MB (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:423)
>>> 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:423)
>>> 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:748)
>>>
>>> --
>>> 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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