Bio-Formats importer broken after latest Fiji update?

[Martin Höhne]

Dear All,

Fiji just did it´s auto-update after startup, and it seems that the bioformats-importer is broken.

Plugin > Bio-Formats > Bio-Formats Importer

gives the error message pasted below. Is this a general problem or only my configuration (Latest Fiji on Win7)

Thanks
Martin

---------
(Fiji Is Just) ImageJ 2.0.0-rc-26/1.49p; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 23MB of 2975MB (<1%)
 
java.lang.NoClassDefFoundError: Could not initialize class loci.common.Location
        at loci.plugins.in.ImporterOptions.parseArg(ImporterOptions.java:171)
        at loci.plugins.in.Importer.parseOptions(Importer.java:112)
        at loci.plugins.in.Importer.run(Importer.java:69)
        at loci.plugins.LociImporter.run(LociImporter.java:78)
        at ij.IJ.runUserPlugIn(IJ.java:199)
        at ij.IJ.runPlugIn(IJ.java:163)
        at ij.Executer.runCommand(Executer.java:131)
        at ij.Executer.run(Executer.java:64)
        at java.lang.Thread.run(Thread.java:662)

[Aryeh Weiss]

On 3/24/15 12:25 PM, Martin Höhne wrote:

> Dear All,
>
> Fiji just did it´s auto-update after startup, and it seems that the
> bioformats-importer is broken.
>
> Plugin > Bio-Formats > Bio-Formats Importer
>
> gives the error message pasted below. Is this a general problem or only my
> configuration (Latest Fiji on Win7)
>
> Thanks
> Martin
>
> ---------
> (Fiji Is Just) ImageJ 2.0.0-rc-26/1.49p; Java 1.6.0_24 [64-bit]; Windows 7
> 6.1; 23MB of 2975MB (<1%)
>  
> java.lang.NoClassDefFoundError: Could not initialize class
> loci.common.Location
> at loci.plugins.in.ImporterOptions.parseArg(ImporterOptions.java:171)
> at loci.plugins.in.Importer.parseOptions(Importer.java:112)
> at loci.plugins.in.Importer.run(Importer.java:69)
> at loci.plugins.LociImporter.run(LociImporter.java:78)
> at ij.IJ.runUserPlugIn(IJ.java:199)
> at ij.IJ.runPlugIn(IJ.java:163)
> at ij.Executer.runCommand(Executer.java:131)
> at ij.Executer.run(Executer.java:64)
> at java.lang.Thread.run(Thread.java:662)
>
>
>

I confirm this on OSX Yosemite. You can work around by deselecting the
Bioformats update site, so that you get Bioformats from the Fiji update
site. They are still at 5.0.7, and it works. However, if you read
complicated ND2 files, you will need the 5.0.2 version of the gpl jar file.

--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

[lechristophe]

I confirm this, had to deselect the Bio-Format update site.

On Tue, Mar 24, 2015 at 12:22 PM, Aryeh Weiss <[hidden email]> wrote:

> On 3/24/15 12:25 PM, Martin Höhne wrote:
>
>> Dear All,
>>
>> Fiji just did it´s auto-update after startup, and it seems that the
>> bioformats-importer is broken.
>>
>> Plugin > Bio-Formats > Bio-Formats Importer
>>
>> gives the error message pasted below. Is this a general problem or only my
>> configuration (Latest Fiji on Win7)
>>
>> Thanks
>> Martin
>>
>> ---------
>> (Fiji Is Just) ImageJ 2.0.0-rc-26/1.49p; Java 1.6.0_24 [64-bit]; Windows 7
>> 6.1; 23MB of 2975MB (<1%)
>>   java.lang.NoClassDefFoundError: Could not initialize class
>> loci.common.Location
>>         at loci.plugins.in.ImporterOptions.parseArg(
>> ImporterOptions.java:171)
>>         at loci.plugins.in.Importer.parseOptions(Importer.java:112)
>>         at loci.plugins.in.Importer.run(Importer.java:69)
>>         at loci.plugins.LociImporter.run(LociImporter.java:78)
>>         at ij.IJ.runUserPlugIn(IJ.java:199)
>>         at ij.IJ.runPlugIn(IJ.java:163)
>>         at ij.Executer.runCommand(Executer.java:131)
>>         at ij.Executer.run(Executer.java:64)
>>         at java.lang.Thread.run(Thread.java:662)
>>
>>
>>
>>
> I confirm this on OSX Yosemite. You can work around by deselecting the
> Bioformats update site, so that you get Bioformats from the Fiji update
> site. They are still at 5.0.7, and it works. However, if you read
> complicated ND2 files, you will need the 5.0.2 version of the gpl jar file.
>
> --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

[Mark Hiner]

Hi all,

 Sorry for the inconvenience. Yesterday on the Fiji bugzilla[1] it was
reported that consumers of Bio-Formats were broken by the Bio-Formats
update site. Thank you for pointing out that core functionality is broken
as well!

 The Bio-Formats update site is certainly mixing 5.1.x and 5.0.x
Bio-Formats components. We'll look into it and hope to have a fix shortly.

Thanks!
- Mark

[1] http://fiji.sc/bugzilla/show_bug.cgi?id=1034

On Tue, Mar 24, 2015 at 7:06 AM, Christophe Leterrier <
[hidden email]> wrote:

> I confirm this, had to deselect the Bio-Format update site.
>
> On Tue, Mar 24, 2015 at 12:22 PM, Aryeh Weiss <[hidden email]> wrote:
>
> > On 3/24/15 12:25 PM, Martin Höhne wrote:
> >
> >> Dear All,
> >>
> >> Fiji just did it´s auto-update after startup, and it seems that the
> >> bioformats-importer is broken.
> >>
> >> Plugin > Bio-Formats > Bio-Formats Importer
> >>
> >> gives the error message pasted below. Is this a general problem or only
> my
> >> configuration (Latest Fiji on Win7)
> >>
> >> Thanks
> >> Martin
> >>
> >> ---------
> >> (Fiji Is Just) ImageJ 2.0.0-rc-26/1.49p; Java 1.6.0_24 [64-bit];
> Windows 7
> >> 6.1; 23MB of 2975MB (<1%)
> >>   java.lang.NoClassDefFoundError: Could not initialize class
> >> loci.common.Location
> >>         at loci.plugins.in.ImporterOptions.parseArg(
> >> ImporterOptions.java:171)
> >>         at loci.plugins.in.Importer.parseOptions(Importer.java:112)
> >>         at loci.plugins.in.Importer.run(Importer.java:69)
> >>         at loci.plugins.LociImporter.run(LociImporter.java:78)
> >>         at ij.IJ.runUserPlugIn(IJ.java:199)
> >>         at ij.IJ.runPlugIn(IJ.java:163)
> >>         at ij.Executer.runCommand(Executer.java:131)
> >>         at ij.Executer.run(Executer.java:64)
> >>         at java.lang.Thread.run(Thread.java:662)
> >>
> >>
> >>
> >>
> > I confirm this on OSX Yosemite. You can work around by deselecting the
> > Bioformats update site, so that you get Bioformats from the Fiji update
> > site. They are still at 5.0.7, and it works. However, if you read
> > complicated ND2 files, you will need the 5.0.2 version of the gpl jar
> file.
> >
> > --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
>

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

[Melissa Linkert-2]

Hi all,

>  Sorry for the inconvenience. Yesterday on the Fiji bugzilla[1] it was
> reported that consumers of Bio-Formats were broken by the Bio-Formats
> update site. Thank you for pointing out that core functionality is broken
> as well!
>
>  The Bio-Formats update site is certainly mixing 5.1.x and 5.0.x
> Bio-Formats components. We'll look into it and hope to have a fix shortly.

Our understanding is that this is a packaging issue related to mixing of
Bio-Formats 5.0.x (stable) and Bio-Formats 5.1.x (development) lines
within a Fiji install, and not an issue with Bio-Formats itself.  Let us
know if we can be of any assistance.

Regards,
-Melissa

On Tue, Mar 24, 2015 at 08:23:28AM -0500, Mark Hiner wrote:

> Hi all,
>
>  Sorry for the inconvenience. Yesterday on the Fiji bugzilla[1] it was
> reported that consumers of Bio-Formats were broken by the Bio-Formats
> update site. Thank you for pointing out that core functionality is broken
> as well!
>
>  The Bio-Formats update site is certainly mixing 5.1.x and 5.0.x
> Bio-Formats components. We'll look into it and hope to have a fix shortly.
>
> Thanks!
> - Mark
>
> [1] http://fiji.sc/bugzilla/show_bug.cgi?id=1034
>
> On Tue, Mar 24, 2015 at 7:06 AM, Christophe Leterrier <
> [hidden email]> wrote:
>
> > I confirm this, had to deselect the Bio-Format update site.
> >
> > On Tue, Mar 24, 2015 at 12:22 PM, Aryeh Weiss <[hidden email]> wrote:
> >
> > > On 3/24/15 12:25 PM, Martin Höhne wrote:
> > >
> > >> Dear All,
> > >>
> > >> Fiji just did it´s auto-update after startup, and it seems that the
> > >> bioformats-importer is broken.
> > >>
> > >> Plugin > Bio-Formats > Bio-Formats Importer
> > >>
> > >> gives the error message pasted below. Is this a general problem or only
> > my
> > >> configuration (Latest Fiji on Win7)
> > >>
> > >> Thanks
> > >> Martin
> > >>
> > >> ---------
> > >> (Fiji Is Just) ImageJ 2.0.0-rc-26/1.49p; Java 1.6.0_24 [64-bit];
> > Windows 7
> > >> 6.1; 23MB of 2975MB (<1%)
> > >>   java.lang.NoClassDefFoundError: Could not initialize class
> > >> loci.common.Location
> > >>         at loci.plugins.in.ImporterOptions.parseArg(
> > >> ImporterOptions.java:171)
> > >>         at loci.plugins.in.Importer.parseOptions(Importer.java:112)
> > >>         at loci.plugins.in.Importer.run(Importer.java:69)
> > >>         at loci.plugins.LociImporter.run(LociImporter.java:78)
> > >>         at ij.IJ.runUserPlugIn(IJ.java:199)
> > >>         at ij.IJ.runPlugIn(IJ.java:163)
> > >>         at ij.Executer.runCommand(Executer.java:131)
> > >>         at ij.Executer.run(Executer.java:64)
> > >>         at java.lang.Thread.run(Thread.java:662)
> > >>
> > >>
> > >>
> > >>
> > > I confirm this on OSX Yosemite. You can work around by deselecting the
> > > Bioformats update site, so that you get Bioformats from the Fiji update
> > > site. They are still at 5.0.7, and it works. However, if you read
> > > complicated ND2 files, you will need the 5.0.2 version of the gpl jar
> > file.
> > >
> > > --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
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

[ctrueden]

Hi all,

The Bio-Formats update site is now fixed. For those affected: please run
Help > Update... again and let us know if you continue to have problems.

For those curious: the issue was not related to mixing BF5.0 and BF5.1
libraries, but rather with some libraries needed by BF5.1 (e.g., guava)
being erroneously removed from the update site. We have fixed the
configuration to avoid this issue in the future.

Regards,
Curtis

On Tue, Mar 24, 2015 at 10:55 AM, Melissa Linkert <
[hidden email]> wrote:

> Hi all,
>
> >  Sorry for the inconvenience. Yesterday on the Fiji bugzilla[1] it was
> > reported that consumers of Bio-Formats were broken by the Bio-Formats
> > update site. Thank you for pointing out that core functionality is broken
> > as well!
> >
> >  The Bio-Formats update site is certainly mixing 5.1.x and 5.0.x
> > Bio-Formats components. We'll look into it and hope to have a fix
> shortly.
>
> Our understanding is that this is a packaging issue related to mixing of
> Bio-Formats 5.0.x (stable) and Bio-Formats 5.1.x (development) lines
> within a Fiji install, and not an issue with Bio-Formats itself.  Let us
> know if we can be of any assistance.
>
> Regards,
> -Melissa
>
> On Tue, Mar 24, 2015 at 08:23:28AM -0500, Mark Hiner wrote:
> > Hi all,
> >
> >  Sorry for the inconvenience. Yesterday on the Fiji bugzilla[1] it was
> > reported that consumers of Bio-Formats were broken by the Bio-Formats
> > update site. Thank you for pointing out that core functionality is broken
> > as well!
> >
> >  The Bio-Formats update site is certainly mixing 5.1.x and 5.0.x
> > Bio-Formats components. We'll look into it and hope to have a fix
> shortly.
> >
> > Thanks!
> > - Mark
> >
> > [1] http://fiji.sc/bugzilla/show_bug.cgi?id=1034
> >
> > On Tue, Mar 24, 2015 at 7:06 AM, Christophe Leterrier <
> > [hidden email]> wrote:
> >
> > > I confirm this, had to deselect the Bio-Format update site.
> > >
> > > On Tue, Mar 24, 2015 at 12:22 PM, Aryeh Weiss <[hidden email]>
> wrote:
> > >
> > > > On 3/24/15 12:25 PM, Martin Höhne wrote:
> > > >
> > > >> Dear All,
> > > >>
> > > >> Fiji just did it´s auto-update after startup, and it seems that the
> > > >> bioformats-importer is broken.
> > > >>
> > > >> Plugin > Bio-Formats > Bio-Formats Importer
> > > >>
> > > >> gives the error message pasted below. Is this a general problem or
> only
> > > my
> > > >> configuration (Latest Fiji on Win7)
> > > >>
> > > >> Thanks
> > > >> Martin
> > > >>
> > > >> ---------
> > > >> (Fiji Is Just) ImageJ 2.0.0-rc-26/1.49p; Java 1.6.0_24 [64-bit];
> > > Windows 7
> > > >> 6.1; 23MB of 2975MB (<1%)
> > > >>   java.lang.NoClassDefFoundError: Could not initialize class
> > > >> loci.common.Location
> > > >>         at loci.plugins.in.ImporterOptions.parseArg(
> > > >> ImporterOptions.java:171)
> > > >>         at loci.plugins.in.Importer.parseOptions(Importer.java:112)
> > > >>         at loci.plugins.in.Importer.run(Importer.java:69)
> > > >>         at loci.plugins.LociImporter.run(LociImporter.java:78)
> > > >>         at ij.IJ.runUserPlugIn(IJ.java:199)
> > > >>         at ij.IJ.runPlugIn(IJ.java:163)
> > > >>         at ij.Executer.runCommand(Executer.java:131)
> > > >>         at ij.Executer.run(Executer.java:64)
> > > >>         at java.lang.Thread.run(Thread.java:662)
> > > >>
> > > >>
> > > >>
> > > >>
> > > > I confirm this on OSX Yosemite. You can work around by deselecting
> the
> > > > Bioformats update site, so that you get Bioformats from the Fiji
> update
> > > > site. They are still at 5.0.7, and it works. However, if you read
> > > > complicated ND2 files, you will need the 5.0.2 version of the gpl jar
> > > file.
> > > >
> > > > --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
> > >
> >
> > --
> > 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

[Ignacio Arganda-Carreras]

Hello Curtis,

I updated Fiji and consequently Bioformats but the problem remains. I have
the same exception as before and also this one:

(Fiji Is Just) ImageJ 2.0.0-rc-26/1.49p; Java 1.6.0_24 [64-bit]; Linux
3.13.0-48-generic; 31MB of 30000MB (<1%)

java.lang.NoClassDefFoundError: com/google/common/collect/MapMaker
at loci.common.Location.<clinit>(Location.java:88)
at loci.plugins.in.ImporterOptions.parseArg(ImporterOptions.java:171)
at loci.plugins.in.Importer.parseOptions(Importer.java:112)
at loci.plugins.in.Importer.run(Importer.java:69)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:199)
at ij.IJ.runPlugIn(IJ.java:163)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:662)
Caused by: java.lang.ClassNotFoundException:
com.google.common.collect.MapMaker
at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
... 10 more

I hope it helps!

ignacio


On Tue, Mar 24, 2015 at 5:10 PM, Curtis Rueden <[hidden email]> wrote:

> Hi all,
>
> The Bio-Formats update site is now fixed. For those affected: please run
> Help > Update... again and let us know if you continue to have problems.
>
> For those curious: the issue was not related to mixing BF5.0 and BF5.1
> libraries, but rather with some libraries needed by BF5.1 (e.g., guava)
> being erroneously removed from the update site. We have fixed the
> configuration to avoid this issue in the future.
>
> Regards,
> Curtis
>
> On Tue, Mar 24, 2015 at 10:55 AM, Melissa Linkert <
> [hidden email]> wrote:
>
> > Hi all,
> >
> > >  Sorry for the inconvenience. Yesterday on the Fiji bugzilla[1] it was
> > > reported that consumers of Bio-Formats were broken by the Bio-Formats
> > > update site. Thank you for pointing out that core functionality is
> broken
> > > as well!
> > >
> > >  The Bio-Formats update site is certainly mixing 5.1.x and 5.0.x
> > > Bio-Formats components. We'll look into it and hope to have a fix
> > shortly.
> >
> > Our understanding is that this is a packaging issue related to mixing of
> > Bio-Formats 5.0.x (stable) and Bio-Formats 5.1.x (development) lines
> > within a Fiji install, and not an issue with Bio-Formats itself.  Let us
> > know if we can be of any assistance.
> >
> > Regards,
> > -Melissa
> >
> > On Tue, Mar 24, 2015 at 08:23:28AM -0500, Mark Hiner wrote:
> > > Hi all,
> > >
> > >  Sorry for the inconvenience. Yesterday on the Fiji bugzilla[1] it was
> > > reported that consumers of Bio-Formats were broken by the Bio-Formats
> > > update site. Thank you for pointing out that core functionality is
> broken
> > > as well!
> > >
> > >  The Bio-Formats update site is certainly mixing 5.1.x and 5.0.x
> > > Bio-Formats components. We'll look into it and hope to have a fix
> > shortly.
> > >
> > > Thanks!
> > > - Mark
> > >
> > > [1] http://fiji.sc/bugzilla/show_bug.cgi?id=1034
> > >
> > > On Tue, Mar 24, 2015 at 7:06 AM, Christophe Leterrier <
> > > [hidden email]> wrote:
> > >
> > > > I confirm this, had to deselect the Bio-Format update site.
> > > >
> > > > On Tue, Mar 24, 2015 at 12:22 PM, Aryeh Weiss <[hidden email]>
> > wrote:
> > > >
> > > > > On 3/24/15 12:25 PM, Martin Höhne wrote:
> > > > >
> > > > >> Dear All,
> > > > >>
> > > > >> Fiji just did it´s auto-update after startup, and it seems that
> the
> > > > >> bioformats-importer is broken.
> > > > >>
> > > > >> Plugin > Bio-Formats > Bio-Formats Importer
> > > > >>
> > > > >> gives the error message pasted below. Is this a general problem or
> > only
> > > > my
> > > > >> configuration (Latest Fiji on Win7)
> > > > >>
> > > > >> Thanks
> > > > >> Martin
> > > > >>
> > > > >> ---------
> > > > >> (Fiji Is Just) ImageJ 2.0.0-rc-26/1.49p; Java 1.6.0_24 [64-bit];
> > > > Windows 7
> > > > >> 6.1; 23MB of 2975MB (<1%)
> > > > >>   java.lang.NoClassDefFoundError: Could not initialize class
> > > > >> loci.common.Location
> > > > >>         at loci.plugins.in.ImporterOptions.parseArg(
> > > > >> ImporterOptions.java:171)
> > > > >>         at
> loci.plugins.in.Importer.parseOptions(Importer.java:112)
> > > > >>         at loci.plugins.in.Importer.run(Importer.java:69)
> > > > >>         at loci.plugins.LociImporter.run(LociImporter.java:78)
> > > > >>         at ij.IJ.runUserPlugIn(IJ.java:199)
> > > > >>         at ij.IJ.runPlugIn(IJ.java:163)
> > > > >>         at ij.Executer.runCommand(Executer.java:131)
> > > > >>         at ij.Executer.run(Executer.java:64)
> > > > >>         at java.lang.Thread.run(Thread.java:662)
> > > > >>
> > > > >>
> > > > >>
> > > > >>
> > > > > I confirm this on OSX Yosemite. You can work around by deselecting
> > the
> > > > > Bioformats update site, so that you get Bioformats from the Fiji
> > update
> > > > > site. They are still at 5.0.7, and it works. However, if you read
> > > > > complicated ND2 files, you will need the 5.0.2 version of the gpl
> jar
> > > > file.
> > > > >
> > > > > --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
> > > >
> > >
> > > --
> > > 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
>

--
Ignacio Arganda-Carreras, Ph.D.
Seung's lab, 46-5065
Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St.
Cambridge, MA 02139
USA

Phone: [phone]
Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html

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

[ctrueden]

Hi Ignacio,

> java.lang.NoClassDefFoundError: com/google/common/collect/MapMaker

Please check:
* Help > Update...
* Advanced mode
* View Options -> View all files
* Search -> guava

Do you have "jars/guava.jar" with Status of "Up-to-date" on Update Site
"Bio-Formats"?

Regards,
Curtis

On Tue, Mar 24, 2015 at 11:40 AM, Ignacio Arganda-Carreras <
[hidden email]> wrote:

> Hello Curtis,
>
> I updated Fiji and consequently Bioformats but the problem remains. I have
> the same exception as before and also this one:
>
> (Fiji Is Just) ImageJ 2.0.0-rc-26/1.49p; Java 1.6.0_24 [64-bit]; Linux
> 3.13.0-48-generic; 31MB of 30000MB (<1%)
>
> java.lang.NoClassDefFoundError: com/google/common/collect/MapMaker
> at loci.common.Location.<clinit>(Location.java:88)
> at loci.plugins.in.ImporterOptions.parseArg(ImporterOptions.java:171)
> at loci.plugins.in.Importer.parseOptions(Importer.java:112)
> at loci.plugins.in.Importer.run(Importer.java:69)
> at loci.plugins.LociImporter.run(LociImporter.java:78)
> at ij.IJ.runUserPlugIn(IJ.java:199)
> at ij.IJ.runPlugIn(IJ.java:163)
> at ij.Executer.runCommand(Executer.java:131)
> at ij.Executer.run(Executer.java:64)
> at java.lang.Thread.run(Thread.java:662)
> Caused by: java.lang.ClassNotFoundException:
> com.google.common.collect.MapMaker
> at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
> at java.security.AccessController.doPrivileged(Native Method)
> at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
> ... 10 more
>
> I hope it helps!
>
> ignacio
>
>
> On Tue, Mar 24, 2015 at 5:10 PM, Curtis Rueden <[hidden email]> wrote:
>
> > Hi all,
> >
> > The Bio-Formats update site is now fixed. For those affected: please run
> > Help > Update... again and let us know if you continue to have problems.
> >
> > For those curious: the issue was not related to mixing BF5.0 and BF5.1
> > libraries, but rather with some libraries needed by BF5.1 (e.g., guava)
> > being erroneously removed from the update site. We have fixed the
> > configuration to avoid this issue in the future.
> >
> > Regards,
> > Curtis
> >
> > On Tue, Mar 24, 2015 at 10:55 AM, Melissa Linkert <
> > [hidden email]> wrote:
> >
> > > Hi all,
> > >
> > > >  Sorry for the inconvenience. Yesterday on the Fiji bugzilla[1] it
> was
> > > > reported that consumers of Bio-Formats were broken by the Bio-Formats
> > > > update site. Thank you for pointing out that core functionality is
> > broken
> > > > as well!
> > > >
> > > >  The Bio-Formats update site is certainly mixing 5.1.x and 5.0.x
> > > > Bio-Formats components. We'll look into it and hope to have a fix
> > > shortly.
> > >
> > > Our understanding is that this is a packaging issue related to mixing
> of
> > > Bio-Formats 5.0.x (stable) and Bio-Formats 5.1.x (development) lines
> > > within a Fiji install, and not an issue with Bio-Formats itself.  Let
> us
> > > know if we can be of any assistance.
> > >
> > > Regards,
> > > -Melissa
> > >
> > > On Tue, Mar 24, 2015 at 08:23:28AM -0500, Mark Hiner wrote:
> > > > Hi all,
> > > >
> > > >  Sorry for the inconvenience. Yesterday on the Fiji bugzilla[1] it
> was
> > > > reported that consumers of Bio-Formats were broken by the Bio-Formats
> > > > update site. Thank you for pointing out that core functionality is
> > broken
> > > > as well!
> > > >
> > > >  The Bio-Formats update site is certainly mixing 5.1.x and 5.0.x
> > > > Bio-Formats components. We'll look into it and hope to have a fix
> > > shortly.
> > > >
> > > > Thanks!
> > > > - Mark
> > > >
> > > > [1] http://fiji.sc/bugzilla/show_bug.cgi?id=1034
> > > >
> > > > On Tue, Mar 24, 2015 at 7:06 AM, Christophe Leterrier <
> > > > [hidden email]> wrote:
> > > >
> > > > > I confirm this, had to deselect the Bio-Format update site.
> > > > >
> > > > > On Tue, Mar 24, 2015 at 12:22 PM, Aryeh Weiss <[hidden email]
> >
> > > wrote:
> > > > >
> > > > > > On 3/24/15 12:25 PM, Martin Höhne wrote:
> > > > > >
> > > > > >> Dear All,
> > > > > >>
> > > > > >> Fiji just did it´s auto-update after startup, and it seems that
> > the
> > > > > >> bioformats-importer is broken.
> > > > > >>
> > > > > >> Plugin > Bio-Formats > Bio-Formats Importer
> > > > > >>
> > > > > >> gives the error message pasted below. Is this a general problem
> or
> > > only
> > > > > my
> > > > > >> configuration (Latest Fiji on Win7)
> > > > > >>
> > > > > >> Thanks
> > > > > >> Martin
> > > > > >>
> > > > > >> ---------
> > > > > >> (Fiji Is Just) ImageJ 2.0.0-rc-26/1.49p; Java 1.6.0_24 [64-bit];
> > > > > Windows 7
> > > > > >> 6.1; 23MB of 2975MB (<1%)
> > > > > >>   java.lang.NoClassDefFoundError: Could not initialize class
> > > > > >> loci.common.Location
> > > > > >>         at loci.plugins.in.ImporterOptions.parseArg(
> > > > > >> ImporterOptions.java:171)
> > > > > >>         at
> > loci.plugins.in.Importer.parseOptions(Importer.java:112)
> > > > > >>         at loci.plugins.in.Importer.run(Importer.java:69)
> > > > > >>         at loci.plugins.LociImporter.run(LociImporter.java:78)
> > > > > >>         at ij.IJ.runUserPlugIn(IJ.java:199)
> > > > > >>         at ij.IJ.runPlugIn(IJ.java:163)
> > > > > >>         at ij.Executer.runCommand(Executer.java:131)
> > > > > >>         at ij.Executer.run(Executer.java:64)
> > > > > >>         at java.lang.Thread.run(Thread.java:662)
> > > > > >>
> > > > > >>
> > > > > >>
> > > > > >>
> > > > > > I confirm this on OSX Yosemite. You can work around by
> deselecting
> > > the
> > > > > > Bioformats update site, so that you get Bioformats from the Fiji
> > > update
> > > > > > site. They are still at 5.0.7, and it works. However, if you read
> > > > > > complicated ND2 files, you will need the 5.0.2 version of the gpl
> > jar
> > > > > file.
> > > > > >
> > > > > > --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
> > > > >
> > > >
> > > > --
> > > > 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
> >
>
>
>
> --
> Ignacio Arganda-Carreras, Ph.D.
> Seung's lab, 46-5065
> Department of Brain and Cognitive Sciences
> Massachusetts Institute of Technology
> 43 Vassar St.
> Cambridge, MA 02139
> USA
>
> Phone: [phone]
> Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.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

[Ignacio Arganda-Carreras]

Hello Curtis,


> Do you have "jars/guava.jar" with Status of "Up-to-date" on Update Site
> "Bio-Formats"?
>

Nope, it was not installed. I did it and now everything works :)

Thank you very much!

ignacio



--
Ignacio Arganda-Carreras, Ph.D.
Seung's lab, 46-5065
Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St.
Cambridge, MA 02139
USA

Phone: [phone]
Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html

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