http://imagej.273.s1.nabble.com/Bio-Formats-importer-broken-after-latest-Fiji-update-tp5012127p5012139.html
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.
being erroneously removed from the update site. We have fixed the
> 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: 972-3-7384051
> > > >
> > > >
> > > > --
> > > > 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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