http://imagej.273.s1.nabble.com/Bio-Formats-importer-broken-after-latest-Fiji-update-tp5012127p5012145.html
> 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: 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> > >
> > > --
> > > 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: (001) 617-324-3747
> Website:
http://bioweb.cnb.csic.es/~iarganda/index_EN.html>
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