Unfortunately the problem persists ... I will try it on Linux and Windows to confirm it is not a Mac specific thing once more ...
On Aug 8, 2012, at 18:13 , Curtis Rueden wrote: > Hi Steffi, > > I had problems building Fiji from source from a fresh clone. Johannes & I > debugged it, and found a problem with how Fiji's build system was resolving > versions. That is now fixed and pushed to master. Afterwards, I tried opening > one of your sample LSMs, and was able to do so successfully. So my hope is > that this versioning issue is the same problem afflicting your setup as well. > > Can you please give it a try with the latest Fiji master and let us know how > it goes? > > Regards, > Curtis > > > On Wed, Aug 8, 2012 at 3:33 PM, Stephan Preibisch <[email protected]> > wrote: > No, I can only see > > jars/ > MD5 (scifio.jar) = 9e101ed5cd590534f74d0001b98c1918 > MD5 (loci-common.jar) = 10d372b14b99965ec8c8f809d5973853 > > plugins/ > MD5 (loci_plugins.jar) = 9b4a563016f5c2e9e1347a2c969bba05 > > For some files I get a different error: > Caused by: java.lang.NoSuchMethodError: > loci.formats.meta.MetadataStore.setImageObjectiveSettingsID(Ljava/lang/String;I)V > at > loci.formats.in.ZeissLSMReader.populateMetadataStore(ZeissLSMReader.java:1249) > at loci.formats.in.ZeissLSMReader.initMetadata(ZeissLSMReader.java:1168) > at loci.formats.in.ZeissLSMReader.initFile(ZeissLSMReader.java:520) > at loci.formats.FormatReader.setId(FormatReader.java:1105) > at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482) > at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146) > at loci.plugins.in.Importer.showDialogs(Importer.java:141) > at loci.plugins.in.Importer.run(Importer.java:79) > at loci.plugins.LociImporter.run(LociImporter.java:81) > at ij.IJ.runUserPlugIn(IJ.java:185) > at ij.IJ.runPlugIn(IJ.java:152) > ... 8 more > > Beanshell reports for: > print( loci.formats.meta.MetadataStore.class.getResource( > "/loci/formats/meta/MetadataStore.class" )); > jar:file:/Users/preibischs/workspace/fiji/jars/scifio.jar!/loci/formats/meta/MetadataStore.class > > Thanks for looking into it, > Steffi > > On Aug 8, 2012, at 16:22 , Curtis Rueden wrote: > >> Hi Steffi, >> >> > The same happens when I make a new clone of Fiji ... >> >> I am doing a full build of Fiji to help diagnose. >> >> The problem is certainly that there is a mismatch between JAR versions. >> >> Is there a loci_tools.jar anywhere? If so, delete it. If not, the problem >> must be that an old bio-formats.jar is lying around somewhere—that stack >> trace indicates an old ZeissLSMReader. >> >> I'll write back with any additional insight after some more testing. >> >> -Curtis >> >> >> On Wed, Aug 8, 2012 at 3:20 PM, Stephan Preibisch <[email protected]> >> wrote: >> The same happens when I make a new clone of Fiji ... >> >> git clone ... >> git submoule init modules/imglib (without that Colocalization_Analysis and >> Fiji does not compile btw) >> git submodule update >> Build >> ImageJ >> Plugins > LOCI > Import ... choose LSM >> >> > crash >> >> Steffi >> >> On Aug 8, 2012, at 15:59 , Stephan Preibisch wrote: >> >> > Hi guys, >> > >> > during the last hour LOCI stopped working on all my machines when I try to >> > open LSM files (Fiji checkout master, Build clean, Build): >> > >> > an example is here: http://fly.mpi-cbg.de/preibisch/nm/HisYFP-SPIM.zip >> > >> > preibischs-lm1:fiji preibischs$ ./ImageJ >> > SLF4J: Class path contains multiple SLF4J bindings. >> > SLF4J: Found binding in >> > [jar:file:/Users/preibischs/workspace/fiji/jars/slf4j-log4j12-1.5.10.jar!/org/slf4j/impl/StaticLoggerBinder.class] >> > SLF4J: Found binding in >> > [jar:file:/Users/preibischs/workspace/fiji/jars/slf4j-log4j12.jar!/org/slf4j/impl/StaticLoggerBinder.class] >> > SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an >> > explanation. >> > [ERROR] "loci.formats.in.PovrayReader" is not valid. >> > [ERROR] "loci.formats.in.IMODReader" is not valid. >> > [ERROR] "loci.formats.in.OperettaReader" is not valid. >> > [ERROR] "loci.formats.in.ZeissTIFFReader" is not valid. >> > [ERROR] "loci.formats.in.HRDGDFReader" is not valid. >> > [ERROR] "loci.formats.in.CanonRawReader" is not valid. >> > [INFO ] Reading LSM metadata for series #0 >> > java.lang.reflect.InvocationTargetException >> > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) >> > at >> > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) >> > at >> > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) >> > at java.lang.reflect.Method.invoke(Method.java:597) >> > at ij.Command.runPlugIn(Command.java:146) >> > at ij.Command.runCommand(Command.java:95) >> > at ij.Executer.run(Executer.java:64) >> > at java.lang.Thread.run(Thread.java:680) >> > Caused by: java.lang.NoSuchMethodError: >> > loci.formats.meta.MetadataStore.setImageObjectiveSettingsID(Ljava/lang/String;I)V >> > at >> > loci.formats.in.ZeissLSMReader.populateMetadataStore(ZeissLSMReader.java:1249) >> > at >> > loci.formats.in.ZeissLSMReader.initMetadata(ZeissLSMReader.java:1168) >> > at loci.formats.in.ZeissLSMReader.initFile(ZeissLSMReader.java:520) >> > at loci.formats.FormatReader.setId(FormatReader.java:1105) >> > at >> > loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482) >> > at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146) >> > at loci.plugins.in.Importer.showDialogs(Importer.java:141) >> > at loci.plugins.in.Importer.run(Importer.java:79) >> > at loci.plugins.LociImporter.run(LociImporter.java:81) >> > at ij.IJ.runUserPlugIn(IJ.java:185) >> > at ij.IJ.runPlugIn(IJ.java:152) >> > ... 8 more >> > [INFO ] Reading IFDs >> > [INFO ] Populating metadata >> > [INFO ] Checking comment style >> > [INFO ] Populating OME metadata >> > >> > >> > I tried replacing scifio, loci_plugins, anything that starts or includes >> > loci with different versions (from the download version of Fiji and an >> > older checkout where it still works) - but it will continue failing. >> > >> > I was just working on my SPIM code and suddenly it broke upon a ./Build >> > where I changed nothing but my files ... >> > >> > Does anybody have a suggestion? >> > >> > Thanks a lot, >> > Steffi >> > >> > -- >> > Please avoid top-posting, and please make sure to reply-to-all! >> > >> > Mailing list web interface: http://groups.google.com/group/fiji-devel >> >> -- >> Please avoid top-posting, and please make sure to reply-to-all! >> >> Mailing list web interface: http://groups.google.com/group/fiji-devel >> > > > -- > Please avoid top-posting, and please make sure to reply-to-all! > > Mailing list web interface: http://groups.google.com/group/fiji-devel >
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