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<div class="">Hi Again </div>
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Is there any other component, or combination of components that I can try ?
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<div class="">Thanks</div>
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<div class="">Ian</div>
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<div class="">On 31 Mar 2017, at 10:29, Munro, Ian <<a href="mailto:i.munro@imperial.ac.uk" class="">i.munro@imperial.ac.uk</a>> wrote:</div>
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Hi Sebastien
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<div class="">Unfortunately replacing bioformats_package.jar with loci_tools.jar has simply replaced the previous warning </div>
<div class="">with :</div>
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<div class="">SLF4J: Class path contains multiple SLF4J bindings.</div>
<div class="">SLF4J: Found binding in [jar:file:/Applications/MATLAB/MATLAB_Runtime/v91/java/jarext/slf4j/slf4j-log4j12.jar!/org/slf4j/impl/StaticLoggerBinder.class]</div>
<div class="">SLF4J: Found binding in [jar:file:/Users/imunro/Library/Application%20Support/.mcrCache9.1/FLIMfi0/BFMatlab/loci_tools.jar!/org/slf4j/impl/StaticLoggerBinder.class]</div>
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<div class="">Best,</div>
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<div class="">Ian</div>
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<div class="">On 30 Mar 2017, at 14:40, Munro, Ian <<a href="mailto:i.munro@imperial.ac.uk" class="">i.munro@imperial.ac.uk</a>> wrote:</div>
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Thanks Sebastien
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<div class="">I’ll give that a try and let you know.</div>
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<div class="">Ian</div>
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<div class="">On 30 Mar 2017, at 14:32, Sebastien Besson (Staff) <<a href="mailto:s.besson@dundee.ac.uk" class="">s.besson@dundee.ac.uk</a>> wrote:</div>
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Hi Ian,
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<div class="">I think Curtis summarised the nature of the warning which should be harmless albeit</div>
<div class="">annoying. For reference, OME was historically using log4j and switched to logback</div>
<div class="">as the default logging implementation a few years ago [1].</div>
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<div class="">Moving towards individual JARs as Curtis suggests might be the best way to enable full</div>
<div class="">control of the dependencies and prevent conflict in an environment like MATLAB.</div>
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<div class="">In the short term, a third alternative might be to use the loci_tools.jar rather than</div>
<div class="">bioformats_package.jar. The only difference between both bundle JARs is effectively the</div>
<div class="">logging implementation shipped (log4j vs logback).</div>
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<div class="">Best,</div>
<div class="">Sebastien</div>
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<div class="">[1] <a href="https://github.com/openmicroscopy/bioformats/pull/889/" class="">https://github.com/openmicroscopy/bioformats/pull/889/</a> </div>
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<div class="">On 30 Mar 2017, at 13:49, Munro, Ian <<a href="mailto:i.munro@imperial.ac.uk" class="">i.munro@imperial.ac.uk</a>> wrote:</div>
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Thanks Curtis
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<div class="">Sounds like 2) would be the way to go then.</div>
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<div class="">Ian</div>
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<div class="">On 30 Mar 2017, at 13:30, Curtis Rueden <<a href="mailto:ctrueden@wisc.edu" class="">ctrueden@wisc.edu</a>> wrote:</div>
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<div dir="ltr" class="">Hi Ian,
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<div class="">> SLF4J: Class path contains multiple SLF4J bindings.</div>
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<div class="">Maybe the docs about that are helpful?</div>
<div class=""><a href="https://www.slf4j.org/codes.html#multiple_bindings" target="_blank" class="">https://www.slf4j.org/codes.<wbr class="">html#multiple_bindings</a><br class="">
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<div class="">> if anyone has any thoughts on a work-around that would be great.</div>
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<div class="">The error message suggests that MATLAB now ships its own SLF4J binding. This makes sense, since best practice is for apps (like MATLAB and Fiji) to choose and ship a binding, rather than for libraries to mandate one. Otherwise, this situation
can happen. Bio-Formats embeds an SLF4J binding into the bioformats_package.jar via its dependency on logback-classic. (Specifically: metakit and ome-common and bio-formats_plugins and bio-formats_tools all depend on it.)</div>
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<div class="">Fiji's strategy is to ship logback-classic as its chosen SLF4J binding; fortunately, Fiji bundles no other libraries with conflicting bindings. But since MATLAB now ships its own, a different solution is needed. There are a couple of possibilities:</div>
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<div class="">1) Change Bio-Formats to no longer depend on any JARs which include an SLF4J binding. This would be a desirable change in general.</div>
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<div class="">2) Change FLIMfit to stop using bioformats_package in favor of the individual Bio-Formats JARs, and exclude the logback-classic dependency from its dependency hierarchy.</div>
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<div class="">Regards,<br class="">
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<div class="">Curtis</div>
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<div class=""><span style="font-size:12.8px" class="">--</span></div>
<div class=""><span style="font-size:12.8px" class="">Curtis Rueden</span><br class="">
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<div class=""><span style="font-size:12.8px" class="">LOCI software architect - <a href="https://loci.wisc.edu/software" target="_blank" class="">
https://loci.wisc.edu/software</a></span></div>
<div class="">ImageJ2 lead, Fiji maintainer - <span style="font-size:12.8px" class=""><a href="https://imagej.net/User:Rueden" target="_blank" class="">https://imagej.net/User:<wbr class="">Rueden</a></span></div>
<div class="">Did you know ImageJ has a forum? <a href="http://forum.imagej.net/" target="_blank" class="">
http://forum.imagej.net/</a></div>
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<div class="gmail_quote">On Thu, Mar 30, 2017 at 5:34 AM, Munro, Ian <span dir="ltr" class="">
<<a href="mailto:i.munro@imperial.ac.uk" target="_blank" class="">i.munro@imperial.ac.uk</a>></span> wrote:<br class="">
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Good afternoon<br class="">
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I wondered if anyone has any thoughts on an issue we’re currently having.<br class="">
The next release of our FLIMfit application is nearly ready for release.<br class="">
However when running the deployed version we get a warning:<br class="">
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SLF4J: Class path contains multiple SLF4J bindings.<br class="">
SLF4J: Found binding in [jar:file:/Applications/MATLAB<wbr class="">/MATLAB_Runtime/v91/java/<wbr class="">jarext/slf4j/slf4j-log4j12.<wbr class="">jar!/org/slf4j/impl/StaticLogg<wbr class="">erBinder.class]<br class="">
SLF4J: Found binding in [jar:file:/Users/imunro/Librar<wbr class="">y/Application%20Support/.<wbr class="">mcrCache9.1/FLIMfi0/BFMatlab/b<wbr class="">ioformats_package.jar!/org/slf<wbr class="">4j/impl/StaticLoggerBinder.cla<wbr class="">ss]<br class="">
SLF4J: See <a href="http://www.slf4j.org/codes.html#multiple_bindings" rel="noreferrer" target="_blank" class="">
http://www.slf4j.org/codes.htm<wbr class="">l#multiple_bindings</a> for an explanation.<br class="">
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see also <a href="https://github.com/flimfit/FLIMfit/issues/299" rel="noreferrer" target="_blank" class="">
https://github.com/flimfit/FLI<wbr class="">Mfit/issues/299</a><br class="">
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Thiis seems to be a warning only but if anyone has any thoughts on a work-around that would be great.<br class="">
NB this arose with the recent move to Matlab 2016b.<br class="">
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Many Thanks<br class="">
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Ian<br class="">
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