<div dir="ltr">Hi Ian,<div><br></div><div><div>> Is there any other component, or combination of components that I can</div><div>> try ?</div></div><div><br></div><div>Two possibilities come to mind:</div><div><br></div><div>1) Use the Bio-Formats JARs piecemeal, excluding the logback-common dependency from your dependency hierarchy. You can lean on Maven to resolve your dependencies.</div><div><br></div><div>2) Massage the bioformats_package/loci_tools archive to stop shipping any SLF4J bindings.<br></div><div><br></div><div>I filed PR #300 which pursues option (2); maybe it helps you.</div><div><a href="https://github.com/flimfit/FLIMfit/pull/300" target="_blank">https://github.com/flimfit/FLI<wbr>Mfit/pull/300</a><br></div><div><br></div><div>In the longer term, I encourage the Bio-Formats team to purge the logback-classic dependency. It should be bundled only with the command line tools.</div><div><br></div><div>Regards,</div><div>Curtis</div><div class="gmail_extra"><br clear="all"><div><div class="m_2461107495403341533m_-6949419526036133203m_-5146209036269288843m_-1040860127368940751gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><span style="font-size:12.8px">--</span></div><div><span style="font-size:12.8px">Curtis Rueden</span><br></div><div><span style="font-size:12.8px">LOCI software architect - <a href="https://loci.wisc.edu/software" target="_blank">https://loci.wisc.edu/software</a></span></div><div>ImageJ2 lead, Fiji maintainer - <span style="font-size:12.8px"><a href="https://imagej.net/User:Rueden" target="_blank">https://imagej.net/User:Rued<wbr>en</a></span></div><div>Did you know ImageJ has a forum? <a href="http://forum.imagej.net/" target="_blank">http://forum.imagej.net/</a></div><div><br></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Fri, Mar 31, 2017 at 8:41 AM, Munro, Ian <span dir="ltr"><<a href="mailto:i.munro@imperial.ac.uk" target="_blank">i.munro@imperial.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">



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<div>Hi Again </div>
<div><br>
</div>
Is there any other component, or combination of components that I can try ?
<div><br>
</div>
<div>Thanks</div><span class="m_2461107495403341533m_-6949419526036133203m_-5146209036269288843m_-1040860127368940751HOEnZb"><font color="#888888">
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<div>Ian</div></font></span><div><div class="m_2461107495403341533m_-6949419526036133203m_-5146209036269288843m_-1040860127368940751h5">
<div><br>
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<div>
<blockquote type="cite">
<div>On 31 Mar 2017, at 10:29, Munro, Ian <<a href="mailto:i.munro@imperial.ac.uk" target="_blank">i.munro@imperial.ac.uk</a>> wrote:</div>
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Hi Sebastien
<div><br>
</div>
<div>Unfortunately replacing bioformats_package.jar with loci_tools.jar has simply replaced the previous warning </div>
<div>with :</div>
<div><br>
</div>
<div>
<div>SLF4J: Class path contains multiple SLF4J bindings.</div>
<div>SLF4J: Found binding in [jar:file:/Applications/MATLAB<wbr>/MATLAB_Runtime/v91/java/jarex<wbr>t/slf4j/slf4j-log4j12.jar!/org<wbr>/slf4j/impl/StaticLoggerBinder<wbr>.class]</div>
<div>SLF4J: Found binding in [jar:file:/Users/imunro/Librar<wbr>y/Application%20Support/.mcrCa<wbr>che9.1/FLIMfi0/BFMatlab/loci_t<wbr>ools.jar!/org/slf4j/impl/Stati<wbr>cLoggerBinder.class]</div>
<div><br>
</div>
<div><br>
</div>
<div>Best,</div>
<div><br>
</div>
<div>Ian</div>
<div><br>
</div>
<div>
<blockquote type="cite">
<div>On 30 Mar 2017, at 14:40, Munro, Ian <<a href="mailto:i.munro@imperial.ac.uk" target="_blank">i.munro@imperial.ac.uk</a>> wrote:</div>
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Thanks Sebastien
<div><br>
</div>
<div>I’ll give that a try and let you know.</div>
<div><br>
</div>
<div>Ian</div>
<div><br>
</div>
<div><br>
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<blockquote type="cite">
<div>On 30 Mar 2017, at 14:32, Sebastien Besson (Staff) <<a href="mailto:s.besson@dundee.ac.uk" target="_blank">s.besson@dundee.ac.uk</a>> wrote:</div>
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Hi Ian,
<div><br>
</div>
<div>I think Curtis summarised the nature of the warning which should be harmless albeit</div>
<div>annoying. For reference, OME was historically using log4j and switched to logback</div>
<div>as the default logging implementation a few years ago [1].</div>
<div><br>
</div>
<div>Moving towards individual JARs as Curtis suggests might be the best way to enable full</div>
<div>control of the dependencies and prevent conflict in an environment like MATLAB.</div>
<div><br>
</div>
<div>In the short term, a third alternative might be to use the loci_tools.jar rather than</div>
<div>bioformats_package.jar. The only difference between both bundle JARs is effectively the</div>
<div>logging implementation shipped (log4j vs logback).</div>
<div><br>
</div>
<div>Best,</div>
<div>Sebastien</div>
<div><br>
</div>
<div>[1] <a href="https://github.com/openmicroscopy/bioformats/pull/889/" target="_blank">https://github.com/openmic<wbr>roscopy/bioformats/pull/889/</a> </div>
<div><br>
<div>
<blockquote type="cite">
<div>On 30 Mar 2017, at 13:49, Munro, Ian <<a href="mailto:i.munro@imperial.ac.uk" target="_blank">i.munro@imperial.ac.uk</a>> wrote:</div>
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<div style="word-wrap:break-word">
Thanks Curtis 
<div><br>
</div>
<div>Sounds like 2) would be the way to go then.</div>
<div><br>
</div>
<div>Ian</div>
<div><br>
</div>
<div><br>
<div>
<blockquote type="cite">
<div>On 30 Mar 2017, at 13:30, Curtis Rueden <<a href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</a>> wrote:</div>
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<div dir="ltr">Hi Ian,
<div><br>
</div>
<div>> SLF4J: Class path contains multiple SLF4J bindings.</div>
<div><br>
</div>
<div>Maybe the docs about that are helpful?</div>
<div><a href="https://www.slf4j.org/codes.html#multiple_bindings" target="_blank">https://www.slf4j.org/codes.ht<wbr>ml#multiple_bindings</a><br>
</div>
<div><br>
</div>
<div>> if anyone has any thoughts on a work-around that would be great.</div>
<div><br>
</div>
<div>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>
<div><br>
</div>
<div>
<div>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>
</div>
<div><br>
</div>
<div>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>
<div><br>
</div>
<div>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>
<div><br>
</div>
<div>Regards,<br>
</div>
<div>Curtis</div>
<div class="gmail_extra"><br clear="all">
<div>
<div class="m_2461107495403341533m_-6949419526036133203m_-5146209036269288843m_-1040860127368940751m_27506431077288657m_-5738650066751389869gmail_signature" data-smartmail="gmail_signature">
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<div><span style="font-size:12.8px">--</span></div>
<div><span style="font-size:12.8px">Curtis Rueden</span><br>
</div>
<div><span style="font-size:12.8px">LOCI software architect - <a href="https://loci.wisc.edu/software" target="_blank">
https://loci.wisc.edu/software</a></span></div>
<div>ImageJ2 lead, Fiji maintainer - <span style="font-size:12.8px"><a href="https://imagej.net/User:Rueden" target="_blank">https://imagej.net/User:Rued<wbr>en</a></span></div>
<div>Did you know ImageJ has a forum? <a href="http://forum.imagej.net/" target="_blank">
http://forum.imagej.net/</a></div>
<div><br>
</div>
</div>
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</div>
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<br>
<div class="gmail_quote">On Thu, Mar 30, 2017 at 5:34 AM, Munro, Ian <span dir="ltr">
<<a href="mailto:i.munro@imperial.ac.uk" target="_blank">i.munro@imperial.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Good afternoon<br>
<br>
I wondered if anyone has any thoughts on an issue we’re currently having.<br>
The next release of our FLIMfit application is nearly ready for release.<br>
However when running the deployed version we get a warning:<br>
<br>
SLF4J: Class path contains multiple SLF4J bindings.<br>
SLF4J: Found binding in [jar:file:/Applications/MATLAB<wbr>/MATLAB_Runtime/v91/java/jarex<wbr>t/slf4j/slf4j-log4j12.jar!/org<wbr>/slf4j/impl/StaticLoggerBinder<wbr>.class]<br>
SLF4J: Found binding in [jar:file:/Users/imunro/Librar<wbr>y/Application%20Support/.mcrCa<wbr>che9.1/FLIMfi0/BFMatlab/biofor<wbr>mats_package.jar!/org/slf4j/im<wbr>pl/StaticLoggerBinder.class]<br>
SLF4J: See <a href="http://www.slf4j.org/codes.html#multiple_bindings" rel="noreferrer" target="_blank">
http://www.slf4j.org/codes.htm<wbr>l#multiple_bindings</a> for an explanation.<br>
<br>
see also <a href="https://github.com/flimfit/FLIMfit/issues/299" rel="noreferrer" target="_blank">
https://github.com/flimfit/FLI<wbr>Mfit/issues/299</a><br>
<br>
Thiis seems to be a warning only but if anyone has any thoughts on a work-around that would be great.<br>
NB this arose with the recent move to Matlab 2016b.<br>
<br>
Many Thanks<br>
<br>
Ian<br>
<br>
<br>
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