<div dir="ltr">Hi Ian,<div><br></div><div>Quick searches suggest that that error is some macOS Cocoa error message. I am guessing it is generated by MATLAB itself. I doubt there is anything you can do about it, although perhaps the old "binary code search" trick might help you isolate what triggers it. That is: comment out half your code, such that the remaining half still runs. Run it. See if the error happens. If the error happens, command another half of the remaining code. Or if it doesn't occur, uncomment half of the commented code. Ideally, this process can eventually whittle down the commented code to a single line. You can then investigate whether there is an alternative approach to that line of code, which avoids triggering the issue.</div><div><br></div><div>You could also write a support ticket to Mathworks, although of course you should still create a MCVE to send to them. So you'll want to narrow down the problem regardless.</div><div><br></div><div>Regards,</div><div>Curtis</div><div class="gmail_extra"><br clear="all"><div><div class="gmail_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:Rueden</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 1:25 PM, 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">



<div style="word-wrap:break-word">
<div>Evening all</div>
<div><br>
</div>
So Curtis’ suggested solution, which is to remove the sl4j bindings from bioformats-package.jar as follows:
<div><br>
</div>
<div>
<div>zip -d bfmatlab/bioformats_package.<wbr>jar 'org/slf4j/impl/*’</div>
<div><br>
</div>
<div>seems to work. Thanks Curtis.</div>
<div><br>
</div>
<div>However I now get:</div>
<div>"2017-03-31 19:15:14.579 FLIMfit[29709:165086] Failed to connect (typePopUp) outlet from (NSViewController) to (NSPopUpButton): missing setter or instance variable”</div>
<div>with the deployed version only.</div>
<div><br>
</div>
<div>Does anyone have any idea how messing with bio-formats_package could generate that or has anyone even seen anything similar?</div>
<div><br>
</div>
<div>Thanks </div><span class="HOEnZb"><font color="#888888">
<div><br>
</div>
<div>Ian</div></font></span><div><div class="h5">
<div><br>
</div>
<div><br>
</div>
<div>
<div>
<blockquote type="cite">
<div>On 31 Mar 2017, at 15:30, Munro, Ian <<a href="mailto:i.munro@imperial.ac.uk" target="_blank">i.munro@imperial.ac.uk</a>> wrote:</div>
<br class="m_1158078619137304844Apple-interchange-newline">
<div>
<div style="word-wrap:break-word">
Thanks Curtis 
<div><br>
</div>
<div>Ian</div>
<div><br>
</div>
<div><br>
<div>
<blockquote type="cite">
<div>On 31 Mar 2017, at 15:28, Curtis Rueden <<a href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</a>> wrote:</div>
<br class="m_1158078619137304844Apple-interchange-newline">
<div>
<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_1158078619137304844m_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">
<div style="word-wrap:break-word">
<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_1158078619137304844m_2461107495403341533m_-6949419526036133203m_-5146209036269288843m_-1040860127368940751HOEnZb"><font color="#888888">
<div><br>
</div>
<div>Ian</div>
</font></span>
<div>
<div class="m_1158078619137304844m_2461107495403341533m_-6949419526036133203m_-5146209036269288843m_-1040860127368940751h5">
<div><br>
</div>
<div><br>
<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>
<br class="m_1158078619137304844m_2461107495403341533m_-6949419526036133203m_-5146209036269288843m_-1040860127368940751m_27506431077288657Apple-interchange-newline">
<div>
<div style="word-wrap:break-word">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>
<br class="m_1158078619137304844m_2461107495403341533m_-6949419526036133203m_-5146209036269288843m_-1040860127368940751m_27506431077288657Apple-interchange-newline">
<div>
<div style="word-wrap:break-word">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>
<div>
<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>
<br class="m_1158078619137304844m_2461107495403341533m_-6949419526036133203m_-5146209036269288843m_-1040860127368940751m_27506431077288657Apple-interchange-newline">
<div>
<div style="word-wrap:break-word">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>
<br class="m_1158078619137304844m_2461107495403341533m_-6949419526036133203m_-5146209036269288843m_-1040860127368940751m_27506431077288657Apple-interchange-newline">
<div>
<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>
<br class="m_1158078619137304844m_2461107495403341533m_-6949419526036133203m_-5146209036269288843m_-1040860127368940751m_27506431077288657Apple-interchange-newline">
<div>
<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_1158078619137304844m_2461107495403341533m_-6949419526036133203m_-5146209036269288843m_-1040860127368940751m_27506431077288657m_-5738650066751389869gmail_signature" data-smartmail="gmail_signature">
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<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 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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