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Thanks Curtis.
<div class="">I just wondered if anyone had come across this while working on the BF Matlab plugin as it must be related somehow, although how </div>
<div class="">changing that can affect Cocoa I really can’t imagine.</div>
<div class=""><br class="">
</div>
<div class="">Ian</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 31 Mar 2017, at 19:48, Curtis Rueden <<a href="mailto:ctrueden@wisc.edu" class="">ctrueden@wisc.edu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Hi Ian,
<div class=""><br class="">
</div>
<div class="">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 class=""><br class="">
</div>
<div class="">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 class=""><br class="">
</div>
<div class="">Regards,</div>
<div class="">Curtis</div>
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<div class=""><span style="font-size:12.8px" class="">Curtis Rueden</span><br class="">
</div>
<div class=""><span style="font-size:12.8px" class="">LOCI software architect - <a href="https://loci.wisc.edu/software" target="_blank" class="">
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<div class="gmail_quote">On Fri, Mar 31, 2017 at 1:25 PM, 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="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word" class="">
<div class="">Evening all</div>
<div class=""><br class="">
</div>
So Curtis’ suggested solution, which is to remove the sl4j bindings from bioformats-package.jar as follows:
<div class=""><br class="">
</div>
<div class="">
<div class="">zip -d bfmatlab/bioformats_package.<wbr class="">jar 'org/slf4j/impl/*’</div>
<div class=""><br class="">
</div>
<div class="">seems to work. Thanks Curtis.</div>
<div class=""><br class="">
</div>
<div class="">However I now get:</div>
<div class="">"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 class="">with the deployed version only.</div>
<div class=""><br class="">
</div>
<div class="">Does anyone have any idea how messing with bio-formats_package could generate that or has anyone even seen anything similar?</div>
<div class=""><br class="">
</div>
<div class="">Thanks </div>
<span class="HOEnZb"><font color="#888888" class="">
<div class=""><br class="">
</div>
<div class="">Ian</div>
</font></span>
<div class="">
<div class="h5">
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 31 Mar 2017, at 15:30, Munro, Ian <<a href="mailto:i.munro@imperial.ac.uk" target="_blank" class="">i.munro@imperial.ac.uk</a>> wrote:</div>
<br class="m_1158078619137304844Apple-interchange-newline">
<div class="">
<div style="word-wrap:break-word" class="">Thanks Curtis
<div class=""><br class="">
</div>
<div class="">Ian</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 31 Mar 2017, at 15:28, Curtis Rueden <<a href="mailto:ctrueden@wisc.edu" target="_blank" class="">ctrueden@wisc.edu</a>> wrote:</div>
<br class="m_1158078619137304844Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Hi Ian,
<div class=""><br class="">
</div>
<div class="">
<div class="">> Is there any other component, or combination of components that I can</div>
<div class="">> try ?</div>
</div>
<div class=""><br class="">
</div>
<div class="">Two possibilities come to mind:</div>
<div class=""><br class="">
</div>
<div class="">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 class=""><br class="">
</div>
<div class="">2) Massage the bioformats_package/loci_tools archive to stop shipping any SLF4J bindings.<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">I filed PR #300 which pursues option (2); maybe it helps you.</div>
<div class=""><a href="https://github.com/flimfit/FLIMfit/pull/300" target="_blank" class="">https://github.com/flimfit/FLI<wbr class="">Mfit/pull/300</a><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">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 class=""><br class="">
</div>
<div class="">Regards,</div>
<div class="">Curtis</div>
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<div class=""><span style="font-size:12.8px" class="">Curtis Rueden</span><br class="">
</div>
<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>
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<br class="">
<div class="gmail_quote">On Fri, Mar 31, 2017 at 8:41 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="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word" class="">
<div class="">Hi Again </div>
<div class=""><br class="">
</div>
Is there any other component, or combination of components that I can try ?
<div class=""><br class="">
</div>
<div class="">Thanks</div>
<span class="m_1158078619137304844m_2461107495403341533m_-6949419526036133203m_-5146209036269288843m_-1040860127368940751HOEnZb"><font color="#888888" class="">
<div class=""><br class="">
</div>
<div class="">Ian</div>
</font></span>
<div class="">
<div class="m_1158078619137304844m_2461107495403341533m_-6949419526036133203m_-5146209036269288843m_-1040860127368940751h5">
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 31 Mar 2017, at 10:29, Munro, Ian <<a href="mailto:i.munro@imperial.ac.uk" target="_blank" class="">i.munro@imperial.ac.uk</a>> wrote:</div>
<br class="m_1158078619137304844m_2461107495403341533m_-6949419526036133203m_-5146209036269288843m_-1040860127368940751m_27506431077288657Apple-interchange-newline">
<div class="">
<div style="word-wrap:break-word" class="">Hi Sebastien
<div class=""><br class="">
</div>
<div class="">Unfortunately replacing bioformats_package.jar with loci_tools.jar has simply replaced the previous warning </div>
<div class="">with :</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">SLF4J: Class path contains multiple SLF4J bindings.</div>
<div class="">SLF4J: Found binding in [jar:file:/Applications/MATLAB<wbr class="">/MATLAB_Runtime/v91/java/jarex<wbr class="">t/slf4j/slf4j-log4j12.jar!/org<wbr class="">/slf4j/impl/StaticLoggerBinder<wbr class="">.class]</div>
<div class="">SLF4J: Found binding in [jar:file:/Users/imunro/Librar<wbr class="">y/Application%20Support/.mcrCa<wbr class="">che9.1/FLIMfi0/BFMatlab/loci_t<wbr class="">ools.jar!/org/slf4j/impl/Stati<wbr class="">cLoggerBinder.class]</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class=""><br class="">
</div>
<div class="">Ian</div>
<div class=""><br class="">
</div>
<div class="">
<blockquote type="cite" class="">
<div class="">On 30 Mar 2017, at 14:40, Munro, Ian <<a href="mailto:i.munro@imperial.ac.uk" target="_blank" class="">i.munro@imperial.ac.uk</a>> wrote:</div>
<br class="m_1158078619137304844m_2461107495403341533m_-6949419526036133203m_-5146209036269288843m_-1040860127368940751m_27506431077288657Apple-interchange-newline">
<div class="">
<div style="word-wrap:break-word" class="">Thanks Sebastien
<div class=""><br class="">
</div>
<div class="">I’ll give that a try and let you know.</div>
<div class=""><br class="">
</div>
<div class="">Ian</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 30 Mar 2017, at 14:32, Sebastien Besson (Staff) <<a href="mailto:s.besson@dundee.ac.uk" target="_blank" class="">s.besson@dundee.ac.uk</a>> wrote:</div>
<br class="m_1158078619137304844m_2461107495403341533m_-6949419526036133203m_-5146209036269288843m_-1040860127368940751m_27506431077288657Apple-interchange-newline">
<div class="">
<div style="word-wrap:break-word" class="">Hi Ian,
<div class=""><br class="">
</div>
<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>
<div class=""><br class="">
</div>
<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>
<div class=""><br class="">
</div>
<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>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
</div>
<div class="">[1] <a href="https://github.com/openmicroscopy/bioformats/pull/889/" target="_blank" class="">https://github.com/openmic<wbr class="">roscopy/bioformats/pull/889/</a> </div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 30 Mar 2017, at 13:49, Munro, Ian <<a href="mailto:i.munro@imperial.ac.uk" target="_blank" class="">i.munro@imperial.ac.uk</a>> wrote:</div>
<br class="m_1158078619137304844m_2461107495403341533m_-6949419526036133203m_-5146209036269288843m_-1040860127368940751m_27506431077288657Apple-interchange-newline">
<div class="">
<div style="word-wrap:break-word" class="">Thanks Curtis
<div class=""><br class="">
</div>
<div class="">Sounds like 2) would be the way to go then.</div>
<div class=""><br class="">
</div>
<div class="">Ian</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 30 Mar 2017, at 13:30, Curtis Rueden <<a href="mailto:ctrueden@wisc.edu" target="_blank" class="">ctrueden@wisc.edu</a>> wrote:</div>
<br class="m_1158078619137304844m_2461107495403341533m_-6949419526036133203m_-5146209036269288843m_-1040860127368940751m_27506431077288657Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Hi Ian,
<div class=""><br class="">
</div>
<div class="">> SLF4J: Class path contains multiple SLF4J bindings.</div>
<div class=""><br class="">
</div>
<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.ht<wbr class="">ml#multiple_bindings</a><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">> if anyone has any thoughts on a work-around that would be great.</div>
<div class=""><br class="">
</div>
<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>
<div class=""><br class="">
</div>
<div class="">
<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>
</div>
<div class=""><br class="">
</div>
<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>
<div class=""><br class="">
</div>
<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>
<div class=""><br class="">
</div>
<div class="">Regards,<br class="">
</div>
<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="">
</div>
<div class=""><span style="font-size:12.8px" class="">LOCI software architect - <a href="https://loci.wisc.edu/software" target="_blank" class="">
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<br class="">
<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="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Good afternoon<br class="">
<br class="">
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="">
<br class="">
SLF4J: Class path contains multiple SLF4J bindings.<br class="">
SLF4J: Found binding in [jar:file:/Applications/MATLAB<wbr class="">/MATLAB_Runtime/v91/java/jarex<wbr class="">t/slf4j/slf4j-log4j12.jar!/org<wbr class="">/slf4j/impl/StaticLoggerBinder<wbr class="">.class]<br class="">
SLF4J: Found binding in [jar:file:/Users/imunro/Librar<wbr class="">y/Application%20Support/.mcrCa<wbr class="">che9.1/FLIMfi0/BFMatlab/biofor<wbr class="">mats_package.jar!/org/slf4j/im<wbr class="">pl/StaticLoggerBinder.class]<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="">
<br class="">
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="">
<br class="">
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="">
<br class="">
Many Thanks<br class="">
<br class="">
Ian<br class="">
<br class="">
<br class="">
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