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<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.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>
<div class=""><br class="">
</div>
<div class="">Ian</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">
<div>
<blockquote type="cite" class="">
<div class="">On 31 Mar 2017, at 15:30, Munro, Ian <<a href="mailto:i.munro@imperial.ac.uk" class="">i.munro@imperial.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" 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" 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="">
<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="">--</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="">
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:Rued<wbr class="">en</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_2461107495403341533m_-6949419526036133203m_-5146209036269288843m_-1040860127368940751HOEnZb"><font color="#888888" class="">
<div class=""><br class="">
</div>
<div class="">Ian</div>
</font></span>
<div class="">
<div class="m_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_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_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_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_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_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="">
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:Rued<wbr class="">en</a></span></div>
<div class="">Did you know ImageJ has a forum? <a href="http://forum.imagej.net/" 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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