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HI Sebastien
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<div class="">Thanks for the detailed reply.</div>
<div class="">The warnings are only present using the runtime.</div>
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<div class="">It appears that you already offer the capability I was suggesting in any case.</div>
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<div class="">Best Wishes</div>
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<div class="">Ian</div>
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<div class="">On 21 Aug 2017, at 09:15, Sebastien Besson (Staff) <<a href="mailto:s.besson@dundee.ac.uk" class="">s.besson@dundee.ac.uk</a>> wrote:</div>
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<div class="">Hi Ian,</div>
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<div class="">you are correct the Bio-Formats uber JARs bundle all dependencies incl.</div>
<div class="">the ones already shipped in MATLAB like the logging JARs. Is this behavior </div>
<div class="">only present with the MATLAB runtime or do you get the same warnings</div>
<div class="">when using MATLAB?</div>
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<div class="">For end-users, these warnings should not affect the application despite their</div>
<div class="">verbosity. As you said, there would be a couple of ways to address them:</div>
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<div class="">- creating a separate uber JAR without the conflicting dependencies i.e. the</div>
<div class=""> equivalent of you are currently doing</div>
<div class="">- using individual JARs: the bioformats_package.jar bundled with Bio-Formats</div>
<div class=""> MATLAB is only used as a fallback if the Bio-Formats JARs are not found in</div>
<div class=""> the Java class path.</div>
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<div class="">Depending on your build system, it might be possible to write a simple pom.xml</div>
<div class="">file that copies all Bio-Formats dependencies for a given version into the right</div>
<div class="">location excluding the conflicting ones.</div>
<div class="">See [1] for an example of such POM used by OME to update the decoupled JARs</div>
<div class="">in Fiji.</div>
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<div class="">Seb</div>
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<div class="">[1] <a href="https://github.com/openmicroscopy/bio-formats-fiji/blob/master/pom.xml" class="">https://github.com/openmicroscopy/bio-formats-fiji/blob/master/pom.xml</a></div>
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<div class="">On 16 Aug 2017, at 12:32, Munro, Ian <<a href="mailto:i.munro@imperial.ac.uk" class="">i.munro@imperial.ac.uk</a>> wrote:</div>
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Hello All
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<div class="">After a recent upgrade to Matlab 2016b we started to see warnings like those below in our deployed Matlab application:</div>
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<div class=""><span style="color: rgb(36, 41, 46); font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol'; font-size: 14px; background-color: rgb(255, 255, 255);" class="">SLF4J:
Class path contains multiple SLF4J bindings.</span><br style="box-sizing: border-box; color: rgb(36, 41, 46); font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol'; font-size: 14px;" class="">
<span style="color: rgb(36, 41, 46); font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol'; font-size: 14px; background-color: rgb(255, 255, 255);" class="">SLF4J:
Found binding in [jar:file:/Applications/MATLAB/MATLAB_Runtime/v91/java/jarext/slf4j/slf4j-log4j12.jar!/org/slf4j/impl/StaticLoggerBinder.class]</span><br style="box-sizing: border-box; color: rgb(36, 41, 46); font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol'; font-size: 14px;" class="">
<span style="color: rgb(36, 41, 46); font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol'; font-size: 14px; background-color: rgb(255, 255, 255);" class="">SLF4J:
Found binding in [jar:file:/Users/xxxx/Library/Application%20Support/.mcrCache9.1/FLIMfi0/BFMatlab/bioformats_package.jar!/org/slf4j/impl/StaticLoggerBinder.class]</span><br style="box-sizing: border-box; color: rgb(36, 41, 46); font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol'; font-size: 14px;" class="">
<span style="color: rgb(36, 41, 46); font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol'; font-size: 14px; background-color: rgb(255, 255, 255);" class="">SLF4J:
See </span><a href="http://www.slf4j.org/codes.html#multiple_bindings" style="box-sizing: border-box; -webkit-text-decoration-skip: objects; color: rgb(3, 102, 214); text-decoration: none; font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol'; font-size: 14px;" class="">http://www.slf4j.org/codes.html#multiple_bindings</a><span style="color: rgb(36, 41, 46); font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol'; font-size: 14px; background-color: rgb(255, 255, 255);" class=""> for
an explanation.</span></div>
<div class=""><span style="color: rgb(36, 41, 46); font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol'; font-size: 14px; background-color: rgb(255, 255, 255);" class=""><br class="">
</span></div>
<div class=""><span style="color: rgb(36, 41, 46); font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol'; font-size: 14px; background-color: rgb(255, 255, 255);" class="">Should
anyone else encounter this issue.</span></div>
<div class=""><span style="color: rgb(36, 41, 46); font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol'; font-size: 14px; background-color: rgb(255, 255, 255);" class="">The
solution was to add the following line to the build script.</span></div>
<div class=""><span style="color: rgb(36, 41, 46); font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol'; font-size: 14px; background-color: rgb(255, 255, 255);" class="">(Thanks
to Curtis Rueden IIRC for suggesting this)</span></div>
<div class=""><span style="color: rgb(36, 41, 46); font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol'; font-size: 14px; background-color: rgb(255, 255, 255);" class=""><br class="">
</span></div>
<div class=""><span style="color: rgb(36, 41, 46); font-family: SFMono-Regular, Consolas, 'Liberation Mono', Menlo, Courier, monospace; font-size: 12.000000953674316px; white-space: pre; background-color: rgb(255, 255, 255);" class="">zip -d bfmatlab/bioformats_package.jar
</span><span class="pl-s" style="box-sizing: border-box; color: rgb(3, 47, 98); font-family: SFMono-Regular, Consolas, 'Liberation Mono', Menlo, Courier, monospace; font-size: 12.000000953674316px; white-space: pre;"><span class="pl-pds" style="box-sizing: border-box;">'</span>org/slf4j/impl/*<span class="pl-pds" style="box-sizing: border-box;">’</span></span></div>
<div class=""><span class="pl-s" style="box-sizing: border-box; color: rgb(3, 47, 98); font-family: SFMono-Regular, Consolas, 'Liberation Mono', Menlo, Courier, monospace; font-size: 12.000000953674316px; white-space: pre;"><span class="pl-pds" style="box-sizing: border-box;"><br class="">
</span></span></div>
<div class="">It occurs to me that making a .jar file without these components available for download somewhere, might </div>
<div class="">be something the OME team might like to consider.</div>
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<div class="">Best Wishes </div>
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<div class="">Ian</div>
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</div>
<div class=""><span class="pl-s" style="box-sizing: border-box; color: rgb(3, 47, 98); font-family: SFMono-Regular, Consolas, 'Liberation Mono', Menlo, Courier, monospace; font-size: 12.000000953674316px; white-space: pre;"><span class="pl-pds" style="box-sizing: border-box;"><br class="">
</span></span></div>
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</div>
<div class=""><span style="color: rgb(36, 41, 46); font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol'; font-size: 14px; background-color: rgb(255, 255, 255);" class=""><br class="">
</span></div>
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</span></div>
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</span></div>
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</blockquote>
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