[ome-devel] Sl4j classpath issues in deployed Matlab

Fri Mar 31 19:48:08 BST 2017

Hi Ian,

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.

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.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/

On Fri, Mar 31, 2017 at 1:25 PM, Munro, Ian <i.munro at imperial.ac.uk> wrote:

> Evening all
>
> So Curtis’ suggested solution, which is to remove the sl4j bindings from
> bioformats-package.jar as follows:
>
> zip -d bfmatlab/bioformats_package.jar 'org/slf4j/impl/*’
>
> seems to work. Thanks Curtis.
>
> However I now get:
> "2017-03-31 19:15:14.579 FLIMfit[29709:165086] Failed to connect
> (typePopUp) outlet from (NSViewController) to (NSPopUpButton): missing
> setter or instance variable”
> with the deployed version only.
>
> Does anyone have any idea how messing with bio-formats_package could
> generate that or has anyone even seen anything similar?
>
> Thanks
>
> Ian
>
>
> On 31 Mar 2017, at 15:30, Munro, Ian <i.munro at imperial.ac.uk> wrote:
>
> Thanks Curtis
>
> Ian
>
>
> On 31 Mar 2017, at 15:28, Curtis Rueden <ctrueden at wisc.edu> wrote:
>
> Hi Ian,
>
> > Is there any other component, or combination of components that I can
> > try ?
>
> Two possibilities come to mind:
>
> 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.
>
> 2) Massage the bioformats_package/loci_tools archive to stop shipping any
> SLF4J bindings.
>
> I filed PR #300 which pursues option (2); maybe it helps you.
> https://github.com/flimfit/FLIMfit/pull/300
>
> 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.
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Fri, Mar 31, 2017 at 8:41 AM, Munro, Ian <i.munro at imperial.ac.uk>
> wrote:
>
>> Hi Again
>>
>> Is there any other component, or combination of components that I can try
>> ?
>>
>> Thanks
>>
>> Ian
>>
>>
>> On 31 Mar 2017, at 10:29, Munro, Ian <i.munro at imperial.ac.uk> wrote:
>>
>> Hi Sebastien
>>
>> Unfortunately replacing bioformats_package.jar with loci_tools.jar has
>> simply replaced the previous warning
>> with :
>>
>> SLF4J: Class path contains multiple SLF4J bindings.
>> SLF4J: Found binding in [jar:file:/Applications/MATLAB
>> /MATLAB_Runtime/v91/java/jarext/slf4j/slf4j-log4j12.jar!/org
>> /slf4j/impl/StaticLoggerBinder.class]
>> SLF4J: Found binding in [jar:file:/Users/imunro/Librar
>> y/Application%20Support/.mcrCache9.1/FLIMfi0/BFMatlab/loci_t
>> ools.jar!/org/slf4j/impl/StaticLoggerBinder.class]
>>
>>
>> Best,
>>
>> Ian
>>
>> On 30 Mar 2017, at 14:40, Munro, Ian <i.munro at imperial.ac.uk> wrote:
>>
>> Thanks Sebastien
>>
>> I’ll give that a try and let you know.
>>
>> Ian
>>
>>
>> On 30 Mar 2017, at 14:32, Sebastien Besson (Staff) <s.besson at dundee.ac.uk>
>> wrote:
>>
>> Hi Ian,
>>
>> I think Curtis summarised the nature of the warning which should be
>> harmless albeit
>> annoying. For reference, OME was historically using log4j and switched to
>> logback
>> as the default logging implementation a few years ago [1].
>>
>> Moving towards individual JARs as Curtis suggests might be the best way
>> to enable full
>> control of the dependencies and prevent conflict in an environment like
>> MATLAB.
>>
>> In the short term, a third alternative might be to use the loci_tools.jar
>> rather than
>> bioformats_package.jar. The only difference between both bundle JARs is
>> effectively the
>> logging implementation shipped (log4j vs logback).
>>
>> Best,
>> Sebastien
>>
>> [1] https://github.com/openmicroscopy/bioformats/pull/889/
>>
>> On 30 Mar 2017, at 13:49, Munro, Ian <i.munro at imperial.ac.uk> wrote:
>>
>> Thanks Curtis
>>
>> Sounds like 2) would be the way to go then.
>>
>> Ian
>>
>>
>> On 30 Mar 2017, at 13:30, Curtis Rueden <ctrueden at wisc.edu> wrote:
>>
>> Hi Ian,
>>
>> > SLF4J: Class path contains multiple SLF4J bindings.
>>
>> Maybe the docs about that are helpful?
>> https://www.slf4j.org/codes.html#multiple_bindings
>>
>> > if anyone has any thoughts on a work-around that would be great.
>>
>> 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.)
>>
>> 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:
>>
>> 1) Change Bio-Formats to no longer depend on any JARs which include an
>> SLF4J binding. This would be a desirable change in general.
>>
>> 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.
>>
>> Regards,
>> Curtis
>>
>> --
>> Curtis Rueden
>> LOCI software architect - https://loci.wisc.edu/software
>> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
>> Did you know ImageJ has a forum? http://forum.imagej.net/
>>
>>
>> On Thu, Mar 30, 2017 at 5:34 AM, Munro, Ian <i.munro at imperial.ac.uk>
>> wrote:
>>
>>> Good afternoon
>>>
>>> I wondered if anyone has any thoughts on an issue we’re currently having.
>>> The next release of our FLIMfit application is nearly ready for release.
>>> However when running the deployed version we get a warning:
>>>
>>> SLF4J: Class path contains multiple SLF4J bindings.
>>> SLF4J: Found binding in [jar:file:/Applications/MATLAB
>>> /MATLAB_Runtime/v91/java/jarext/slf4j/slf4j-log4j12.jar!/org
>>> /slf4j/impl/StaticLoggerBinder.class]
>>> SLF4J: Found binding in [jar:file:/Users/imunro/Librar
>>> y/Application%20Support/.mcrCache9.1/FLIMfi0/BFMatlab/biofor
>>> mats_package.jar!/org/slf4j/impl/StaticLoggerBinder.class]
>>> SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an
>>> explanation.
>>>
>>> see also https://github.com/flimfit/FLIMfit/issues/299
>>>
>>> Thiis seems to be a warning only but if anyone has any thoughts on a
>>> work-around that would be great.
>>> NB this arose with the recent move to Matlab 2016b.
>>>
>>> Many Thanks
>>>
>>> Ian
>>>
>>>
>>> _______________________________________________
>>> ome-devel mailing list
>>> ome-devel at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>>>
>>
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