[ImageJ-devel] [fiji-devel] LOCI crashes with current Fiji build on runtime

[Jonas Øgaard]

Hi again, Curtis!

> I sat at work all day today pulling my hair - I could not make it
> > work.
>
> My sincerest apologies for the pain. It is almost certainly due to
> problems on the update site, not your configuration.
>

Please don't apologize for providing me with tools for science (;
I will try it out first thing tomorrow. Pretty much done with developing,
now it's time for analysis (:

Besides, I like a challenge - although I have to admit this time I was in
over my head.

Oh, by the way, I'm not sure if the Maven dependencies are all sorted with
regards to a certain Jama package... It looks for version 1.0.2 whereas the
latest release is 1.0.3 so it cannot be found... I managed to get it
working through manually installing 1.0.2. It also works by changing the
pom files of VIB-lib, VIB_ and 3D_viewer making them up to date. Having
said that I only have a faintest clue of the infrastructure of Maven
repositories...

Anyway, it didn't help me with my loci (;

Sincerely,
Jonas


>
> I have updated the Bio-Formats installation in Fiji to the absolute latest
> available, and hopefully ironed out these problems. Can you please run Help
> > Update Fiji to install all the updates, and let me know if Bio-Formats
> becomes functional for you?
>
> Thanks,
> Curtis
>
>
> On Tue, Dec 11, 2012 at 10:55 AM, Jonas Øgaard <jonas at ogaard.no> wrote:
>
>> Hi there,
>>
>> I have a working version of Fiji running at home (where I'm at now) and
>> don't dare to break it, but I sat at work all day today pulling my hair - I
>> could not make it work.
>>
>> I tried fresh downloads (fiji with and without jre), I tried removing one
>> LOCI-jar, then the other, then both. I tried updating both fiji and imagej
>> in two seperate clean setups, and also tried repeating updates to make sure
>> no more components where awaiting updates.
>>
>> It could be that the java-install is not entirely stable/up-to-date -
>> it's running JRE6. Haven't tried 7.
>>
>> I have no clue. Working from home tomorrow where it's safe & stable!
>>
>> Sincerely,
>> Jonas
>>
>>
>> On Tue, Dec 11, 2012 at 5:47 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:
>>
>>> Hi Jonas,
>>>
>>> > I am unable to import files with LOCI, no matter which loci-jar is
>>> > deleted or not...
>>>
>>> I updated Fiji with the 4.4.5 release of Bio-Formats last night, so
>>> these errors are almost certainly my fault.
>>>
>>> Unfortunately, I am unable to replicate the problem. I tried updating an
>>> existing Fiji on another workstation, and all worked fine (though I did
>>> have to click "break the dependency" in response to one prompt). I also
>>> tried with a fresh continuous release downloaded from fiji.sc just now,
>>> and it also worked.
>>>
>>> If you run Help > Update Fiji, click on Advanced mode, what do you see
>>> for "Locally modified files" and "Uninstalled files only"? A fully
>>> up-to-date Fiji should not have any entries.
>>>
>>> -Curtis
>>>
>>>
>>> On Tue, Dec 11, 2012 at 6:31 AM, <jonas.ogaard at gmail.com> wrote:
>>>
>>>> Hi!
>>>>
>>>> I am still having difficulties with the latest Fiji (both w/w/out jre)
>>>> and LOCI. Receiving same errors as described above.
>>>>
>>>> As of now I am unable to import files with LOCI, no matter which
>>>> loci-jar is deleted or not...
>>>>
>>>> Have I magically jinxed my Fiji folder (again) or is this a problem
>>>> shared by others?
>>>>
>>>> Awesome work btw, Johannes (:
>>>>
>>>> //Jonas
>>>>
>>>> On Wednesday, August 1, 2012 7:37:26 PM UTC+2, Johannes Schindelin
>>>> wrote:
>>>>
>>>>> Hi Sebi,
>>>>>
>>>>> On Wed, 1 Aug 2012, sebr... at gmail.com wrote:
>>>>>
>>>>> > I tried to download the most up-to-date version (
>>>>> > http://jenkins.imagej.net/job/**Stable-Fiji/**
>>>>> lastSuccessfulBuild/artifact/**fiji-nojre.zip<http://jenkins.imagej.net/job/Stable-Fiji/lastSuccessfulBuild/artifact/fiji-nojre.zip>)
>>>>>
>>>>> >
>>>>> >
>>>>> > This contains the loci_tools.jar as well as the the individual jars.
>>>>> So
>>>>> > should i just delete which files? This issues is quite critical for
>>>>> us,
>>>>> > since the Loci Bio-Format import is cruicial for us (and customer)
>>>>> to
>>>>> > import the OME-TIFF data produced by our imaging software.
>>>>>
>>>>> Yes, it is safe to delete loci_tools.jar. My work last year on
>>>>> enabling
>>>>> multiple update sites introduced the bug that removing files from
>>>>> update
>>>>> sites does not mark them as obsolete if you updated the files
>>>>> successfully
>>>>> before. We just did not hit that bug because we did not remove files
>>>>> in a
>>>>> long time ;-)
>>>>>
>>>>> > Do you still have an idea when this problem might get solved?
>>>>>
>>>>> It is fixed in the source code, I just have to upload a new version
>>>>> (for
>>>>> which I need to be comfortable with the current state first, though
>>>>> ;-).
>>>>> Should be happening within the hour.
>>>>>
>>>>> Ciao,
>>>>> Dscho
>>>>>
>>>>
>>>> _______________________________________________
>>>> ImageJ-devel mailing list
>>>> ImageJ-devel at imagej.net
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>>>>
>>>>
>>>
>>
>
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