Maven TrackMate Dependency Question

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Maven TrackMate Dependency Question

Jay Warrick-2
Hi All,

I was hoping someone on the list might have a suggestion for the following 2 problems I'm having. First, I'm trying to use TrackMate in my program. I updated my pom to use the new TrackMate version 2.5 instead of version 2.3. I've also checked all the dependency hierarchies of my project modules in Eclipse for dependencies on the old version and only find a dependency on v 2.5.

<dependency>
<groupId>sc.fiji</groupId>
<artifactId>TrackMate_</artifactId>
<version>2.5.0</version>
</dependency>

However, it seems maven still thinks I'm using v 2.3 according to the following error message.

%%%%%%%%%%%%%%%

[WARNING] The POM for sc.fiji:TrackMate_:jar:2.3.0 is invalid, transitive dependencies (if any) will not be available: 1 problem was encountered while building the effective model for sc.fiji:TrackMate_:2.3.0
[ERROR] 'dependencies.dependency.groupId' for ${jama.groupId}:jama:jar with value '${jama.groupId}' does not match a valid id pattern. @ 

%%%%%%%%%%%%%%%

This brings me to the second problem... how can I resolve this above warning/error message? Is there something I should be doing differently in general when I want to specifically depend on similar FIJI plugin? This issue appears to be preventing the inclusion of my own "wrapper plugin" which depends on this jar/plugin as all my wrapper plugins are listed in my application when run except for the wrapper plugin that depends on the TrackMate jar.

Here's what I've tried... I forced update of snapshots and releases from within Eclipse for all modules of my project. I turned off "Build Automatically" within Eclipse and went to the command line and ran 'mvn -e -U clean install'. I even deleted my ~/.m2/repository contents as a last ditch effort. 

As background information, my parent pom is scijava

<parent>
<groupId>org.scijava</groupId>
<artifactId>pom-scijava</artifactId>
<version>3.4</version>
</parent>

 but I depend on imagej with the following...

<dependencyManagement>
<dependencies>
<dependency>
<groupId>net.imagej</groupId>
<artifactId>pom-imagej</artifactId>
<version>2.49</version>
<type>pom</type>
<scope>import</scope>
</dependency>
</dependencies>
</dependencyManagement>

Any suggestions?

Thanks!!!

Jay


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Re: Maven TrackMate Dependency Question

Jean-Yves Tinevez-2
On 13-Sep-14 13:44, Jay Warrick wrote:
Hi All,

I was hoping someone on the list might have a suggestion for the following 2 problems I'm having. First, I'm trying to use TrackMate in my program. I updated my pom to use the new TrackMate version 2.5 instead of version 2.3. I've also checked all the dependency hierarchies of my project modules in Eclipse for dependencies on the old version and only find a dependency on v 2.5.

<dependency>
<groupId>sc.fiji</groupId>
<artifactId>TrackMate_</artifactId>
<version>2.5.0</version>
</dependency>

However, it seems maven still thinks I'm using v 2.3 according to the following error message.

%%%%%%%%%%%%%%%

[WARNING] The POM for sc.fiji:TrackMate_:jar:2.3.0 is invalid, transitive dependencies (if any) will not be available: 1 problem was encountered while building the effective model for sc.fiji:TrackMate_:2.3.0

Hi Jay

Ok, that's very odd. The TrackMate-example depends on TrackMate this way and it works:
https://github.com/fiji/MaMuT/blob/master/pom.xmlhttps://github.com/fiji/MaMuT/blob/master/pom.xml

Could you post the whole pom.xml to let us see through it?
best
jy



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Re: Maven TrackMate Dependency Question

Jay Warrick-2
Hi Jean-Yves,

Thanks for the quick reply! Here are the poms for my multi module project. I added to the default "pom.xml" names to make things easier to follow. The Master pom is the parent pom for each of my project modules. The parent of Master is scijava. The JEX module has essentially one class, Main which calls the main class in Core. Core contains essentially the whole program including the dependency on TrackMate. Broken contains broken code for one reason or another but doesn't really come into play as the Broken module is not part of the build process. It is "disabled" using a profile within the JEX module. Despite this, I still confirmed it didn't depend on TrackMate 2.3 using the Eclipse dependency hierarchy viewer, just in case.






Likewise, if it is easier, my git repo for this project is https://github.com/jaywarrick/JEX.

Thanks so much for helping me with this.

Regards,

Jay

On Sep 13, 2014, at 7:27 AM, Jean-Yves Tinevez <[hidden email]> wrote:

On 13-Sep-14 13:44, Jay Warrick wrote:
Hi All,

I was hoping someone on the list might have a suggestion for the following 2 problems I'm having. First, I'm trying to use TrackMate in my program. I updated my pom to use the new TrackMate version 2.5 instead of version 2.3. I've also checked all the dependency hierarchies of my project modules in Eclipse for dependencies on the old version and only find a dependency on v 2.5.

<dependency>
<groupId>sc.fiji</groupId>
<artifactId>TrackMate_</artifactId>
<version>2.5.0</version>
</dependency>

However, it seems maven still thinks I'm using v 2.3 according to the following error message.

%%%%%%%%%%%%%%%

[WARNING] The POM for sc.fiji:TrackMate_:jar:2.3.0 is invalid, transitive dependencies (if any) will not be available: 1 problem was encountered while building the effective model for sc.fiji:TrackMate_:2.3.0

Hi Jay

Ok, that's very odd. The TrackMate-example depends on TrackMate this way and it works:
https://github.com/fiji/MaMuT/blob/master/pom.xmlhttps://github.com/fiji/MaMuT/blob/master/pom.xml

Could you post the whole pom.xml to let us see through it?
best
jy



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Re: Maven TrackMate Dependency Question

Jean-Yves Tinevez-2
On 13-Sep-14 16:01, Jay Warrick wrote:
Hi Jean-Yves,

Thanks for the quick reply! Here are the poms for my multi module project. I added to the default "pom.xml" names to make things easier to follow. The Master pom is the parent pom for each of my project modules. The parent of Master is scijava. The JEX module has essentially one class, Main which calls the main class in Core. Core contains essentially the whole program including the dependency on TrackMate. Broken contains broken code for one reason or another but doesn't really come into play as the Broken module is not part of the build process. It is "disabled" using a profile within the JEX module. Despite this, I still confirmed it didn't depend on TrackMate 2.3 using the Eclipse dependency hierarchy viewer, just in case.

Ok thank you for the crystal clear report.
We are on the verge of what I know of maven. However I remember having a similar issue that was fixed by making the parent of the master pom the fiji plugin pom, like for TrackMate pom.

Any chance you could just try that first?
jy



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Re: Maven TrackMate Dependency Question

Jay Warrick-2
I can certainly try it. That will at least give us an indication of things. Long term, I'm not sure how that will go but we can at least try this for now. I'll follow up on your suggestion when I can next work on it. Thanks again so much.

Dscho - would you have any other suggestions. The error message references '${jama.groupId}' property. Do you know where this is likely defined? I poked around some poms but didn't see it. Can I just define it and it will work? I suppose I'll try that as well.

Cheers,

Jay

On Sep 13, 2014, at 9:20 AM, Jean-Yves Tinevez <[hidden email]> wrote:

On 13-Sep-14 16:01, Jay Warrick wrote:
Hi Jean-Yves,

Thanks for the quick reply! Here are the poms for my multi module project. I added to the default "pom.xml" names to make things easier to follow. The Master pom is the parent pom for each of my project modules. The parent of Master is scijava. The JEX module has essentially one class, Main which calls the main class in Core. Core contains essentially the whole program including the dependency on TrackMate. Broken contains broken code for one reason or another but doesn't really come into play as the Broken module is not part of the build process. It is "disabled" using a profile within the JEX module. Despite this, I still confirmed it didn't depend on TrackMate 2.3 using the Eclipse dependency hierarchy viewer, just in case.

Ok thank you for the crystal clear report.
We are on the verge of what I know of maven. However I remember having a similar issue that was fixed by making the parent of the master pom the fiji plugin pom, like for TrackMate pom.

Any chance you could just try that first?
jy



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Re: Maven TrackMate Dependency Question

Jay Warrick-2
In reply to this post by Jean-Yves Tinevez-2
Hi JY,

Could it be a problem with the TrackMate groupId? Searching the internet with the error string brought up this past issue with jama and SPIM...


When I look at the TrackMate pom, I don't think I see a "groupId" defined for the TrackMate plugin. Hard for me to completely decipher in the issue discussion if this would cause the problem I'm seeing or if it would merely prevent the imageJ/Fiji folks from "seeing" that such a problem exists.

Stephan Preibisch, Curtis, and Dscho - Does that sound like the right track? Thoughts?

Thanks,

Jay

On Sep 13, 2014, at 9:20 AM, Jean-Yves Tinevez <[hidden email]> wrote:

On 13-Sep-14 16:01, Jay Warrick wrote:
Hi Jean-Yves,

Thanks for the quick reply! Here are the poms for my multi module project. I added to the default "pom.xml" names to make things easier to follow. The Master pom is the parent pom for each of my project modules. The parent of Master is scijava. The JEX module has essentially one class, Main which calls the main class in Core. Core contains essentially the whole program including the dependency on TrackMate. Broken contains broken code for one reason or another but doesn't really come into play as the Broken module is not part of the build process. It is "disabled" using a profile within the JEX module. Despite this, I still confirmed it didn't depend on TrackMate 2.3 using the Eclipse dependency hierarchy viewer, just in case.

Ok thank you for the crystal clear report.
We are on the verge of what I know of maven. However I remember having a similar issue that was fixed by making the parent of the master pom the fiji plugin pom, like for TrackMate pom.

Any chance you could just try that first?
jy



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Re: Maven TrackMate Dependency Question

Jay Warrick-2
If this might be on the right track, is there any way to test this on my end? Use offline mode and go into my .m2 repository and muck with poms or something?
On Sep 14, 2014, at 6:11 AM, Jay Warrick <[hidden email]> wrote:

Hi JY,

Could it be a problem with the TrackMate groupId? Searching the internet with the error string brought up this past issue with jama and SPIM...


When I look at the TrackMate pom, I don't think I see a "groupId" defined for the TrackMate plugin. Hard for me to completely decipher in the issue discussion if this would cause the problem I'm seeing or if it would merely prevent the imageJ/Fiji folks from "seeing" that such a problem exists.

Stephan Preibisch, Curtis, and Dscho - Does that sound like the right track? Thoughts?

Thanks,

Jay

On Sep 13, 2014, at 9:20 AM, Jean-Yves Tinevez <[hidden email]> wrote:

On 13-Sep-14 16:01, Jay Warrick wrote:
Hi Jean-Yves,

Thanks for the quick reply! Here are the poms for my multi module project. I added to the default "pom.xml" names to make things easier to follow. The Master pom is the parent pom for each of my project modules. The parent of Master is scijava. The JEX module has essentially one class, Main which calls the main class in Core. Core contains essentially the whole program including the dependency on TrackMate. Broken contains broken code for one reason or another but doesn't really come into play as the Broken module is not part of the build process. It is "disabled" using a profile within the JEX module. Despite this, I still confirmed it didn't depend on TrackMate 2.3 using the Eclipse dependency hierarchy viewer, just in case.

Ok thank you for the crystal clear report.
We are on the verge of what I know of maven. However I remember having a similar issue that was fixed by making the parent of the master pom the fiji plugin pom, like for TrackMate pom.

Any chance you could just try that first?
jy



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Re: Maven TrackMate Dependency Question

Jay Warrick-2
I think never mind. Still learning about Maven, but it looks like the groupID is assumed the same as the parent so you TrackMate doesn't need to define it. Should have guessed this based on how everything else seems to work in Maven.

On Sep 14, 2014, at 6:15 AM, Jay Warrick <[hidden email]> wrote:

If this might be on the right track, is there any way to test this on my end? Use offline mode and go into my .m2 repository and muck with poms or something?
On Sep 14, 2014, at 6:11 AM, Jay Warrick <[hidden email]> wrote:

Hi JY,

Could it be a problem with the TrackMate groupId? Searching the internet with the error string brought up this past issue with jama and SPIM...


When I look at the TrackMate pom, I don't think I see a "groupId" defined for the TrackMate plugin. Hard for me to completely decipher in the issue discussion if this would cause the problem I'm seeing or if it would merely prevent the imageJ/Fiji folks from "seeing" that such a problem exists.

Stephan Preibisch, Curtis, and Dscho - Does that sound like the right track? Thoughts?

Thanks,

Jay

On Sep 13, 2014, at 9:20 AM, Jean-Yves Tinevez <[hidden email]> wrote:

On 13-Sep-14 16:01, Jay Warrick wrote:
Hi Jean-Yves,

Thanks for the quick reply! Here are the poms for my multi module project. I added to the default "pom.xml" names to make things easier to follow. The Master pom is the parent pom for each of my project modules. The parent of Master is scijava. The JEX module has essentially one class, Main which calls the main class in Core. Core contains essentially the whole program including the dependency on TrackMate. Broken contains broken code for one reason or another but doesn't really come into play as the Broken module is not part of the build process. It is "disabled" using a profile within the JEX module. Despite this, I still confirmed it didn't depend on TrackMate 2.3 using the Eclipse dependency hierarchy viewer, just in case.

Ok thank you for the crystal clear report.
We are on the verge of what I know of maven. However I remember having a similar issue that was fixed by making the parent of the master pom the fiji plugin pom, like for TrackMate pom.

Any chance you could just try that first?
jy



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Re: Maven TrackMate Dependency Question

Jay Warrick-2
Ok. So this makes more sense...  TrackMate v 2.3 uses the <groupId>${jama.groupId}</groupId> which causes the error, which was fixed by TrackMate v2.5 which uses <groupId>gov.nist.math</groupId>.

So the whole issue boils down to, "Why is maven trying to do ANYTHING with v 2.3 when I can't find a single dependency on this version? If I can get Maven to stop looking for v 2.3 my issue will be solved.

Thoughts on where to search for hidden/residual links to v 2.3 given what I've checked already?

Thanks,

Jay

On Sep 14, 2014, at 6:45 AM, Jay Warrick <[hidden email]> wrote:

I think never mind. Still learning about Maven, but it looks like the groupID is assumed the same as the parent so you TrackMate doesn't need to define it. Should have guessed this based on how everything else seems to work in Maven.

On Sep 14, 2014, at 6:15 AM, Jay Warrick <[hidden email]> wrote:

If this might be on the right track, is there any way to test this on my end? Use offline mode and go into my .m2 repository and muck with poms or something?
On Sep 14, 2014, at 6:11 AM, Jay Warrick <[hidden email]> wrote:

Hi JY,

Could it be a problem with the TrackMate groupId? Searching the internet with the error string brought up this past issue with jama and SPIM...


When I look at the TrackMate pom, I don't think I see a "groupId" defined for the TrackMate plugin. Hard for me to completely decipher in the issue discussion if this would cause the problem I'm seeing or if it would merely prevent the imageJ/Fiji folks from "seeing" that such a problem exists.

Stephan Preibisch, Curtis, and Dscho - Does that sound like the right track? Thoughts?

Thanks,

Jay

On Sep 13, 2014, at 9:20 AM, Jean-Yves Tinevez <[hidden email]> wrote:

On 13-Sep-14 16:01, Jay Warrick wrote:
Hi Jean-Yves,

Thanks for the quick reply! Here are the poms for my multi module project. I added to the default "pom.xml" names to make things easier to follow. The Master pom is the parent pom for each of my project modules. The parent of Master is scijava. The JEX module has essentially one class, Main which calls the main class in Core. Core contains essentially the whole program including the dependency on TrackMate. Broken contains broken code for one reason or another but doesn't really come into play as the Broken module is not part of the build process. It is "disabled" using a profile within the JEX module. Despite this, I still confirmed it didn't depend on TrackMate 2.3 using the Eclipse dependency hierarchy viewer, just in case.

Ok thank you for the crystal clear report.
We are on the verge of what I know of maven. However I remember having a similar issue that was fixed by making the parent of the master pom the fiji plugin pom, like for TrackMate pom.

Any chance you could just try that first?
jy



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pom-fiji TrackMate update?

Jay Warrick-2
I changed the subject line from Re: [ImageJ-devel] Maven TrackMate Dependency Question because of the following...

Oh boy, really at the extent of my knowledge... but I think I may have it, is this what is happening??? Is maven pulling TrackMate v 2.3 via TrackMate v2.5 and fiji?

In TrackMate v 2.5 pom there is...

<parent>
<groupId>sc.fiji</groupId>
<artifactId>pom-fiji</artifactId>
<version>2.0.0-beta-1-SNAPSHOT</version>
<relativePath/>
</parent>
<artifactId>TrackMate_</artifactId>
<version>2.5.0</version>
<name>plugins/TrackMate_.jar</name>

which thus pulls in pom-fiji 2.0.0-beta-1-SNAPSHOT where there is the following...

<fiji-compat.version>2.0.0-SNAPSHOT</fiji-compat.version>

and 

<dependency>
<groupId>sc.fiji</groupId>
<artifactId>fiji-compat</artifactId>
</dependency>

The pom for fiji-compat uses pom-fiji 2.0.0-SNAPSHOT as parent

<parent>
<groupId>sc.fiji</groupId>
<artifactId>pom-fiji</artifactId>
<version>2.0.0-SNAPSHOT</version>
<relativePath/>
</parent><
artifactId>fiji-compat</artifactId>
<name>jars/fiji-compat.jar</name>

The pom-fiji 2.0.0-SNAPSHOT has the following

<TrackMate.version>2.3.0-SNAPSHOT</TrackMate.version>

and 

<dependency>
<groupId>sc.fiji</groupId>
<artifactId>TrackMate_</artifactId>
<version>${TrackMate.version}</version>
</dependency>

Thus, ?maybe? with TrackMate v 2.5's pom parent being pom-fiji 2.0.0-beta-1-SNAPSHOT, fiji-compate 2.0.0-SNAPSHOT gets pulled in which pulls pom-fiji 2.0.0-SNAPSHOT which tries to pulls in TrackMate v 2.3 which then tries to use <groupId>${jama.groupId}</groupId> instead of <groupId>gov.nist.math</groupId> for jama. 

Is this counter to what is intended or is there some maven magic which should right this "wrong"? If it is not intended and could be affecting things, what might be the fix? 

Thanks all,

Jay


On Sep 14, 2014, at 6:51 AM, Jay Warrick <[hidden email]> wrote:

Ok. So this makes more sense...  TrackMate v 2.3 uses the <groupId>${jama.groupId}</groupId> which causes the error, which was fixed by TrackMate v2.5 which uses <groupId>gov.nist.math</groupId>.

So the whole issue boils down to, "Why is maven trying to do ANYTHING with v 2.3 when I can't find a single dependency on this version? If I can get Maven to stop looking for v 2.3 my issue will be solved.

Thoughts on where to search for hidden/residual links to v 2.3 given what I've checked already?

Thanks,

Jay

On Sep 14, 2014, at 6:45 AM, Jay Warrick <[hidden email]> wrote:

I think never mind. Still learning about Maven, but it looks like the groupID is assumed the same as the parent so you TrackMate doesn't need to define it. Should have guessed this based on how everything else seems to work in Maven.

On Sep 14, 2014, at 6:15 AM, Jay Warrick <[hidden email]> wrote:

If this might be on the right track, is there any way to test this on my end? Use offline mode and go into my .m2 repository and muck with poms or something?
On Sep 14, 2014, at 6:11 AM, Jay Warrick <[hidden email]> wrote:

Hi JY,

Could it be a problem with the TrackMate groupId? Searching the internet with the error string brought up this past issue with jama and SPIM...


When I look at the TrackMate pom, I don't think I see a "groupId" defined for the TrackMate plugin. Hard for me to completely decipher in the issue discussion if this would cause the problem I'm seeing or if it would merely prevent the imageJ/Fiji folks from "seeing" that such a problem exists.

Stephan Preibisch, Curtis, and Dscho - Does that sound like the right track? Thoughts?

Thanks,

Jay

On Sep 13, 2014, at 9:20 AM, Jean-Yves Tinevez <[hidden email]> wrote:

On 13-Sep-14 16:01, Jay Warrick wrote:
Hi Jean-Yves,

Thanks for the quick reply! Here are the poms for my multi module project. I added to the default "pom.xml" names to make things easier to follow. The Master pom is the parent pom for each of my project modules. The parent of Master is scijava. The JEX module has essentially one class, Main which calls the main class in Core. Core contains essentially the whole program including the dependency on TrackMate. Broken contains broken code for one reason or another but doesn't really come into play as the Broken module is not part of the build process. It is "disabled" using a profile within the JEX module. Despite this, I still confirmed it didn't depend on TrackMate 2.3 using the Eclipse dependency hierarchy viewer, just in case.

Ok thank you for the crystal clear report.
We are on the verge of what I know of maven. However I remember having a similar issue that was fixed by making the parent of the master pom the fiji plugin pom, like for TrackMate pom.

Any chance you could just try that first?
jy



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Re: Maven TrackMate Dependency Question

Curtis Rueden
In reply to this post by Jay Warrick-2

Hi Jay,

Eclipse has tools to understand where deps are coming from. Double click the pom.xml and see the Dependency Hierarchy tab. Much faster than guesswork and experimentation.

-Curtis

On Sep 14, 2014 6:52 AM, "Jay Warrick" <[hidden email]> wrote:
Ok. So this makes more sense...  TrackMate v 2.3 uses the <groupId>${jama.groupId}</groupId> which causes the error, which was fixed by TrackMate v2.5 which uses <groupId>gov.nist.math</groupId>.

So the whole issue boils down to, "Why is maven trying to do ANYTHING with v 2.3 when I can't find a single dependency on this version? If I can get Maven to stop looking for v 2.3 my issue will be solved.

Thoughts on where to search for hidden/residual links to v 2.3 given what I've checked already?

Thanks,

Jay

On Sep 14, 2014, at 6:45 AM, Jay Warrick <[hidden email]> wrote:

I think never mind. Still learning about Maven, but it looks like the groupID is assumed the same as the parent so you TrackMate doesn't need to define it. Should have guessed this based on how everything else seems to work in Maven.

On Sep 14, 2014, at 6:15 AM, Jay Warrick <[hidden email]> wrote:

If this might be on the right track, is there any way to test this on my end? Use offline mode and go into my .m2 repository and muck with poms or something?
On Sep 14, 2014, at 6:11 AM, Jay Warrick <[hidden email]> wrote:

Hi JY,

Could it be a problem with the TrackMate groupId? Searching the internet with the error string brought up this past issue with jama and SPIM...


When I look at the TrackMate pom, I don't think I see a "groupId" defined for the TrackMate plugin. Hard for me to completely decipher in the issue discussion if this would cause the problem I'm seeing or if it would merely prevent the imageJ/Fiji folks from "seeing" that such a problem exists.

Stephan Preibisch, Curtis, and Dscho - Does that sound like the right track? Thoughts?

Thanks,

Jay

On Sep 13, 2014, at 9:20 AM, Jean-Yves Tinevez <[hidden email]> wrote:

On 13-Sep-14 16:01, Jay Warrick wrote:
Hi Jean-Yves,

Thanks for the quick reply! Here are the poms for my multi module project. I added to the default "pom.xml" names to make things easier to follow. The Master pom is the parent pom for each of my project modules. The parent of Master is scijava. The JEX module has essentially one class, Main which calls the main class in Core. Core contains essentially the whole program including the dependency on TrackMate. Broken contains broken code for one reason or another but doesn't really come into play as the Broken module is not part of the build process. It is "disabled" using a profile within the JEX module. Despite this, I still confirmed it didn't depend on TrackMate 2.3 using the Eclipse dependency hierarchy viewer, just in case.

Ok thank you for the crystal clear report.
We are on the verge of what I know of maven. However I remember having a similar issue that was fixed by making the parent of the master pom the fiji plugin pom, like for TrackMate pom.

Any chance you could just try that first?
jy



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Re: Maven TrackMate Dependency Question

Jay Warrick-2
Hi Curtis,

I updated maven and at least now it appears my plugin which depends on TrackMate 2.5 successfully gets included/built into the final app. I still get the warning about TrackMate 2.3 but at least it doesn't appear to be getting in the way of my TrackMate 2.5 dependent plugin (if it ever was).

Thus, not an "emergency" for any of your assistance that you graciously offered, but this brings up a question... How does maven deal with reciprocally dependent jar's such as TrackMate and Fiji where the plugin depends on Fiji while it also seems that Fiji depends on the plugin. Is this all fine and dandy for maven in general or is it typically managed via "scope"? I didn't notice any specification for "scope" with respect to the TrackMate dependency. Can scope be specified elsewhere as a property of group of dependencies?

Cheers and thanks,

Jay

On Sep 14, 2014, at 8:11 AM, Curtis Rueden <[hidden email]> wrote:

If you still haven't solved in by tomorrow, I'll take a look when I'm in front of a computer tomorrow then.

On Sep 14, 2014 8:10 AM, "Jay Warrick" <[hidden email]> wrote:
I already mentioned that I did that. You pointed it out to me before and it has been extremely useful since then. However, in this case, it is showing that there are no TrackMate 2.3 dependencies yet when running maven from command line, I get an issue when, for some reason, it tries to pull it in.

Thanks,

Jay

On Sep 14, 2014, at 8:07 AM, Curtis Rueden <[hidden email]> wrote:

Hi Jay,

Eclipse has tools to understand where deps are coming from. Double click the pom.xml and see the Dependency Hierarchy tab. Much faster than guesswork and experimentation.

-Curtis

On Sep 14, 2014 6:52 AM, "Jay Warrick" <[hidden email]> wrote:
Ok. So this makes more sense...  TrackMate v 2.3 uses the <groupId>${jama.groupId}</groupId> which causes the error, which was fixed by TrackMate v2.5 which uses <groupId>gov.nist.math</groupId>.

So the whole issue boils down to, "Why is maven trying to do ANYTHING with v 2.3 when I can't find a single dependency on this version? If I can get Maven to stop looking for v 2.3 my issue will be solved.

Thoughts on where to search for hidden/residual links to v 2.3 given what I've checked already?

Thanks,

Jay

On Sep 14, 2014, at 6:45 AM, Jay Warrick <[hidden email]> wrote:

I think never mind. Still learning about Maven, but it looks like the groupID is assumed the same as the parent so you TrackMate doesn't need to define it. Should have guessed this based on how everything else seems to work in Maven.

On Sep 14, 2014, at 6:15 AM, Jay Warrick <[hidden email]> wrote:

If this might be on the right track, is there any way to test this on my end? Use offline mode and go into my .m2 repository and muck with poms or something?
On Sep 14, 2014, at 6:11 AM, Jay Warrick <[hidden email]> wrote:

Hi JY,

Could it be a problem with the TrackMate groupId? Searching the internet with the error string brought up this past issue with jama and SPIM...


When I look at the TrackMate pom, I don't think I see a "groupId" defined for the TrackMate plugin. Hard for me to completely decipher in the issue discussion if this would cause the problem I'm seeing or if it would merely prevent the imageJ/Fiji folks from "seeing" that such a problem exists.

Stephan Preibisch, Curtis, and Dscho - Does that sound like the right track? Thoughts?

Thanks,

Jay

On Sep 13, 2014, at 9:20 AM, Jean-Yves Tinevez <[hidden email]> wrote:

On 13-Sep-14 16:01, Jay Warrick wrote:
Hi Jean-Yves,

Thanks for the quick reply! Here are the poms for my multi module project. I added to the default "pom.xml" names to make things easier to follow. The Master pom is the parent pom for each of my project modules. The parent of Master is scijava. The JEX module has essentially one class, Main which calls the main class in Core. Core contains essentially the whole program including the dependency on TrackMate. Broken contains broken code for one reason or another but doesn't really come into play as the Broken module is not part of the build process. It is "disabled" using a profile within the JEX module. Despite this, I still confirmed it didn't depend on TrackMate 2.3 using the Eclipse dependency hierarchy viewer, just in case.

Ok thank you for the crystal clear report.
We are on the verge of what I know of maven. However I remember having a similar issue that was fixed by making the parent of the master pom the fiji plugin pom, like for TrackMate pom.

Any chance you could just try that first?
jy



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Re: pom-fiji TrackMate update?

Curtis Rueden
In reply to this post by Jay Warrick-2
Hi Jay,

> In TrackMate v 2.5 pom there is...
> <parent>
> <groupId>sc.fiji</groupId>
> <artifactId>pom-fiji</artifactId>
> <version>2.0.0-beta-1-SNAPSHOT</version>
> <relativePath/>
> </parent>
> <artifactId>TrackMate_</artifactId>
> <version>2.5.0</version>
> <name>plugins/TrackMate_.jar</name>

OK, I finally made a little time to look at this.

Yes, this is a major problem with TrackMate's releases. Version 2.5.0 inherits from sc.fiji:pom-fiji:2.0.0-beta-1-SNAPSHOT. This is forbidden in Maven terms -- a release must depend only on other releases.

This is a consequence of the fact that Fiji artifacts do not use the maven-release-plugin for releases, and hence nothing ever actually enforces that stipulation. The solution will be for all Fiji plugins to extend a _release_ version of the pom-fiji parent, not a SNAPSHOT version.

We are moving in that direction... but until we complete that migration, downstream artifacts such as JEX will _not_ be stable when they depend on a Fiji project such as TrackMate, _even if_ the dependency purports to be a "release" version! Caveat emptor.

Regards,
Curtis

On Sun, Sep 14, 2014 at 7:40 AM, Jay Warrick <[hidden email]> wrote:
I changed the subject line from Re: [ImageJ-devel] Maven TrackMate Dependency Question because of the following...

Oh boy, really at the extent of my knowledge... but I think I may have it, is this what is happening??? Is maven pulling TrackMate v 2.3 via TrackMate v2.5 and fiji?

In TrackMate v 2.5 pom there is...

<parent>
<groupId>sc.fiji</groupId>
<artifactId>pom-fiji</artifactId>
<version>2.0.0-beta-1-SNAPSHOT</version>
<relativePath/>
</parent>
<artifactId>TrackMate_</artifactId>
<version>2.5.0</version>
<name>plugins/TrackMate_.jar</name>

which thus pulls in pom-fiji 2.0.0-beta-1-SNAPSHOT where there is the following...

<fiji-compat.version>2.0.0-SNAPSHOT</fiji-compat.version>

and 

<dependency>
<groupId>sc.fiji</groupId>
<artifactId>fiji-compat</artifactId>
</dependency>

The pom for fiji-compat uses pom-fiji 2.0.0-SNAPSHOT as parent

<parent>
<groupId>sc.fiji</groupId>
<artifactId>pom-fiji</artifactId>
<version>2.0.0-SNAPSHOT</version>
<relativePath/>
</parent><
artifactId>fiji-compat</artifactId>
<name>jars/fiji-compat.jar</name>

The pom-fiji 2.0.0-SNAPSHOT has the following

<TrackMate.version>2.3.0-SNAPSHOT</TrackMate.version>

and 

<dependency>
<groupId>sc.fiji</groupId>
<artifactId>TrackMate_</artifactId>
<version>${TrackMate.version}</version>
</dependency>

Thus, ?maybe? with TrackMate v 2.5's pom parent being pom-fiji 2.0.0-beta-1-SNAPSHOT, fiji-compate 2.0.0-SNAPSHOT gets pulled in which pulls pom-fiji 2.0.0-SNAPSHOT which tries to pulls in TrackMate v 2.3 which then tries to use <groupId>${jama.groupId}</groupId> instead of <groupId>gov.nist.math</groupId> for jama. 

Is this counter to what is intended or is there some maven magic which should right this "wrong"? If it is not intended and could be affecting things, what might be the fix? 

Thanks all,

Jay


On Sep 14, 2014, at 6:51 AM, Jay Warrick <[hidden email]> wrote:

Ok. So this makes more sense...  TrackMate v 2.3 uses the <groupId>${jama.groupId}</groupId> which causes the error, which was fixed by TrackMate v2.5 which uses <groupId>gov.nist.math</groupId>.

So the whole issue boils down to, "Why is maven trying to do ANYTHING with v 2.3 when I can't find a single dependency on this version? If I can get Maven to stop looking for v 2.3 my issue will be solved.

Thoughts on where to search for hidden/residual links to v 2.3 given what I've checked already?

Thanks,

Jay

On Sep 14, 2014, at 6:45 AM, Jay Warrick <[hidden email]> wrote:

I think never mind. Still learning about Maven, but it looks like the groupID is assumed the same as the parent so you TrackMate doesn't need to define it. Should have guessed this based on how everything else seems to work in Maven.

On Sep 14, 2014, at 6:15 AM, Jay Warrick <[hidden email]> wrote:

If this might be on the right track, is there any way to test this on my end? Use offline mode and go into my .m2 repository and muck with poms or something?
On Sep 14, 2014, at 6:11 AM, Jay Warrick <[hidden email]> wrote:

Hi JY,

Could it be a problem with the TrackMate groupId? Searching the internet with the error string brought up this past issue with jama and SPIM...


When I look at the TrackMate pom, I don't think I see a "groupId" defined for the TrackMate plugin. Hard for me to completely decipher in the issue discussion if this would cause the problem I'm seeing or if it would merely prevent the imageJ/Fiji folks from "seeing" that such a problem exists.

Stephan Preibisch, Curtis, and Dscho - Does that sound like the right track? Thoughts?

Thanks,

Jay

On Sep 13, 2014, at 9:20 AM, Jean-Yves Tinevez <[hidden email]> wrote:

On 13-Sep-14 16:01, Jay Warrick wrote:
Hi Jean-Yves,

Thanks for the quick reply! Here are the poms for my multi module project. I added to the default "pom.xml" names to make things easier to follow. The Master pom is the parent pom for each of my project modules. The parent of Master is scijava. The JEX module has essentially one class, Main which calls the main class in Core. Core contains essentially the whole program including the dependency on TrackMate. Broken contains broken code for one reason or another but doesn't really come into play as the Broken module is not part of the build process. It is "disabled" using a profile within the JEX module. Despite this, I still confirmed it didn't depend on TrackMate 2.3 using the Eclipse dependency hierarchy viewer, just in case.

Ok thank you for the crystal clear report.
We are on the verge of what I know of maven. However I remember having a similar issue that was fixed by making the parent of the master pom the fiji plugin pom, like for TrackMate pom.

Any chance you could just try that first?
jy



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Re: pom-fiji TrackMate update?

Jay Warrick-2
Thanks Curtis.

Cheers,

Jay


On Oct 3, 2014, at 12:53 PM, Curtis Rueden <[hidden email]> wrote:

Hi Jay,

> In TrackMate v 2.5 pom there is...
> <parent>
> <groupId>sc.fiji</groupId>
> <artifactId>pom-fiji</artifactId>
> <version>2.0.0-beta-1-SNAPSHOT</version>
> <relativePath/>
> </parent>
> <artifactId>TrackMate_</artifactId>
> <version>2.5.0</version>
> <name>plugins/TrackMate_.jar</name>

OK, I finally made a little time to look at this.

Yes, this is a major problem with TrackMate's releases. Version 2.5.0 inherits from sc.fiji:pom-fiji:2.0.0-beta-1-SNAPSHOT. This is forbidden in Maven terms -- a release must depend only on other releases.

This is a consequence of the fact that Fiji artifacts do not use the maven-release-plugin for releases, and hence nothing ever actually enforces that stipulation. The solution will be for all Fiji plugins to extend a _release_ version of the pom-fiji parent, not a SNAPSHOT version.

We are moving in that direction... but until we complete that migration, downstream artifacts such as JEX will _not_ be stable when they depend on a Fiji project such as TrackMate, _even if_ the dependency purports to be a "release" version! Caveat emptor.

Regards,
Curtis

On Sun, Sep 14, 2014 at 7:40 AM, Jay Warrick <[hidden email]> wrote:
I changed the subject line from Re: [ImageJ-devel] Maven TrackMate Dependency Question because of the following...

Oh boy, really at the extent of my knowledge... but I think I may have it, is this what is happening??? Is maven pulling TrackMate v 2.3 via TrackMate v2.5 and fiji?

In TrackMate v 2.5 pom there is...

<parent>
<groupId>sc.fiji</groupId>
<artifactId>pom-fiji</artifactId>
<version>2.0.0-beta-1-SNAPSHOT</version>
<relativePath/>
</parent>
<artifactId>TrackMate_</artifactId>
<version>2.5.0</version>
<name>plugins/TrackMate_.jar</name>

which thus pulls in pom-fiji 2.0.0-beta-1-SNAPSHOT where there is the following...

<fiji-compat.version>2.0.0-SNAPSHOT</fiji-compat.version>

and 

<dependency>
<groupId>sc.fiji</groupId>
<artifactId>fiji-compat</artifactId>
</dependency>

The pom for fiji-compat uses pom-fiji 2.0.0-SNAPSHOT as parent

<parent>
<groupId>sc.fiji</groupId>
<artifactId>pom-fiji</artifactId>
<version>2.0.0-SNAPSHOT</version>
<relativePath/>
</parent><
artifactId>fiji-compat</artifactId>
<name>jars/fiji-compat.jar</name>

The pom-fiji 2.0.0-SNAPSHOT has the following

<TrackMate.version>2.3.0-SNAPSHOT</TrackMate.version>

and 

<dependency>
<groupId>sc.fiji</groupId>
<artifactId>TrackMate_</artifactId>
<version>${TrackMate.version}</version>
</dependency>

Thus, ?maybe? with TrackMate v 2.5's pom parent being pom-fiji 2.0.0-beta-1-SNAPSHOT, fiji-compate 2.0.0-SNAPSHOT gets pulled in which pulls pom-fiji 2.0.0-SNAPSHOT which tries to pulls in TrackMate v 2.3 which then tries to use <groupId>${jama.groupId}</groupId> instead of <groupId>gov.nist.math</groupId> for jama. 

Is this counter to what is intended or is there some maven magic which should right this "wrong"? If it is not intended and could be affecting things, what might be the fix? 

Thanks all,

Jay


On Sep 14, 2014, at 6:51 AM, Jay Warrick <[hidden email]> wrote:

Ok. So this makes more sense...  TrackMate v 2.3 uses the <groupId>${jama.groupId}</groupId> which causes the error, which was fixed by TrackMate v2.5 which uses <groupId>gov.nist.math</groupId>.

So the whole issue boils down to, "Why is maven trying to do ANYTHING with v 2.3 when I can't find a single dependency on this version? If I can get Maven to stop looking for v 2.3 my issue will be solved.

Thoughts on where to search for hidden/residual links to v 2.3 given what I've checked already?

Thanks,

Jay

On Sep 14, 2014, at 6:45 AM, Jay Warrick <[hidden email]> wrote:

I think never mind. Still learning about Maven, but it looks like the groupID is assumed the same as the parent so you TrackMate doesn't need to define it. Should have guessed this based on how everything else seems to work in Maven.

On Sep 14, 2014, at 6:15 AM, Jay Warrick <[hidden email]> wrote:

If this might be on the right track, is there any way to test this on my end? Use offline mode and go into my .m2 repository and muck with poms or something?
On Sep 14, 2014, at 6:11 AM, Jay Warrick <[hidden email]> wrote:

Hi JY,

Could it be a problem with the TrackMate groupId? Searching the internet with the error string brought up this past issue with jama and SPIM...


When I look at the TrackMate pom, I don't think I see a "groupId" defined for the TrackMate plugin. Hard for me to completely decipher in the issue discussion if this would cause the problem I'm seeing or if it would merely prevent the imageJ/Fiji folks from "seeing" that such a problem exists.

Stephan Preibisch, Curtis, and Dscho - Does that sound like the right track? Thoughts?

Thanks,

Jay

On Sep 13, 2014, at 9:20 AM, Jean-Yves Tinevez <[hidden email]> wrote:

On 13-Sep-14 16:01, Jay Warrick wrote:
Hi Jean-Yves,

Thanks for the quick reply! Here are the poms for my multi module project. I added to the default "pom.xml" names to make things easier to follow. The Master pom is the parent pom for each of my project modules. The parent of Master is scijava. The JEX module has essentially one class, Main which calls the main class in Core. Core contains essentially the whole program including the dependency on TrackMate. Broken contains broken code for one reason or another but doesn't really come into play as the Broken module is not part of the build process. It is "disabled" using a profile within the JEX module. Despite this, I still confirmed it didn't depend on TrackMate 2.3 using the Eclipse dependency hierarchy viewer, just in case.

Ok thank you for the crystal clear report.
We are on the verge of what I know of maven. However I remember having a similar issue that was fixed by making the parent of the master pom the fiji plugin pom, like for TrackMate pom.

Any chance you could just try that first?
jy



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Re: pom-fiji TrackMate update?

Jean-Yves Tinevez-2
In reply to this post by Curtis Rueden

> OK, I finally made a little time to look at this.
>
> Yes, this is a major problem with TrackMate's releases. Version 2.5.0
> inherits from sc.fiji:pom-fiji:2.0.0-beta-1-SNAPSHOT. This is
> forbidden in Maven terms -- a release must depend only on other releases.



Woops sorry I did not know.
How can I fix this?
best
jy

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Re: pom-fiji TrackMate update?

Mark Hiner
Hi J-Y,

>Woops sorry I did not know.

When TrackMate 2.5.0 was released there actually wasn't a pom-fiji release to pin to.. so don't be too hard on yourself. :)

>How can I fix this?

You could update TrackMate's parent pom to the latest pom-fiji release. However, that beta-0 release is fairly old (last commit is from July 24th) so you may need something more recent. Also, it doesn't completely solve the issue since you do have other sc.fiji dependencies in TrackMate... so until we convert everything to a release coupling, things won't truly be stable and reproducible.

Johannes is out for the weekend.. I will talk with him on Monday about how we want to release pom-fiji:beta-1, and transition everything to release couplings.

Regards,
Mark



On Fri, Oct 3, 2014 at 2:54 PM, Jean-Yves Tinevez <[hidden email]> wrote:

OK, I finally made a little time to look at this.

Yes, this is a major problem with TrackMate's releases. Version 2.5.0 inherits from sc.fiji:pom-fiji:2.0.0-beta-1-SNAPSHOT. This is forbidden in Maven terms -- a release must depend only on other releases.



Woops sorry I did not know.
How can I fix this?
best
jy

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Re: pom-fiji TrackMate update?

Jay Warrick-2
Thanks all.

On Oct 3, 2014, at 3:23 PM, Mark Hiner <[hidden email]> wrote:

Hi J-Y,

>Woops sorry I did not know.

When TrackMate 2.5.0 was released there actually wasn't a pom-fiji release to pin to.. so don't be too hard on yourself. :)

>How can I fix this?

You could update TrackMate's parent pom to the latest pom-fiji release. However, that beta-0 release is fairly old (last commit is from July 24th) so you may need something more recent. Also, it doesn't completely solve the issue since you do have other sc.fiji dependencies in TrackMate... so until we convert everything to a release coupling, things won't truly be stable and reproducible.

Johannes is out for the weekend.. I will talk with him on Monday about how we want to release pom-fiji:beta-1, and transition everything to release couplings.

Regards,
Mark



On Fri, Oct 3, 2014 at 2:54 PM, Jean-Yves Tinevez <[hidden email]> wrote:

OK, I finally made a little time to look at this.

Yes, this is a major problem with TrackMate's releases. Version 2.5.0 inherits from sc.fiji:pom-fiji:2.0.0-beta-1-SNAPSHOT. This is forbidden in Maven terms -- a release must depend only on other releases.



Woops sorry I did not know.
How can I fix this?
best
jy

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pom-fiji beta 1, was Re: pom-fiji TrackMate update?

dscho
Administrator
In reply to this post by Mark Hiner
Hi Mark,

On Fri, 3 Oct 2014, Mark Hiner wrote:

> You could update TrackMate's parent pom to the latest pom-fiji release
> <https://github.com/fiji/pom-fiji/releases>. However, that beta-0
> release is fairly old (last commit is from July 24th) so you may need
> something more recent.

I really tried to push for a beta-1 that actually has release couplings
all over. It is very tedious a battle, though, because a couple of Fiji
subprojects seem to want to be in eternal snapshot land...

Ciao,
Dscho

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