Building TrakEM2 from source

I checked out the current TrakEM2 master branch, then imported the maven project in Eclipse, then run the pom.xml as Maven install (or Maven build, or Maven generate sources) and this does not generate the ‘target’ folder in which I should be finding the generated xxx.jar (there is also no xxx.jar anywhere).
The Eclipse console is below. Am I doing something wrong ?
Thanks for your help

[INFO] Scanning for projects...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Aggregator project for Albert Cardona's TrakEM2 software suite 2.0.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.3.1:enforce (enforce-rules) @ pom-trakem2 ---
[INFO] Adding ignorable dependency: null:jcodings:null
[INFO]   Adding ignore: org/jcodings/*
[INFO] Adding ignorable dependency: null:jnr-constants:null
[INFO]   Adding ignore: com/kenai/constantine/*
[INFO]   Adding ignore: jnr/constants/*
[INFO] Adding ignorable dependency: null:jnr-ffi:null
[INFO]   Adding ignore: jnr/ffi/*
[INFO] Adding ignorable dependency: null:joda-time:null
[INFO]   Adding ignore: *
[INFO] Adding ignorable dependency: null:slf4j-log4j12:null
[INFO]   Adding ignore: org/slf4j/impl/*
[INFO] Adding ignorable dependency: batik:batik:null
[INFO]   Adding ignore: *
[INFO] Adding ignorable dependency: jama:jama:null
[INFO]   Adding ignore: Jama/*
[INFO] Adding ignorable dependency: com.sun:tools:null
[INFO]   Adding ignore: *
[INFO] 
[INFO] --- build-helper-maven-plugin:1.9.1:regex-property (sanitize-version) @ pom-trakem2 ---
[INFO] 
[INFO] --- buildnumber-maven-plugin:1.3:create (default) @ pom-trakem2 ---
[INFO] Executing: cmd.exe /X /C "git rev-parse --verify HEAD"
[INFO] Working directory: D:\Research\FijiJavaDevel\TrakEM2
[INFO] Storing buildNumber: UNKNOWN at timestamp: 1457436372396
[WARNING] Cannot get the branch information from the git repository: 
Detecting the current branch failed: 'git' is not recognized as an internal or external command,
operable program or batch file.

[INFO] Executing: cmd.exe /X /C "git rev-parse --verify HEAD"
[INFO] Working directory: D:\Research\FijiJavaDevel\TrakEM2
[INFO] Storing buildScmBranch: UNKNOWN_BRANCH
[INFO] 
[INFO] --- scijava-maven-plugin:0.5.1:set-rootdir (set-rootdir) @ pom-trakem2 ---
[INFO] Setting rootdir: D:\Research\FijiJavaDevel\TrakEM2
[INFO] 
[INFO] --- maven-source-plugin:2.3:jar-no-fork (default) @ pom-trakem2 ---
[INFO] 
[INFO] --- maven-source-plugin:2.3:jar-no-fork (attach-sources) @ pom-trakem2 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:2.9.1:jar (attach-javadocs) @ pom-trakem2 ---
[INFO] Not executing Javadoc as the project is not a Java classpath-capable package
[INFO] 
[INFO] --- maven-install-plugin:2.5.1:install (default-install) @ pom-trakem2 ---
[INFO] Installing D:\Research\FijiJavaDevel\TrakEM2\pom.xml to C:\Users\templier\.m2\repository\sc\fiji\pom-trakem2\2.0.0-SNAPSHOT\pom-trakem2-2.0.0-SNAPSHOT.pom
[INFO] 
[INFO] --- imagej-maven-plugin:0.6.0:copy-jars (copy-jars) @ pom-trakem2 ---
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 3.478 s
[INFO] Finished at: 2016-03-08T12:26:13+01:00
[INFO] Final Memory: 21M/491M
[INFO] ------------------------------------------------------------------------

The TrakEM2 repository contains an aggregator project for TrakEM2_ and its subprojects/dependencies.

Try building the actual sub-project:

cd TrakEM2_
mvn -Djavadoc.skip

Then it should say:

[INFO] ------------------------------------------------------------------------
[INFO] Building plugins/TrakeEM2_.jar 1.0h-SNAPSHOT
[INFO] ------------------------------------------------------------------------

and you should be able to find TrakEM2_-1.0h-SNAPSHOT.jar in the trakem2/TrakEM2_/target directory.

2 Likes

Thanks @imagejan. Unfortunately, in Eclipse I right click on TrakEM2\TrakEM2_\pom.xml , make a maven build and get in the Eclipse console:

[INFO] Scanning for projects...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building plugins/TrakEM2_.jar 1.0h-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[WARNING] The POM for sc.fiji:VectorString:jar:2.0.0-SNAPSHOT is missing, no dependency information available
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1.550 s
[INFO] Finished at: 2016-03-08T15:34:59+01:00
[INFO] Final Memory: 19M/491M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project TrakEM2_: Could not resolve dependencies for project sc.fiji:TrakEM2_:jar:1.0h-SNAPSHOT: Failure to find sc.fiji:VectorString:jar:2.0.0-SNAPSHOT in http://maven.imagej.net/content/groups/public was cached in the local repository, resolution will not be reattempted until the update interval of imagej.public has elapsed or updates are forced -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException

My eclipse is configured with these dependencies (see image below) that are pointing to a freshly downloaded Fiji. Something wrong again on my side ?
Thanks for your help

Sorry, I don’t know how to set this up correctly in Eclipse. Building from the command line worked well for me (except that I had to disable the javadoc generation, see above). You can always turn off automatic building in Eclipse and build from the command line.

Maybe the TrakEM2 maintainers can comment on this: @axtimwalde, @hinerm, @ctrueden, any instructions how to work with aggregator projects in Eclipse?

The thing about aggregator projects is that they need to have valid modules! :wink: Looks like the modules didn’t get uncommented after the last release, so the latest SNAPSHOT versions never got deployed (and builds from the top-level would do nothing).

Anyway, fixed on master for now.

I would import the pom-trakem2 project and use that as the base directory instead. That way it will build and install all the modules and ensure they are coupled together properly. Your other configuration looks good. Here’s what my configuration looks like:

2 Likes

Thanks @imagejan and @hinerm.
Could you please detail what you mean by [quote=“hinerm, post:8, topic:1037”]
import the pom-trakem2 project
[/quote]
?
In the picture below which of the pom should I choose ? Only the one that is highlighted: TrakEM2_/pom.xml ?

I have tried importing either only this one or all. If I import only this one like here

and build the TrakEM2/pom.xml I get:

[INFO] Scanning for projects...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building plugins/TrakEM2_.jar 1.0h-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[WARNING] The POM for sc.fiji:VectorString:jar:2.0.0-SNAPSHOT is missing, no dependency information available
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1.633 s
[INFO] Finished at: 2016-03-08T16:58:25+01:00
[INFO] Final Memory: 19M/491M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project TrakEM2_: Could not resolve dependencies for project sc.fiji:TrakEM2_:jar:1.0h-SNAPSHOT: Failure to find sc.fiji:VectorString:jar:2.0.0-SNAPSHOT in http://maven.imagej.net/content/groups/public was cached in the local repository, resolution will not be reattempted until the update interval of imagej.public has elapsed or updates are forced -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException

When I try to set up the workspace to what you advised there is no pom-trakem2.
Thanks for your help

You should have all of them checked. When I said:

I meant sc.fiji:pom-trakem2, which is the top entry of your import dialog.

My Eclipse projects look like this:

Here I have all the TrakEM2 projects (5 libraries + the aggregator, pom-trakem2) ordered under a Working Set called trakem2.

In my Maven configuration, for the Base directory, I used Browse Workspace... to select the pom-trakem2 project as the base.

Let me know if you have any more questions about this configuration.

1 Like

Thanks @hinerm, your explanations are clear but I do not get it to work. I show you my steps:

  1. I import all maven projects, and tick the add project to working set at the bottom:

  2. I select the pom-trakem2 working set :

  3. I build the TrakEM2_/pom.xml and set the TrakEM2 as the base directory (note that there is no workspace_loc:/pom-trakem2 available unlike your configuration)

  4. In the Eclipse console I get :

[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] Aggregator project for Albert Cardona's TrakEM2 software suite
[INFO] jars/VectorString.jar
[INFO] plugins/TrakEM2_.jar
[INFO] jars/T2-NIT.jar
[INFO] jars/T2-TreelineGraph.jar
[INFO] mpicbg-trakem2
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Aggregator project for Albert Cardona's TrakEM2 software suite 2.0.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.3.1:enforce (enforce-rules) @ pom-trakem2 ---
[INFO] Adding ignorable dependency: null:jcodings:null
[INFO]   Adding ignore: org/jcodings/*
[INFO] Adding ignorable dependency: null:jnr-constants:null
[INFO]   Adding ignore: com/kenai/constantine/*
[INFO]   Adding ignore: jnr/constants/*
[INFO] Adding ignorable dependency: null:jnr-ffi:null
[INFO]   Adding ignore: jnr/ffi/*
[INFO] Adding ignorable dependency: null:joda-time:null
[INFO]   Adding ignore: *
[INFO] Adding ignorable dependency: null:slf4j-log4j12:null
[INFO]   Adding ignore: org/slf4j/impl/*
[INFO] Adding ignorable dependency: batik:batik:null
[INFO]   Adding ignore: *
[INFO] Adding ignorable dependency: jama:jama:null
[INFO]   Adding ignore: Jama/*
[INFO] Adding ignorable dependency: com.sun:tools:null
[INFO]   Adding ignore: *
[INFO] 
[INFO] --- build-helper-maven-plugin:1.9.1:regex-property (sanitize-version) @ pom-trakem2 ---
[INFO] 
[INFO] --- buildnumber-maven-plugin:1.3:create (default) @ pom-trakem2 ---
[INFO] Executing: cmd.exe /X /C "git rev-parse --verify HEAD"
[INFO] Working directory: D:\Research\FijiJavaDevel\TrakEM2
[INFO] Storing buildNumber: UNKNOWN at timestamp: 1457456193250
[WARNING] Cannot get the branch information from the git repository: 
Detecting the current branch failed: 'git' is not recognized as an internal or external command,
operable program or batch file.

[INFO] Executing: cmd.exe /X /C "git rev-parse --verify HEAD"
[INFO] Working directory: D:\Research\FijiJavaDevel\TrakEM2
[INFO] Storing buildScmBranch: UNKNOWN_BRANCH
[INFO] 
[INFO] --- scijava-maven-plugin:0.5.1:set-rootdir (set-rootdir) @ pom-trakem2 ---
[INFO] Setting rootdir: D:\Research\FijiJavaDevel\TrakEM2
[INFO] 
[INFO] --- maven-source-plugin:2.3:jar-no-fork (default) @ pom-trakem2 ---
[INFO] 
[INFO] --- maven-source-plugin:2.3:jar-no-fork (attach-sources) @ pom-trakem2 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:2.9.1:jar (attach-javadocs) @ pom-trakem2 ---
[INFO] Not executing Javadoc as the project is not a Java classpath-capable package
[INFO] 
[INFO] --- maven-install-plugin:2.5.1:install (default-install) @ pom-trakem2 ---
[INFO] Installing D:\Research\FijiJavaDevel\TrakEM2\pom.xml to C:\Users\templier\.m2\repository\sc\fiji\pom-trakem2\2.0.0-SNAPSHOT\pom-trakem2-2.0.0-SNAPSHOT.pom
[INFO] 
[INFO] --- imagej-maven-plugin:0.6.0:copy-jars (copy-jars) @ pom-trakem2 ---
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building jars/VectorString.jar 2.0.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.3.1:enforce (enforce-rules) @ VectorString ---
[INFO] Skipping Rule Enforcement.
[INFO] 
[INFO] --- build-helper-maven-plugin:1.9.1:regex-property (sanitize-version) @ VectorString ---
[INFO] 
[INFO] --- buildnumber-maven-plugin:1.3:create (default) @ VectorString ---
[INFO] 
[INFO] --- scijava-maven-plugin:0.5.1:set-rootdir (set-rootdir) @ VectorString ---
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ VectorString ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ VectorString ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ VectorString ---
[INFO] Not copying test resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:testCompile (default-testCompile) @ VectorString ---
[INFO] Not compiling test sources
[INFO] 
[INFO] --- maven-surefire-plugin:2.17:test (default-test) @ VectorString ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:2.5:jar (default-jar) @ VectorString ---
[INFO] 
[INFO] --- maven-source-plugin:2.3:jar-no-fork (default) @ VectorString ---
[INFO] 
[INFO] --- maven-source-plugin:2.3:jar-no-fork (attach-sources) @ VectorString ---
[INFO] 
[INFO] --- maven-javadoc-plugin:2.9.1:jar (attach-javadocs) @ VectorString ---
[INFO] 
Loading source files for package ini.trakem2.vector...
Constructing Javadoc information...
Standard Doclet version 1.8.0_71
Building tree for all the packages and classes...
Generating D:\Research\FijiJavaDevel\TrakEM2\VectorString\target\apidocs\ini\trakem2\vector\Editions.html...
Generating D:\Research\FijiJavaDevel\TrakEM2\VectorString\target\apidocs\ini\trakem2\vector\Editions.Chunk.html...
Generating D:\Research\FijiJavaDevel\TrakEM2\VectorString\target\apidocs\ini\trakem2\vector\SkinMaker.html...
Generating D:\Research\FijiJavaDevel\TrakEM2\VectorString\target\apidocs\ini\trakem2\vector\SkinMaker.Match.html...
Generating D:\Research\FijiJavaDevel\TrakEM2\VectorString\target\apidocs\ini\trakem2\vector\Util.html...
Generating D:\Research\FijiJavaDevel\TrakEM2\VectorString\target\apidocs\ini\trakem2\vector\Util.CircularSequence.html...
Generating D:\Research\FijiJavaDevel\TrakEM2\VectorString\target\apidocs\ini\trakem2\vector\VectorString.html...
Generating D:\Research\FijiJavaDevel\TrakEM2\VectorString\target\apidocs\ini\trakem2\vector\VectorString2D.html...
Generating D:\Research\FijiJavaDevel\TrakEM2\VectorString\target\apidocs\ini\trakem2\vector\VectorString3D.html...
Generating D:\Research\FijiJavaDevel\TrakEM2\VectorString\target\apidocs\ini\trakem2\vector\package-frame.html...
Generating D:\Research\FijiJavaDevel\TrakEM2\VectorString\target\apidocs\ini\trakem2\vector\package-summary.html...
Generating D:\Research\FijiJavaDevel\TrakEM2\VectorString\target\apidocs\ini\trakem2\vector\package-tree.html...
Generating D:\Research\FijiJavaDevel\TrakEM2\VectorString\target\apidocs\constant-values.html...
Building index for all the packages and classes...
Generating D:\Research\FijiJavaDevel\TrakEM2\VectorString\target\apidocs\overview-tree.html...
Generating D:\Research\FijiJavaDevel\TrakEM2\VectorString\target\apidocs\index-all.html...
Generating D:\Research\FijiJavaDevel\TrakEM2\VectorString\target\apidocs\deprecated-list.html...
Building index for all classes...
Generating D:\Research\FijiJavaDevel\TrakEM2\VectorString\target\apidocs\allclasses-frame.html...
Generating D:\Research\FijiJavaDevel\TrakEM2\VectorString\target\apidocs\allclasses-noframe.html...
Generating D:\Research\FijiJavaDevel\TrakEM2\VectorString\target\apidocs\index.html...
Generating D:\Research\FijiJavaDevel\TrakEM2\VectorString\target\apidocs\help-doc.html...
3 errors
100 warnings
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] Aggregator project for Albert Cardona's TrakEM2 software suite SUCCESS [  3.381 s]
[INFO] jars/VectorString.jar .............................. FAILURE [  9.377 s]
[INFO] plugins/TrakEM2_.jar ............................... SKIPPED
[INFO] jars/T2-NIT.jar .................................... SKIPPED
[INFO] jars/T2-TreelineGraph.jar .......................... SKIPPED
[INFO] mpicbg-trakem2 ..................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 13.389 s
[INFO] Finished at: 2016-03-08T17:56:43+01:00
[INFO] Final Memory: 30M/622M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-javadoc-plugin:2.9.1:jar (attach-javadocs) on project VectorString: MavenReportException: Error while creating archive:
[ERROR] Exit code: 1 - D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Editions.java:83: warning: no @return
[ERROR] public double getSimilarity(final boolean skip_ends, final int max_mut, final float min_chunk) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Editions.java:129: warning: no @param for skip_ends
[ERROR] public double getSimilarity2(boolean skip_ends, final int max_mut, final float min_chunk) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Editions.java:129: warning: no @param for max_mut
[ERROR] public double getSimilarity2(boolean skip_ends, final int max_mut, final float min_chunk) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Editions.java:129: warning: no @param for min_chunk
[ERROR] public double getSimilarity2(boolean skip_ends, final int max_mut, final float min_chunk) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Editions.java:129: warning: no @return
[ERROR] public double getSimilarity2(boolean skip_ends, final int max_mut, final float min_chunk) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Editions.java:201: warning: no @param for skip_ends
[ERROR] public double getPhysicalDistance(final boolean skip_ends, final int max_mut, final float min_chunk, final boolean average) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Editions.java:201: warning: no @param for max_mut
[ERROR] public double getPhysicalDistance(final boolean skip_ends, final int max_mut, final float min_chunk, final boolean average) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Editions.java:201: warning: no @param for min_chunk
[ERROR] public double getPhysicalDistance(final boolean skip_ends, final int max_mut, final float min_chunk, final boolean average) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Editions.java:201: warning: no @param for average
[ERROR] public double getPhysicalDistance(final boolean skip_ends, final int max_mut, final float min_chunk, final boolean average) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Editions.java:201: warning: no @return
[ERROR] public double getPhysicalDistance(final boolean skip_ends, final int max_mut, final float min_chunk, final boolean average) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Editions.java:290: warning: no @param for skip_ends
[ERROR] public double[] getStatistics(final boolean skip_ends, final int max_mut, final float min_chunk, final boolean score_mut_only) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Editions.java:290: warning: no @param for max_mut
[ERROR] public double[] getStatistics(final boolean skip_ends, final int max_mut, final float min_chunk, final boolean score_mut_only) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Editions.java:290: warning: no @param for min_chunk
[ERROR] public double[] getStatistics(final boolean skip_ends, final int max_mut, final float min_chunk, final boolean score_mut_only) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Editions.java:290: warning: no @param for score_mut_only
[ERROR] public double[] getStatistics(final boolean skip_ends, final int max_mut, final float min_chunk, final boolean score_mut_only) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Editions.java:290: warning: no @return
[ERROR] public double[] getStatistics(final boolean skip_ends, final int max_mut, final float min_chunk, final boolean score_mut_only) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Editions.java:758: warning: no @param for separator
[ERROR] public String prettyPrint(String separator) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Editions.java:758: warning: no @return
[ERROR] public String prettyPrint(String separator) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Editions.java:897: warning: no @param for max_non_mut
[ERROR] public Editions recreateFromCenter(final int max_non_mut) throws Exception {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Editions.java:897: warning: no @return
[ERROR] public Editions recreateFromCenter(final int max_non_mut) throws Exception {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Editions.java:897: warning: no @throws for java.lang.Exception
[ERROR] public Editions recreateFromCenter(final int max_non_mut) throws Exception {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\SkinMaker.java:36: warning: no @param for vs1
[ERROR] static public double[][] getMorphedPerimeter(final VectorString2D vs1, final VectorString2D vs2, final double alpha, final Editions ed) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\SkinMaker.java:36: warning: no @param for vs2
[ERROR] static public double[][] getMorphedPerimeter(final VectorString2D vs1, final VectorString2D vs2, final double alpha, final Editions ed) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\SkinMaker.java:36: warning: no @param for alpha
[ERROR] static public double[][] getMorphedPerimeter(final VectorString2D vs1, final VectorString2D vs2, final double alpha, final Editions ed) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\SkinMaker.java:36: warning: no @param for ed
[ERROR] static public double[][] getMorphedPerimeter(final VectorString2D vs1, final VectorString2D vs2, final double alpha, final Editions ed) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\SkinMaker.java:36: warning: no @return
[ERROR] static public double[][] getMorphedPerimeter(final VectorString2D vs1, final VectorString2D vs2, final double alpha, final Editions ed) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\SkinMaker.java:123: warning: no @param for vs1
[ERROR] static public double[][][] getMorphedPerimeters(final VectorString2D vs1, final VectorString2D vs2, int n_morphed_perimeters, final Editions ed) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\SkinMaker.java:123: warning: no @param for vs2
[ERROR] static public double[][][] getMorphedPerimeters(final VectorString2D vs1, final VectorString2D vs2, int n_morphed_perimeters, final Editions ed) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\SkinMaker.java:123: warning: no @param for n_morphed_perimeters
[ERROR] static public double[][][] getMorphedPerimeters(final VectorString2D vs1, final VectorString2D vs2, int n_morphed_perimeters, final Editions ed) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\SkinMaker.java:123: warning: no @param for ed
[ERROR] static public double[][][] getMorphedPerimeters(final VectorString2D vs1, final VectorString2D vs2, int n_morphed_perimeters, final Editions ed) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\SkinMaker.java:123: warning: no @return
[ERROR] static public double[][][] getMorphedPerimeters(final VectorString2D vs1, final VectorString2D vs2, int n_morphed_perimeters, final Editions ed) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\SkinMaker.java:138: warning: no @param for vs
[ERROR] static public ArrayList<SkinMaker.Match> getMorphedPerimeters(final VectorString2D[] vs, final int n_morphed_perimeters, final double delta_, final boolean closed) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\SkinMaker.java:138: warning: no @param for n_morphed_perimeters
[ERROR] static public ArrayList<SkinMaker.Match> getMorphedPerimeters(final VectorString2D[] vs, final int n_morphed_perimeters, final double delta_, final boolean closed) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\SkinMaker.java:138: warning: no @param for delta_
[ERROR] static public ArrayList<SkinMaker.Match> getMorphedPerimeters(final VectorString2D[] vs, final int n_morphed_perimeters, final double delta_, final boolean closed) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\SkinMaker.java:138: warning: no @param for closed
[ERROR] static public ArrayList<SkinMaker.Match> getMorphedPerimeters(final VectorString2D[] vs, final int n_morphed_perimeters, final double delta_, final boolean closed) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\SkinMaker.java:138: warning: no @return
[ERROR] static public ArrayList<SkinMaker.Match> getMorphedPerimeters(final VectorString2D[] vs, final int n_morphed_perimeters, final double delta_, final boolean closed) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\SkinMaker.java:323: warning: no @param for vs
[ERROR] static public List<Point3f> generateTriangles(final VectorString2D[] vs, final int n_morphed_perimeters, final double delta_, final boolean closed) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\SkinMaker.java:323: warning: no @param for n_morphed_perimeters
[ERROR] static public List<Point3f> generateTriangles(final VectorString2D[] vs, final int n_morphed_perimeters, final double delta_, final boolean closed) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\SkinMaker.java:323: warning: no @param for delta_
[ERROR] static public List<Point3f> generateTriangles(final VectorString2D[] vs, final int n_morphed_perimeters, final double delta_, final boolean closed) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\SkinMaker.java:323: warning: no @param for closed
[ERROR] static public List<Point3f> generateTriangles(final VectorString2D[] vs, final int n_morphed_perimeters, final double delta_, final boolean closed) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\SkinMaker.java:323: warning: no @return
[ERROR] static public List<Point3f> generateTriangles(final VectorString2D[] vs, final int n_morphed_perimeters, final double delta_, final boolean closed) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\SkinMaker.java:209: warning: no @param for closed
[ERROR] public List<Point3f> generateTriangles(final boolean closed) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\SkinMaker.java:209: warning: no @return
[ERROR] public List<Point3f> generateTriangles(final boolean closed) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Util.java:6: warning: no @param for a
[ERROR] static public final double[] copy(final double[] a, final int new_length) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Util.java:6: warning: no @param for new_length
[ERROR] static public final double[] copy(final double[] a, final int new_length) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Util.java:6: warning: no @return
[ERROR] static public final double[] copy(final double[] a, final int new_length) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Util.java:24: warning: no @param for x
[ERROR] static public final double getAngle(final double x, final double y) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Util.java:24: warning: no @param for y
[ERROR] static public final double getAngle(final double x, final double y) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Util.java:24: warning: no @return
[ERROR] static public final double getAngle(final double x, final double y) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Util.java:43: warning: no @param for a
[ERROR] static public final void reverse(final double[] a) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Util.java:151: warning: no @param for p
[ERROR] final static public DoublePolygon createInterpolatedPolygon(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Util.java:151: warning: no @param for interval
[ERROR] final static public DoublePolygon createInterpolatedPolygon(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Util.java:151: warning: no @param for isLine
[ERROR] final static public DoublePolygon createInterpolatedPolygon(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Util.java:151: warning: no @return
[ERROR] final static public DoublePolygon createInterpolatedPolygon(
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Util.java:107: error: malformed HTML
[ERROR] /** Will wrap around if k<0 or k>size. */
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Util.java:107: error: bad use of '>'
[ERROR] /** Will wrap around if k<0 or k>size. */
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Util.java:108: warning: no @param for k
[ERROR] final public int setPosition(final int k) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Util.java:108: warning: no @return
[ERROR] final public int setPosition(final int k) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Util.java:115: warning: no @param for inc
[ERROR] final public int move(final int inc) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Util.java:115: warning: no @return
[ERROR] final public int move(final int inc) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\Util.java:86: error: no tag name after @
[ERROR] /** A sequence of integers from 0 to {@param size}
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString.java:37: warning: no @param for dim
[ERROR] public double[] getPoints(int dim);
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString.java:37: warning: no @return
[ERROR] public double[] getPoints(int dim);
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString.java:40: warning: no @param for dim
[ERROR] public double getPoint(int dim, int i);
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString.java:40: warning: no @param for i
[ERROR] public double getPoint(int dim, int i);
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString.java:40: warning: no @return
[ERROR] public double getPoint(int dim, int i);
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString2D.java:305: warning: no @param for cal
[ERROR] public void calibrate(final Calibration cal) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString2D.java:50: warning: no @param for x
[ERROR] public VectorString2D(double[] x, double[] y, double z, boolean closed) throws Exception {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString2D.java:50: warning: no @param for y
[ERROR] public VectorString2D(double[] x, double[] y, double z, boolean closed) throws Exception {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString2D.java:50: warning: no @param for z
[ERROR] public VectorString2D(double[] x, double[] y, double z, boolean closed) throws Exception {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString2D.java:50: warning: no @param for closed
[ERROR] public VectorString2D(double[] x, double[] y, double z, boolean closed) throws Exception {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString2D.java:50: warning: no @throws for java.lang.Exception
[ERROR] public VectorString2D(double[] x, double[] y, double z, boolean closed) throws Exception {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString3D.java:80: warning: no @param for a
[ERROR] public void addDependent(final double[] a) throws Exception {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString3D.java:80: warning: no @throws for java.lang.Exception
[ERROR] public void addDependent(final double[] a) throws Exception {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString3D.java:98: warning: no @return
[ERROR] public double getAverageDelta() {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString3D.java:658: warning: no @return
[ERROR] public ArrayList<ArrayList<Point3d>> getSource() { return this.source; }
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString3D.java:660: warning: no @return
[ERROR] public int getNSources() { return n_sources; }
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString3D.java:871: warning: no @param for target_delta
[ERROR] public void equalize(final double target_delta) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString3D.java:914: warning: no @param for cal
[ERROR] public void calibrate(final Calibration cal) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString3D.java:934: warning: no @param for cal
[ERROR] public void setCalibration(final Calibration cal) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString3D.java:975: warning: no @param for other
[ERROR] public VectorString3D createInterpolated(final VectorString3D other, final Editions ed, final double alpha) throws Exception {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString3D.java:975: warning: no @param for ed
[ERROR] public VectorString3D createInterpolated(final VectorString3D other, final Editions ed, final double alpha) throws Exception {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString3D.java:975: warning: no @param for alpha
[ERROR] public VectorString3D createInterpolated(final VectorString3D other, final Editions ed, final double alpha) throws Exception {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString3D.java:975: warning: no @return
[ERROR] public VectorString3D createInterpolated(final VectorString3D other, final Editions ed, final double alpha) throws Exception {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString3D.java:975: warning: no @throws for java.lang.Exception
[ERROR] public VectorString3D createInterpolated(final VectorString3D other, final Editions ed, final double alpha) throws Exception {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString3D.java:1134: warning: no @param for axis
[ERROR] public void mirror(final int axis) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString3D.java:1172: warning: no @return
[ERROR] public double computeLength() {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString3D.java:1196: warning: no @return
[ERROR] public Vector3d sumVector() {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString3D.java:1228: warning: no @param for i
[ERROR] public final double distance(final int i, final Point3d p) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString3D.java:1228: warning: no @param for p
[ERROR] public final double distance(final int i, final Point3d p) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString3D.java:1228: warning: no @return
[ERROR] public final double distance(final int i, final Point3d p) {
[ERROR] ^
[ERROR] D:\Research\FijiJavaDevel\TrakEM2\VectorString\src\main\java\ini\trakem2\vector\VectorString3D.java:1323: warning: no @param for ed
[ERROR] static public VectorString3D createInterpolatedPoints(final Editions ed, final double alpha) {
[ERROR] ^


Where am I wrong ?
Thanks

There are currently problems with the javadoc generation in Java 8 (lots of invalid javadoc tags being caught).

You can either specify Java 7 in the Maven run configuration:

Or add another Maven parameter:

javadoc.skip, with the value true

I think your pom-trakem2 also got imported as TrakEM2_ because you have two projects with that name in your workspace.

The actual build looks like it was proceeding as intended (looking at the “Reactor Build Order” section, it looks correct). So I’m thinking if you fix the Java version, or skip javadoc generation, everything will work.

FYI, the only thing my using pom-trakem2 workspace loc actually did for me was tell Maven to run in the top-level TrakEM2 folder (e.g. the top of the Git repository). You could also specify that manually. i assume for you that would just be D:\Research\FijiJavaDevel\TrakEM2

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solved the problem (my mistake, I should have done it earlier based on @imagejan’s previous answer

)

Thanks for your help @hinerm and @imagejan

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