I can't reproduce this problem. The warnings don't disappear when I press F5, they stay were they are.

Strange, I just tried again by also deleting my ~/.eclipse folder and with a complete new workspace. Still the same.
I will try on another machine tomorrow and let you know.

I can reproduce this on 2 more machines, one running Ubuntu 12.04 too and one running Windows 7 32 bit. Both with Java 8. Both with a complete fresh install of ScalaIDE (not .eclipse folder, no workspace). So I could reproduce this issue on 3 different machines running 2 different OS.
The only difference was on Windows 7 the warnings stayed after importing, but as soon as you cleaned the project and then selected it and hit F5 the warnings disappeared from the Problems tab too.

@sschaef On which system did you try to reproduce?

Ok, I can reproduce the problem now with the 4.1 build. However, on the nightly build everything works as it should. @mkurz Could you please also have a look if it works in the nightly for you?

Where can I get the latest nightly?

I mean is there a packaged .zip or tar.gz file like for the stable releases?

No, there is only an update site: http://scala-ide.org/download/nightly.html

I still happens for me with the latest Nightly on my Ubuntu machine. Did not try Windows.
Whenever I hit F5 or click around a bit, open other projects, switch back to the project, open a file in the project, whatever, the warnings disappear...

reproducing...

reproducible on Windows as well. Slightly different behavior. When Project -> Build Automatically is on warnings appear and disappear after a short moment. Even errors disappear. Continuing...

"Build Automatically" was always on when I tested as well, sorry I didn't mentioned it, I thought it's the default anyway.

Matthias,
problem concerns java warning and errors only (no scala issue) when F5 I guess.
So I see that problem is when we delete java markers from java files. Scala i working correctly because markers are restored from analysis cache as well. Java part doesn't have it. I need to ponder a little on solution

Yeah, that's possible.

So unfortunately there is no good solution for sbt 0.13.6 because in this version there is no information about java compilation result available for sbt.
There is a snippet from BuildScopeUnit:

  private def resetJavaMarkers(javaFiles: Set[IFile]): Set[IFile] = {
    javaFiles.foreach { _.deleteMarkers(IJavaModelMarker.JAVA_MODEL_PROBLEM_MARKER, true, IResource.DEPTH_INFINITE) }
    javaFiles
  }

but line where markers are deleted cannot be removed. It protect us in scenario when for example scala file defines method used in java file but the visibility of this method is insufficient (is private for example). Then after a fix in scala file sbt knows that scala file needs to be rebuilt but because java hasn't be changed java file isn't. If markers weren't be removed then eclipse would still be showing that something wrong is in java file.

It seems that in 0.13.8 java is complied with reporter which can keep problems from compilation. Below is related code snippet of AggressiveCompile from 0.13.8

            val loader = ClasspathUtilities.toLoader(searchClasspath)
            timed("Java compilation", log) {
              try javac.compileWithReporter(javaSrcs.toArray, absClasspath.toArray, output, options.javacOptions.toArray, reporter, log)
              catch {
                // Handle older APIs
                case _: NoSuchMethodError =>
                  javac.compile(javaSrcs.toArray, absClasspath.toArray, output, options.javacOptions.toArray, log)
              }
            }

In 0.13.6 this guy is called only:

 javac.compile(javaSrcs.toArray, absClasspath.toArray, output, options.javacOptions.toArray, log)

I will drill it but I recommend to implement this functionality with #1002481 (Upgrade sbt to version 0.13.8)

Fix for #1002486

Solves problem with not compiled java files when they depend on scala
files. Additionally there was a problem of disappearing error markers.

Fix #1002486

Branch: master
Commit: scala-ide:fbef29a8af

Fix for #1002486

Solves problem with not compiled java files when they depend on scala
files. Additionally there was a problem of disappearing error markers.

Fix #1002486

Branch: ide-release-4.1.1
Commit: scala-ide:c19493cfb6