[Debian-med-packaging] Bug#893184: artemis FTBFS with openjdk-9

[Andreas Tille]

Hi,

On Sat, Mar 17, 2018 at 10:27:38AM +0200, Adrian Bunk wrote:
> Source: artemis
> Version: 16.0.17+dfsg-3
> Severity: serious

I injected Artemis 17.0.1 into Git which seems to fix this issue.

Unfortunately there are other Build problems:

...
/build/artemis-17.0.1+dfsg/uk/ac/sanger/artemis/j2ssh/SshFileManager.java:437: warning: [removal] destroy() in Thread has been deprecated and marked for removal
    public void destroy()
                ^
/build/artemis-17.0.1+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:565: error: cannot find symbol
      FTPSeekableStream fss = new FTPSeekableStream(new URL(alignmentFile), ftpSocketTimeout);
      ^
  symbol:   class FTPSeekableStream
  location: class BamView
/build/artemis-17.0.1+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:565: error: cannot find symbol
      FTPSeekableStream fss = new FTPSeekableStream(new URL(alignmentFile), ftpSocketTimeout);
                                  ^
  symbol:   class FTPSeekableStream
  location: class BamView
/build/artemis-17.0.1+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:4204: error: cannot find symbol
            (sam.isSecondaryAlignment() ? "yes" : "no"), Level.DEBUG);
                ^
  symbol:   method isSecondaryAlignment()
  location: variable sam of type SAMRecord
...


I suspect these are compatibility issues with latest samtools.

Could somebody more familiar with this like me please have a look.

Kind regards

       Andreas.

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