Help needed for Artemis

[Andreas Tille <andreas@an3as.eu>]

Hi,

I try to build the latest version of Artemis[1] but when I try
to build the current state in Git I get:

...
CLASSPATH=/usr/share/java/biojava.jar:/usr/share/java/j2ssh-core.jar:/usr/share/java/ibatis.jar:/usr/share/java/log4j-1.2.jar:/usr/share/java/postgresql-jdbc3.jar:/usr/share/java/picard.jar:/usr/share/java/htsjdk.jar:/usr/share/java/commons-net.jar:/usr/share/java/commons-lang3.jar:/usr/share/java/batik-all.jar:/usr/share/java/batik-awt-util.jar:/usr/share/java/batik-dom.jar:/usr/share/java/batik-ext.jar:/usr/share/java/batik-svggen.jar:/usr/share/java/batik-util.jar:/usr/share/java/batik-xml.jar:/usr/share/EMBOSS/jemboss/lib/jemboss.jar:/build/artemis-17.0.1+dfsg javac -source 1.8 -target 1.8   uk/ac/sanger/artemis/MegaBlastComparisonData.java
warning: [options] bootstrap class path not set in conjunction with -source 8
/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
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
2 errors
2 warnings
...

Any help would be welcome.

Kind regards

      Andreas.

[1] https://salsa.debian.org/med-team/artemis

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