java.net.SocketException: Network is unreachable (Eclipse on Windows 8)

Question

I am having problems with running my code by using Eclipse on Windows 8. The code below runs smoothly in Eclipse on Linux but not in Windows 8.

    package first

    import org.biojava.bio.structure.Atom
    import org.biojava.bio.structure.Structure
    import org.biojava.bio.structure.StructureTools
    import org.biojava.bio.structure.align.StructureAlignment
    import org.biojava.bio.structure.align.StructureAlignmentFactory
    import org.biojava.bio.structure.align.fatcat.FatCatRigid
    import org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
    import org.biojava.bio.structure.align.gui.StructureAlignmentDisplay
    import org.biojava.bio.structure.align.model.AFPChain
    import org.biojava.bio.structure.align.util.AtomCache
    import org.biojava.bio.structure.gui.BiojavaJmol
    import org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol

    object Alignment {

      def main(args: Array[String]){

          val name1 = "1YYO.A"
          val name2 = "1YYW.A"
          val cache = new AtomCache()
          val algorithm = StructureAlignmentFactory.getAlgorithm(FatCatRigid.algorithmName)
          val ca1: Array[Atom] = StructureTools.getAtomCAArray(cache.getStructure(name1))
          val ca2: Array[Atom] = StructureTools.getAtomCAArray(cache.getStructure(name2))
          val params: FatCatParameters = new FatCatParameters()
          val afpchain: AFPChain = algorithm.align(ca1, ca2, params)
          afpchain.setName1(name1)
          afpchain.setName2(name2)
          println(afpchain.toFatcat(ca1,ca2))
          StructureAlignmentDisplay.display(afpchain, ca1, ca2)

      }
    }

Basically getStructure method tries to download the PDB file but it fails and gives the error below.

Problem while downloading PDB ID 1yyo from FTP server.
Failed URL: ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/yy/pdb1yyo.ent.gz
java.net.SocketException: Network is unreachable: connect
    at java.net.TwoStacksPlainSocketImpl.socketConnect(Native Method)
    at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339)
    at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200)
    at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182)
    at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:172)
    at java.net.Socket.connect(Socket.java:579)
    at java.net.Socket.connect(Socket.java:528)
    at sun.net.ftp.impl.FtpClient.openPassiveDataConnection(FtpClient.java:671)
    at sun.net.ftp.impl.FtpClient.openDataConnection(FtpClient.java:710)
    at sun.net.ftp.impl.FtpClient.getFileStream(FtpClient.java:1284)
    at sun.net.www.protocol.ftp.FtpURLConnection.getInputStream(FtpURLConnection.java:428)
    at java.net.URL.openStream(URL.java:1037)
    at org.biojava.bio.structure.io.util.FileDownloadUtils.downloadGzipCompressedFile(FileDownloadUtils.java:96)
    at org.biojava.bio.structure.io.PDBFileReader.downloadPDB(PDBFileReader.java:677)
    at org.biojava.bio.structure.io.PDBFileReader.downloadAndGetInputStream(PDBFileReader.java:795)
    at org.biojava.bio.structure.io.PDBFileReader.getInputStream(PDBFileReader.java:433)
    at org.biojava.bio.structure.io.PDBFileReader.getStructureById(PDBFileReader.java:875)
    at org.biojava.bio.structure.align.util.AtomCache.loadStructureFromPdbByPdbId(AtomCache.java:1173)
    at org.biojava.bio.structure.align.util.AtomCache.getStructure(AtomCache.java:501)
    at first.Alignment$.main(Alignment.scala:24)
    at first.Alignment.main(Alignment.scala)
problem loading:1YYO.A 

I tried to reinstall and update JDK, turned my firewall off, added -Djava.net.preferIPv4Stack=true but I still can't solve the problem. Any suggestions will be greatly appreciated. Many thanks in advance!

Answer 1

It could be the following Windows issue:

http://support.microsoft.com/kb/2754804

That one is for Windows 7, not sure if it works the same for Windows 8.