[Debian-med-packaging] Bug#696947: biojava3-live: FTBFS without Internet access

[Ilya Barygin]

Package: biojava3-live
Version: 3.0.5-1
Severity: serious
Tags: upstream
Justification: fails to build from source (but built successfully in the past)

biojava3-live fails to build without Internet access. One of the tests fails:

test:
    [junit] Running org.biojava3.ronn.JronnTest
    [junit] Testsuite: org.biojava3.ronn.JronnTest
    [junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 2.203 sec
    [junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 2.203 sec
    [junit] 
    [junit] Testcase: verifyRanges took 2.192 sec
    [junit] Running org.biojava3.ronn.NonstandardProteinCompoundTest
    [junit] Testsuite: org.biojava3.ronn.NonstandardProteinCompoundTest
    [junit] Tests run: 1, Failures: 1, Errors: 0, Time elapsed: 0.042 sec
    [junit] Tests run: 1, Failures: 1, Errors: 0, Time elapsed: 0.042 sec
    [junit] ------------- Standard Error -----------------
    [junit] Dec 06, 2012 5:15:54 PM org.biojava3.core.sequence.loader.UniprotProxySequenceReader getUniprotXML
    [junit] INFO: Loading http://www.uniprot.org/uniprot/?query=O30642&format=xml
    [junit] java.net.UnknownHostException: www.uniprot.org
    [junit] 	at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:178)
[...]

Build logs can be found at
https://launchpad.net/ubuntu/+source/biojava3-live/3.0.5-1

-- System Information:
Debian Release: wheezy/sid
  APT prefers quantal-updates
  APT policy: (500, 'quantal-updates'), (500, 'quantal-security'), (500, 'quantal-proposed'), (500, 'quantal'), (100, 'quantal-backports')
Architecture: i386 (i686)

Kernel: Linux 3.5.0-21-generic (SMP w/2 CPU cores)
Locale: LANG=ru_RU.UTF-8, LC_CTYPE=ru_RU.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash