[Debian-med-packaging] Bug#795685: Bug#795685: biojava4-live: FTBFS: UnknownHostException: eutils.ncbi.nlm.nih.gov

[olivier.sallou at codeless.fr]

On 08/16/2015 11:28 AM, Chris West (Faux) wrote:
> Source: biojava4-live
> Version: 4.1.0+dfsg-1
> Severity: serious
> Justification: fails to build from source
> Tags: sid stretch
> User: reproducible-builds at lists.alioth.debian.org
> Usertags: ftbfs
> X-Debbugs-CC: reproducible-builds at lists.alioth.debian.org
>
> Dear Maintainer,
>
> The package fails to build without networking, which we believe is a
> policy violation.  Ubuntu may have a patch, as they also enforce this:
>
>     [junit] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest
>     [junit] Testsuite: org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest
>     [junit] Tests run: 16, Failures: 0, Errors: 8, Skipped: 0, Time elapsed: 0.095 sec
>     [junit] Tests run: 16, Failures: 0, Errors: 8, Skipped: 0, Time elapsed: 0.095 sec
>     [junit] ------------- Standard Error -----------------
>     [junit] SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
>     [junit] SLF4J: Defaulting to no-operation (NOP) logger implementation
>     [junit] SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
>     [junit] ------------- ---------------- ---------------
>     [junit] 
>     [junit] Testcase: testProteinSequenceFactoring[0] took 0.038 sec
>     [junit] 	Caused an ERROR
>     [junit] eutils.ncbi.nlm.nih.gov
>     [junit] java.net.UnknownHostException: eutils.ncbi.nlm.nih.gov
>     [junit] 	at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:178)
> ...
>     [junit] 	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1301)
>     [junit] 	at org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader.getEutilsInputStream(GenbankProxySequenceReader.java:141)
>     [junit] 	at org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader.getBufferedInputStream(GenbankProxySequenceReader.java:109)
>     [junit] 	at org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader.<init>(GenbankProxySequenceReader.java:83)
>     [junit] 	at org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest.testProteinSequenceFactoring(GenbankProxySequenceReaderTest.java:84)
>     [junit] 
>     [junit] Testcase: testFeatures[0] took 0 sec
>     [junit] Testcase: testProteinSequenceFactoring[1] took 0.001 sec
>     [junit] 	Caused an ERROR
>     [junit] eutils.ncbi.nlm.nih.gov
>     [junit] java.net.UnknownHostException: eutils.ncbi.nlm.nih.gov
Thanks for the report. I already disabled some network tests, those ones
are certainly new "remote" tests introduced in this release.
I gonna patch this soon.
>
> -- System Information:
> Debian Release: stretch/sid
> APT prefers unstable
> APT policy: (500, 'unstable')
> Architecture: amd64 (x86_64)
>
> Kernel: Linux 3.19.0-23-generic (SMP w/8 CPU cores)
> Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
> Shell: /bin/sh linked to /bin/dash
> Init: systemd (via /run/systemd/system)
>
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> -- 
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