Your message dated Tue, 07 Feb 2023 10:50:33 +0000
with message-id <[email protected]>
and subject line Bug#1030728: fixed in biojava6-live 6.1.0+dfsg-4
has caused the Debian Bug report #1030728,
regarding Subject: FTBFS: tests fail, requiring network access
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1030728: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1030728
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: biojava6-live
Version: 6.1.0+dfsg-3
Severity: serious
Tag: ftbfs patch
Dear Maintainer,
biojava6-live currently fails to build from source with test failures:
[ERROR] Failures:
[ERROR] FileDownloadUtilsTest$URLMethods.pingGoogleOK:161 expected:
<true> but was: <false>
The attached patch disables this and another test which require network
access. With these disabled, the package built successfully.
For more details, see either the build log from reproducible builds or
when the package was synced to Ubuntu
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/biojava6-live.html
https://launchpad.net/ubuntu/+source/biojava6-live/6.1.0+dfsg-3/+build/25558013
-- System Information:
Debian Release: bookworm/sid
APT prefers unstable
APT policy: (500, 'unstable')
Architecture: amd64 (x86_64)
Kernel: Linux 6.0.0-6-amd64 (SMP w/3 CPU threads; PREEMPT)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8),
LANGUAGE=en_US:en
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
--
mvh / best regards
Hans Joachim Desserud
http://desserud.org
Description: Disable tests which require network access
Disable two tests which require network access when running.
To be honest, I don't see exactly how TestJmolSymmetryScriptGenerator ends up
calling network resources. I did see that when running the test suite with it
enabled it will send a request to https://models.rcsb.org/ presumably fetching
the models.
---
--- biojava6-live-6.1.0+dfsg.orig/biojava-core/src/test/java/org/biojava/nbio/core/util/FileDownloadUtilsTest.java
+++ biojava6-live-6.1.0+dfsg/biojava-core/src/test/java/org/biojava/nbio/core/util/FileDownloadUtilsTest.java
@@ -12,6 +12,7 @@ import java.io.FileOutputStream;
import java.io.IOException;
import java.nio.file.Files;
+import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
@@ -156,6 +157,7 @@ class FileDownloadUtilsTest {
class URLMethods {
final String availableUrl = "https://www.google.com";;
+ @Disabled("Requires network access")
@Test
void pingGoogleOK(){
assertTrue(FileDownloadUtils.ping(availableUrl, 1000));
--- biojava6-live-6.1.0+dfsg.orig/biojava-structure-gui/src/test/java/org/biojava/nbio/structure/symmetry/TestJmolSymmetryScriptGenerator.java
+++ biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/test/java/org/biojava/nbio/structure/symmetry/TestJmolSymmetryScriptGenerator.java
@@ -39,6 +39,7 @@ import org.biojava.nbio.structure.symmet
import org.biojava.nbio.structure.symmetry.core.SymmetryPerceptionMethod;
import org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorDn;
import org.junit.Before;
+import org.junit.Ignore;
import org.junit.Test;
/**
@@ -50,6 +51,7 @@ public class TestJmolSymmetryScriptGener
public void setUp() {
}
+ @Ignore
@Test
public void testPolygon() throws IOException, StructureException {
Structure struc = StructureIO.getStructure("4hhb");
@@ -64,4 +66,4 @@ public class TestJmolSymmetryScriptGener
String expected = "draw polyhedronD30 line{30.02,-39.95,0.59}{29.24,-0.53,40.00}{30.02,38.89,0.59}{30.80,-0.53,-38.82}{30.02,-39.95,0.59}{-30.00,-39.95,-0.60}{-30.79,-0.53,38.81}{-30.00,38.89,-0.60}{-29.22,-0.53,-40.01}{-30.00,-39.95,-0.60}width 0.45 color [x42ffd9] off;draw polyhedronD31 line{29.24,-0.53,40.00}{-30.79,-0.53,38.81}width 0.45 color [x42ffd9] off;draw polyhedronD32 line{30.02,38.89,0.59}{-30.00,38.89,-0.60}width 0.45 color [x42ffd9] off;draw polyhedronD33 line{30.80,-0.53,-38.82}{-29.22,-0.53,-40.01}width 0.45 color [x42ffd9] off;";
assertEquals(expected, poly);
}
-}
\ No newline at end of file
+}
--- End Message ---
--- Begin Message ---
Source: biojava6-live
Source-Version: 6.1.0+dfsg-4
Done: Pierre Gruet <[email protected]>
We believe that the bug you reported is fixed in the latest version of
biojava6-live, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Pierre Gruet <[email protected]> (supplier of updated biojava6-live package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 07 Feb 2023 10:14:19 +0100
Source: biojava6-live
Architecture: source
Version: 6.1.0+dfsg-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Pierre Gruet <[email protected]>
Closes: 1030728
Changes:
biojava6-live (6.1.0+dfsg-4) unstable; urgency=medium
.
* Excluding two more tests accessing the network during build-time tests,
thanks to Hans Joachim Desserud! (Closes: #1030728)
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