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
+}
