Bug#849025: marked as done (jalview: FTBFS: error: cannot find symbol EnumCallback)

[Debian Bug Tracking System]

Your message dated Sun, 07 Feb 2021 06:33:21 +
with message-id 
and subject line Bug#849025: fixed in jalview 2.11.1.3+dfsg2-1
has caused the Debian Bug report #849025,
regarding jalview: FTBFS: error: cannot find symbol EnumCallback
to be marked as done.

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849025: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=849025
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--- Begin Message ---
Source: jalview
Version: 2.7.dfsg-5
Severity: serious
Justification: fails to build from source
User: reproducible-bui...@lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-b...@lists.alioth.debian.org

Dear Maintainer,

jalview fails to build from source in unstable/amd64:

  […]

  [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:952: 
error: cannot find symbol
  [javac]   public void notifyCallback(EnumCallback type, Object[] data)
  [javac]  ^
  [javac]   symbol:   class EnumCallback
  [javac]   location: class JalviewJmolBinding
  [javac] «BUILDDIR»/src/jalview/ext/jmol/JalviewJmolBinding.java:1006: 
error: cannot find symbol
  [javac]   public boolean notifyEnabled(EnumCallback callbackPick)
  [javac]^
  [javac]   symbol:   class EnumCallback
  [javac]   location: class JalviewJmolBinding
  [javac] «BUILDDIR»/src/jalview/ws/EnfinEnvision2OneWay.java:67: error: 
package com.lowagie.text.html does not exist
  [javac] import com.lowagie.text.html.HtmlEncoder;
  [javac] ^
  [javac] «BUILDDIR»/src/jalview/ws/rest/params/SeqVector.java:37: error: 
cannot find symbol
  [javac] import org.jmol.util.ArrayUtil;
  [javac] ^
  [javac]   symbol:   class ArrayUtil
  [javac]   location: package org.jmol.util
  [javac] «BUILDDIR»/src/jalview/appletgui/AppletJmol.java:32: error: 
cannot find symbol
  [javac] import org.jmol.viewer.JmolConstants;
  [javac]   ^
  [javac]   symbol:   class JmolConstants
  [javac]   location: package org.jmol.viewer
  [javac] «BUILDDIR»/src/jalview/appletgui/AppletJmolBinding.java:30: 
error: cannot find symbol
  [javac] import org.jmol.popup.JmolPopup;
  [javac]  ^
  [javac]   symbol:   class JmolPopup
  [javac]   location: package org.jmol.popup
  [javac] «BUILDDIR»/src/jalview/bin/Jalview.java:756: warning: non-varargs 
call of varargs method with inexact argument type for last parameter;
  [javac] gbcons = gbindingc.getConstructor(null);
  [javac]   ^
  [javac]   cast to Class for a varargs call
  [javac]   cast to Class[] for a non-varargs call and to suppress this 
warning
  [javac] «BUILDDIR»/src/jalview/bin/Jalview.java:757: warning: non-varargs 
call of varargs method with inexact argument type for last parameter;
  [javac] gbinding = gbcons.newInstance(null);
  [javac]   ^
  [javac]   cast to Object for a varargs call
  [javac]   cast to Object[] for a non-varargs call and to suppress this 
warning
  [javac] «BUILDDIR»/src/jalview/gui/Desktop.java:2177: warning: 
non-varargs call of varargs method with inexact argument type for last 
parameter;
  [javac]   Constructor gccons = gcClass.getConstructor(null);
  [javac]   ^
  [javac]   cast to Class for a varargs call
  [javac]   cast to Class[] for a non-varargs call and to suppress this 
warning
  [javac] «BUILDDIR»/src/jalview/gui/Desktop.java:2181: warning: 
non-varargs call of varargs method with inexact argument type for last 
parameter;
  [javac]   java.lang.reflect.Method run = gcClass.getMethod("run", 
null);
  [javac]   ^
  [javac]   cast to Class for a varargs call
  [javac]   cast to Class[] for a non-varargs call and to suppress this 
warning
  [javac] «BUILDDIR»/src/jalview/gui/Desktop.java:2182: warning: 
non-varargs call of varargs method with inexact argument type for last 
parameter;
  [javac]   Object gc = gccons.newInstance(null);
  [javac]  ^
  [javac]   cast to Object for a varargs call
  [javac]   cast to Object[] for a non-varargs call and to suppress this 
warning
  [javac] «BUILDDIR»/src/jalview/gui/Desktop.java:2185: warning: 
non-varargs call of varargs method 

jalview_2.11.1.3+dfsg2-1_source.changes ACCEPTED into unstable

[Debian FTP Masters]

Accepted:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Sat, 06 Feb 2021 23:04:36 +0100
Source: jalview
Architecture: source
Version: 2.11.1.3+dfsg2-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Java Maintainers 

Changed-By: Pierre Gruet 
Closes: 849025 897294
Changes:
 jalview (2.11.1.3+dfsg2-1) unstable; urgency=medium
 .
   [ Pierre Gruet ]
   * New upstream version (Closes: #849025)
   * New uploader (Closes: #897294)
   * Using version 4 in d/watch to remove files
   * Using secure URI in d/watch
   * Switching from cdbs to dh
   * Depending on debhelper-compat 13
   * Making the build with Maven instead of upstream's gradle
   * Removing call to classgraph, not needed for a Debian run
   * Updating build-dependencies list and d/jalview.classpath
   * Modifying the jar launcher by setting properly the jar manifest
   * Updating Vcs-* and Homepage fields in d/control
   * Refreshing d/copyright
   * Bump Standards version to 4.5.1:
 - Providing a FreeDesktop entry instead of former menu entry
 - Rules-Requires-Root: no
 - Using the https form of the copyright-format URL
   * Updating manpage
   * Deactivating Google Analytics, using a non-packaged and improperly
 licensed software
   * Adding Mime types in d/jalview.desktop and d/jalview-mime.xml
   * Adding autopkgtests
   * Integrating the patch of upstream to control the way the web services are
 launched
 .
   [ Steffen Moeller ]
   * Reintroduced debian/upstream/edam file
   * Created debian/upstream/metadata
 - references to papers
 - references to registries
   * Added prior forgotten PMID in metadata
   * d/u/metadata: syntax fixed(?) and URLs added
   * Added ref to conda, RRID->SciCrunch
 .
   [ Andreas Tille ]
   * d/rules: enforce LC_ALL=C.UTF-8 to cope with UTF-8 characters
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jalview_2.11.1.3+dfsg2-1.debian.tar.xz
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ecj_3.16.0-1~bpo9+1_source.changes ACCEPTED into stretch-backports->backports-policy

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Accepted:

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Hash: SHA256

Format: 1.8
Date: Sun, 07 Feb 2021 00:25:51 +0100
Source: ecj
Binary: ecj libecj-java
Architecture: source
Version: 3.16.0-1~bpo9+1
Distribution: stretch-backports
Urgency: medium
Maintainer: Debian Java Maintainers 

Changed-By: Emmanuel Bourg 
Description:
 ecj- standalone version of the Eclipse Java compiler
 libecj-java - Eclipse Java compiler (library)
Changes:
 ecj (3.16.0-1~bpo9+1) stretch-backports; urgency=medium
 .
   * Rebuild for stretch-backports.
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Bug#973135: Bug#973070: libsis-base-java: FTBFS: Could not delete the directory targets/unit-test-wd/ch.syst

[Ivo De Decker]

Hi,

On Thu, Oct 29, 2020 at 03:24:29PM +0100, Markus Koschany wrote:
> Am 29.10.20 um 15:11 schrieb Andreas Tille:
> > Hi,
> > 
> > here is a suggested patch for commons-io that would prevent making the
> > test in libsis-base-java fail.
> 
> It seems this is a six year old unresolved upstream bug.
> 
> https://issues.apache.org/jira/browse/IO-449
> 
> This should be fixed upstream in my opinion and not only in Debian. Other
> projects may rely exactly on that behavior.

Given that there is no clear consensus about what the exact behaviour should
be, I guess it's probably best to disable this test for now. I can confirm
that just commenting out the 2 tests in
src/test/java/org/codehaus/plexus/components/io/attributes/SymlinkUtilsTest.java
fixes the build.

As a side node: it seems that some of the builds succeed in the
reproducible-builds tests, while others do not. So the issue doesn't show up
in all cases. Maybe it's related to the type of filesystem used.

https://tests.reproducible-builds.org/debian/history/plexus-io.html

Cheers,

Ivo

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