[Debian-med-packaging] Bug#849929: Time to remove biojava3 ? [was: Bug#849929: biojava3-live: FTBFS (error: cannot find symbol)]

[Andreas Tille]

Hi,

since we hae biojava 4 (and legacy biojava 1) I think it is time to
remove biojava 3.  Anybody who insists in keeping it please provide a
patch to solve this bug.

Kind regards

     Andreas.

----- Forwarded message from Santiago Vila <sanvila at debian.org> -----

Date: Mon, 02 Jan 2017 12:01:21 +0000
From: Santiago Vila <sanvila at debian.org>
To: Debian BTS <submit at bugs.debian.org>
Subject: Bug#849929: biojava3-live: FTBFS (error: cannot find symbol)
X-Debian-PR-Message: report 849929
X-Debian-PR-Package: src:biojava3-live
X-Debian-PR-Keywords: 
X-Debian-PR-Source: biojava3-live

Package: src:biojava3-live
Version: 3.1.0+dfsg-2
Severity: serious

Dear maintainer:

I tried to build this package in stretch with "dpkg-buildpackage -A"
(which is what the "Arch: all" autobuilder would do to build it)
but it failed:

--------------------------------------------------------------------------------
[...]
 debian/rules build-indep
dh build-indep  --with javahelper
dh: Compatibility levels before 9 are deprecated (level 8 in use)
   dh_testdir -i
   dh_update_autotools_config -i
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/biojava3-live-3.1.0+dfsg'
dh_auto_configure
dh_auto_configure: Compatibility levels before 9 are deprecated (level 8 in use)
sed -e 's/BJLIB/biojava3-forester/g' debian/build.xml > biojava3-forester/build.xml
sed -e 's/BJLIB/biojava3-aa-prop/g' debian/build.xml > biojava3-aa-prop/build.xml
sed -e 's/BJLIB/biojava3-core/g' debian/build.xml > biojava3-core/build.xml
sed -e 's/BJLIB/biojava3-alignment/g' debian/build.xml > biojava3-alignment/build.xml

[... snipped ...]

    [javac]   location: class AsaCalculator
    [javac] /<<BUILDDIR>>/biojava3-live-3.1.0+dfsg/biojava3-structure/src/main/java/org/biojava/bio/structure/asa/AsaCalculator.java:256: error: cannot find symbol
    [javac] 	    Point3d[] points = new Point3d[nSpherePoints];
    [javac] 	                           ^
    [javac]   symbol:   class Point3d
    [javac]   location: class AsaCalculator
    [javac] /<<BUILDDIR>>/biojava3-live-3.1.0+dfsg/biojava3-structure/src/main/java/org/biojava/bio/structure/asa/AsaCalculator.java:263: error: cannot find symbol
    [javac] 	        points[k] = new Point3d(Math.cos(phi)*r, y, Math.sin(phi)*r);
    [javac] 	                        ^
    [javac]   symbol:   class Point3d
    [javac]   location: class AsaCalculator
    [javac] /<<BUILDDIR>>/biojava3-live-3.1.0+dfsg/biojava3-structure/src/main/java/org/biojava/bio/structure/asa/AsaCalculator.java:307: error: cannot find symbol
    [javac]         for (Point3d point: spherePoints){
    [javac]              ^
    [javac]   symbol:   class Point3d
    [javac]   location: class AsaCalculator
    [javac] /<<BUILDDIR>>/biojava3-live-3.1.0+dfsg/biojava3-structure/src/main/java/org/biojava/bio/structure/asa/AsaCalculator.java:309: error: cannot find symbol
    [javac]             Point3d test_point = new Point3d(point.x*radius + atom_i.getX(),
    [javac]             ^
    [javac]   symbol:   class Point3d
    [javac]   location: class AsaCalculator
    [javac] /<<BUILDDIR>>/biojava3-live-3.1.0+dfsg/biojava3-structure/src/main/java/org/biojava/bio/structure/asa/AsaCalculator.java:309: error: cannot find symbol
    [javac]             Point3d test_point = new Point3d(point.x*radius + atom_i.getX(),
    [javac]                                      ^
    [javac]   symbol:   class Point3d
    [javac]   location: class AsaCalculator
    [javac] /<<BUILDDIR>>/biojava3-live-3.1.0+dfsg/biojava3-structure/src/main/java/org/biojava/bio/structure/asa/AsaCalculator.java:327: error: cannot find symbol
    [javac]                 double diff_sq = test_point.distanceSquared(new Point3d(atom_j.getCoords()));
    [javac]                                                                 ^
    [javac]   symbol:   class Point3d
    [javac]   location: class AsaCalculator
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 10 errors

BUILD FAILED
/<<BUILDDIR>>/biojava3-live-3.1.0+dfsg/biojava3-structure/build.xml:72: Compile failed; see the compiler error output for details.

Total time: 10 seconds
debian/rules:28: recipe for target 'override_dh_auto_build' failed
make[1]: *** [override_dh_auto_build] Error 1
make[1]: Leaving directory '/<<BUILDDIR>>/biojava3-live-3.1.0+dfsg'
debian/rules:10: recipe for target 'build-indep' failed
make: *** [build-indep] Error 2
dpkg-buildpackage: error: debian/rules build-indep gave error exit status 2
--------------------------------------------------------------------------------

The relevant part of the build log is included above.

If this is really a bug in one of the build-depends, please use reassign and affects,
so that this is still visible in the page for this package.

If you could not reproduce this using sbuild on a single CPU virtual machine (as I did),
please do not downgrade or mark as unreproducible, I would then consider giving you access
to a virtual machine on which I can reproduce it so that you can as well.
(In such case, please contact me off-list for details).

Thanks.

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