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 <sanv...@debian.org> -----
Date: Mon, 02 Jan 2017 12:01:21 +0000
From: Santiago Vila <sanv...@debian.org>
To: Debian BTS <sub...@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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----- End forwarded message -----
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