Bug#724120: cdk: FTBFS: [javac] /«PKGBUILDDIR»/build/src/extra/org/openscience/cdk/geometry/alignment/KabschAlignment.java:34: error: package Jama does not exist

[David Suárez]

Source: cdk
Version: 1:1.2.10-4
Severity: serious
Tags: jessie sid
User: debian-qa at lists.debian.org
Usertags: qa-ftbfs-20130922 qa-ftbfs
Justification: FTBFS on amd64

Hi,

During a rebuild of all packages in sid, your package failed to build on
amd64.

Relevant part (hopefully): 
> compile-module:
>      [echo] Compiling classes for CDK's extra module from src/main...
>      [echo] Datafiles defined: true
>      [echo] Extra files defined: ${module.extrafiles.present}
>      [echo] CDK dependencies defined: true
>      [echo] Library dependencies defined: true
>      [echo] Developer Library dependencies defined: ${module.devellibdepends.present}
>      [echo] Autogenerated files specified: ${module.autogenerated.present}
>     [mkdir] Created dir: /«PKGBUILDDIR»/build/src/extra
>     [mkdir] Created dir: /«PKGBUILDDIR»/build/extra
>      [copy] Copying 79 files to /«PKGBUILDDIR»/build/src/extra
>     [javac] Compiling 79 source files to /«PKGBUILDDIR»/build/extra
>     [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.5
>     [javac] /«PKGBUILDDIR»/build/src/extra/org/openscience/cdk/geometry/alignment/KabschAlignment.java:34: error: package Jama does not exist
>     [javac] import Jama.EigenvalueDecomposition;
>     [javac]            ^
>     [javac] /«PKGBUILDDIR»/build/src/extra/org/openscience/cdk/geometry/alignment/KabschAlignment.java:35: error: package Jama does not exist
>     [javac] import Jama.Matrix;
>     [javac]            ^
>     [javac] /«PKGBUILDDIR»/build/src/extra/org/openscience/cdk/geometry/alignment/KabschAlignment.java:290: error: cannot find symbol
>     [javac]         Matrix tmp;
>     [javac]         ^
>     [javac]   symbol:   class Matrix
>     [javac]   location: class KabschAlignment
>     [javac] /«PKGBUILDDIR»/build/src/extra/org/openscience/cdk/geometry/alignment/KabschAlignment.java:329: error: cannot find symbol
>     [javac]         tmp = new Matrix(tR);
>     [javac]                   ^
>     [javac]   symbol:   class Matrix
>     [javac]   location: class KabschAlignment
>     [javac] /«PKGBUILDDIR»/build/src/extra/org/openscience/cdk/geometry/alignment/KabschAlignment.java:335: error: cannot find symbol
>     [javac]         Matrix jamaR = new Matrix(R);
>     [javac]         ^
>     [javac]   symbol:   class Matrix
>     [javac]   location: class KabschAlignment
>     [javac] /«PKGBUILDDIR»/build/src/extra/org/openscience/cdk/geometry/alignment/KabschAlignment.java:335: error: cannot find symbol
>     [javac]         Matrix jamaR = new Matrix(R);
>     [javac]                            ^
>     [javac]   symbol:   class Matrix
>     [javac]   location: class KabschAlignment
>     [javac] /«PKGBUILDDIR»/build/src/extra/org/openscience/cdk/geometry/alignment/KabschAlignment.java:340: error: cannot find symbol
>     [javac]         Matrix jamaRtR = new Matrix(RtR);
>     [javac]         ^
>     [javac]   symbol:   class Matrix
>     [javac]   location: class KabschAlignment
>     [javac] /«PKGBUILDDIR»/build/src/extra/org/openscience/cdk/geometry/alignment/KabschAlignment.java:340: error: cannot find symbol
>     [javac]         Matrix jamaRtR = new Matrix(RtR);
>     [javac]                              ^
>     [javac]   symbol:   class Matrix
>     [javac]   location: class KabschAlignment
>     [javac] /«PKGBUILDDIR»/build/src/extra/org/openscience/cdk/geometry/alignment/KabschAlignment.java:341: error: cannot find symbol
>     [javac]         EigenvalueDecomposition ed = jamaRtR.eig();
>     [javac]         ^
>     [javac]   symbol:   class EigenvalueDecomposition
>     [javac]   location: class KabschAlignment
>     [javac] /«PKGBUILDDIR»/build/src/extra/org/openscience/cdk/validate/BasicValidator.java:321: warning: [deprecation] getBondOrderSum(IAtom) in AtomContainer has been deprecated
>     [javac]             int bos = (int)molecule.getBondOrderSum(atom);
>     [javac]                                    ^
>     [javac] Note: Some input files use unchecked or unsafe operations.
>     [javac] Note: Recompile with -Xlint:unchecked for details.
>     [javac] 9 errors
>     [javac] 2 warnings
> 
> BUILD FAILED
> /«PKGBUILDDIR»/build.xml:529: The following error occurred while executing this line:
> /«PKGBUILDDIR»/build.xml:367: Compile failed; see the compiler error output for details.
> 
> Total time: 41 seconds
> make: *** [debian/stamp-ant-build] Error 1

The full build log is available from:
   http://aws-logs.debian.net/ftbfs-logs/2013/09/22/cdk_1.2.10-4_unstable.log

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.