Your message dated Tue, 31 Dec 2013 00:33:27 +0000 with message-id <e1vxngx-0006af...@franck.debian.org> and subject line Bug#724120: fixed in cdk 1:1.2.10-5 has caused the Debian Bug report #724120, regarding cdk: FTBFS: [javac] /«PKGBUILDDIR»/build/src/extra/org/openscience/cdk/geometry/alignment/KabschAlignment.java:34: error: package Jama does not exist to be marked as done.
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--- Begin Message ---Source: cdk Version: 1:1.2.10-4 Severity: serious Tags: jessie sid User: debian...@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.
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--- Begin Message ---Source: cdk Source-Version: 1:1.2.10-5 We believe that the bug you reported is fixed in the latest version of cdk, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 724...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. tony mancill <tmanc...@debian.org> (supplier of updated cdk package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Mon, 30 Dec 2013 16:14:46 -0800 Source: cdk Binary: libcdk-java Architecture: source all Version: 1:1.2.10-5 Distribution: unstable Urgency: medium Maintainer: Debian Java Maintainers <pkg-java-maintain...@lists.alioth.debian.org> Changed-By: tony mancill <tmanc...@debian.org> Description: libcdk-java - Chemistry Development Kit (CDK) Java libraries Closes: 724120 Changes: cdk (1:1.2.10-5) unstable; urgency=medium . * Team upload. * Update Jama dependency for 1.0.3 for FTBFS bug. (Closes: #724120) * Bump Standards-Version to 3.9.5. * Use debhelper 9 instead of 7; correct debian/compat (was 5) * Update Vcs- fields to use canonical URLs. Checksums-Sha1: 7c9943cccf8a18efd597db01d4d1cff7d23ca663 2143 cdk_1.2.10-5.dsc 0805fa602fcd0a37286fe023b928910f6b6c9ab0 11901 cdk_1.2.10-5.debian.tar.gz 9428b405093bade414a4df0053459ea2b469e95a 4792388 libcdk-java_1.2.10-5_all.deb Checksums-Sha256: 0cce29ed132e526d98f5ce07e10fb4d28a16f055930b7f112fe82b847287fcbb 2143 cdk_1.2.10-5.dsc 536ffd0a1f6a77a0e29d25ac08c67b8b1a9245b0a193d03d268f4f4b9592ad3e 11901 cdk_1.2.10-5.debian.tar.gz 1a4ff1f1ad15eb0cf63d0254f7d1952a64c6c142507ba9ffa4fce227b862b93d 4792388 libcdk-java_1.2.10-5_all.deb Files: 9f9aee096418a16e3e508f1f4c722f51 2143 java optional cdk_1.2.10-5.dsc 76c700d01401f92bb988c347a09942f7 11901 java optional cdk_1.2.10-5.debian.tar.gz 6e68334c81ac5353436a123d185ddb76 4792388 java optional libcdk-java_1.2.10-5_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.15 (GNU/Linux) iQIcBAEBCgAGBQJSwg24AAoJECHSBYmXSz6WyegQAM2dH7cMoVAJlBYcKUYoIRYb AehXP+/XEfIH98nYpYvr7e2JB9YuaaYt9GC6LvLmaXE0XOwsj9dar9AUS9zn74GO ZjxxTItfbsqajZz1TNNZzXobSJPx+f03dp13Ai6RCEG1E0LdBthl+bqpQa0nutTs 1tFzaq0cZVAk3NvnufCgRsWbWgTsegr29Txi95DQ9+Wp5gzawS+BR+KAyU+fqBHj Vy0xbLLIoZ1yk+PNmQUMCtRKWOMS/+sLviAk0j29U6D6P2JFtA/vlQMccWcEkaRd fNXRkJ5jmESGHPKACLsXycLsHE2jbf0qKgsMF3LVGqy7OjuFL/8QUIhs+yFNzEjx ORPbDzykvHEMA3SzsKlVT1fGcuv/sNAXgRyMpqPOUfAYxQPCgSIdEQeJxIvK1hpA az8ad9pHmXQTiD6KtVRAF20SzRYzJ0cx+Bf48Nu+dZOWu0RqvMQYqfrRxIH/NZ/O VKuQcaTfot4fPBVx5V3trbhiCHGj7TtMEg9pUkViQ9wiYAHVIz8jj2bH1566M6gq AcnsEqBXOwVWfcQIOZhQUy7A95hWGs48/V8kRU2SmlT8yaNP/eo3F/7kS8uUK1fE glogU/nc6MP4JR04BcbuV0pH8DY1SsPjBIM2fQG6xsm1Hp4/gxcrSNorGRB8OxtY XOmlHKPiMHvbdb9YhlhX =4qXZ -----END PGP SIGNATURE-----
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