Perhaps some final problems to update fastqc? (Was: libsis-jhdf5-java_14.12.1-1_amd64.changes ACCEPTED into unstable, unstable)
Hi Olivier,
yes I noticed that this package appeared in unstable and I was just
trying to build. Unfortunately some build errors are remaining:
init:
[mkdir] Created dir: /build/fastqc-0.11.4+dfsg/bin
[copy] Copying 78 files to /build/fastqc-0.11.4+dfsg/bin
build-project:
[echo] FastQC: /build/fastqc-0.11.4+dfsg/build.xml
[javac] Compiling 72 source files to /build/fastqc-0.11.4+dfsg/bin
[javac] warning: [options] bootstrap class path not set in conjunction with -source 1.5
[javac] /build/fastqc-0.11.4+dfsg/uk/ac/babraham/FastQC/FastQCMenuBar.java:39: error: duplicate class: uk.ac.babraham.FastQC.FastQCMenuBar
[javac] public class FastQCMenuBar extends JMenuBar implements ActionListener {
[javac] ^
[javac] /build/fastqc-0.11.4+dfsg/uk/ac/babraham/FastQC/Modules/AdapterContent.java:46: error: duplicate class: uk.ac.babraham.FastQC.Modules.AdapterContent
[javac] public class AdapterContent extends AbstractQCModule {
[javac] ^
[javac] /build/fastqc-0.11.4+dfsg/uk/ac/babraham/FastQC/Modules/ModuleConfig.java:33: error: duplicate class: uk.ac.babraham.FastQC.Modules.ModuleConfig
[javac] public class ModuleConfig {
[javac] ^
[javac] /build/fastqc-0.11.4+dfsg/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.java:33: error: duplicate class: uk.ac.babraham.FastQC.Sequence.Contaminant.ContaminentFinder
[javac] public class ContaminentFinder {
[javac] ^
[javac] /build/fastqc-0.11.4+dfsg/uk/ac/babraham/FastQC/Sequence/Fast5File.java:25: error: package ch.systemsx.cisd.hdf5 does not exist
[javac] import ch.systemsx.cisd.hdf5.HDF5Factory;
[javac] ^
[javac] /build/fastqc-0.11.4+dfsg/uk/ac/babraham/FastQC/Sequence/Fast5File.java:26: error: package ch.systemsx.cisd.hdf5 does not exist
[javac] import ch.systemsx.cisd.hdf5.IHDF5SimpleReader;
[javac] ^
[javac] /build/fastqc-0.11.4+dfsg/uk/ac/babraham/FastQC/Sequence/Fast5File.java:39: error: cannot find symbol
[javac] IHDF5SimpleReader reader = HDF5Factory.openForReading(file);
[javac] ^
[javac] symbol: class IHDF5SimpleReader
[javac] location: class Fast5File
[javac] /build/fastqc-0.11.4+dfsg/uk/ac/babraham/FastQC/Sequence/Fast5File.java:39: error: cannot find symbol
[javac] IHDF5SimpleReader reader = HDF5Factory.openForReading(file);
[javac] ^
[javac] symbol: variable HDF5Factory
[javac] location: class Fast5File
[javac] Note: Some input files use unchecked or unsafe operations.
[javac] Note: Recompile with -Xlint:unchecked for details.
[javac] 8 errors
[javac] 1 warning
BUILD FAILED
/build/fastqc-0.11.4+dfsg/build.xml:36: Compile failed; see the compiler error output for details.
May be I did something worng (Git repository is updated)?
Kind regards
Andreas.
On Wed, Nov 25, 2015 at 01:03:15PM +0100, Olivier Sallou wrote:
>
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA256
>
> It has been accepted, I think it is the dependency you were waiting for.
>
> Olivier
>
>
> - -------- Forwarded Message --------
> Subject: [Debian-med-packaging]
> libsis-jhdf5-java_14.12.1-1_amd64.changes ACCEPTED into unstable, unstable
> Date: Wed, 25 Nov 2015 12:00:21 +0000
> From: Debian FTP Masters <ftpmaster@ftp-master.debian.org>
> To: Debian Med Packaging Team
> <debian-med-packaging@lists.alioth.debian.org>, Tim Booth
> <tbooth@ceh.ac.uk>, osallou@debian.org
>
>
>
>
> Accepted:
>
> Format: 1.8
> Date: Wed, 12 Aug 2015 12:15:17 +0100
> Source: libsis-jhdf5-java
> Binary: libsis-jhdf5-java libsis-jhdf5-jni
> Architecture: source all amd64
> Version: 14.12.1-1
> Distribution: unstable
> Urgency: medium
> Maintainer: Debian Med Packaging Team
> <debian-med-packaging@lists.alioth.debian.org>
> Changed-By: Tim Booth <tbooth@ceh.ac.uk>
> Description:
> libsis-jhdf5-java - easy-to-use HDF library for Java
> libsis-jhdf5-jni - native libs used by libsis-jhdf5-java package
> Closes: 796390
> Changes:
> libsis-jhdf5-java (14.12.1-1) unstable; urgency=medium
> .
> * [ Team upload ]
> First package (Closes: #796390 ).
> Checksums-Sha1:
> ab5a30f35ff1d3f5a2948e3bc23b80e22e15f59f 2301
> libsis-jhdf5-java_14.12.1-1.dsc
> e750632f427b3edd6c020bc52eaf737847660d65 794418
> libsis-jhdf5-java_14.12.1.orig.tar.gz
> 492a82861499e8887011a927fc5448dfe9d0bebd 7336
> libsis-jhdf5-java_14.12.1-1.debian.tar.xz
> 6e72879348243f3b81252a478b9c9f85dde3889a 1299712
> libsis-jhdf5-java_14.12.1-1_all.deb
> 1215ae0d7580b3da8dfa800e91b42cef81bfb3c7 111604
> libsis-jhdf5-jni_14.12.1-1_amd64.deb
> Checksums-Sha256:
> 8849563cfd2b05203b9be79728a3d34908a51010145887b928e7846f05282563 2301
> libsis-jhdf5-java_14.12.1-1.dsc
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> libsis-jhdf5-java_14.12.1.orig.tar.gz
> ebbef40be5eec08d9ee71c325ad5ee69e9609bb72e5d543acb37fa802fc040d1 7336
> libsis-jhdf5-java_14.12.1-1.debian.tar.xz
> f434e1c50e0a1e58d9d85857b53ee7e823a22b83f3c2578fae65ca8003767611
> 1299712 libsis-jhdf5-java_14.12.1-1_all.deb
> 2c3d9f7d4b15f39e093821b4455c195837dc276858623d45466b71a0ed32638b 111604
> libsis-jhdf5-jni_14.12.1-1_amd64.deb
> Files:
> be92381750029b9e20c42e7c94c3ab3f 2301 java optional
> libsis-jhdf5-java_14.12.1-1.dsc
> 940dacb9f9c44d9c54d8b2a32c70a349 794418 java optional
> libsis-jhdf5-java_14.12.1.orig.tar.gz
> a188a8967a158ae6908b8a1bfc79efa4 7336 java optional
> libsis-jhdf5-java_14.12.1-1.debian.tar.xz
> dbd570e561c06da46239022636161cf9 1299712 java optional
> libsis-jhdf5-java_14.12.1-1_all.deb
> ebb4c9d42cb90b73743c3f8967197d95 111604 java optional
> libsis-jhdf5-jni_14.12.1-1_amd64.deb
>
>
>
> Thank you for your contribution to Debian.
>
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