FastQC preconditions should be there but it does not build (Perhaps some final problems to update fastqc? (Was: libsis-jhdf5-java_14.12.1-1_amd64.changes ACCEPTED into unstable, unstable))
Hi Debian Java folks,
I had no success with this question on Debian Med list. The new version
of FastQC needed two new dependencies which arrived in unstable but the
build does not work. The packaging is at
git://git.debian.org/git/debian-med/fastqc.git
Any help is welcome
Andreas.
----- Forwarded message from Andreas Tille <andreas@fam-tille.de> -----
Date: Thu, 26 Nov 2015 08:22:03 +0100
From: Andreas Tille <andreas@fam-tille.de>
To: Olivier Sallou <olivier.sallou@irisa.fr>
Cc: Debian Med Project List <debian-med@lists.debian.org>
Subject: 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
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> 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:
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> libsis-jhdf5-java_14.12.1-1.debian.tar.xz
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> 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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> Debian-med-packaging@lists.alioth.debian.org
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