Re: Best/recommended way to search if a Java library or class is packaged

[Sergio Fernández]

I always use the following bash-based solution:

dpkg -l | grep java | awk '{ print $2 }' | xargs -I {} dpkg -L  {} | grep
jar | xargs -I {} grep "javax.servlet.Servlet" {}

But I'm pretty sure there is much better tolling for such tasks...


On Thu, Dec 3, 2015 at 9:19 PM, Emmanuel Bourg  wrote:

> Le 3/12/2015 19:16, Miguel Landaeta a écrit :
>
> > Since jar-content.txt Torsten's file is not being updated since a long
> > time, I was wondering what's the current recommended way to quickly
> > check if a Java library is packaged in Debian.
>
> Maybe we could revive this tool. If the source is available somewhere I
> can host the service on my server.
>
>
> > I know I can use apt-file or apt-cache but sometimes that's not
> > enough (IMO).
>
> I often use sources.debian.net with queries like 'class Foo' or 'package
> org.bar' to locate the source package containing a class or a package.
>
> Emmanuel Bourg
>
>


-- 
Sergio Fernández
Partner Technology Manager
Redlink GmbH
m: +43 6602747925
e: sergio.fernan...@redlink.co
w: http://redlink.co

Re: Best/recommended way to search if a Java library or class is packaged

[Mikołaj Izdebski]

Hi Emmanuel,

On 12/3/15, Emmanuel Bourg  wrote:
> Le 3/12/2015 19:16, Miguel Landaeta a écrit :
>
>> Since jar-content.txt Torsten's file is not being updated since a long
>> time, I was wondering what's the current recommended way to quickly
>> check if a Java library is packaged in Debian.
>
> Maybe we could revive this tool. If the source is available somewhere I
> can host the service on my server.

If you want to host service for searching for classes (and other
things) then the following project may be interesting for you:

http://java-deptools.fedorainfracloud.org/
https://github.com/msimacek/java-deptools

It is a web application where you can search for classes and manifest
headers of all JARs in particular OS version. There are plans to
extend it with other capabilities, such as searching for other things
(eg. pom.xml and pom.properties embedded in JARs) and analysing
dependencies between JAR files and distro packages.

Currently only rpm packages are supported, but it should be fairly
easy to add support for deb. It should even be possible to have a
single instance where you would be able to search in various deb- and
rpm-based distros.

--
Mikołaj

Re: Best/recommended way to search if a Java library or class is packaged

[Paul Wise]

On Fri, Dec 4, 2015 at 2:16 AM, Miguel Landaeta wrote:

> Since jar-content.txt Torsten's file is not being updated since a long
> time, I was wondering what's the current recommended way to quickly
> check if a Java library is packaged in Debian.

The future of this sort of thing (mapping between $foo in language
$bar and package $baz) is DEP-11. It is currently focussed on mapping
packages to "apps" but is in theory aimed at more general mappings,
allowing one to eventually do things like this:

apt-get install java-class:javax.servlet.Servlet

https://wiki.debian.org/DEP-11
https://wiki.debian.org/AppStream

-- 
bye,
pabs

https://wiki.debian.org/PaulWise

Re: Best/recommended way to search if a Java library or class is packaged

[Miguel Landaeta]

Thanks to everyone for the helpful answers.

-- 
Miguel Landaeta, nomadium at debian.org
secure email with PGP 0x6E608B637D8967E9 available at http://miguel.cc/key.
"Faith means not wanting to know what is true." -- Nietzsche


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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))

[Andreas Tille]

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  -

Date: Thu, 26 Nov 2015 08:22:03 +0100
From: Andreas Tille 
To: Olivier Sallou 
Cc: Debian Med Project List 
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 +
> From: Debian FTP Masters 
> To: Debian Med Packaging Team
> , Tim Booth
> , osal...@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
> 
> Changed-By: Tim Booth 
> 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-jav

Re: 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))

[Emmanuel Bourg]

Le 4/12/2015 18:28, Andreas Tille a écrit :

> Any help is welcome

Hi Andreas,

I pushed a fix for the compilation issues to the repository. The
build.xml file is still missing a target building the jar after
compiling the classes.

Emmanuel Bourg