Re: Packaging maven-scala-plugin (Was: Help needed for gatk)

2016-02-01 Thread David Bernard
Andreas, the latest version of maven-scala-plugin is available at https://github.com/davidB/scala-maven-plugin/tree/v2.15.2 (both plugin share the same history, repo,...) this version work for maven 2 and didn't rely on zinc. and it should match your initial requirement. As the version 3 also chan

Re: Packaging maven-scala-plugin (Was: Help needed for gatk)

2016-02-01 Thread Andreas Tille
Hi David, On Mon, Feb 01, 2016 at 10:41:53PM +0100, David Bernard wrote: > zinc is optional at runtime, but required at build time (part of the code > depends of it). That actually was my question: Do you see any chance to patch the code to not require zinc at build time. If I do not intend to

Re: Packaging maven-scala-plugin (Was: Help needed for gatk)

2016-02-01 Thread David Bernard
zinc is optional at runtime, but required at build time (part of the code depends of it). I don't know the package policy of Debian (I use ArchLinux). Is it mandatarory to build every package (like in a gentoo)? If yes you'll have to build all the dependency of plugin, jars, ... from source and in

Re: Packaging maven-scala-plugin (Was: Help needed for gatk)

2016-02-01 Thread Andreas Tille
Hi David, On Mon, Feb 01, 2016 at 09:38:44PM +0100, David Bernard wrote: > > TBH, I don't understand why you package a maven plugin ? I can understand that from a maven plugin author this sounds totally crazy since maven is designed to download what is missing. However, the Debian archive has t

Re: Packaging maven-scala-plugin (Was: Help needed for gatk)

2016-02-01 Thread Andreas Tille
On Mon, Feb 01, 2016 at 02:38:19PM +0100, Emmanuel Bourg wrote: > > I wonder whether I could really skip the Zinc dependency. I'm also > > afraid that if Zinc is not available I need at least xsbti - so just > > another package I need to create. Is this correct? > > You ignored the zinc dependen

Re: Packaging maven-scala-plugin (Was: Help needed for gatk)

2016-02-01 Thread Emmanuel Bourg
Le 1/02/2016 14:35, Andreas Tille a écrit : > I wonder whether I could really skip the Zinc dependency. I'm also > afraid that if Zinc is not available I need at least xsbti - so just > another package I need to create. Is this correct? You ignored the zinc dependency, but now you need to patch

Re: Packaging maven-scala-plugin (Was: Help needed for gatk)

2016-02-01 Thread Andreas Tille
Hi, [Upstream in CC. David for better understanding you might like to read my mail https://lists.debian.org/debian-java/2016/02/msg0.html and the related patch https://anonscm.debian.org/cgit/pkg-java/maven-scala-plugin.git/tree/debian/patches/disable_zinc.patch If you read below the

Re: Packaging maven-scala-plugin (Was: Help needed for gatk)

2016-02-01 Thread Andrew Schurman
On Mon, 2016-02-01 at 12:18 +0100, Andreas Tille wrote: >  I admit I have no idea how > to > craft the suggested publishedRule. The maven.publishedRules usually gets generated with comments to help you if you used mh_make. If not, check another project for reference such as [1]. Adding the line be

Re: Packaging maven-scala-plugin (Was: Help needed for gatk)

2016-02-01 Thread Andreas Tille
Hi Andrew, On Mon, Feb 01, 2016 at 03:05:32AM -0800, Andrew Schurman wrote: > On Mon, 2016-02-01 at 09:51 +0100, Andreas Tille wrote: > > Thanks for "reading aloud" for me - this might be due to my partial > > blindness for Java problems. :-) > > No worries. Sometimes people overlook the simplest

Re: Packaging maven-scala-plugin (Was: Help needed for gatk)

2016-02-01 Thread Andrew Schurman
On Mon, 2016-02-01 at 09:51 +0100, Andreas Tille wrote: > Thanks for "reading aloud" for me - this might be due to my partial > blindness for Java problems. :-) No worries. Sometimes people overlook the simplest solutions because they've been tackling a problem for too long.  > > The next stumb

Re: Packaging maven-scala-plugin (Was: Help needed for gatk)

2016-02-01 Thread Andreas Tille
Hi Andrew, On Sat, Jan 30, 2016 at 01:05:00PM -0800, Andrew Schurman wrote: > > artifact com.typesafe.zinc:zinc:jar:debian has not been downloaded > > All the details are in the error output. I've highlighted the line you > should pay attention to. It says you're missing the project > com.typesaf

Re: Packaging maven-scala-plugin (Was: Help needed for gatk)

2016-01-30 Thread Andrew Schurman
On Sat, 2016-01-30 at 18:05 +0100, Andreas Tille wrote: > [ERROR] Failed to execute goal on project scala-maven-plugin: Could > not resolve dependencies for project net.alchim31.maven:scala-maven- > plugin:maven-plugin:3.2.2: Cannot access central > (https://repo.maven.apache.org/maven2) in offline

Re: Packaging maven-scala-plugin (Was: Help needed for gatk)

2016-01-30 Thread Andreas Tille
iHi Emmanuel, On Sat, Jan 30, 2016 at 03:46:01PM +0100, Emmanuel Bourg wrote: > Le 30/01/2016 14:59, Andreas Tille a écrit : > Add --no-parent for this pom in debian/.poms, this will > ignore the parent oss-parent pom. This helped a step further and I also added junit as Build-Depends. The next s

Re: Packaging maven-scala-plugin (Was: Help needed for gatk)

2016-01-30 Thread Emmanuel Bourg
Le 30/01/2016 14:59, Andreas Tille a écrit : > Any help would be welcome Add --no-parent for this pom in debian/.poms, this will ignore the parent oss-parent pom. Emmanuel Bourg

Re: Packaging maven-scala-plugin (Was: Help needed for gatk)

2016-01-30 Thread Andreas Tille
On Thu, Jan 28, 2016 at 07:32:06PM +0100, Andreas Tille wrote: > > Hmmm, I'm missing my mail from some hours ago to the list but to > push things a bit forward I injected > >git://anonscm.debian.org/pkg-java/maven-scala-plugin.git According to different hints I dropped the idea to package ve

Re: Help needed for gatk

2016-01-29 Thread Andreas Tille
Hi Andrew, On Fri, Jan 29, 2016 at 10:44:07AM -0800, Andrew Schurman wrote: > > Based on the history of the repo, it appears to be the same project by > the same author. I don't think it's too much of a stretch to use this > new repo. If you want to be extra cautious, you could compare source of

Re: Help needed for gatk

2016-01-29 Thread Andrew Schurman
On Thu, 2016-01-28 at 16:26 +0100, Andreas Tille wrote: > As far as I understand its renamed by the same author. You're right. I didn't realize this. > I perfectly agree - but I have no idea how to find the according > source > code.  I feel a bit unsafe to checkout the new repository and > chec

Packaging maven-scala-plugin (Was: Help needed for gatk)

2016-01-28 Thread Andreas Tille
On Wed, Jan 27, 2016 at 02:52:55PM -0800, Andrew Schurman wrote: > > Just to make sure I'm > > heading in the right direction: > > > >   scala: https://github.com/davidB/scala-maven-plugin > >    (this seems to be outdated: http://scala-tools.org/mvnsites/maven- > > scala-plugin/) > > The one fro

Re: Help needed for gatk

2016-01-28 Thread Andreas Tille
Hi Andrew, On Wed, Jan 27, 2016 at 02:52:55PM -0800, Andrew Schurman wrote: > On Wed, 2016-01-27 at 15:08 +0100, Andreas Tille wrote: > > Reading "compile" and "link" would tell me > > that these are not needed only for testing, right? > > Don't confused with . Goals are named subroutines from >

Re: Help needed for gatk

2016-01-27 Thread Andrew Schurman
On Wed, 2016-01-27 at 15:08 +0100, Andreas Tille wrote: > Reading "compile" and "link" would tell me > that these are not needed only for testing, right? Don't confused with . Goals are named subroutines from the plugin. Phases are standard Maven names. If you prefer, goals tell Maven what to use

Re: Help needed for gatk

2016-01-27 Thread Andreas Tille
On Thu, Jan 21, 2016 at 11:02:58AM +0100, Emmanuel Bourg wrote: > Le 21/01/2016 10:46, Andreas Tille a écrit : > > > Considering that I can not find anything matching "maven > > {scala,junction}" via apt-cache search does that mean that these plugins > > need to be packaged first? If yes, is ther

Re: Help needed for gatk

2016-01-21 Thread Emmanuel Bourg
Le 21/01/2016 10:46, Andreas Tille a écrit : > Considering that I can not find anything matching "maven > {scala,junction}" via apt-cache search does that mean that these plugins > need to be packaged first? If yes, is there some similar example where > I could start? If they are used in the bui

Re: Help needed for gatk

2016-01-21 Thread Andreas Tille
On Thu, Jan 21, 2016 at 10:27:03AM +0100, Emmanuel Bourg wrote: > I don't think the unversionned plugins are the issue, this works fine > usually. This is more likely to be caused by missing plugins or > dependencies. maven-scala-plugin and maven-junction-plugin are missing > for example. Consider

Re: Help needed for gatk

2016-01-21 Thread Emmanuel Bourg
I don't think the unversionned plugins are the issue, this works fine usually. This is more likely to be caused by missing plugins or dependencies. maven-scala-plugin and maven-junction-plugin are missing for example. Emmanuel Bourg

Re: Help needed for gatk

2016-01-21 Thread Thorsten Glaser
On Thu, 21 Jan 2016, Andreas Tille wrote: > Please try > >git clone ssh://git.debian.org/git/debian-med/gatk.git OK, that works better. Indeed, all those plugins are not versioned: org.scala-tools maven-scala-plugin

Re: Help needed for gatk

2016-01-21 Thread gregor herrmann
On Thu, 21 Jan 2016 10:02:48 +0100, Andreas Tille wrote: > On Thu, Jan 21, 2016 at 09:51:37AM +0100, Thorsten Glaser wrote: > > tglase@tglase:/tmp $ git clone git://anonscm.debian.org/debian-med/gatk.git > > Cloning into 'gatk'... > > Permission denied (publickey). > > fatal: Could not read from r

Re: Help needed for gatk

2016-01-21 Thread Andreas Tille
On Thu, Jan 21, 2016 at 09:51:37AM +0100, Thorsten Glaser wrote: > On Thu, 21 Jan 2016, Andreas Tille wrote: > > > I'm lost again with a Java package: gatk[1]. The confusing part from > > tglase@tglase:/tmp $ git clone git://anonscm.debian.org/debian-med/gatk.git > Cloning into 'gatk'... > Permi

Re: Help needed for gatk

2016-01-21 Thread Thorsten Glaser
On Thu, 21 Jan 2016, Andreas Tille wrote: > I'm lost again with a Java package: gatk[1]. The confusing part from tglase@tglase:/tmp $ git clone git://anonscm.debian.org/debian-med/gatk.git Cloning into 'gatk'... Permission denied (publickey). fatal: Could not read from remote repository. > [WAR

Help needed for gatk

2016-01-21 Thread Andreas Tille
Hi, I'm lost again with a Java package: gatk[1]. The confusing part from the build log is: ... /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar:/usr/lib/jvm/default-java/lib/tools.jar -Dmaven.home=/usr/share/maven -Dmaven.