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From Stian Soiland-Reyes <st...@apache.org>
Subject Re: Snapshot issue when releasing taverna language
Date Mon, 01 Feb 2016 14:42:42 GMT
I think it is caused by this:

https://github.com/apache/incubator-taverna-language/blob/master/pom.xml#L48
https://issues.apache.org/jira/browse/TAVERNA-867
https://issues.apache.org/jira/browse/TAVERNA-869


Does it work with Java 8?



On 1 February 2016 at 12:35, Menaka Madushanka <menaka12350@gmail.com> wrote:
> Hello,
> I get this error when building tavlang tool....
>
> [ERROR] Failed to execute goal
> org.apache.maven.plugins:maven-javadoc-plugin:2.9:jar (attach-javadocs) on
> project taverna-language-commandline: MavenReportException: Error while
> creating archive:
> [ERROR] Exit code: 1 - javadoc: error - invalid flag: -Xdoclint:none
> [ERROR]
> [ERROR] Command line was: /usr/lib/jvm/java-7-oracle/jre/../bin/javadoc
> @options @packages
> [ERROR]
> [ERROR] Refer to the generated Javadoc files in
> '/media/menaka/7567da6f-cbe0-4f3e-9277-7ff83266e516/incubator-taverna-language/taverna-language-commandline/target/apidocs'
> dir.
> [ERROR] -> [Help 1]
> [ERROR]
> [ERROR] To see the full stack trace of the errors, re-run Maven with the -e
> switch.
> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
> [ERROR]
> [ERROR] For more information about the errors and possible solutions,
> please read the following articles:
> [ERROR] [Help 1]
> http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
>
>
> Has anyone got this error before?
>
>
> On 1 February 2016 at 17:06, Menaka Madushanka <menaka12350@gmail.com>
> wrote:
>
>> I'll change the module name as suggested.
>>
>> Cheers
>>
>> On 1 February 2016 at 15:53, Stian Soiland-Reyes <stain@apache.org> wrote:
>>
>>> Thanks for the fixes, Menaka, applied :)
>>>
>>> (I did the git pull as it said in the automated git email)
>>>
>>>
>>>
>>> Gale, perhaps you could have a look if the tavlang help screens are
>>> now OK? Feel free to fix anything missed :)
>>>
>>> It should work fine to build just the taverna-language-commandline module
>>> within
>>> https://git-wip-us.apache.org/repos/asf/incubator-taverna-language.git -
>>> or you can download the latest JAR from
>>>
>>> https://builds.apache.org/user/stain/my-views/view/taverna/job/incubator-taverna-language/lastSuccessfulBuild/org.apache.taverna.language$taverna-language-commandline/
>>> and run it with java -jar
>>>
>>> e.g.
>>>
>>> stain@biggie
>>> :~/src/taverna/incubator-taverna-language/taverna-language-commandline/target$
>>> java -jar taverna-language-commandline-0.15.1-incubating-SNAPSHOT.jar
>>> help
>>> usage: tavlang <command> [<args>]
>>>
>>> The most commonly used tavlang commands are:
>>>     convert    Convert the given workflow
>>>     help       Display help information about Tvarna
>>>     inspect    Inspect the given workflow and show the results on the
>>> terminal
>>>     stats      Shows the workflow statistics
>>>     validate   validate the given workflow
>>>     version    Show version informantion
>>>
>>> See 'tavlang help <command>' for more information on a specific command.
>>>
>>>
>>> Menaka and others - perhaps we should rename the module from
>>> "taverna-language-commandline" to taverna-tavlang ?  Might reduce the
>>> confusion against the taverna-commandline..
>>> Raised as https://issues.apache.org/jira/browse/TAVERNA-889
>>>
>>> On 31 January 2016 at 16:06, Menaka Madushanka <menaka12350@gmail.com>
>>> wrote:
>>> > Hello all,
>>> >
>>> > I corrected the typo issues and removed some unnecessary comments.......
>>> > Thank you very much Gale..!!!
>>> >
>>> > What could we do for the Iwir issue?
>>> >
>>> > I added it because in the Readme.md file of  taverna-scufl2-api
>>> > <
>>> https://github.com/apache/incubator-taverna-language/tree/master/taverna-scufl2-api
>>> >,
>>> > says about the iwir support.
>>> >
>>> > Cheers
>>> >
>>> > On 30 January 2016 at 01:58, Gale Naylor <GaleN@noventussolutions.com>
>>> > wrote:
>>> >
>>> >> It seems that the iwir capability is already commented out in
>>> >> Scufl2Convert.java? (LInes 185-188) Or am I not reading this right?
>>> >>
>>> >>
>>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/convert/Scufl2Convert.java
>>> >>
>>> >> Also, there seem to be some typos in CommandLineTool.java that may be
>>> >> something users can see and, therefore, maybe we should change (see
>>> below)?
>>> >>
>>> >>
>>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/CommandLineTool.java
>>> >>
>>> >> Two instances of bund*el* instead of bund*le*: in description and one
>>> >> Tvarna instead of Taverna.
>>> >>     line 86: @Option(name = "--wfbundle", description = "Convert the
>>> >> workflow file to wfbundel"
>>> >>     line 89: @Option(name = "--robundle", description = "Convert given
>>> >> bundel in to Research Object bundel")
>>> >>     line 178: "Tvarna" should be Taverna --> description = "Display
>>> help
>>> >> information about Tvarna"
>>> >>
>>> >> Thanks,
>>> >> Gale
>>> >>
>>> >> On Fri, Jan 29, 2016 at 11:17 AM Gale Naylor <
>>> GaleN@noventussolutions.com>
>>> >> wrote:
>>> >>
>>> >> > @stain, when you said maybe scufl2-iwir "should move to
>>> >> >
>>> >> > taverna-extras Github organisations, which we said was for plugins
>>> with
>>> >> > LGPL or GPL licences/dependencies," is taverna-extras one of the
>>> github
>>> >> > source code repos or something else?
>>> >> >
>>> >> > Also, @stain, if Menaka added IWIR support to the tavtool, does
that
>>> mean
>>> >> > he is *not* using the iwirTool to provide that support? If so,
then
>>> can
>>> >> we
>>> >> > leave the iwir capability in the taverna-language-commandline
>>> >> documentation?
>>> >> >
>>> >> > Thanks,
>>> >> > Gale
>>> >> >
>>> >> > On Fri, Jan 29, 2016 at 10:58 AM Gale Naylor <
>>> >> GaleN@noventussolutions.com>
>>> >> > wrote:
>>> >> >
>>> >> >> I am a little confused about the licensing. This Apache webpage
>>> seems to
>>> >> >> say that we cannot use anything with an LGPL license:
>>> >> >> http://www.apache.org/legal/resolved.html#category-x. But it's
>>> okay if
>>> >> >> the dependency is optional?
>>> >> >>
>>> >> >> Regarding documentation: do we want to remove any mention of
iwir
>>> >> >> completely?
>>> >> >>
>>> >> >> Thanks,
>>> >> >>
>>> >> >> Gale
>>> >> >>
>>> >> >> On Fri, Jan 29, 2016 at 7:14 AM Ian Dunlop <
>>> ian.dunlop@manchester.ac.uk
>>> >> >
>>> >> >> wrote:
>>> >> >>
>>> >> >>> Hello,
>>> >> >>>
>>> >> >>> I'm just trying to figure out the dependency spaghetti!
The
>>> scufl2-iwir
>>> >> >>> jar seems to be in the 'tavtool' lib forlder:
>>> >> >>>
>>> >> >>> ls
>>> >> taverna-language-commandline/target/taverna-language-commandline/lib/
>>> >> >>> (...lots of jars)
>>> >> >>>      scufl2-iwir-0.2-20150619.152911-2.jar
>>> >> >>>
>>> >> >>> It is marked as an optional in the taverna-language-commandline
pom
>>> >> >>>
>>> >> >>>          <dependency>
>>> >> >>>                 <groupId>no.s11.scufl2</groupId>
>>> >> >>>                 <artifactId>scufl2-iwir</artifactId>
>>> >> >>>                 <version>0.2-SNAPSHOT</version>
>>> >> >>>         <optional>true</optional>
>>> >> >>>     </dependency>
>>> >> >>>
>>> >> >>> I commented the dependency out and there were no problems
with mvn
>>> >> clean
>>> >> >>> install plus the jar is no longer in the lib. I'm not 100%
clear
>>> why
>>> >> >>> this dependency is here anyway, isn't the conversion done
by the
>>> >> >>> workflow bundle tool?
>>> >> >>> So, looks like you can remove the dependency from the tavtool
>>> although
>>> >> >>> you will probably need some doc updates to point out that
iwir is
>>> not
>>> >> >>> supported now.
>>> >> >>>
>>> >> >>> Cheers,
>>> >> >>>
>>> >> >>> Ian
>>> >> >>>
>>> >> >>>
>>> >> >>> On 26/01/2016 14:14, Stian Soiland-Reyes wrote:
>>> >> >>> > On 26 Jan 2016 13:45, "Ian Dunlop" <ian.dunlop@manchester.ac.uk>
>>> >> >>> wrote:
>>> >> >>> >>
>>> >> >>> >> Hello,
>>> >> >>> >>
>>> >> >>> >> The scufl2-iwir tool pom
>>> >> >>> >> https://github.com/stain/scufl2-iwir/blob/master/pom.xml
lists
>>> an
>>> >> >>> LGPL
>>> >> >>> >> dependency
>>> >> >>> >>
>>> >> >>> >> <groupId>org.shiwa.fgi.iwir</groupId>
>>> >> >>> >> <artifactId>iwirTool</artifactId>
>>> >> >>> >> <version>1.1.11</version>
>>> >> >>> >> <!-- WARNING: LGPL dependency -->
>>> >> >>> >> <!-- See http://sourceforge.net/projects/iwirtool/
-->
>>> >> >>> >>
>>> >> >>> >> Is that a problem for an Apache release?
>>> >> >>> >
>>> >> >>> > Ouch, scufl2-iwir is a dependency Menaka added to
tavtool, as
>>> one of
>>> >> >>> the
>>> >> >>> > conversion formats.
>>> >> >>> >
>>> >> >>> > It should not be a problem as long as it is an optional
>>> dependency
>>> >> >>> which is
>>> >> >>> > not pulled into use inadvertently. It might be worth
checking the
>>> >> >>> tavtool
>>> >> >>> > lib folder after compilation if it does so.
>>> >> >>> >
>>> >> >>> > As I was not sure at the time (plus this was experimental)
I put
>>> the
>>> >> >>> IWIR
>>> >> >>> > support in a separate repository. Perhaps this should
move to
>>> >> >>> > taverna-extras Github organisations, which we said
was for
>>> plugins
>>> >> with
>>> >> >>> > LGPL or GPL licences/dependencies.
>>> >> >>> >
>>> >> >>> > Do we need this ependency to compile (e.g. release)
or can
>>> >> scufl2-iwir
>>> >> >>> > dependency be commented out / moved to a Maven profile?
>>> >> >>> >
>>> >> >>> > I guess this is a bit of spaghetti leftover :/ as
scufl2-iwir is
>>> a
>>> >> >>> plugin
>>> >> >>> > for scufl2-api to deal with the IWIR format, but Menaka
added
>>> IWIR
>>> >> >>> support
>>> >> >>> > to the tavtool, and both are part of taverna-language
while
>>> >> >>> scufl2-iwir is
>>> >> >>> > outside Apache Taverna.
>>> >> >>> >
>>> >> >>> > I am not sure why this dependency is SNAPSHOT though,
I can try
>>> to
>>> >> >>> release
>>> >> >>> > it, and to a better repository (Central?)
>>> >> >>> >
>>> >> >>> > Really the scufl2 command line tool might need a pluggable
>>> structure
>>> >> so
>>> >> >>> > third-party plugins (even if that third party in this
case is
>>> me!)
>>> >> can
>>> >> >>> be
>>> >> >>> > dropped into say the lib folder rather than by editing
the
>>> pom.xml
>>> >> >>> >
>>> >> >>> >>
>>> >> >>> >> Cheers,
>>> >> >>> >>
>>> >> >>> >> Ian
>>> >> >>> >>
>>> >> >>> >> On 26/01/2016 12:15, Ian Dunlop wrote:
>>> >> >>> >>> Hello,
>>> >> >>> >>>
>>> >> >>> >>> Looks like https://github.com/stain/scufl2-iwir
needs to be
>>> >> released
>>> >> >>> >>> without SNAPSHOT version. The SNAPSHOT is
available from the
>>> mygrid
>>> >> >>> repo
>>> >> >>> >>>
>>> >> >>> >
>>> >> >>>
>>> >>
>>> http://repository.mygrid.org.uk/artifactory/mygrid-snapshots/no/s11/scufl2/scufl2-iwir/0.2-SNAPSHOT/
>>> >> >>> >>>
>>> >> >>> >>> Cheers,
>>> >> >>> >>>
>>> >> >>> >>> Ian
>>> >> >>> >>>
>>> >> >>> >>> On 26/01/2016 12:09, Ian Dunlop wrote:
>>> >> >>> >>>> Hello,
>>> >> >>> >>>>
>>> >> >>> >>>> Yes it is in
>>> >> >>> >>>>
>>> >> >>> >
>>> >> >>>
>>> >>
>>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-language-commandline/pom.xml
>>> >> >>> >>>> which (IIRC) is the module that menaka
built for GSOC. I
>>> think the
>>> >> >>> last
>>> >> >>> >>>> release did not include this module -
>>> >> >>> >>>>
>>> >> >>> >
>>> >> >>>
>>> >>
>>> https://github.com/apache/incubator-taverna-language/commit/349460af1447cd04bfea59b047a99ab85652c185
>>> >> >>> > .
>>> >> >>> >>>>
>>> >> >>> >>>> <dependency>
>>> >> >>> >>>>      <groupId>no.s11.scufl2</groupId>
>>> >> >>> >>>>      <artifactId>scufl2-iwir</artifactId>
>>> >> >>> >>>>      <version>0.2-SNAPSHOT</version>
>>> >> >>> >>>>      <optional>true</optional>
>>> >> >>> >>>> </dependency>
>>> >> >>> >>>>
>>> >> >>> >>>> So it looks like we need to get the no.s11.scufl2:scufl2-iwir
>>> >> >>> > dependency
>>> >> >>> >>>> deployed 'properly'
>>> >> >>> >>>>
>>> >> >>> >>>> Cheers,
>>> >> >>> >>>>
>>> >> >>> >>>> Ian
>>> >> >>> >>>>
>>> >> >>> >>>> On 25/01/2016 17:27, Andy Seaborne wrote:
>>> >> >>> >>>>> On 25/01/16 16:37, Ian Dunlop wrote:
>>> >> >>> >>>>>> Hello
>>> >> >>> >>>>>>
>>> >> >>> >>>>>> Pasted from IRC chat!
>>> >> >>> >>>>>>
>>> >> >>> >>>>>> "Was going to try a taverna-language
release but mvn
>>> >> >>> release:prepare
>>> >> >>> >>>>>> asked if I wanted to resolve some
SNAPSHOT dependencies
>>> >> >>> >>>>>> [15:42] <IanD_> I said no
which resulted in: [ERROR] Failed
>>> to
>>> >> >>> > execute
>>> >> >>> >>>>>> goal
>>> org.apache.maven.plugins:maven-release-plugin:2.5.2:prepare
>>> >> >>> >>>>>> (default-cli) on project taverna-language:
Can't release
>>> project
>>> >> >>> due
>>> >> >>> > to
>>> >> >>> >>>>>> non released dependencies : [ERROR]
>>> >> >>> >>>>>> no.s11.scufl2:scufl2-iwir:jar:0.2-SNAPSHOT:compile
>>> >> >>> >>>>>> [15:43] <IanD_> [ERROR]
in project 'Apache Taverna Language
>>> >> >>> > Commandline'
>>> >> >>> >>>>>>
>>> >> >>> >
>>> >> >>>
>>> >>
>>> (org.apache.taverna.language:taverna-language-commandline:jar:0.15.1-incubating-SNAPSHOT)"
>>> >> >>> >>>>>>
>>> >> >>> >>>>>>
>>> >> >>> >>>>>> Any ideas?
>>> >> >>> >>>>>> Cheers,
>>> >> >>> >>>>>>
>>> >> >>> >>>>>> Ian
>>> >> >>> >>>>>>
>>> >> >>> >>>>>
>>> >> >>> >>>>> One reason this can happen is when,
somewhere, a module
>>> depends
>>> >> on
>>> >> >>> a
>>> >> >>> >>>>> SNAPSHOT and it's getting that SNAPSHOT
from the repo, not as
>>> >> part
>>> >> >>> of
>>> >> >>> >>>>> the build.
>>> >> >>> >>>>>
>>> >> >>> >>>>>     Andy
>>> >> >>> >>>>>
>>> >> >>> >>>>>
>>> >> >>> >>>>>
>>> >> >>> >>>>
>>> >> >>> >>>
>>> >> >>> >>
>>> >> >>> >> --
>>> >> >>> >> Ian Dunlop, eScience Lab
>>> >> >>> >> School of Computer Science
>>> >> >>> >> The University of Manchester
>>> >> >>> >> http://orcid.org/0000-0001-7066-3350
>>> >> >>> >
>>> >> >>>
>>> >> >>> --
>>> >> >>> Ian Dunlop, eScience Lab
>>> >> >>> School of Computer Science
>>> >> >>> The University of Manchester
>>> >> >>> http://orcid.org/0000-0001-7066-3350
>>> >> >>>
>>> >> >>
>>> >>
>>> >
>>> >
>>> >
>>> > --
>>> > Menaka Madushanka Jayawardena
>>> > Faculty of Engineering, <http://www.pdn.ac.lk/eng>
>>> > University of Peradeniyaya.
>>> > LinkedIn <http://lk.linkedin.com/in/menakajayawardena>
>>>
>>>
>>>
>>> --
>>> Stian Soiland-Reyes
>>> Apache Taverna (incubating), Apache Commons RDF (incubating)
>>> http://orcid.org/0000-0001-9842-9718
>>>
>>
>>
>>
>> --
>> Menaka Madushanka Jayawardena
>> Faculty of Engineering, <http://www.pdn.ac.lk/eng>
>> University of Peradeniyaya.
>> LinkedIn <http://lk.linkedin.com/in/menakajayawardena>
>>
>
>
>
> --
> Menaka Madushanka Jayawardena
> Faculty of Engineering, <http://www.pdn.ac.lk/eng>
> University of Peradeniyaya.
> LinkedIn <http://lk.linkedin.com/in/menakajayawardena>



-- 
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718

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