Nextflow joint build running on hold version

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Nextflow joint build running on hold version

Paolo Di Tommaso
Upgrading the Nextflow project to latest Groovy version (2.4.12) I got several errors related to this issue: 



I was a bit surprised because the joint build in the community Team-City server is reporting all tests green: 



When running in the CI server the groovy deps are overridden by this snippet in gradle build file and the groovy version is provided by the `CI_GROOVY_VERSION  ` env variable. 

Looking in the log that variable looks outdated: 

[03:21:46] : [Step 1/1] Overriden Groovy dependency to use 2.4.4-SNAPSHOT


Would it be possible to update the config to have NF compiled against the latest snapshot ? 


Thanks you,
Paolo

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Re: Nextflow joint build running on hold version

paulk_asert
Now set to 2.4.13-SNAPSHOT

On Sun, Jun 25, 2017 at 11:03 PM, Paolo Di Tommaso <[hidden email]> wrote:
Upgrading the Nextflow project to latest Groovy version (2.4.12) I got several errors related to this issue: 



I was a bit surprised because the joint build in the community Team-City server is reporting all tests green: 



When running in the CI server the groovy deps are overridden by this snippet in gradle build file and the groovy version is provided by the `CI_GROOVY_VERSION  ` env variable. 

Looking in the log that variable looks outdated: 

[03:21:46] : [Step 1/1] Overriden Groovy dependency to use 2.4.4-SNAPSHOT


Would it be possible to update the config to have NF compiled against the latest snapshot ? 


Thanks you,
Paolo


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Re: Nextflow joint build running on hold version

Paolo Di Tommaso
OK, now the `CI_GROOVY_VERSION` is correctly defined, however this still does not solve the issue. 

I've added a test to verify that the SNAPSHOT version is correctly used by the build and it turns out that it is not. It just uses the groovy runtime define in the project not the one specified by the `CI_GROOVY_VERSION`. 

Condition not satisfied:

System.getenv('CI_GROOVY_VERSION') == GroovySystem.getVersion()
       |                           |               |
       2.4.13-SNAPSHOT             |               2.4.11
                                   false
                                   10 differences (33% similarity)
                                   2.4.1(3-SNAPSHOT)
                                   2.4.1(1---------)


 
This is also explain why the 2.5.x build was compiling successfully, while it doesn't on my local build. 

Nextflow uses a Gradle build in which this snippet, contributed by Cédric Champeau, is supposed to override the project groovy libraries with the latest snapshot. 

Frankly it's not clear to me how that snippet is supposed to work, thus I don't know if it's problem with the CI server configuration or with my build file. 


Any suggestion is welcome. 


Cheers,
Paolo




On Mon, Jun 26, 2017 at 12:55 PM, Paul King <[hidden email]> wrote:
Now set to 2.4.13-SNAPSHOT

On Sun, Jun 25, 2017 at 11:03 PM, Paolo Di Tommaso <[hidden email]> wrote:
Upgrading the Nextflow project to latest Groovy version (2.4.12) I got several errors related to this issue: 



I was a bit surprised because the joint build in the community Team-City server is reporting all tests green: 



When running in the CI server the groovy deps are overridden by this snippet in gradle build file and the groovy version is provided by the `CI_GROOVY_VERSION  ` env variable. 

Looking in the log that variable looks outdated: 

[03:21:46] : [Step 1/1] Overriden Groovy dependency to use 2.4.4-SNAPSHOT


Would it be possible to update the config to have NF compiled against the latest snapshot ? 


Thanks you,
Paolo



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