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GMOD / Apollo

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.
http://genomearchitect.readthedocs.io/
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Apollo-2.0.3 Build Successful - with Multiple Errors #1232

Closed entzn closed 8 years ago

entzn commented 8 years ago

Hi - attempting to install Apollo - It shows "BUILD SUCCESSFUL" But multiple Error messages

[SNIP] Installing Perl prerequisites ...Prerequisites installed, finished. :javac :gwtc

BUILD SUCCESSFUL

Total time: 55.713 secs

This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.ht| Configuring classpath | Error Resolve error obtaining dependencies: The following artifacts could not be resolved: org.codehaus.groovy:groovy-all:jar:2.4.4, org.apache.httpcomponents:httpcore:jar:4.3.2, org.apache.httpcomponents:httpclient:jar:4.3.2, org.apache.httpcomponents:httpmime:jar:4.3.3, org.grails.plugins:tomcat:zip:7.0.55.2, org.grails.plugins:coveralls:zip:0.1.3, org.grails.plugins:rest-client-builder:zip:2.1.1: Could not transfer artifact org.codehaus.groovy:groovy-all:jar:2.4.4 from/to grailsCentral (https://repo.grails.org/grails/plugins): repo.grails.org (Use --stacktrace to see the full trace) | Error Resolve error obtaining dependencies: The following artifacts could not be resolved: org.codehaus.groovy:groovy-all:jar:2.4.4, org.springframework:spring-webmvc:jar:4.1.8.RELEASE, org.springframework:spring-context-support:jar:4.1.8.RELEASE, org.springframework:spring-jdbc:jar:4.1.8.RELEASE, org.springframework:spring-context:jar:4.1.8.RELEASE, org.springframework:spring-core:jar:4.1.8.RELEASE, org.springframework:spring-beans:jar:4.1.8.RELEASE, org.springframework:spring-web:jar:4.1.8.RELEASE, org.springframework:spring-tx:jar:4.1.8.RELEASE, org.springframework:spring-test:jar:4.1.8.RELEASE, cglib:cglib-nodep:jar:2.2.2, mysql:mysql-connector-java:jar:5.1.29, org.postgresql:postgresql:jar:9.3-1101-jdbc41, commons-codec:commons-codec:jar:1.2, org.json:json:jar:20140107, org.hibernate:hibernate-tools:jar:3.2.0.ga, org.grails:grails-datastore-test-support:jar:1.0.2-grails-2.4, org.grails.plugins:rest-api-doc:zip:0.6, org.grails.plugins:scaffolding:zip:2.1.2, org.grails.plugins:cache:zip:1.1.8, org.grails.plugins:cache-ehcache:zip:1.0.5, org.grails.plugins:asset-pipeline:zip:2.1.5, org.grails.plugins:spring-websocket:zip:1.2.0, org.grails.plugins:shiro:zip:1.2.1, org.grails.plugins:audit-logging:zip:1.0.3, org.grails.plugins:hibernate4:zip:4.3.8.1, org.grails.plugins:database-migration:zip:1.4.1, org.grails.plugins:jquery-ui:zip:1.10.4, org.grails.plugins:jquery:zip:1.11.1, org.grails.plugins:twitter-bootstrap:zip:3.3.5, org.grails.plugins:yammer-metrics:zip:3.0.1-2, org.grails.plugins:rest-client-builder:zip:2.1.1, org.grails.plugins:code-coverage:zip:2.0.3-3: Could not transfer artifact org.codehaus.groovy:groovy-all:jar:2.4.4 from/to grailsCentral (https://repo.grails.org/grails/plugins): repo.grails.org (Use --stacktrace to see the full trace) | Error Resolve error obtaining dependencies: The following artifacts could not be resolved: org.codehaus.groovy:groovy-all:jar:2.4.4, org.springframework:spring-webmvc:jar:4.1.8.RELEASE, org.springframework:spring-context-support:jar:4.1.8.RELEASE, org.springframework:spring-jdbc:jar:4.1.8.RELEASE, org.springframework:spring-context:jar:4.1.8.RELEASE, org.springframework:spring-core:jar:4.1.8.RELEASE, org.springframework:spring-beans:jar:4.1.8.RELEASE, org.springframework:spring-web:jar:4.1.8.RELEASE, org.springframework:spring-tx:jar:4.1.8.RELEASE, mysql:mysql-connector-java:jar:5.1.29, org.postgresql:postgresql:jar:9.3-1101-jdbc41, commons-codec:commons-codec:jar:1.2, org.json:json:jar:20140107, org.hibernate:hibernate-tools:jar:3.2.0.ga, org.grails.plugins:rest-api-doc:zip:0.6, org.grails.plugins:scaffolding:zip:2.1.2, org.grails.plugins:cache:zip:1.1.8, org.grails.plugins:cache-ehcache:zip:1.0.5, org.grails.plugins:asset-pipeline:zip:2.1.5, org.grails.plugins:spring-websocket:zip:1.2.0, org.grails.plugins:shiro:zip:1.2.1, org.grails.plugins:audit-logging:zip:1.0.3, org.grails.plugins:hibernate4:zip:4.3.8.1, org.grails.plugins:database-migration:zip:1.4.1, org.grails.plugins:jquery-ui:zip:1.10.4, org.grails.plugins:jquery:zip:1.11.1, org.grails.plugins:twitter-bootstrap:zip:3.3.5, org.grails.plugins:yammer-metrics:zip:3.0.1-2, org.grails.plugins:rest-client-builder:zip:2.1.1: Could not transfer artifact org.codehaus.groovy:groovy-all:jar:2.4.4 from/to grailsCentral (https://repo.grails.org/grails/plugins): repo.grails.org (Use --stacktrace to see the full trace) | Error Resolve error obtaining dependencies: The following artifacts could not be resolved: org.codehaus.groovy:groovy-all:jar:2.4.4, org.springframework:spring-webmvc:jar:4.1.8.RELEASE, org.springframework:spring-context-support:jar:4.1.8.RELEASE, org.springframework:spring-jdbc:jar:4.1.8.RELEASE, org.springframework:spring-context:jar:4.1.8.RELEASE, org.springframework:spring-core:jar:4.1.8.RELEASE, org.springframework:spring-beans:jar:4.1.8.RELEASE, org.springframework:spring-web:jar:4.1.8.RELEASE, org.springframework:spring-tx:jar:4.1.8.RELEASE, commons-codec:commons-codec:jar:1.2, org.json:json:jar:20140107, org.hibernate:hibernate-tools:jar:3.2.0.ga, org.grails.plugins:rest-api-doc:zip:0.6, org.grails.plugins:scaffolding:zip:2.1.2, org.grails.plugins:cache:zip:1.1.8, org.grails.plugins:cache-ehcache:zip:1.0.5, org.grails.plugins:asset-pipeline:zip:2.1.5, org.grails.plugins:spring-websocket:zip:1.2.0, org.grails.plugins:shiro:zip:1.2.1, org.grails.plugins:audit-logging:zip:1.0.3, org.grails.plugins:yammer-metrics:zip:3.0.1-2: Could not transfer artifact org.codehaus.groovy:groovy-all:jar:2.4.4 from/to grailsCentral (https://repo.grails.org/grails/plugins): repo.grails.org (Use --stacktrace to see the full trace) | Error The following artifacts could not be resolved: org.codehaus.groovy:groovy-all:jar:2.4.4, org.apache.httpcomponents:httpcore:jar:4.3.2, org.apache.httpcomponents:httpclient:jar:4.3.2, org.apache.httpcomponents:httpmime:jar:4.3.3, org.grails.plugins:tomcat:zip:7.0.55.2, org.grails.plugins:coveralls:zip:0.1.3, org.grails.plugins:rest-client-builder:zip:2.1.1: Could not transfer artifact org.codehaus.groovy:groovy-all:jar:2.4.4 from/to grailsCentral (https://repo.grails.org/grails/plugins): repo.grails.org | Run 'grails dependency-report' for further information. | Configuring classpath | Error Resolve error obtaining dependencies: The following artifacts could not be resolved: org.codehaus.groovy:groovy-all:jar:2.4.4, org.apache.httpcomponents:httpcore:jar:4.3.2, org.apache.httpcomponents:httpclient:jar:4.3.2, org.apache.httpcomponents:httpmime:jar:4.3.3, org.grails.plugins:tomcat:zip:7.0.55.2, org.grails.plugins:coveralls:zip:0.1.3, org.grails.plugins:rest-client-builder:zip:2.1.1: Could not transfer artifact org.codehaus.groovy:groovy-all:jar:2.4.4 from/to grailsCentral (https://repo.grails.org/grails/plugins): repo.grails.org (Use --stacktrace to see the full trace) | Error Resolve error obtaining dependencies: The following artifacts could not be resolved: org.codehaus.groovy:groovy-all:jar:2.4.4, org.springframework:spring-webmvc:jar:4.1.8.RELEASE, org.springframework:spring-context-support:jar:4.1.8.RELEASE, org.springframework:spring-jdbc:jar:4.1.8.RELEASE, org.springframework:spring-context:jar:4.1.8.RELEASE, org.springframework:spring-core:jar:4.1.8.RELEASE, org.springframework:spring-beans:jar:4.1.8.RELEASE, org.springframework:spring-web:jar:4.1.8.RELEASE, org.springframework:spring-tx:jar:4.1.8.RELEASE, org.springframework:spring-test:jar:4.1.8.RELEASE, cglib:cglib-nodep:jar:2.2.2, mysql:mysql-connector-java:jar:5.1.29, org.postgresql:postgresql:jar:9.3-1101-jdbc41, commons-codec:commons-codec:jar:1.2, org.json:json:jar:20140107, org.hibernate:hibernate-tools:jar:3.2.0.ga, org.grails:grails-datastore-test-support:jar:1.0.2-grails-2.4, org.grails.plugins:rest-api-doc:zip:0.6, org.grails.plugins:scaffolding:zip:2.1.2, org.grails.plugins:cache:zip:1.1.8, org.grails.plugins:cache-ehcache:zip:1.0.5, org.grails.plugins:asset-pipeline:zip:2.1.5, org.grails.plugins:spring-websocket:zip:1.2.0, org.grails.plugins:shiro:zip:1.2.1, org.grails.plugins:audit-logging:zip:1.0.3, org.grails.plugins:hibernate4:zip:4.3.8.1, org.grails.plugins:database-migration:zip:1.4.1, org.grails.plugins:jquery-ui:zip:1.10.4, org.grails.plugins:jquery:zip:1.11.1, org.grails.plugins:twitter-bootstrap:zip:3.3.5, org.grails.plugins:yammer-metrics:zip:3.0.1-2, org.grails.plugins:rest-client-builder:zip:2.1.1, org.grails.plugins:code-coverage:zip:2.0.3-3: Could not transfer artifact org.codehaus.groovy:groovy-all:jar:2.4.4 from/to grailsCentral (https://repo.grails.org/grails/plugins): repo.grails.org (Use --stacktrace to see the full trace) | Error Resolve error obtaining dependencies: The following artifacts could not be resolved: org.codehaus.groovy:groovy-all:jar:2.4.4, org.springframework:spring-webmvc:jar:4.1.8.RELEASE, org.springframework:spring-context-support:jar:4.1.8.RELEASE, org.springframework:spring-jdbc:jar:4.1.8.RELEASE, org.springframework:spring-context:jar:4.1.8.RELEASE, org.springframework:spring-core:jar:4.1.8.RELEASE, org.springframework:spring-beans:jar:4.1.8.RELEASE, org.springframework:spring-web:jar:4.1.8.RELEASE, org.springframework:spring-tx:jar:4.1.8.RELEASE, mysql:mysql-connector-java:jar:5.1.29, org.postgresql:postgresql:jar:9.3-1101-jdbc41, commons-codec:commons-codec:jar:1.2, org.json:json:jar:20140107, org.hibernate:hibernate-tools:jar:3.2.0.ga, org.grails.plugins:rest-api-doc:zip:0.6, org.grails.plugins:scaffolding:zip:2.1.2, org.grails.plugins:cache:zip:1.1.8, org.grails.plugins:cache-ehcache:zip:1.0.5, org.grails.plugins:asset-pipeline:zip:2.1.5, org.grails.plugins:spring-websocket:zip:1.2.0, org.grails.plugins:shiro:zip:1.2.1, org.grails.plugins:audit-logging:zip:1.0.3, org.grails.plugins:hibernate4:zip:4.3.8.1, org.grails.plugins:database-migration:zip:1.4.1, org.grails.plugins:jquery-ui:zip:1.10.4, org.grails.plugins:jquery:zip:1.11.1, org.grails.plugins:twitter-bootstrap:zip:3.3.5, org.grails.plugins:yammer-metrics:zip:3.0.1-2, org.grails.plugins:rest-client-builder:zip:2.1.1: Could not transfer artifact org.codehaus.groovy:groovy-all:jar:2.4.4 from/to grailsCentral (https://repo.grails.org/grails/plugins): repo.grails.org (Use --stacktrace to see the full trace) | Error Resolve error obtaining dependencies: The following artifacts could not be resolved: org.codehaus.groovy:groovy-all:jar:2.4.4, org.springframework:spring-webmvc:jar:4.1.8.RELEASE, org.springframework:spring-context-support:jar:4.1.8.RELEASE, org.springframework:spring-jdbc:jar:4.1.8.RELEASE, org.springframework:spring-context:jar:4.1.8.RELEASE, org.springframework:spring-core:jar:4.1.8.RELEASE, org.springframework:spring-beans:jar:4.1.8.RELEASE, org.springframework:spring-web:jar:4.1.8.RELEASE, org.springframework:spring-tx:jar:4.1.8.RELEASE, commons-codec:commons-codec:jar:1.2, org.json:json:jar:20140107, org.hibernate:hibernate-tools:jar:3.2.0.ga, org.grails.plugins:rest-api-doc:zip:0.6, org.grails.plugins:scaffolding:zip:2.1.2, org.grails.plugins:cache:zip:1.1.8, org.grails.plugins:cache-ehcache:zip:1.0.5, org.grails.plugins:asset-pipeline:zip:2.1.5, org.grails.plugins:spring-websocket:zip:1.2.0, org.grails.plugins:shiro:zip:1.2.1, org.grails.plugins:audit-logging:zip:1.0.3, org.grails.plugins:yammer-metrics:zip:3.0.1-2: Could not transfer artifact org.codehaus.groovy:groovy-all:jar:2.4.4 from/to grailsCentral (https://repo.grails.org/grails/plugins): repo.grails.org (Use --stacktrace to see the full trace) | Error The following artifacts could not be resolved: org.codehaus.groovy:groovy-all:jar:2.4.4, org.apache.httpcomponents:httpcore:jar:4.3.2, org.apache.httpcomponents:httpclient:jar:4.3.2, org.apache.httpcomponents:httpmime:jar:4.3.3, org.grails.plugins:tomcat:zip:7.0.55.2, org.grails.plugins:coveralls:zip:0.1.3, org.grails.plugins:rest-client-builder:zip:2.1.1: Could not transfer artifact org.codehaus.groovy:groovy-all:jar:2.4.4 from/to grailsCentral (https://repo.grails.org/grails/plugins): repo.grails.org | Run 'grails dependency-report' for further information. | Error The following artifacts could not be resolved: org.codehaus.groovy:groovy-all:jar:2.4.4, org.springframework:spring-webmvc:jar:4.1.8.RELEASE, org.springframework:spring-context-support:jar:4.1.8.RELEASE, org.springframework:spring-jdbc:jar:4.1.8.RELEASE, org.springframework:spring-context:jar:4.1.8.RELEASE, org.springframework:spring-core:jar:4.1.8.RELEASE, org.springframework:spring-beans:jar:4.1.8.RELEASE, org.springframework:spring-web:jar:4.1.8.RELEASE, org.springframework:spring-tx:jar:4.1.8.RELEASE, commons-codec:commons-codec:jar:1.2, org.json:json:jar:20140107, org.hibernate:hibernate-tools:jar:3.2.0.ga, org.grails.plugins:rest-api-doc:zip:0.6, org.grails.plugins:scaffolding:zip:2.1.2, org.grails.plugins:cache:zip:1.1.8, org.grails.plugins:cache-ehcache:zip:1.0.5, org.grails.plugins:asset-pipeline:zip:2.1.5, org.grails.plugins:spring-websocket:zip:1.2.0, org.grails.plugins:shiro:zip:1.2.1, org.grails.plugins:audit-logging:zip:1.0.3, org.grails.plugins:yammer-metrics:zip:3.0.1-2: Could not transfer artifact org.codehaus.groovy:groovy-all:jar:2.4.4 from/to grailsCentral (https://repo.grails.org/grails/plugins): repo.grails.org | Run 'grails dependency-report' for further information. | Error The following artifacts could not be resolved: org.codehaus.groovy:groovy-all:jar:2.4.4, org.springframework:spring-webmvc:jar:4.1.8.RELEASE, org.springframework:spring-context-support:jar:4.1.8.RELEASE, org.springframework:spring-jdbc:jar:4.1.8.RELEASE, org.springframework:spring-context:jar:4.1.8.RELEASE, org.springframework:spring-core:jar:4.1.8.RELEASE, org.springframework:spring-beans:jar:4.1.8.RELEASE, org.springframework:spring-web:jar:4.1.8.RELEASE, org.springframework:spring-tx:jar:4.1.8.RELEASE, mysql:mysql-connector-java:jar:5.1.29, org.postgresql:postgresql:jar:9.3-1101-jdbc41, commons-codec:commons-codec:jar:1.2, org.json:json:jar:20140107, org.hibernate:hibernate-tools:jar:3.2.0.ga, org.grails.plugins:rest-api-doc:zip:0.6, org.grails.plugins:scaffolding:zip:2.1.2, org.grails.plugins:cache:zip:1.1.8, org.grails.plugins:cache-ehcache:zip:1.0.5, org.grails.plugins:asset-pipeline:zip:2.1.5, org.grails.plugins:spring-websocket:zip:1.2.0, org.grails.plugins:shiro:zip:1.2.1, org.grails.plugins:audit-logging:zip:1.0.3, org.grails.plugins:hibernate4:zip:4.3.8.1, org.grails.plugins:database-migration:zip:1.4.1, org.grails.plugins:jquery-ui:zip:1.10.4, org.grails.plugins:jquery:zip:1.11.1, org.grails.plugins:twitter-bootstrap:zip:3.3.5, org.grails.plugins:yammer-metrics:zip:3.0.1-2, org.grails.plugins:rest-client-builder:zip:2.1.1: Could not transfer artifact org.codehaus.groovy:groovy-all:jar:2.4.4 from/to grailsCentral (https://repo.grails.org/grails/plugins): repo.grails.org | Run 'grails dependency-report' for further information. | Error The following artifacts could not be resolved: org.codehaus.groovy:groovy-all:jar:2.4.4, org.springframework:spring-webmvc:jar:4.1.8.RELEASE, org.springframework:spring-context-support:jar:4.1.8.RELEASE, org.springframework:spring-jdbc:jar:4.1.8.RELEASE, org.springframework:spring-context:jar:4.1.8.RELEASE, org.springframework:spring-core:jar:4.1.8.RELEASE, org.springframework:spring-beans:jar:4.1.8.RELEASE, org.springframework:spring-web:jar:4.1.8.RELEASE, org.springframework:spring-tx:jar:4.1.8.RELEASE, org.springframework:spring-test:jar:4.1.8.RELEASE, cglib:cglib-nodep:jar:2.2.2, mysql:mysql-connector-java:jar:5.1.29, org.postgresql:postgresql:jar:9.3-1101-jdbc41, commons-codec:commons-codec:jar:1.2, org.json:json:jar:20140107, org.hibernate:hibernate-tools:jar:3.2.0.ga, org.grails:grails-datastore-test-support:jar:1.0.2-grails-2.4, org.grails.plugins:rest-api-doc:zip:0.6, org.grails.plugins:scaffolding:zip:2.1.2, org.grails.plugins:cache:zip:1.1.8, org.grails.plugins:cache-ehcache:zip:1.0.5, org.grails.plugins:asset-pipeline:zip:2.1.5, org.grails.plugins:spring-websocket:zip:1.2.0, org.grails.plugins:shiro:zip:1.2.1, org.grails.plugins:audit-logging:zip:1.0.3, org.grails.plugins:hibernate4:zip:4.3.8.1, org.grails.plugins:database-migration:zip:1.4.1, org.grails.plugins:jquery-ui:zip:1.10.4, org.grails.plugins:jquery:zip:1.11.1, org.grails.plugins:twitter-bootstrap:zip:3.3.5, org.grails.plugins:yammer-metrics:zip:3.0.1-2, org.grails.plugins:rest-client-builder:zip:2.1.1, org.grails.plugins:code-coverage:zip:2.0.3-3: Could not transfer artifact org.codehaus.groovy:groovy-all:jar:2.4.4 from/to grailsCentral (https://repo.grails.org/grails/plugins): repo.grails.org | Run 'grails dependency-report' for further information. | Environment set to development. | Error The following artifacts could not be resolved: org.codehaus.groovy:groovy-all:jar:2.4.4, org.apache.httpcomponents:httpcore:jar:4.3.2, org.apache.httpcomponents:httpclient:jar:4.3.2, org.apache.httpcomponents:httpmime:jar:4.3.3, org.grails.plugins:tomcat:zip:7.0.55.2, org.grails.plugins:coveralls:zip:0.1.3, org.grails.plugins:rest-client-builder:zip:2.1.1: Could not transfer artifact org.codehaus.groovy:groovy-all:jar:2.4.4 from/to grailsCentral (https://repo.grails.org/grails/plugins): repo.grails.org (scope: build) (Use --stacktrace to see the full trace)

nathandunn commented 8 years ago

@entzn Some questions to try and find the problem:

0 - You should use 2.0.4, the latest release if possible: https://github.com/GMOD/Apollo/releases/tag/2.0.4 1 - What command did you use to build with? 2 - What version of Java are you using? 3 - Do you have grails installed? If so, what version? (you don't need to install it, it will download automatically) 4 - Are you running it from within the Apollo directory (i.e. did you change into the directory you cloned / downloaded into before running the command)?

entzn commented 8 years ago

0 - You should use 2.0.4, the latest release if possible: https://github.com/GMOD/Apollo/releases/tag/2.0.4 ok

1 - What command did you use to build with? ./apollo run-local 2 - What version of Java are you using? java version "1.7.0_75" 3 - Do you have grails installed? If so, what version? (you don't need to install it, it will download automatically) Auto install done by using SDKMANhttp://sdkman.io/ – grails 2.5.5 4 - Are you running it from within the Apollo directory (i.e. did you change into the directory you cloned / downloaded into before running the command)? Yes

Thanks, keith.mcwhite@bayer.commailto:keith.mcwhite@bayer.com To request work: http://jira.be.bayercropsciencehttp://jira.be.bayercropscience/

From: Nathan Dunn [mailto:notifications@github.com] Sent: Monday, August 29, 2016 3:59 PM To: GMOD/Apollo Cc: Keith McWhite; Mention Subject: Re: [GMOD/Apollo] Apollo-2.0.3 Build Successful - with Multiple Errors (#1232)

@entznhttps://github.com/entzn Some questions to try and find the problem:

0 - You should use 2.0.4, the latest release if possible: https://github.com/GMOD/Apollo/releases/tag/2.0.4 1 - What command did you use to build with? 2 - What version of Java are you using? 3 - Do you have grails installed? If so, what version? (you don't need to install it, it will download automatically) 4 - Are you running it from within the Apollo directory (i.e. did you change into the directory you cloned / downloaded into before running the command)?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/GMOD/Apollo/issues/1232#issuecomment-243237201, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ART3skbFp6RZgQF3VxE7vDsg0eoWgD6jks5qkzoTgaJpZM4Jv1LX.

nathandunn commented 8 years ago

That all looks good. 2.0.4 vs 2.0.3 shouldn't make any difference. More questions to see if I can't reproduce / fix:

1 - What happens if you run grails dependency-report? 2 - What OS are you running? 3 - I'm assuming you have other grails and/or maven projects?

nathandunn commented 8 years ago

Also, I wonder if you are able to see this link (to determine if its a firewall issue):

https://repo.grails.org/grails/plugins/

entzn commented 8 years ago

1 - What happens if you run grails dependency-report? -- attached

2 - What OS are you running? Description: Red Hat Enterprise Linux Server release 6.8 (Santiago) Release: 6.8 Codename: Santiago

3 - I'm assuming you have other grails and/or maven projects? - I can uninstall/reinstall

Thanks, keith.mcwhite@bayer.commailto:keith.mcwhite@bayer.com To request work: http://jira.be.bayercropsciencehttp://jira.be.bayercropscience/

From: Nathan Dunn [mailto:notifications@github.com] Sent: Monday, August 29, 2016 4:17 PM To: GMOD/Apollo Cc: Keith McWhite; Mention Subject: Re: [GMOD/Apollo] Apollo-2.0.3 Build Successful - with Multiple Errors (#1232)

That all looks good. 2.0.4 vs 2.0.3 shouldn't make any difference. More questions to see if I can't reproduce / fix:

1 - What happens if you run grails dependency-report? 2 - What OS are you running? 3 - I'm assuming you have other grails and/or maven projects?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/GMOD/Apollo/issues/1232#issuecomment-243242050, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ART3sk8obVVyzvP5MvUp6qqc5CFjOeQFks5qkz4ggaJpZM4Jv1LX.

nathandunn commented 8 years ago

Usually, when I run into this error I remove the grails and maven cache and that will typically fix it:

rm -rf ~/.grails/ivy-cache/*

If that doesn't work doing a re-deploy:

rm -rf ~/.grails/*

Finally if that doesn't work try this via a re-deploy:

rm -rf ~/.m2/repository/*

Let me know how it goes.

entzn commented 8 years ago

Yes – I see the link

Thanks, keith.mcwhite@bayer.commailto:keith.mcwhite@bayer.com To request work: http://jira.be.bayercropsciencehttp://jira.be.bayercropscience/

From: Nathan Dunn [mailto:notifications@github.com] Sent: Monday, August 29, 2016 4:20 PM To: GMOD/Apollo Cc: Keith McWhite; Mention Subject: Re: [GMOD/Apollo] Apollo-2.0.3 Build Successful - with Multiple Errors (#1232)

Also, I wonder if you are able to see this link (to determine if its a firewall issue):

https://repo.grails.org/grails/plugins/

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/GMOD/Apollo/issues/1232#issuecomment-243242856, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ART3sjttkowSlD8SKQabNOllf7p1Oop3ks5qkz7agaJpZM4Jv1LX.

entzn commented 8 years ago

Again, BUILD SUCCESSFUL

[entzn@ausress9810] Apollo-2.0.4 $ ./apollo run-local Defining custom 'build' task when using the standard Gradle lifecycle plugins has been deprecated and is scheduled to be removed in Gradle 3.0 No log file found in classpath. final JBrowse settings [git:[url:https://github.com/gmod/jbrowse, tag:1.12.2-apollo, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]] final plugins [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]] Copying apollo plugin handling jbrowse release [git:[url:https://github.com/gmod/jbrowse, tag:1.12.2-apollo, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]] handling jbrowse [git:[url:https://github.com/gmod/jbrowse, tag:1.12.2-apollo, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]] :evaluateJBrowseConfigs UP-TO-DATE :installJBrowse installing jbrowse [git:[url:https://github.com/gmod/jbrowse, tag:1.12.2-apollo, alwaysPull:false, alwaysRecheck:false], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]] Cloning: https://github.com/gmod/jbrowse into jbrowse-download. using bower to install: gmod/jbrowse#1.12.2-apollo bower jbrowse#1.12.2-apollo cached https://github.com/gmod/jbrowse.git#1.12.2-apollo bower jbrowse#1.12.2-apollo validate 1.12.2-apollo against https://github.com/gmod/jbrowse.git#1.12.2-apollo bower jDataView#* not-cached https://github.com/rbuels/jDataView.git# bower jDataView#* resolve https://github.com/rbuels/jDataView.git# bower jszlib#* not-cached https://github.com/rbuels/jszlib.git# bower jszlib#* resolve https://github.com/rbuels/jszlib.git# bower FileSaver#* not-cached https://github.com/dkasenberg/FileSaver.js.git# bower FileSaver#* resolve https://github.com/dkasenberg/FileSaver.js.git# bower lazyload#amd not-cached https://github.com/rbuels/lazyload.git#amd bower lazyload#amd resolve https://github.com/rbuels/lazyload.git#amd bower dbind#* not-cached https://github.com/rbuels/dbind.git# bower dbind#* resolve https://github.com/rbuels/dbind.git# bower util#1.9.8 cached https://github.com/dojo/util.git#1.9.8 bower util#1.9.8 validate 1.9.8 against https://github.com/dojo/util.git#1.9.8 bower json-schema#0.2.1 cached https://github.com/kriszyp/json-schema.git#0.2.1 bower json-schema#0.2.1 validate 0.2.1 against https://github.com/kriszyp/json-schema.git#0.2.1 bower dojo#1.9.8 cached https://github.com/dojo/dojo.git#1.9.8 bower dojo#1.9.8 validate 1.9.8 against https://github.com/dojo/dojo.git#1.9.8 bower dojox#1.9.8 cached https://github.com/dojo/dojox.git#1.9.8 bower dojox#1.9.8 validate 1.9.8 against https://github.com/dojo/dojox.git#1.9.8 bower put-selector#0.3.6 cached https://github.com/kriszyp/put-selector.git#0.3.6 bower put-selector#0.3.6 validate 0.3.6 against https://github.com/kriszyp/put-selector.git#0.3.6 bower dgrid#0.3.17 cached https://github.com/SitePen/dgrid.git#0.3.17 bower dgrid#0.3.17 validate 0.3.17 against https://github.com/SitePen/dgrid.git#0.3.17 bower dijit#1.9.8 cached https://github.com/dojo/dijit.git#1.9.8 bower dijit#1.9.8 validate 1.9.8 against https://github.com/dojo/dijit.git#1.9.8 bower xstyle#0.3.1 cached https://github.com/kriszyp/xstyle.git#0.3.1 bower xstyle#0.3.1 validate 0.3.1 against https://github.com/kriszyp/xstyle.git#0.3.1 bower jszlib#* checkout master bower jDataView#* checkout master bower lazyload#amd checkout amd bower FileSaver#* checkout master bower dbind#* checkout master bower jszlib#* resolved https://github.com/rbuels/jszlib.git#18cd14e592 bower jDataView#* resolved https://github.com/rbuels/jDataView.git#db0893d468 bower FileSaver#* invalid-meta The "name" is recommended to be lowercase, can contain digits, dots, dashes bower FileSaver#* resolved https://github.com/dkasenberg/FileSaver.js.git#4f79d8e666 bower dbind#* resolved https://github.com/rbuels/dbind.git#2b70834f3b bower lazyload#amd resolved https://github.com/rbuels/lazyload.git#d428749c54 bower jbrowse#1.12.2-apollo install jbrowse#1.12.2-apollo bower json-schema#0.2.1 install json-schema#0.2.1 bower util#1.9.8 install util#1.9.8 bower put-selector#0.3.6 install put-selector#0.3.6 bower dojo#1.9.8 install dojo#1.9.8 bower dojox#1.9.8 install dojox#1.9.8 bower xstyle#0.3.1 install xstyle#0.3.1 bower dijit#1.9.8 install dijit#1.9.8 bower dgrid#0.3.17 install dgrid#0.3.17 bower jszlib#* install jszlib#18cd14e592 bower jDataView#* install jDataView#db0893d468 bower FileSaver#* install FileSaver#4f79d8e666 bower dbind#* install dbind#2b70834f3b bower lazyload#amd install lazyload#d428749c54

jbrowse#1.12.2-apollo bower_components/jbrowse ├── FileSaver#4f79d8e666 ├── dbind#2b70834f3b ├── dgrid#0.3.17 ├── dijit#1.9.8 ├── dojo#1.9.8 ├── dojox#1.9.8 ├── jDataView#db0893d468 ├── json-schema#0.2.1 ├── jszlib#18cd14e592 ├── lazyload#d428749c54 ├── put-selector#0.3.6 ├── util#1.9.8 └── xstyle#0.3.1

json-schema#0.2.1 bower_components/json-schema

util#1.9.8 bower_components/util

put-selector#0.3.6 bower_components/put-selector

dojo#1.9.8 bower_components/dojo

dojox#1.9.8 bower_components/dojox

xstyle#0.3.1 bower_components/xstyle

dijit#1.9.8 bower_components/dijit

dgrid#0.3.17 bower_components/dgrid

jszlib#18cd14e592 bower_components/jszlib

jDataView#db0893d468 bower_components/jDataView

FileSaver#4f79d8e666 bower_components/FileSaver

dbind#2b70834f3b bower_components/dbind

lazyload#d428749c54 bower_components/lazyload Moving JBrowse into position gmod/jbrowse#1.12.2-apollo Dojo does not exist, installing bower FileSaver#* invalid-meta The "name" is recommended to be lowercase, can contain digits, dots, dashes Installing Perl prerequisites ... done.

Formatting Volvox example data ... failed. See setup.log file for error messages.

Formatting Yeast example data ... failed. See setup.log file for error messages.

Building and installing legacy wiggle format support (superseded by BigWig tracks) ... done.

Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ... done. :copyApolloPlugin :installJBrowsePlugins installing jbrowse plugins [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]] Evaluating plugin WebApollo=[included:true] Plugin jbrowse-download/plugins/WebApollo exists and appears valid. Evaluating plugin RegexSequenceSearch=[included:true] Plugin jbrowse-download/plugins/RegexSequenceSearch exists and appears valid. Evaluating plugin HideTrackLabels=[included:true] Plugin jbrowse-download/plugins/HideTrackLabels exists and appears valid. :handleJBrowse :copy.apollo.plugin.webapp :setup-jbrowse [ant:echo] copying plugin to jbrowse git ... [ant:echo] Will be setting up jbrowse :copy-resources :copyResourcesDev found jbrowse directory false Installing Perl prerequisites ...Prerequisites installed, finished. :javac Note: /gpfs/rtp/.filesets/biogrid_root/tools/bioinfo/app/Apollo-2.0.4/src/gwt/org/bbop/apollo/gwt/client/ReferenceSequenceOracle.java uses or overrides a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. :gwtc

BUILD SUCCESSFUL

Total time: 4 mins 11.424 secs

This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.ht| Configuring classpath | Error Resolve error obtaining dependencies: The following artifacts could not be resolved: org.codehaus.groovy:groovy-all:jar:2.4.4, org.apache.httpcomponents:httpcore:jar:4.3.2, org.apache.httpcomponents:httpclient:jar:4.3.2, org.apache.httpcomponents:httpmime:jar:4.3.3, org.grails.plugins:tomcat:zip:7.0.55.2, org.grails.plugins:coveralls:zip:0.1.3, org.grails.plugins:rest-client-builder:zip:2.1.1: Could not transfer artifact org.codehaus.groovy:groovy-all:jar:2.4.4 from/to grailsCentral (https://repo.grails.org/grails/plugins): repo.grails.org (Use --stacktrace to see the full trace) | Error Resolve error obtaining dependencies: The following artifacts could not be resolved: org.codehaus.groovy:groovy-all:jar:2.4.4, org.springframework:spring-webmvc:jar:4.1.8.RELEASE, org.springframework:spring-context-support:jar:4.1.8.RELEASE, org.springframework:spring-jdbc:jar:4.1.8.RELEASE, org.springframework:spring-context:jar:4.1.8.RELEASE, org.springframework:spring-core:jar:4.1.8.RELEASE, org.springframework:spring-beans:jar:4.1.8.RELEASE, org.springframework:spring-web:jar:4.1.8.RELEASE, org.springframework:spring-tx:jar:4.1.8.RELEASE, org.springframework:spring-test:jar:4.1.8.RELEASE, cglib:cglib-nodep:jar:2.2.2, mysql:mysql-connector-java:jar:5.1.29, org.postgresql:postgresql:jar:9.3-1101-jdbc41, commons-codec:commons-codec:jar:1.2, org.json:json:jar:20140107, org.hibernate:hibernate-tools:jar:3.2.0.ga, org.grails:grails-datastore-test-support:jar:1.0.2-grails-2.4, org.grails.plugins:rest-api-doc:zip:0.6, org.grails.plugins:scaffolding:zip:2.1.2, org.grails.plugins:cache:zip:1.1.8, org.grails.plugins:cache-ehcache:zip:1.0.5, org.grails.plugins:asset-pipeline:zip:2.1.5, org.grails.plugins:spring-websocket:zip:1.2.0, org.grails.plugins:shiro:zip:1.2.1, org.grails.plugins:audit-logging:zip:1.0.3, org.grails.plugins:hibernate4:zip:4.3.8.1, org.grails.plugins:database-migration:zip:1.4.1, org.grails.plugins:jquery-ui:zip:1.10.4, org.grails.plugins:jquery:zip:1.11.1, org.grails.plugins:twitter-bootstrap:zip:3.3.5, org.grails.plugins:yammer-metrics:zip:3.0.1-2, org.grails.plugins:rest-client-builder:zip:2.1.1, org.grails.plugins:code-coverage:zip:2.0.3-3: Could not transfer artifact org.codehaus.groovy:groovy-all:jar:2.4.4 from/to grailsCentral (https://repo.grails.org/grails/plugins): repo.grails.org (Use --stacktrace to see the full trace) | Error Resolve error obtaining dependencies: The following artifacts could not be resolved: org.codehaus.groovy:groovy-all:jar:2.4.4, org.springframework:spring-webmvc:jar:4.1.8.RELEASE, org.springframework:spring-context-support:jar:4.1.8.RELEASE, org.springframework:spring-jdbc:jar:4.1.8.RELEASE, org.springframework:spring-context:jar:4.1.8.RELEASE, org.springframework:spring-core:jar:4.1.8.RELEASE, org.springframework:spring-beans:jar:4.1.8.RELEASE, org.springframework:spring-web:jar:4.1.8.RELEASE, org.springframework:spring-tx:jar:4.1.8.RELEASE, mysql:mysql-connector-java:jar:5.1.29, org.postgresql:postgresql:jar:9.3-1101-jdbc41, commons-codec:commons-codec:jar:1.2, org.json:json:jar:20140107, org.hibernate:hibernate-tools:jar:3.2.0.ga, org.grails.plugins:rest-api-doc:zip:0.6, org.grails.plugins:scaffolding:zip:2.1.2, org.grails.plugins:cache:zip:1.1.8, org.grails.plugins:cache-ehcache:zip:1.0.5, org.grails.plugins:asset-pipeline:zip:2.1.5, org.grails.plugins:spring-websocket:zip:1.2.0, org.grails.plugins:shiro:zip:1.2.1, org.grails.plugins:audit-logging:zip:1.0.3, org.grails.plugins:hibernate4:zip:4.3.8.1, org.grails.plugins:database-migration:zip:1.4.1, org.grails.plugins:jquery-ui:zip:1.10.4, org.grails.plugins:jquery:zip:1.11.1, org.grails.plugins:twitter-bootstrap:zip:3.3.5, org.grails.plugins:yammer-metrics:zip:3.0.1-2, org.grails.plugins:rest-client-builder:zip:2.1.1: Could not transfer artifact org.codehaus.groovy:groovy-all:jar:2.4.4 from/to grailsCentral (https://repo.grails.org/grails/plugins): repo.grails.org (Use --stacktrace to see the full trace) | Error Resolve error obtaining dependencies: The following artifacts could not be resolved: org.codehaus.groovy:groovy-all:jar:2.4.4, org.springframework:spring-webmvc:jar:4.1.8.RELEASE, org.springframework:spring-context-support:jar:4.1.8.RELEASE, org.springframework:spring-jdbc:jar:4.1.8.RELEASE, org.springframework:spring-context:jar:4.1.8.RELEASE, org.springframework:spring-core:jar:4.1.8.RELEASE, org.springframework:spring-beans:jar:4.1.8.RELEASE, org.springframework:spring-web:jar:4.1.8.RELEASE, org.springframework:spring-tx:jar:4.1.8.RELEASE, commons-codec:commons-codec:jar:1.2, org.json:json:jar:20140107, org.hibernate:hibernate-tools:jar:3.2.0.ga, org.grails.plugins:rest-api-doc:zip:0.6, org.grails.plugins:scaffolding:zip:2.1.2, org.grails.plugins:cache:zip:1.1.8, org.grails.plugins:cache-ehcache:zip:1.0.5, org.grails.plugins:asset-pipeline:zip:2.1.5, org.grails.plugins:spring-websocket:zip:1.2.0, org.grails.plugins:shiro:zip:1.2.1, org.grails.plugins:audit-logging:zip:1.0.3, org.grails.plugins:yammer-metrics:zip:3.0.1-2: Could not transfer artifact org.codehaus.groovy:groovy-all:jar:2.4.4 from/to grailsCentral (https://repo.grails.org/grails/plugins): repo.grails.org (Use --stacktrace to see the full trace) | Error The following artifacts could not be resolved: org.codehaus.groovy:groovy-all:jar:2.4.4, org.apache.httpcomponents:httpcore:jar:4.3.2, org.apache.httpcomponents:httpclient:jar:4.3.2, org.apache.httpcomponents:httpmime:jar:4.3.3, org.grails.plugins:tomcat:zip:7.0.55.2, org.grails.plugins:coveralls:zip:0.1.3, org.grails.plugins:rest-client-builder:zip:2.1.1: Could not transfer artifact org.codehaus.groovy:groovy-all:jar:2.4.4 from/to grailsCentral (https://repo.grails.org/grails/plugins): repo.grails.org | Run 'grails dependency-report' for further information.

entzn commented 8 years ago

grails dependency-report

[entzn@ausress9810] app $ Downloading: cglib-2.2.2.jar :: problems summary :: :::: WARNINGS module not found: org.codehaus.groovy#groovy-all;2.4.4 ==== grailsPlugins: tried -- artifact org.codehaus.groovy#groovy-all;2.4.4!groovy-all.jar: /gpfs/rtp/.filesets/biogrid_root/tools/bioinfo/app/lib/groovy-all-2.4.4.jar ==== grailsHome: tried /home/entzn/.sdkman/candidates/grails/current/lib/org.codehaus.groovy/groovy-all/ivy-2.4.4.xml -- artifact org.codehaus.groovy#groovy-all;2.4.4!groovy-all.jar: /home/entzn/.sdkman/candidates/grails/current/lib/org.codehaus.groovy/groovy-all/jars/groovy-all-2.4.4.jar /home/entzn/.sdkman/candidates/grails/current/lib/org.codehaus.groovy/groovy-all/bundles/groovy-all-2.4.4.jar ==== grailsHome: tried /home/entzn/.sdkman/candidates/grails/current/dist/groovy-all-2.4.4.pom -- artifact org.codehaus.groovy#groovy-all;2.4.4!groovy-all.jar: /home/entzn/.sdkman/candidates/grails/current/dist/groovy-all-2.4.4.jar ==== grailsHome: tried /home/entzn/.grails/2.5.5/cached-installed-plugins/groovy-all-2.4.4.xml -- artifact org.codehaus.groovy#groovy-all;2.4.4!groovy-all.jar: /home/entzn/.grails/2.5.5/cached-installed-plugins/groovy-all-2.4.4.jar ==== grailsHome: tried /home/entzn/.sdkman/candidates/grails/current/plugins/groovy-all-2.4.4.pom -- artifact org.codehaus.groovy#groovy-all;2.4.4!groovy-all.jar: /home/entzn/.sdkman/candidates/grails/current/plugins/groovy-all-2.4.4.jar 
            ::          UNRESOLVED DEPENDENCIES         ::
            ::::::::::::::::::::::::::::::::::::::::::::::
            :: org.codehaus.groovy#groovy-all;2.4.4: not found
            ::::::::::::::::::::::::::::::::::::::::::::::

| Error Resolve error obtaining dependencies: Failed to resolve dependencies (Set log level to 'warn' in BuildConfig.groovy for more information):

| Error Resolve error obtaining dependencies: Failed to resolve dependencies (Set log level to 'warn' in BuildConfig.groovy for more information):

| Error Resolve error obtaining dependencies: Failed to resolve dependencies (Set log level to 'warn' in BuildConfig.groovy for more information):

| Run 'grails dependency-report' for further information. | Error Failed to resolve dependencies (Set log level to 'warn' in BuildConfig.groovy for more information):

| Run 'grails dependency-report' for further information. | Error Failed to resolve dependencies (Set log level to 'warn' in BuildConfig.groovy for more information):

| Run 'grails dependency-report' for further information. | Error /gpfs/rtp/.filesets/biogrid_root/tools/bioinfo/app does not appear to be part of a Grails application. | Error The following commands are supported outside of a project: add-proxy clear-proxy create-app create-multi-project-build create-plugin help install-app-templates list-plugins package-plugin plugin-info remove-proxy set-proxy | Run 'grails help' for a complete list of available scripts. [entzn@ausress9810] app $

nathandunn commented 8 years ago

Looking at this the recommend doing this:

rm -rf ~/.sdkman/candidates/grails/2.5.5/
sdk install grails 2.5.5
sdk use grails 2.5.5

Keep in mind that unless you are actually doing development, you don't need to explicitly install grails.

entzn commented 8 years ago

did rm -rf ~/.sdkman/candidates/grails/2.5.5/

then ran [entzn@ausress9810] Apollo-2.0.4 $ ./apollo run-local 8085

BUILD SUCCESSFUL

Total time: 55.16 secs

This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.html Downloading https://github.com/grails/grails-core/releases/download/v2.5.5/grails-2.5.5.zip to /home/entzn/.grails/wrapper/grails-2.5.5-download.zip

Exception in thread "main" java.net.UnknownHostException: github.com at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:178) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) at java.net.Socket.connect(Socket.java:579) at sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:625) at sun.security.ssl.BaseSSLSocketImpl.connect(BaseSSLSocketImpl.java:160) at sun.net.NetworkClient.doConnect(NetworkClient.java:180) at sun.net.www.http.HttpClient.openServer(HttpClient.java:432) at sun.net.www.http.HttpClient.openServer(HttpClient.java:527) at sun.net.www.protocol.https.HttpsClient.(HttpsClient.java:275) at sun.net.www.protocol.https.HttpsClient.New(HttpsClient.java:371) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(AbstractDelegateHttpsURLConnection.java:191) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:933) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:177) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1301) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:254) at org.grails.wrapper.RemoteFileHelper.retrieve(RemoteFileHelper.java:49) at org.grails.wrapper.GrailsWrapper.configureGrailsInstallation(GrailsWrapper.java:137) at org.grails.wrapper.GrailsWrapper.main(GrailsWrapper.java:57)

nathandunn commented 8 years ago

I think you have a firewall or DNS issue if can't find github.

Can you do:

wget https://github.com/grails/grails-core/releases/download/v2.5.5/grails-2.5.5.zip from the same server just to see if it works?

Also note that it does a redirect to AWS, which might also screw up the firewall.

If this doesn't work, you can try installing grails 2.5.5 from sdkman again before you attempt the firewall issues, but I feel like you may end up with additional issues if that isn't resolved.

nathandunn commented 8 years ago

@entzn If internet issues are continuing to cause problems, I'm not sure if installing via docker might make more sense if you have experience with that:

https://hub.docker.com/r/gmod/apollo/tags/

or

https://github.com/GMOD/docker-compose-galaxy-annotation

However, you're still pulling a lot of stuff down remotely, so who knows.

nathandunn commented 8 years ago

@entzn Were you able to resolve your issues? I'm happy to emulate your system to reproduce it.

entzn commented 8 years ago

Hi - We are unable to use Docker - since Docker requires that your kernel must be 3.10 at minimum...Currently at we are at kernel 2.6 for Release 6.8

So currently we [still Receive the Below]

Installing Perl prerequisites ...Prerequisites installed, finished. :javac :gwtc

BUILD SUCCESSFUL

Total time: 56.915 secs

This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.html Downloading https://github.com/grails/grails-core/releases/download/v2.5.5/grails-2.5.5.zip to /home/entzn/.grails/wrapper/grails-2.5.5-download.zip

Exception in thread "main" java.net.UnknownHostException: github.com at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:178) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) at java.net.Socket.connect(Socket.java:579) at sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:625) at sun.security.ssl.BaseSSLSocketImpl.connect(BaseSSLSocketImpl.java:160) at sun.net.NetworkClient.doConnect(NetworkClient.java:180) at sun.net.www.http.HttpClient.openServer(HttpClient.java:432) at sun.net.www.http.HttpClient.openServer(HttpClient.java:527) at sun.net.www.protocol.https.HttpsClient.(HttpsClient.java:275) at sun.net.www.protocol.https.HttpsClient.New(HttpsClient.java:371) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(AbstractDelegateHttpsURLConnection.java:191) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:933) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:177) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1301) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:254) at org.grails.wrapper.RemoteFileHelper.retrieve(RemoteFileHelper.java:49) at org.grails.wrapper.GrailsWrapper.configureGrailsInstallation(GrailsWrapper.java:137) at org.grails.wrapper.GrailsWrapper.main(GrailsWrapper.java:57) [entzn@ausress9810] Apollo-2.0.4 $

nathandunn commented 8 years ago

I think the problem is that your DNS is failing to resolve on your system properly (or minimally have it handle redirects) and you're going to need to talk to your IT group to figure out how to resolve this issue, since it will need to pull from AWS, different maven mirrors, github, cpan, etc. in order to build the system.

So a few more things:

1 - I can provide you with a pre-built image to run ./apollo run-local on, but no guarantee that it will work on your system.

2 - give me a system to emulate. I'll fire off an AWS instance and I'll see if I can't reproduce / fix any issues.

3 - try SDKMAN again. rm -rf ~/.sdkman/candidates/grails/ rm -rf ~/.m2 sdk install grails 2.5.5``./apollo run-local` I think you'll end up running into the exact same issue, though.

nathandunn commented 8 years ago

@entzn I'm going to close this for now as it sounds like a DNS issue. A lot of the folks we work with also have to live life behind a firewall, so it wouldn't hurt to suggest some of these issues to. You may want to post to our list:

apollo@lists.lbl.gov

I'm pretty sure that you can get it up on an secure AWS server (we do this often). If you want me to generate a public image to work off of, let me know (the one we have up there is a bit out of date).

entzn commented 8 years ago

yes - I'm interested in assistance on having this loaded on a secure AWS server

nathandunn commented 8 years ago

Great. If I create a public aws image you'll be able to use it?

Nathan

On Sep 8, 2016, at 6:14 AM, entzn notifications@github.com wrote:

yes - I'm interested in assistance on having this loaded on a secure AWS server

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entzn commented 8 years ago

well I would need the instructions because Bayer has an AWS account with a few instances created

nathandunn commented 8 years ago

I tried to make the most recent version a Community AMI, though it might take awhile for it to appear. The ID is: ami-a74898c7 and it should have honeybee preloaded. The url should be http://:8080/apollo/

screen shot 2016-09-08 at 12 07 12 pm

Obviously moving it into production I would suggest https over apache or nginx, but hopefully this will get you started.

nathandunn commented 8 years ago

Conversely, you could try installing Apollo 2.0.4 directly on an AWS instance, however, I think starting with the AMI will solve a lot of time and hassle.

entzn commented 8 years ago

Hi, Thanks! I’ll look for the instance.

Thanks, keith.mcwhite@bayer.commailto:keith.mcwhite@bayer.com To request work: http://jira.be.bayercropsciencehttp://jira.be.bayercropscience/

From: Nathan Dunn [mailto:notifications@github.com] Sent: Thursday, September 08, 2016 3:10 PM To: GMOD/Apollo Cc: Keith McWhite; Mention Subject: Re: [GMOD/Apollo] Apollo-2.0.3 Build Successful - with Multiple Errors (#1232)

I tried to make the most recent version a Community AMI, though it might take awhile for it to appear. The ID is: ami-a74898c7 and it should have honeybee preloaded. The url should be http://:8080/apollo/

[screen shot 2016-09-08 at 12 07 12 pm]https://cloud.githubusercontent.com/assets/751274/18362964/ebc2a8b6-75bc-11e6-8f17-b2d65367696e.png

Obviously moving it into production I would suggest https over apache or nginx, but hopefully this will get you started.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/GMOD/Apollo/issues/1232#issuecomment-245707018, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ART3svXRP7RAYbowwXVDi1-MnO5JFksdks5qoF2VgaJpZM4Jv1LX.

entzn commented 8 years ago

hi -In Community AMI's - I still get 'No AMI matching' - ami-a74898c7

nathandunn commented 8 years ago

@entzn Ah, it is because it is only in Oregon region. Apologize. I did not think of that. Let me know if you want me to copy it into a different region or if you can use it from there.

entzn commented 8 years ago

hi - yes can you place it in east coast - virginia

nathandunn commented 8 years ago

It should be there now if search ask for Apollo 2.0.4 (the image is ami-a74898c7). Note the login directories. Let me know how it works.

Nathan

On Sep 28, 2016, at 6:40 AM, entzn notifications@github.com wrote:

hi - yes can you place it in east coast - virginia

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