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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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compilation error: startup failed. #1198

Closed arcadeo closed 8 years ago

arcadeo commented 8 years ago

Hi there, I'm trying to test Apollo on my server (RHEL6), but I keep encountering this issue. Any help would be appreciated. ./apollo run-local Buildfile: ~/Apollo/build.xml

copy.apollo.plugin.webapp:

setup-jbrowse:

git.clone: [exec] Result: 128

copy.apollo.plugin.jbrowse: [echo] copying plugin to jbrowse git ... [echo] Will be setting up jbrowse [delete] Deleting directory ~/Apollo/web-app/jbrowse [copy] Copying 1284 files to ~/Apollo/web-app/jbrowse [copy] Copied 582 empty directories to 13 empty directories under ~/Apollo/web-app/jbrowse

install.jbrowse.perl:

copy-resources:

javac: [mkdir] Created dir: ~/Apollo/target/classes/gwt [javac] Compiling 63 source files to ~/Apollo/target/classes/gwt [javac] Note: ~/Apollo/src/gwt/org/bbop/apollo/gwt/client/ReferenceSequenceOracle.java uses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 65 files to ~/Apollo/target/classes [copy] Copied 20 empty directories to 3 empty directories under ~/Apollo/target/classes

gwtc: [java] Compiling module org.bbop.apollo.gwt.Annotator [java] Compiling 5 permutations [java] Compiling permutation 0... [java] Compiling permutation 1... [java] Compiling permutation 2... [java] Compiling permutation 3... [java] Compiling permutation 4... [java] Compile of permutations succeeded [java] Compilation succeeded -- 54.213s [java] Linking into ~/Apollo/web-app/annotator [java] Link succeeded [java] Linking succeeded -- 0.865s

BUILD SUCCESSFUL | Compiling 192 source files. | Error Compilation error: startup failed: ~/Apollo/target/work/plugins/cache-1.1.7/grails-app/services/grails/plugin/cache/GrailsCacheAdminService.groovy: Could not find class for Transformation Processor grails.plugin.cache.compiler.CacheTransformation declared by grails.plugin.cache.CacheEvict ~/Apollo/target/work/plugins/cache-1.1.7/grails-app/services/grails/plugin/cache/GrailsCacheAdminService.groovy: Could not find class for Transformation Processor grails.plugin.cache.compiler.CacheTransformation declared by grails.plugin.cache.CacheEvict

2 errors

Thanks

nathandunn commented 8 years ago

Two quick questions:

1 - what version of Apollo are you using? 2 - what version of Java are you using (should be 7 or above, Oracle or OpenJDK should be fine)

Nathan

On Aug 8, 2016, at 11:57 AM, arcadeo notifications@github.com wrote:

Hi there, I'm trying to test Apollo on my server (RHEL6), but I keep encountering this issue. Any help would be appreciated. ./apollo run-local Buildfile: ~/Apollo/build.xml

copy.apollo.plugin.webapp:

setup-jbrowse:

git.clone: [exec] Result: 128

copy.apollo.plugin.jbrowse: [echo] copying plugin to jbrowse git ... [echo] Will be setting up jbrowse [delete] Deleting directory ~/Apollo/web-app/jbrowse [copy] Copying 1284 files to ~/Apollo/web-app/jbrowse [copy] Copied 582 empty directories to 13 empty directories under ~/Apollo/web-app/jbrowse

install.jbrowse.perl:

copy-resources:

javac: [mkdir] Created dir: ~/Apollo/target/classes/gwt [javac] Compiling 63 source files to ~/Apollo/target/classes/gwt [javac] Note: ~/Apollo/src/gwt/org/bbop/apollo/gwt/client/ReferenceSequenceOracle.java uses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 65 files to ~/Apollo/target/classes [copy] Copied 20 empty directories to 3 empty directories under ~/Apollo/target/classes

gwtc: [java] Compiling module org.bbop.apollo.gwt.Annotator [java] Compiling 5 permutations [java] Compiling permutation 0... [java] Compiling permutation 1... [java] Compiling permutation 2... [java] Compiling permutation 3... [java] Compiling permutation 4... [java] Compile of permutations succeeded [java] Compilation succeeded -- 54.213s [java] Linking into ~/Apollo/web-app/annotator [java] Link succeeded [java] Linking succeeded -- 0.865s

BUILD SUCCESSFUL | Compiling 192 source files. | Error Compilation error: startup failed: ~/Apollo/target/work/plugins/cache-1.1.7/grails-app/services/grails/plugin/cache/GrailsCacheAdminService.groovy: Could not find class for Transformation Processor grails.plugin.cache.compiler.CacheTransformation declared by grails.plugin.cache.CacheEvict ~/Apollo/target/work/plugins/cache-1.1.7/grails-app/services/grails/plugin/cache/GrailsCacheAdminService.groovy: Could not find class for Transformation Processor grails.plugin.cache.compiler.CacheTransformation declared by grails.plugin.cache.CacheEvict

2 errors

Thanks

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arcadeo commented 8 years ago

Hi Nathan, I'm trying to install/use Apollo-2.0.2. And I have Java 7 java version "1.7.0_111" OpenJDK Runtime Environment (rhel-2.6.7.2.el6_8-x86_64 u111-b01) OpenJDK 64-Bit Server VM (build 24.111-b01, mixed mode)

Arcadio

nathandunn commented 8 years ago

I think it has to do with an older version of that cache plugin, which we have since updated.

We are planning to release a 2.0.4 this week (knock on wood). I think what would be the most help is to download and install our third release candidate (we'll have at least one more before we release) and see if it that fixes the issue.

arcadeo commented 8 years ago

Thanks, I'll be on the lookout, and good luck with the release

nathandunn commented 8 years ago

Great. You might want to test this release candidate just to make sure it fixes your issue. Doing the "run-local" as you just did should be a sufficient test to make sure that it has fixed the problem.

monicacecilia commented 8 years ago

@arcadeo for your information, Apollo v 2.0.4 is now released. You can find it at https://github.com/GMOD/Apollo/releases/tag/2.0.4 We are very positive this version has addressed and solved the problem you reported in this issue. Please let us know if there is anything else we can do to help.