JBrowse build Fail - Githubissues

csmibrahim commented 5 years ago

I get this error on Ubuntu when I run ./apollo run-local

Gradle version: 2 Using system gradle 2.11 Node Version: 11 Npm Version: 6 Yarn Version: 1 javac 1.8.0_191 found javac installed JDK 1.8 found: javac 1.8.0_191

:installJBrowseWebOnly JBrowse already exists From https://github.com/gmod/jbrowse

tag 1.16.2-release -> FETCH_HEAD Already up-to-date. yarn install v1.13.0 [1/4] Resolving packages... [2/4] Fetching packages... info fsevents@1.2.4: The platform "linux" is incompatible with this module. info "fsevents@1.2.4" is an optional dependency and failed compatibility check. Excluding it from installation. [3/4] Linking dependencies... warning " > dojo-webpack-plugin@2.7.7" has unmet peer dependency "webpack-sources@>=1.0.1". warning " > extract-text-webpack-plugin@3.0.2" has incorrect peer dependency "webpack@^3.1.0". warning " > url-loader@0.5.7" has unmet peer dependency "file-loader@*". error An unexpected error occurred: "EFAULT: bad address in system call argument, copyfile '/home/XXX/.cache/yarn/v4/npm-@ava-babel-plugin-throws-helper-2.0.0-2fc1fe3c211a71071a4eca7b8f7af5842cd1ae7c/node_modules/@ava/babel-plugin-throws-helper/index.js' -> '/media/XXX/extra/Apollo/jbrowse/node_modules/@ava/babel-plugin-throws-helper/index.js'". info If you think this is a bug, please open a bug report with the information provided in "/media/XXX/extra/Apollo/jbrowse/yarn-error.log". info Visit https://yarnpkg.com/en/docs/cli/install for documentation about this command. :installJBrowseWebOnly FAILED

nathandunn commented 5 years ago

If this an upgrade? If so, you may want to do an:

./apollo clean-all

first.

Also, what version of Ubuntu are you running with?

I’ve done this extensively on Ubuntu 14 and 16 and they seem to work, but every system is a bit different.

This is Apollo 2.3.1, right?

I just tested with node 11, and that should be fine.

Nathan

On May 3, 2019, at 9:57 AM, csmibrahim notifications@github.com wrote:

I get this error on Ubuntu when I run ./apollo run-local

Gradle version: 2 Using system gradle 2.11 Node Version: 11 Npm Version: 6 Yarn Version: 1 javac 1.8.0_191 found javac installed JDK 1.8 found: javac 1.8.0_191

:installJBrowseWebOnly JBrowse already exists From https://github.com/gmod/jbrowse https://github.com/gmod/jbrowse tag 1.16.2-release -> FETCH_HEAD Already up-to-date. yarn install v1.13.0 [1/4] Resolving packages... [2/4] Fetching packages... info fsevents@1.2.4: The platform "linux" is incompatible with this module. info "fsevents@1.2.4" is an optional dependency and failed compatibility check. Excluding it from installation. [3/4] Linking dependencies... warning " > dojo-webpack-plugin@2.7.7" has unmet peer dependency "webpack-sources@>=1.0.1". warning " > extract-text-webpack-plugin@3.0.2" has incorrect peer dependency "webpack@^3.1.0". warning " > url-loader@0.5.7" has unmet peer dependency "file-loader@*". error An unexpected error occurred: "EFAULT: bad address in system call argument, copyfile '/home/XXX/.cache/yarn/v4/npm-@ava-babel-plugin-throws-helper-2.0.0-2fc1fe3c211a71071a4eca7b8f7af5842cd1ae7c/node_modules/@ava/babel-plugin-throws-helper/index.js' -> '/media/XXX/extra/Apollo/jbrowse/node_modules/@ava/babel-plugin-throws-helper/index.js'". info If you think this is a bug, please open a bug report with the information provided in "/media/XXX/extra/Apollo/jbrowse/yarn-error.log". info Visit https://yarnpkg.com/en/docs/cli/install https://yarnpkg.com/en/docs/cli/install for documentation about this command. :installJBrowseWebOnly FAILED

General questions (not bug fixes or feature requests) should be emailed mailto:apollo@lbl.gov or posted to the google group https://groups.google.com/a/lbl.gov/forum/#!forum/apollo.

Search mailing list https://groups.google.com/a/lbl.gov/forum/#!forum/apollo or the archive http://gmod.827538.n3.nabble.com/Apollo-f815553.html.

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csmibrahim commented 5 years ago

Is not Upgrade.

Distributor ID: Ubuntu Description: Ubuntu 16.04.6 LTS Release: 16.04 Codename: xenial

Just new git clone now.

nathandunn commented 5 years ago

@csmibrahim

I would try using node 8 as I was also having problems with node 11 (and let me know if that works).

nvm is ideal if you can use it to switch node versions (and remove the system installed one): https://github.com/nvm-sh/nvm#install--update-script

I'm going to test with a few different versions to see where it breaks and to put in a script for detecting and flagging the node version. At some point I'll get the other stuff working.

csmibrahim commented 5 years ago

Yes, this work. but now I have another issue. The build process continues and then stuck as in the screen for 30 sec. After that as if new terminal open and no error or anything.

nathandunn commented 5 years ago

that compilation step will take awhile. As long as the processors are active, then all is good.

nathandunn commented 5 years ago

but let me know if its not. I'm going to close this for now.

Closed by https://github.com/GMOD/Apollo/commit/f91b610399773249d153d41cc24f3eb0047fd7e3

nathandunn commented 5 years ago

But feel free to continue to comment in this thread if you run into further trouble

csmibrahim commented 5 years ago

Just the same issue after 30 sec the terminal is cleared and nothing come at all

nathandunn commented 5 years ago

What do you see if you type top?

On May 3, 2019, at 2:20 PM, csmibrahim notifications@github.com wrote:

Just the same issue after 30 sec the terminal is cleared and nothing come at all

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csmibrahim commented 5 years ago

Any idea ... when i try localhost:8080/apollo

nathandunn commented 5 years ago

Well, the build is borked.

I would do an

apollo clean-all

and try the installation again and give me the full build dump stack.

When I build I get this:

            9.bundle.js    57 KiB            9  [emitted]  
       browser.bundle.js   563 KiB      browser  [emitted]  browser
dojo/resources/blank.gif  43 bytes               [emitted]  
          main.bundle.js   567 KiB         main  [emitted]  main
   run_jasmine.bundle.js   771 KiB  run_jasmine  [emitted]  run_jasmine
Entrypoint main = main.bundle.js
Entrypoint browser = browser.bundle.js
Entrypoint run_jasmine = run_jasmine.bundle.js
[./build/dojo-webpack-plugin-loader/dojo/dojo.js] 70.1 KiB {main} {browser} {run_jasmine} [built]
[./node_modules/style-loader/index.js!./node_modules/css-loader/index.js!./node_modules/sass-loader/lib/loader.js!./css/genome.scss] ./node_modules/style-loader!./node_modules/css-loader!./node_modules/sass-loader/lib/loader.js!./css/genome.scss 1.18 KiB {11} [built]
[./plugins/BlastView/js/View/Track/CanvasFeatures.js] 5.1 KiB {11} [built]
[./plugins/BlastView/js/View/Track/_FeatureDetailMixin.js] 2.7 KiB {11} [built]
[./plugins/BlastView/js/main.js] 354 bytes {11} [built]
[./plugins/CategoryUrl/js/main.js] 4.37 KiB {11} [built]
[./plugins/DebugEvents/js/main.js] 6.07 KiB {11} [built]
[./plugins/GCContent/js/Store/SeqFeature/GCContent.js] 2.61 KiB {11} [built]
[./plugins/GCContent/js/View/Dialog/WindowSizeDialog.js] 3.21 KiB {11} [built]
[./plugins/GCContent/js/View/Track/GCContent.js] 3.14 KiB {11} [built]
[./plugins/GCContent/js/View/Track/GCContentXY.js] 3.13 KiB {11} [built]
[./plugins/GCContent/js/main.js] 659 bytes {11} [built]
[./src/JBrowse/main.js] 13.2 KiB {main} [built]
[./src/JBrowse/standalone.js] 9.41 KiB {browser} [built]
[./tests/js_tests/main.js] 1.48 KiB {run_jasmine} [built]
    + 1839 hidden modules
:javac
Note: /Users/nathandunn/repositories/nathanApolloMaster/src/gwt/org/bbop/apollo/gwt/client/TrackPanel.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: 53.145 secs
| Compiling 15 source files

| Compiling 234 source files
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
| Compiling 370 source files

| Warning The [pruneTracks] action accepts a parameter of type [org.codehaus.groovy.grails.web.json.JSONArray] which has not been marked with @Validateable.  Data binding will still be applied to this command object but the instance will not be validateable.

       def pruneTracks(JSONArray tracksArray){
       ^
| Compiling 370 source files.....
***
Metrics servlet injected into web.xml
Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
***
| Running Grails application
Configuring Shiro ...
Shiro Configured

That gwtc is the most expensive especially on a smaller machine.

What are the specs of your ubuntu build?

csmibrahim commented 5 years ago

I saved the output in a variable and echo BUILD SUCCESSFUL Total time: 1 mins 11.165 secs This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/ gradle_daemon.html grails: JAVA_HOME environment variable is not set

I created JAVA_HOME and now working fine.

Thanks

GMOD / Apollo

JBrowse build Fail #2152