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[Gmod-ajax] Minification help

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Richard Hayes

[Gmod-ajax] Minification help

Hi all,

I'm not sure if the documentation is up to date. I have a data release coming up this week and I'd like to upgrade to 1.12.3, but I need to apply that defaultTracks bug fix (https://github.com/GMOD/jbrowse/issues/892).

I think my issue might be the closure compiler? I downloaded the most recent:
http://dl.google.com/closure-compiler/compiler-latest.zip

Here is my process:
$ git clone --recursive https://github.com/GMOD/jbrowse.git jbrowse
$ cd jbrowse
$ emacs src/JBrowse/package.json

Local install of bower:
$ npm install --save-dev bower
$ export PATH=<path>/jbrowse/node_modules/.bin:$PATH
$ export CLOSURE_HOME=<path to fresh download>/closure-compiler
$ ./setup.sh
$ make -f build/Makefile release-notest

setup.sh runs perfectly, but the release-min make process repeatedly warns:

starting writing resources...
[Error: This socket is closed.]
Error: This socket is closed.
    at Socket._writeGeneric (net.js:640:19)
    at Socket._write (net.js:694:8)
    at doWrite (_stream_writable.js:292:12)
    at writeOrBuffer (_stream_writable.js:278:5)
    at Socket.Writable.write (_stream_writable.js:207:11)
    at Socket.write (net.js:618:40)
    at Object.proc.write (/opt/services/git/jbrowse/src/util/build/transforms/optimizer/sendJob.js:95:20)
    at sendJob (/opt/services/git/jbrowse/src/util/build/transforms/optimizer/sendJob.js:37:28)
    at /opt/services/git/jbrowse/src/util/build/transforms/optimizer/closure.js:18:7
    at /opt/services/git/jbrowse/src/util/build/node/fs.js:23:9

I tried downloading closure through npm (step 4: "npm install --save-dev bower closure") with no change.

Thanks!

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://phytozome.jgi.doe.gov

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Colin

Re: Minification help

You shouldn't need to install closure compiler manually or separately, it's just packaged with dojo itself and setup.sh probably took care of that.

Is java itself installed on the system? On my system if java isn't installed and the jbrowse build is run, then it produces a different error, so not sure if it's the case on your system

Only other thing I would suggest is not installing closure compiler separately in case it is conflicting somehow

-Colin

On Tue, May 30, 2017 at 3:22 PM, Richard Hayes <[hidden email]> wrote:

Hi all,

I'm not sure if the documentation is up to date. I have a data release coming up this week and I'd like to upgrade to 1.12.3, but I need to apply that defaultTracks bug fix (https://github.com/GMOD/jbrowse/issues/892).

I think my issue might be the closure compiler? I downloaded the most recent:
http://dl.google.com/closure-compiler/compiler-latest.zip

Here is my process:
$ git clone --recursive https://github.com/GMOD/jbrowse.git jbrowse
$ cd jbrowse
$ emacs src/JBrowse/package.json

Local install of bower:
$ npm install --save-dev bower
$ export PATH=<path>/jbrowse/node_modules/.bin:$PATH
$ export CLOSURE_HOME=<path to fresh download>/closure-compiler
$ ./setup.sh
$ make -f build/Makefile release-notest

setup.sh runs perfectly, but the release-min make process repeatedly warns:

starting writing resources...
[Error: This socket is closed.]
Error: This socket is closed.
    at Socket._writeGeneric (net.js:640:19)
    at Socket._write (net.js:694:8)
    at doWrite (_stream_writable.js:292:12)
    at writeOrBuffer (_stream_writable.js:278:5)
    at Socket.Writable.write (_stream_writable.js:207:11)
    at Socket.write (net.js:618:40)
    at Object.proc.write (/opt/services/git/jbrowse/src/util/build/transforms/optimizer/sendJob.js:95:20)
    at sendJob (/opt/services/git/jbrowse/src/util/build/transforms/optimizer/sendJob.js:37:28)
    at /opt/services/git/jbrowse/src/util/build/transforms/optimizer/closure.js:18:7
    at /opt/services/git/jbrowse/src/util/build/node/fs.js:23:9

I tried downloading closure through npm (step 4: "npm install --save-dev bower closure") with no change.

Thanks!

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://phytozome.jgi.doe.gov

------------------------------------------------------------------------------
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Richard Hayes

Re: Minification help

Thanks,

I left off any install or configuration for closure and specified to use a JDK 8 I have with by setting JAVA_HOME and adding $JAVA_HOME/bin to the front of my path. The system default was a JDK 7 that must have been too old.

The above was sufficient to get minification to work correctly.

Best,

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://phytozome.jgi.doe.gov

On Tue, May 30, 2017 at 1:54 PM, Colin <[hidden email]> wrote:

You shouldn't need to install closure compiler manually or separately, it's just packaged with dojo itself and setup.sh probably took care of that.

Is java itself installed on the system? On my system if java isn't installed and the jbrowse build is run, then it produces a different error, so not sure if it's the case on your system

Only other thing I would suggest is not installing closure compiler separately in case it is conflicting somehow

-Colin

On Tue, May 30, 2017 at 3:22 PM, Richard Hayes <[hidden email]> wrote:
Hi all,

I'm not sure if the documentation is up to date. I have a data release coming up this week and I'd like to upgrade to 1.12.3, but I need to apply that defaultTracks bug fix (https://github.com/GMOD/jbrowse/issues/892).

I think my issue might be the closure compiler? I downloaded the most recent:
http://dl.google.com/closure-compiler/compiler-latest.zip

Here is my process:
$ git clone --recursive https://github.com/GMOD/jbrowse.git jbrowse
$ cd jbrowse
$ emacs src/JBrowse/package.json

Local install of bower:
$ npm install --save-dev bower
$ export PATH=<path>/jbrowse/node_modules/.bin:$PATH
$ export CLOSURE_HOME=<path to fresh download>/closure-compiler
$ ./setup.sh
$ make -f build/Makefile release-notest

setup.sh runs perfectly, but the release-min make process repeatedly warns:

starting writing resources...
[Error: This socket is closed.]
Error: This socket is closed.
    at Socket._writeGeneric (net.js:640:19)
    at Socket._write (net.js:694:8)
    at doWrite (_stream_writable.js:292:12)
    at writeOrBuffer (_stream_writable.js:278:5)
    at Socket.Writable.write (_stream_writable.js:207:11)
    at Socket.write (net.js:618:40)
    at Object.proc.write (/opt/services/git/jbrowse/src/util/build/transforms/optimizer/sendJob.js:95:20)
    at sendJob (/opt/services/git/jbrowse/src/util/build/transforms/optimizer/sendJob.js:37:28)
    at /opt/services/git/jbrowse/src/util/build/transforms/optimizer/closure.js:18:7
    at /opt/services/git/jbrowse/src/util/build/node/fs.js:23:9

I tried downloading closure through npm (step 4: "npm install --save-dev bower closure") with no change.

Thanks!

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://phytozome.jgi.doe.gov

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
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[hidden email]
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Colin

Re: Minification help

Good to hear! This says java 7 seems fine so not sure but glad it finally works

https://github.com/google/closure-compiler/wiki/FAQ

-Colin

On Tue, May 30, 2017 at 6:52 PM, Richard Hayes <[hidden email]> wrote:

Thanks,

I left off any install or configuration for closure and specified to use a JDK 8 I have with by setting JAVA_HOME and adding $JAVA_HOME/bin to the front of my path. The system default was a JDK 7 that must have been too old.

The above was sufficient to get minification to work correctly.

Best,

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://phytozome.jgi.doe.gov

On Tue, May 30, 2017 at 1:54 PM, Colin <[hidden email]> wrote:
You shouldn't need to install closure compiler manually or separately, it's just packaged with dojo itself and setup.sh probably took care of that.

Is java itself installed on the system? On my system if java isn't installed and the jbrowse build is run, then it produces a different error, so not sure if it's the case on your system

Only other thing I would suggest is not installing closure compiler separately in case it is conflicting somehow

-Colin

On Tue, May 30, 2017 at 3:22 PM, Richard Hayes <[hidden email]> wrote:
Hi all,

I'm not sure if the documentation is up to date. I have a data release coming up this week and I'd like to upgrade to 1.12.3, but I need to apply that defaultTracks bug fix (https://github.com/GMOD/jbrowse/issues/892).

I think my issue might be the closure compiler? I downloaded the most recent:
http://dl.google.com/closure-compiler/compiler-latest.zip

Here is my process:
$ git clone --recursive https://github.com/GMOD/jbrowse.git jbrowse
$ cd jbrowse
$ emacs src/JBrowse/package.json

Local install of bower:
$ npm install --save-dev bower
$ export PATH=<path>/jbrowse/node_modules/.bin:$PATH
$ export CLOSURE_HOME=<path to fresh download>/closure-compiler
$ ./setup.sh
$ make -f build/Makefile release-notest

setup.sh runs perfectly, but the release-min make process repeatedly warns:

starting writing resources...
[Error: This socket is closed.]
Error: This socket is closed.
    at Socket._writeGeneric (net.js:640:19)
    at Socket._write (net.js:694:8)
    at doWrite (_stream_writable.js:292:12)
    at writeOrBuffer (_stream_writable.js:278:5)
    at Socket.Writable.write (_stream_writable.js:207:11)
    at Socket.write (net.js:618:40)
    at Object.proc.write (/opt/services/git/jbrowse/src/util/build/transforms/optimizer/sendJob.js:95:20)
    at sendJob (/opt/services/git/jbrowse/src/util/build/transforms/optimizer/sendJob.js:37:28)
    at /opt/services/git/jbrowse/src/util/build/transforms/optimizer/closure.js:18:7
    at /opt/services/git/jbrowse/src/util/build/node/fs.js:23:9

I tried downloading closure through npm (step 4: "npm install --save-dev bower closure") with no change.

Thanks!

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://phytozome.jgi.doe.gov

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax