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).http://dl.google.com/closure-compiler/compiler-latest.zip $ 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 |
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:
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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.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:
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Good to hear! This says java 7 seems fine so not sure but glad it finally works -Colin On Tue, May 30, 2017 at 6:52 PM, Richard Hayes <[hidden email]> wrote:
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