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Install JBrowse 1.13.0-dev error #1026

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bhofmei opened this Issue Mar 19, 2018 · 10 comments

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@bhofmei

bhofmei commented Mar 19, 2018

I was trying to update my plugins to work with JBrowse 1.13.0 via zip download of JBrowse-1.13.0-dev at the JBrowse website. I cannot get the sample data to work. I run setup.sh (no plugins installed) and navigate to the sample data url and get this error: TypeError: Cannot read property 'document' of null.

I was able to get JBrowse-1.13.0 (non-dev) to work, but there seems to be an issue with the dev version which I need for plugins.

@cmdcolin

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cmdcolin commented Mar 19, 2018

Do you have a setup.log? It seems like it works on my machine

@kullrich

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kullrich commented Mar 20, 2018

Dear all,
same problem on my side. JBrowse-1.13.0(non-dev) works fine, even with own data.
However, after installing npm and JBrowse-1.13.0-dev to include BioNanoGenomics plugin the examples hangs at ('Loading ...').
Here are some additional warning from npm:
"""npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents@^1.0.0 (node_modules/chokidar/node_modules/fsevents):
npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents@1.1.3: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"})
"""
Architecture: Ubuntu 16.04.4 LTS

Best regards and thank you in anticipation

Kristian

@bhofmei

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bhofmei commented Mar 20, 2018

I do have a setup.log (about 1700 lines) attached. Doesn't seem to have any major errors, just a few warnings. I do get a few deprecated dependencies.

npm WARN deprecated filesaver.js@0.2.0: Unmaintained namespace. Please use the file-saver package: https://www.npmjs.com/package/file-saver
npm WARN deprecated coffee-script@1.12.7: CoffeeScript on NPM has moved to "coffeescript" (no hyphen)
npm WARN deprecated minimatch@0.2.14: Please update to minimatch 3.0.2 or higher to avoid a RegExp DoS issue
npm WARN deprecated minimatch@0.4.0: Please update to minimatch 3.0.2 or higher to avoid a RegExp DoS issue
npm WARN deprecated minimatch@0.3.0: Please update to minimatch 3.0.2 or higher to avoid a RegExp DoS issue
npm WARN prefer global node-gyp@3.6.2 should be installed with -g

I'm running macOS v10.12.6 and using Chrome for web browser.
setup.log

@cmdcolin

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cmdcolin commented Mar 20, 2018

Might be due to too low of a node/npm version. I can reproduce the problem if I use npm3/node6 (default on ubuntu 16, apparently also npm 3 in @bhoefmei setup log).

If I get the homebrewed/linuxbrewed npm5/node9 then it works fine!

Not sure why that is, it might be worth trying to upgrade node versions to see though

@bhofmei

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bhofmei commented Mar 20, 2018

@kullrich

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kullrich commented Mar 20, 2018

For me updating to npm v5.6.0 and nodejs v9.8.0 resolved the issue.
However, after installing the BioNanoGenomics plugin and repeating 'setup.sh' I now run into another error, once I want to add a BioNano track:
"""
Failed to load resource: dojox/widget/Toaster
"""
If this is an issue of the plugin or JBrowse itself I don't know, so that at the moment I will not open another issue.

Best regards
Kristian

@cmdcolin

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cmdcolin commented Mar 20, 2018

Looks like that might because it uses this widget "implicitly" by simply inserting it like this

dom.place('<div data-dojo-type="dojox/widget/Toaster" data-dojo-props="positionDirection:\'br-left\'" id="first_toaster"></div>',window.body());

JBrowse therefore removes it in the production build since its not explicitly included. Good news is that you can fix this pretty simply by adding it to the require list in the BioNanoGenomics main.js

diff --git a/js/main.js b/js/main.js
index 562f40d..51342e2 100644
--- a/js/main.js
+++ b/js/main.js
@@ -9,7 +9,8 @@ define([
            'dijit/MenuItem',
            'JBrowse/Plugin',
            './View/FileDialog',
-           './View/CMapFileDialog'
+           './View/CMapFileDialog',
+           'dojox/widget/Toaster'
        ],
        function(
@cmdcolin

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cmdcolin commented Mar 20, 2018

Might be worth contributing that fix to their repo :)

@kullrich

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kullrich commented Mar 20, 2018

Thank you, I will contact them to include it
Best regards
Kristian

@rbuels

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rbuels commented Mar 20, 2018

I think we need to add a check to setup.sh to check for sufficient npm versions.

Maybe npm >= 4, node >= 6.4?

@rbuels rbuels added this to the 1.13.1 milestone Mar 20, 2018

@rbuels rbuels closed this in efd0832 Mar 23, 2018

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