Error message when I run "serve" command: Uncaught SyntaxError: expected expression, got ')'

[agustin-bilat]

After following the steps in order to install JBrowse Web I finally run the npx serve . command inside de jbrowse2/ directory (obtained with jbrowse create jbrowse2) and when I opened the local port http://localhost:3000 I get an empty white page.

By checking the Web developer tools's debugger I get the error message mentioned in the title (I am using Mozilla Firefox 112.0.1) .

It seems that there is a ')' somewhere but I have no idea how to find it nor how to fix it. When I click, "view source in debugger" though, I notice that the very first character is a ')' :

){case 107:return u(e,":",":"+F)+e;case 101:return u(e,/(.+:)([^;!]+)(;|!.+)?/,"$1"+F+(45===s(e,14)?"inline-":"")+"b

....etcetera.

jbrowse --version

@jbrowse/cli/2.4.2 linux-x64 node-v18.16.0

npx serve --version

14.2.0

Any help would be much appreciated

Best,
Agustin.

[garrettjstevens]

I've tried this with the same version of jbrowse, serve, and Firefox and I can't reproduce the problem. Have you tried a different browser? Also, if you could copy the full error message in the console, including any file name, that could help diagnose it. If you could copy the output of the npx serve . command, too, that might help.

[agustin-bilat]

Have you tried a different browser?

I did, I use google chrome too with the same result.

The image displayed in the console is this:

And the message within the console after navigating into the port http://localhost:3000 as it is seen in the Web dev. tools is:

Uncaught SyntaxError: expected expression, got ')' [Learn More] main.28981932.js:1

If I click main.28981832.js:1 I get this file
Untitled.js.txt

Please let me know if you need any further information.

[garrettjstevens]

That main.28981832.js is missing the beginning, I'm not sure why that would happen. Does the same thing happen if you completely remove the jbrowse2/ directory and create it again with jbrowse create jbrowse2?

[agustin-bilat]

You're right, I've just made what you mentioned (removing the jbrowse2/ and create it again) and what I get as a result is a different syntax error:

Uncaught SyntaxError: expected expression, got '}'

The corresponding file is now:
main.28981932.js:1:8

[garrettjstevens]

It looks like that file is missing the beginning as well. You could try installing it manually. To do this, first you need to remove the jbrowse2 directory and then run these commands:

curl -Lo jbrowse.zip https://github.com/GMOD/jbrowse-components/releases/download/v2.4.2/jbrowse-web-v2.4.2.zip
unzip -d jbrowse2 jbrowse.zip
rm jbrowse.zip

Let me know if this works for you.

[agustin-bilat]

Thanks, I did what you've just mentioned and at least I can see the Volvox sample config file now (not the others though).

[garrettjstevens]

The screenshot in the tutorial is out of date, only seeing Volvox is what is expected, so I think you have everything working now.

[agustin-bilat]

Many thanks for your help and your patience, it seems to be working now.

Best Regards,
Agustin.

[nathanweeks]

I've noticed a similar error recently when jbrowse is installed with jbrowse create. It seems jbrowse create results in a different main.d42b84c7.js vs. manually downloading/unzipping jbrowse-web-v2.5.0.zip:

$ curl -Lo jbrowse.zip https://github.com/GMOD/jbrowse-components/releases/download/v2.5.0/jbrowse-web-v2.5.0.zip
...
$ unzip jbrowse.zip
...
$ echo "$(head -c 50 static/js/main.d42b84c7.js)"
/*! For license information please see main.d42b84
$ jbrowse --version
@jbrowse/cli/2.5.0 linux-x64 node-v18.16.0
$ jbrowse create broken
Fetching https://github.com/GMOD/jbrowse-components/releases/download/v2.5.0/jbrowse-web-v2.5.0.zip...
Unpacked https://github.com/GMOD/jbrowse-components/releases/download/v2.5.0/jbrowse-web-v2.5.0.zip at broken
$ echo "$(head -c 50 broken/static/js/main.d42b84c7.js)"
41===e&&L(e);break;case 92:E()}return y}function R

[nathanweeks]

The error is not observed with node 16.x:

$ nvm use 16
Now using node v16.20.0 (npm v8.19.4)
$ jbrowse --version
@jbrowse/cli/2.5.0 linux-x64 node-v16.20.0
$ jbrowse create not-broken
Fetching https://github.com/GMOD/jbrowse-components/releases/download/v2.5.0/jbrowse-web-v2.5.0.zip...
Unpacked https://github.com/GMOD/jbrowse-components/releases/download/v2.5.0/jbrowse-web-v2.5.0.zip at not-broken
$ echo "$(head -c 50 not-broken/static/js/main.d42b84c7.js)"
/*! For license information please see main.d42b84

[cmdcolin]

@nathanweeks thanks for the extra info. I think the fact it occurs at newer versions of node is true, the nodejs library we used (node-unzipper) has some issues on their github about this. I changed the libraries in this PR #3686 and hopefully can get it released soon!

[cmdcolin]

can see a bunch here ZJONSSON/node-unzipper#271 ZJONSSON/node-unzipper#278 maybe ZJONSSON/node-unzipper#269

[nathanweeks]

@cmdcolin Thanks! It's good to know a fix is slated for the next release, and that there's an easy workaround in the meantime.