Candihub / pixel

A content management platform for quantitative omics data :green_book: :bulb:
BSD 3-Clause "New" or "Revised" License
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make bootstrap: yarn not found #305

Closed lgatto closed 5 years ago

lgatto commented 5 years ago

Following up from my previous issue #302, I now manage to pass all steps but fail due to a missing font module:

Step 25/25 : CMD ["gunicorn", "-c", "/usr/local/etc/gunicorn/pixel.py", "pixel.wsgi:application"]
 ---> Using cache
 ---> 3ecf178890e1
Successfully built 3ecf178890e1
Successfully tagged pixel-dev_web:latest
Waiting until database is up
make[1]: Entering directory '/home/lgatto/tmp/pixel'
Starting pixel-dev_db_1 ... done
Operations to perform:
  Apply all migrations: admin, auth, contenttypes, core, data, sessions, submission, viewflow
Running migrations:
  No migrations to apply.
make[1]: Leaving directory '/home/lgatto/tmp/pixel'
Starting pixel-dev_db_1 ... done
Installed 6 object(s) from 1 fixture(s)
Starting pixel-dev_db_1 ... done
Installed 10 object(s) from 1 fixture(s)
Starting pixel-dev_db_1 ... done
Will generate 3 experiments and 10 pixel sets with 20 pixels each…
Successfully generated fixtures
/bin/sh: line 1: yarn: command not found
make[1]: Entering directory '/home/lgatto/tmp/pixel'
cp: cannot stat 'node_modules/font-awesome/fonts/*': No such file or directory
make[1]: *** [Makefile:65: build-css] Error 1
make[1]: Leaving directory '/home/lgatto/tmp/pixel'
make: *** [Makefile:45: bootstrap] Error 2

I had a look at #59, which seems related - I do not have a node_modules directory in the pixel base dir and I haven't done any installation of yarn nor npm before.

Next I ran

$ docker-compose -p pixel-dev -f docker-compose.yml run --rm node yarn install

giving

Pulling node (node:8)...
8: Pulling from library/node
61be48634cb9: Pull complete
fa696905a590: Pull complete
b6dd2322bbef: Pull complete
32477089adb4: Pull complete
febe7209ec28: Pull complete
4364cbe57162: Pull complete
ace5c680ff94: Pull complete
4acd6a9b7a48: Pull complete
yarn install v1.9.4
[1/4] Resolving packages...
[2/4] Fetching packages...
info fsevents@1.1.2: The platform "linux" is incompatible with this module.
info "fsevents@1.1.2" is an optional dependency and failed compatibility check. Excluding it from installation.
[3/4] Linking dependencies...
[4/4] Building fresh packages...
warning Your current version of Yarn is out of date. The latest version is "1.12.3", while you're on "1.9.4".
info To upgrade, run the following command:
$ curl --compressed -o- -L https://yarnpkg.com/install.sh | bash
Done in 10.40s.

Now I successfully install the missing fonts and have the missing directory, but

$ make bootsrap
[...]
Step 25/25 : CMD ["gunicorn", "-c", "/usr/local/etc/gunicorn/pixel.py", "pixel.wsgi:application"]
 ---> Using cache
 ---> 3ecf178890e1
Successfully built 3ecf178890e1
Successfully tagged pixel-dev_web:latest
Waiting until database is up
make[1]: Entering directory '/home/lgatto/tmp/pixel'
Starting pixel-dev_db_1 ... done
Operations to perform:
  Apply all migrations: admin, auth, contenttypes, core, data, sessions, submission, viewflow
Running migrations:
  No migrations to apply.
make[1]: Leaving directory '/home/lgatto/tmp/pixel'
Starting pixel-dev_db_1 ... done
Installed 6 object(s) from 1 fixture(s)
Starting pixel-dev_db_1 ... done
Installed 10 object(s) from 1 fixture(s)
Starting pixel-dev_db_1 ... done
Will generate 3 experiments and 10 pixel sets with 20 pixels each…
Successfully generated fixtures
/bin/sh: line 1: yarn: command not found
make[1]: Entering directory '/home/lgatto/tmp/pixel'
make[1]: yarn: Command not found
make[1]: *** [Makefile:66: build-css] Error 127
make[1]: Leaving directory '/home/lgatto/tmp/pixel'
make: *** [Makefile:45: bootstrap] Error 2

Not sure where to go from now.

Thank you in advance for your help.

jmaupetit commented 5 years ago

Hey @lgatto :wave: Thanks for the report!

The documentation is unclear on this point. We use system Yarn installation to work on the project, but, things should run smoothly with the node container. We'll improve this in a new PR.

gaellelelandais commented 5 years ago

@jmaupetit Did you fix the documentation on this point ? Many thanks for your reply.

jmaupetit commented 5 years ago

Not yet. I'll do this in the next days.