cBioPortal
Installation errors
Hi I am having trouble installing oncoprintjs on my macbook pro. I have tried installing oncoprintjs on my Mac and in a docker running unbuntu and keep getting the same error. I don't think it is an oncoprintjs error per se, but a problem with the installation. Any guidance is appreciated.
gulp spec [09:16:58] Using gulpfile ~/oncoprintjs/gulpfile.js [09:16:58] Starting 'spec'... [09:16:58] 'spec' errored after 31 ms [09:16:58] Error in plugin 'gulp-jasmine' Message: Cannot find module '../../src/js/sorting.js' Details: code: MODULE_NOT_FOUND
I can confirm this also. The cause seems to be that some files were moved from src/js/ to src/.js/and possible workarounds are either to move all files from the .js folder back to js or to correct the locations of sorting.js, utils.js and main.js in sorting_spec.js, utils_spec.js and gulpfile.js respectively.
I am gald it wasn't just me, but the proposed solution didn't seem to work. After moving all the files in the .js folder to the js folder I get the following errors:
gulp spec [14:27:12] Using gulpfile ~/oncoprintjs/gulpfile.js [14:27:12] Starting 'spec'... ....FFFFFF
Failures:
-
is sample genetically altered shows that an empty sample (no data) is not genetically altered 1.1) TypeError: undefined is not a function
-
is sample genetically altered shows that a clinical-ish sample is not genetically altered 2.1) TypeError: undefined is not a function
-
is sample genetically altered shows that a genetically altered sample as altered 3.1) TypeError: undefined is not a function
-
validate_row_against_rows error if lengths don't match 4.1) Expected function to throw 'Row lengths don't match: 2 and 3', but it threw TypeError: undefined is not a function. 4.2) Expected function to throw 'Row lengths don't match: 3 and 2', but it threw TypeError: undefined is not a function. 4.3) Expected function to throw 'Rows are empty', but it threw TypeError: undefined is not a function.
-
validate_row_against_rows error if samples don't match up exactly 5.1) Expected function to throw 'Sample ids do not match between new row and given rows.', but it threw TypeError: undefined is not a function. 5.2) Expected function to throw 'Sample ids do not match between new row and given rows.', but it threw TypeError: undefined is not a function.
-
validate_row_against_rows returns true if all is well 6.1) TypeError: undefined is not a function
10 specs, 6 failures Finished in 0 seconds [14:27:12] 'spec' errored after 71 ms [14:27:12] Error in plugin 'gulp-jasmine' Message: Tests failed
Again, any guidance is appreciated.
I agree it's strange that the unit tests fail, but I got it running anyway after running gulp test (to generate the test data) and accessing the index.html through http-server.
I started a discussion in the cbioportal google group; maybe there will be further clues: https://groups.google.com/forum/#!topic/cbioportal/3J8OTanYRxg
khalid@FLUX-ProBook:~/Dev/goc/oncoprintjs/src$ gulp test
[19:44:07] Using gulpfile ~/Dev/goc/oncoprintjs/src/gulpfile.js
[19:44:07] Starting 'test'...
Error: Cannot find module 'gl-matrix' from '/home/khalid/Dev/goc/oncoprintjs/src'
at /usr/lib/node_modules/browserify/node_modules/browser-resolve/node_modules/resolve/lib/async.js:46:17
at process (/usr/lib/node_modules/browserify/node_modules/browser-resolve/node_modules/resolve/lib/async.js:173:43)
at ondir (/usr/lib/node_modules/browserify/node_modules/browser-resolve/node_modules/resolve/lib/async.js:188:17)
at load (/usr/lib/node_modules/browserify/node_modules/browser-resolve/node_modules/resolve/lib/async.js:69:43)
at onex (/usr/lib/node_modules/browserify/node_modules/browser-resolve/node_modules/resolve/lib/async.js:92:31)
at /usr/lib/node_modules/browserify/node_modules/browser-resolve/node_modules/resolve/lib/async.js:22:47
at FSReqWrap.oncomplete (fs.js:123:15)
[19:44:07] 'test' errored after 607 ms
[19:44:07] Error in plugin 'gulp-shell'
Message:
Command browserify test.js -o oncoprint-test-bundle.js failed with exit code 1
