vitessce: Can't install with node.js 14.15.3 on windows

Describe the bug An error appeared after using npm install vitessce.

To Reproduce Steps to reproduce the behavior: enter npm install vitessce in the terminal.


PS C:\Users\zyang\Downloads> npm install vitessce
npm ERR! prepareGitDep 1>
npm ERR! prepareGitDep > deasync@0.1.20 install C:\Users\zyang\AppData\Roaming\npm-cache\_cacache\tmp\git-clone-4d07a716\node_modules\deasync
npm ERR! prepareGitDep > node ./build.js
npm ERR! prepareGitDep
npm ERR! prepareGitDep `win32-x64-node-14` exists; testing
npm ERR! prepareGitDep Binary is fine; exiting
npm ERR! prepareGitDep
npm ERR! prepareGitDep > core-js@2.6.11 postinstall C:\Users\zyang\AppData\Roaming\npm-cache\_cacache\tmp\git-clone-4d07a716\node_modules\core-js
npm ERR! prepareGitDep > node -e "try{require('./postinstall')}catch(e){}"
npm ERR! prepareGitDep
npm ERR! prepareGitDep Thank you for using core-js ( https://github.com/zloirock/core-js ) for polyfilling JavaScript standard library!
npm ERR! prepareGitDep
npm ERR! prepareGitDep The project needs your help! Please consider supporting of core-js on Open Collective or Patreon:
npm ERR! prepareGitDep > https://opencollective.com/core-js
npm ERR! prepareGitDep > https://www.patreon.com/zloirock
npm ERR! prepareGitDep
npm ERR! prepareGitDep Also, the author of core-js ( https://github.com/zloirock ) is looking for a good job -)
npm ERR! prepareGitDep
npm ERR! prepareGitDep
npm ERR! prepareGitDep > core-js-pure@3.6.5 postinstall C:\Users\zyang\AppData\Roaming\npm-cache\_cacache\tmp\git-clone-4d07a716\node_modules\core-js-pure
npm ERR! prepareGitDep > node -e "try{require('./postinstall')}catch(e){}"
npm ERR! prepareGitDep
npm ERR! prepareGitDep
npm ERR! prepareGitDep > parcel-bundler@1.12.4 postinstall C:\Users\zyang\AppData\Roaming\npm-cache\_cacache\tmp\git-clone-4d07a716\node_modules\parcel-bundler
npm ERR! prepareGitDep > node -e "console.log('\u001b[35m\u001b[1mLove Parcel? You can now donate to our open collective:\u001b[22m\u001b[39m\n > \u001b[34mhttps://opencollective.com/parcel/donate\u001b[0m')"
npm ERR! prepareGitDep
npm ERR! prepareGitDep Love Parcel? You can now donate to our open collective:
npm ERR! prepareGitDep  > https://opencollective.com/parcel/donate
npm ERR! prepareGitDep
npm ERR! prepareGitDep > geotiff@1.0.0-beta.14 prepare C:\Users\zyang\AppData\Roaming\npm-cache\_cacache\tmp\git-clone-4d07a716
npm ERR! prepareGitDep > npm run build
npm ERR! prepareGitDep
npm ERR! prepareGitDep
npm ERR! prepareGitDep > geotiff@1.0.0-beta.14 build C:\Users\zyang\AppData\Roaming\npm-cache\_cacache\tmp\git-clone-4d07a716
npm ERR! prepareGitDep > npm run build:clean; run-p build:browser build:node;
npm ERR! prepareGitDep
npm ERR! prepareGitDep
npm ERR! prepareGitDep 2> npm WARN install Usage of the `--dev` option is deprecated. Use `--also=dev` instead.
npm ERR! prepareGitDep npm ERR! missing script: build:clean;
npm ERR! prepareGitDep npm ERR!
npm ERR! prepareGitDep npm ERR! Did you mean one of these?
npm ERR! prepareGitDep npm ERR!     build:clean
npm ERR! prepareGitDep npm ERR!     build:node
npm ERR! prepareGitDep npm ERR!     dev:clean
npm ERR! prepareGitDep
npm ERR! prepareGitDep npm ERR! A complete log of this run can be found in:
npm ERR! prepareGitDep npm ERR!     C:\Users\zyang\AppData\Roaming\npm-cache\_logs\2020-12-29T00_08_27_389Z-debug.log
npm ERR! prepareGitDep npm ERR! code ELIFECYCLE
npm ERR! prepareGitDep npm ERR! errno 1
npm ERR! prepareGitDep npm ERR! geotiff@1.0.0-beta.14 build: `npm run build:clean; run-p build:browser build:node;`
npm ERR! prepareGitDep npm ERR! Exit status 1
npm ERR! prepareGitDep npm ERR!
npm ERR! prepareGitDep npm ERR! Failed at the geotiff@1.0.0-beta.14 build script.
npm ERR! prepareGitDep npm ERR! This is probably not a problem with npm. There is likely additional logging output above.
npm ERR! prepareGitDep
npm ERR! prepareGitDep npm ERR! A complete log of this run can be found in:
npm ERR! prepareGitDep npm ERR!     C:\Users\zyang\AppData\Roaming\npm-cache\_logs\2020-12-29T00_08_27_419Z-debug.log
npm ERR! prepareGitDep npm ERR! code ELIFECYCLE
npm ERR! prepareGitDep npm ERR! errno 1
npm ERR! prepareGitDep npm ERR! geotiff@1.0.0-beta.14 prepare: `npm run build`
npm ERR! prepareGitDep npm ERR! Exit status 1
npm ERR! prepareGitDep npm ERR!
npm ERR! prepareGitDep npm ERR! Failed at the geotiff@1.0.0-beta.14 prepare script.
npm ERR! prepareGitDep npm ERR! This is probably not a problem with npm. There is likely additional logging output above.
npm ERR! prepareGitDep
npm ERR! prepareGitDep npm ERR! A complete log of this run can be found in:
npm ERR! prepareGitDep npm ERR!     C:\Users\zyang\AppData\Roaming\npm-cache\_logs\2020-12-29T00_08_27_487Z-debug.log
npm ERR! prepareGitDep
npm ERR! premature close

About this issue

  • Original URL
  • State: closed
  • Created 4 years ago
  • Comments: 16 (6 by maintainers)

Most upvoted comments

To show your own data in Vitessce, you are correct that it currently would require a manual data conversion process. Sorry that this is not clear from our current documentation. We are working on publishing a new documentation website. Our goal is to provide helper functions in the R and Python packages for loading common single-cell data structures like AnnData, Seurat, and now Giotto. These are currently a work in progress and we hope to have initial implementations done for many of them in the next few weeks.

@keller-mark @ilan-gold, it is working!!! I really appreciated it. Overall, the deployment is almost instant on the macOS system while it takes some additional steps to get it to work on Windows. image

One more question, it is possible to replace the current Ruben’s giotto example dataset with a new one. Maybe replace the demo data under some folder? Keller pointed me to an R package which seems to only work with Seurat object at this point (unless I am not aware of new functions for giotto).

image

can you try npm run lint-fix?