Auspice doesn't install correctly

While installing auspice using npm and conda, I encounter errors. I manually installed node.js and updated conda but the result remained the same. Updating npm also gave me errors.

Hi @carr - happy to try and help here - could you send through details of your operating system, the commands you ran & what error messages were printed?

Hi James,
I might have a similar problem. I am using conda 4.9.2:
My server SO is “SUSE Linux Enterprise Server 12 SP1”

The command I use and the errors:

(nextstrain) cdbcexbimollx01:/soft # npm install --global auspice
npm WARN deprecated linspace@1.0.0: I wrote this module a very long time ago; you should use something else.
npm WARN deprecated request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
npm WARN deprecated core-js@2.6.12: core-js@<3 is no longer maintained and not recommended for usage due to the number of issues. Please, upgrade your dependencies to the actual version of core-js@3.
npm WARN deprecated har-validator@5.1.5: this library is no longer supported
npm WARN deprecated urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
npm WARN deprecated resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
npm WARN deprecated chokidar@2.1.8: Chokidar 2 will break on node v14+. Upgrade to chokidar 3 with 15x less dependencies.
npm WARN deprecated fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2.
/root/miniconda3/envs/nextstrain/bin/auspice -> /root/miniconda3/envs/nextstrain/lib/node_modules/auspice/auspice.js

> core-js@2.6.12 postinstall /root/miniconda3/envs/nextstrain/lib/node_modules/auspice/node_modules/babel-runtime/node_modules/core-js
> node -e "try{require('./postinstall')}catch(e){}"

sh: node: command not found
npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents@~2.3.1 (node_modules/auspice/node_modules/chokidar/node_modules/fsevents):
npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents@2.3.2: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"})
npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents@^1.2.7 (node_modules/auspice/node_modules/watchpack-chokidar2/node_modules/chokidar/node_modules/fsevents):
npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents@1.2.13: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"})
npm WARN react-addons-css-transition-group@15.6.2 requires a peer of react@^15.4.2 but none is installed. You must install peer dependencies yourself.
npm WARN react-hot-loader@4.13.0 requires a peer of @types/react@^15.0.0 || ^16.0.0 || ^17.0.0  but none is installed. You must install peer dependencies yourself.

npm ERR! file sh
npm ERR! code ELIFECYCLE
npm ERR! errno ENOENT
npm ERR! syscall spawn
npm ERR! core-js@2.6.12 postinstall: `node -e "try{require('./postinstall')}catch(e){}"`
npm ERR! spawn ENOENT
npm ERR! 
npm ERR! Failed at the core-js@2.6.12 postinstall script.
npm ERR! This is probably not a problem with npm. There is likely additional logging output above.

npm ERR! A complete log of this run can be found in:
npm ERR!     /root/.npm/_logs/2021-02-25T12_00_04_853Z-debug.log

This error, sh: node: command not found, implies that node wasn’t installed into the conda environment. If you could send the commands used to create the environment then I’ll make sure this wasn’t a bug on our end.

The following commands should install node into the environment and allow auspice to be installed:

conda activate <your_environment_name>
conda install -c conda-forge nodejs
npm install --global auspice
1 Like

Hi James,
I managed to install it into a new environment named covid19 with your instructions from the post. So yay!

However for some reason if I follow the installation instructions from the website and try to work with an environment named auspice I get the error:

`conda create --name auspice nodejs=12
WARNING: A conda environment already exists at ‘/root/miniconda3/envs/auspice’
Remove existing environment (y/[n])? y

Collecting package metadata (current_repodata.json): done
Solving environment: done

Package Plan

environment location: /root/miniconda3/envs/auspice

added / updated specs:
- nodejs=12

The following NEW packages will be INSTALLED:

_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
ca-certificates conda-forge/linux-64::ca-certificates-2020.12.5-ha878542_0
icu conda-forge/linux-64::icu-68.1-h58526e2_0
libgcc-ng conda-forge/linux-64::libgcc-ng-9.3.0-h2828fa1_18
libgomp conda-forge/linux-64::libgomp-9.3.0-h2828fa1_18
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.3.0-h6de172a_18
libuv pkgs/main/linux-64::libuv-1.40.0-h7b6447c_0
nodejs conda-forge/linux-64::nodejs-12.19.0-hfa01f41_2
openssl conda-forge/linux-64::openssl-1.1.1j-h7f98852_0
zlib conda-forge/linux-64::zlib-1.2.11-h516909a_1010

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

To activate this environment, use

$ conda activate auspice

To deactivate an active environment, use

$ conda deactivate

(covid19) cdbcexbimollx01:/datos/NextSeq/NextSeq_Output # conda activate auspice
(auspice) cdbcexbimollx01:/datos/NextSeq/NextSeq_Output # npm install --global auspice
npm WARN deprecated linspace@1.0.0: I wrote this module a very long time ago; you should use something else.
npm WARN deprecated request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
npm WARN deprecated core-js@2.6.12: core-js@<3 is no longer maintained and not recommended for usage due to the number of issues. Please, upgrade your dependencies to the actual version of core-js@3.
npm WARN deprecated har-validator@5.1.5: this library is no longer supported
npm WARN deprecated urix@0.1.0: Please see /lydell/urix#deprecated
npm WARN deprecated resolve-url@0.2.1: ydell/resolve-url#deprecated
npm WARN deprecated chokidar@2.1.8: Chokidar 2 will break on node v14+. Upgrade to chokidar 3 with 15x less dependencies.
npm WARN deprecated fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2.
/root/miniconda3/envs/auspice/bin/auspice → /root/miniconda3/envs/auspice/lib/node_modules/auspice/auspice.js

core-js@2.6.12 postinstall /root/miniconda3/envs/auspice/lib/node_modules/auspice/node_modules/babel-runtime/node_modules/core-js
node -e “try{require(’./postinstall’)}catch(e){}”

sh: node: command not found
npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents@~2.3.1 (node_modules/auspice/node_modules/chokidar/node_modules/fsevents):
npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents@2.3.2: wanted {“os”:“darwin”,“arch”:“any”} (current: {“os”:“linux”,“arch”:“x64”})
npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents@^1.2.7 (node_modules/auspice/node_modules/watchpack-chokidar2/node_modules/chokidar/node_modules/fsevents):
npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents@1.2.13: wanted {“os”:“darwin”,“arch”:“any”} (current: {“os”:“linux”,“arch”:“x64”})
npm WARN react-addons-css-transition-group@15.6.2 requires a peer of react@^15.4.2 but none is installed. You must install peer dependencies yourself.
npm WARN react-hot-loader@4.13.0 requires a peer of @types/react@^15.0.0 || ^16.0.0 || ^17.0.0 but none is installed. You must install peer dependencies yourself.

npm ERR! code ELIFECYCLE
npm ERR! syscall spawn
npm ERR! file sh
npm ERR! errno ENOENT
npm ERR! core-js@2.6.12 postinstall: node -e "try{require('./postinstall')}catch(e){}"
npm ERR! spawn ENOENT
npm ERR!
npm ERR! Failed at the core-js@2.6.12 postinstall script.
npm ERR! This is probably not a problem with npm. There is likely additional logging output above.

npm ERR! A complete log of this run can be found in:
npm ERR! 8_201Z-debug.log
`

PS: new users can only put 2 links in a post, had to remove stuff.