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3 is no longer maintained and not recommended for usage due to the number of issues.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.

Glad you got it working!

Those errors can be really tricky to sort out as they’re coming from dependencies of auspice, not auspice itself. For this reason (and others) we’ve been working on making auspice avaliable as a conda package (e.g. conda install auspice or similar). The install instructions should change in the next few days to reflect this :smiley: