Issues encountered in PREPARATION

[Daniel-Mietchen]

I am now ignoring my existing installation and going through the instructions in https://github.com/ContentMine/FutureTDM/blob/master/README.md for the recommended local installation, logging the problems on the way.

Upon

sudo npm install getpapers

I got

npm WARN deprecated [email protected]: use uuid module instead
npm WARN deprecated [email protected]: ReDoS vulnerability parsing Set-Cookie https://nodesecurity.io/advisories/130
- [email protected] node_modules/bluebird

which I ignored as well as the long Node package tree, which was followed by

npm WARN enoent ENOENT: no such file or directory, open '/Users/danielmietchen/package.json'
npm WARN danielmietchen No description
npm WARN danielmietchen No repository field.
npm WARN danielmietchen No README data
npm WARN danielmietchen No license field.

I tried to use https://github.com/ContentMine/getpapers/blob/master/package.json as a fix but that got me

sudo npm install getpapers
npm ERR! Darwin 16.3.0
npm ERR! argv "/Users/danielmietchen/.nvm/versions/node/v7.1.0/bin/node" "/Users/danielmietchen/.nvm/versions/node/v7.1.0/bin/npm" "install" "getpapers"
npm ERR! node v7.1.0
npm ERR! npm  v3.10.9
npm ERR! code ENOSELF

npm ERR! Refusing to install getpapers as a dependency of itself
npm ERR! 
npm ERR! If you need help, you may report this error at:
npm ERR!     <https://github.com/npm/npm/issues>

npm ERR! Please include the following file with any support request:
npm ERR!     /Users/danielmietchen/Programming/FutureTDM/FutureTDM-master/npm-debug.log

I circumvented that by copying over the package.json from my existing installation, but I guess there should be better documentation as to what to do at this point.

Also, the installation instructions are inconsistent:

• https://github.com/ContentMine/contentmine.github.io/blob/master/osx.md says "npm install getpapers"
• https://github.com/ContentMine/getpapers/blob/master/README.md says "npm install --global getpapers"

After getpapers, the tutorial lists norma as the next dependency to install, but https://github.com/ContentMine/norma refers to http://contentmine.github.io/ , which brought me to http://contentmine.github.io/osx.html , which then points to "the zip" at https://github.com/ContentMine/norma/releases .

The instruction at http://contentmine.github.io/osx.html to "Add the bin directory that you unzipped to your path" is something I remember having had trouble with in the past, which was fixed by PMR who sat next to me. That kind of troubleshooting is not available with the tutorial, so the documentation should be improved.

Since both norma and ami are already in my path, and no newer releases are available, I did not install them again.

In terms of installing Python3 and Jupyter, some word on how to handle existing installations would also be useful, or on how to check compatibility with ContentMine. Both are already installed on my system, so I am ignoring this part.

https://github.com/ContentMine/FutureTDM/blob/master/README.md does not list a version for pyCProject, but pip install pycproject went smoothly and resulted in Successfully installed pycproject-0.0.6.dev0.

[tarrow]

You want to install using npm install --global getpapers or npm install -g getpapers. I'll fix up this omission on contentmine.github.io

I think you should also be able to do this without sudo.