v1.13.0 upgrade issues (checkPermissions)

dcook

I am currently running 1.12.2, I ran the upgrade process as I normally do:

git fetch
git checkout v1.13.x
git merge origin/v1.13.x
./nodebb upgrade

However this time I get screen full of errors:

bgc@server1:~/nodebb$ ./nodebb upgrade
Dependencies outdated or not yet installed.
Installing them now...

npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/@babel/runtime/node_modules/regenerator-runtime
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/@babel/runtime
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/@commitlint/cli/node_modules/supports-color
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/@commitlint/cli/node_modules/chalk
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/arr-diff
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/arr-flatten
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/arr-union
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/array-unique
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/assign-symbols
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/atob
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/copy-descriptor
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/cosmiconfig/node_modules/js-yaml
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/decode-uri-component
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/eslint-restricted-globals
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/eslint/node_modules/ajv
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/eslint/node_modules/js-yaml
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/find-parent-dir
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/flat/node_modules/is-buffer
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/fn-name
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/for-in
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/get-value
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/globby/node_modules/pify
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/has-values/node_modules/kind-of
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/has-values
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/inquirer/node_modules/mute-stream
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/is-accessor-descriptor/node_modules/kind-of
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/is-accessor-descriptor
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/is-ci
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/is-data-descriptor/node_modules/kind-of
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/is-data-descriptor
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/is-descriptor/node_modules/kind-of
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/is-descriptor
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/class-utils/node_modules/define-property
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/expand-brackets/node_modules/define-property
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/is-extendable
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/braces/node_modules/extend-shallow
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/expand-brackets/node_modules/extend-shallow
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/extglob/node_modules/extend-shallow
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/fill-range/node_modules/extend-shallow
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/is-number/node_modules/kind-of
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/is-path-in-cwd
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/is-windows
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/isobject
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/has-value
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/is-plain-object
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/extend-shallow/node_modules/is-extendable
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/extend-shallow
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/kind-of
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/base/node_modules/is-accessor-descriptor
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/base/node_modules/is-data-descriptor
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/base/node_modules/is-descriptor
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/base/node_modules/define-property
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/define-property/node_modules/is-accessor-descriptor
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/define-property/node_modules/is-data-descriptor
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/define-property/node_modules/is-descriptor
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/define-property
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/extglob/node_modules/is-accessor-descriptor
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/extglob/node_modules/is-data-descriptor
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/extglob/node_modules/is-descriptor
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/extglob/node_modules/define-property
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/map-cache
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/fragment-cache
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/matcher
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/mixin-deep/node_modules/is-extendable
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/mixin-deep
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/mocha/node_modules/cliui/node_modules/string-width
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/mocha/node_modules/invert-kv
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/mocha/node_modules/js-yaml
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/mocha/node_modules/lcid
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/mocha/node_modules/os-locale
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/mocha/node_modules/string-width/node_modules/ansi-regex
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/mocha/node_modules/string-width/node_modules/strip-ansi
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/npm-path
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/npm-which
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/object-copy/node_modules/define-property
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/object-copy/node_modules/kind-of
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/object-copy
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/object-visit
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/map-visit
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/collection-visit
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/object.pick
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/optionator/node_modules/wordwrap
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/pascalcase
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/path-is-inside
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/posix-character-classes
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/property-expr
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/repeat-element
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/repeat-string
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/resolve-url
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/ret
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/safe-regex
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/regex-not
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/set-value/node_modules/extend-shallow
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/simple-git/node_modules/ms
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/simple-git/node_modules/debug
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/simple-git
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/g-status
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/snapdragon-node/node_modules/is-accessor-descriptor
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/snapdragon-node/node_modules/is-data-descriptor
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/snapdragon-node/node_modules/is-descriptor
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/snapdragon-node/node_modules/define-property
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/snapdragon-util/node_modules/kind-of
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/snapdragon-util
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/snapdragon-node
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/snapdragon/node_modules/define-property
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/snapdragon/node_modules/extend-shallow
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/snapdragon/node_modules/source-map
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/source-map-url
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/split-string
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/set-value
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/staged-git-files
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/static-extend/node_modules/define-property
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/static-extend
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/class-utils
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/synchronous-promise
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/table/node_modules/ajv
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/to-object-path/node_modules/kind-of
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/to-object-path
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/to-regex
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/toposort
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/union-value
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/unset-value/node_modules/has-value/node_modules/isobject
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/unset-value/node_modules/has-values
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/unset-value/node_modules/has-value
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/unset-value
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/cache-base
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/base
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/urix
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/source-map-resolve
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/use
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/snapdragon
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/expand-brackets
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/extglob
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/nanomatch
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/yargs-unparser/node_modules/get-caller-file
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/yargs-unparser/node_modules/invert-kv
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/yargs-unparser/node_modules/lcid
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/yargs-unparser/node_modules/os-locale
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/yargs-unparser/node_modules/require-main-filename
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/yup
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/nodebb-plugin-spam-be-gone
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/@babel/runtime/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/@commitlint/cli/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/cosmiconfig/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/eslint/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/flat/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/globby/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/has-values/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/inquirer/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/is-accessor-descriptor/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/is-data-descriptor/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/is-descriptor/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/class-utils/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/expand-brackets/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/braces/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/extglob/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/fill-range/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/is-number/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/extend-shallow/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/base/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/define-property/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/mixin-deep/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/mocha/node_modules/cliui/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/mocha/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/mocha/node_modules/string-width/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/object-copy/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/optionator/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/set-value/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/simple-git/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/snapdragon-node/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/snapdragon-util/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/snapdragon/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/static-extend/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/table/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/to-object-path/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/unset-value/node_modules/has-value/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/unset-value/node_modules
npm WARN checkPermissions Missing write access to /home/bgc/nodebb/node_modules/yargs-unparser/node_modules
npm WARN [email protected] requires a peer of moment-timezone@^0.4.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of nodebb-plugin-emoji@^2.0.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of textcomplete@^0.14.2 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of canvas@^2.5.0 but none is installed. You must install peer dependencies yourself.

npm ERR! code EACCES
npm ERR! syscall access
npm ERR! path /home/bgc/nodebb/node_modules/@babel/runtime/node_modules/regenerator-runtime
npm ERR! errno -13
npm ERR! Error: EACCES: permission denied, access '/home/bgc/nodebb/node_modules/@babel/runtime/node_modules/regenerator-runtime'
npm ERR!  { [Error: EACCES: permission denied, access '/home/bgc/nodebb/node_modules/@babel/runtime/node_modules/regenerator-runtime']
npm ERR!   stack:
npm ERR!    'Error: EACCES: permission denied, access \'/home/bgc/nodebb/node_modules/@babel/runtime/node_modules/regenerator-runtime\'',
npm ERR!   errno: -13,
npm ERR!   code: 'EACCES',
npm ERR!   syscall: 'access',
npm ERR!   path:
npm ERR!    '/home/bgc/nodebb/node_modules/@babel/runtime/node_modules/regenerator-runtime' }
npm ERR!
npm ERR! The operation was rejected by your operating system.
npm ERR! It is likely you do not have the permissions to access this file as the current user
npm ERR!
npm ERR! If you believe this might be a permissions issue, please double-check the
npm ERR! permissions of the file and its containing directories, or try running
npm ERR! the command again as root/Administrator.

npm ERR! A complete log of this run can be found in:
npm ERR!     /home/bgc/.npm/_logs/2019-12-02T15_01_51_895Z-debug.log
Error installing dependencies!
message: Command failed: npm install --production
stdout: null
stderr: null
/home/bgc/nodebb/src/cli/package-install.js:52
                throw e;
                ^

Error: Command failed: npm install --production
    at checkExecSyncError (child_process.js:629:11)
    at Object.execSync (child_process.js:666:13)
    at Object.installAll (/home/bgc/nodebb/src/cli/package-install.js:43:9)
    at Object.<anonymous> (/home/bgc/nodebb/src/cli/index.js:60:18)
    at Module._compile (internal/modules/cjs/loader.js:778:30)
    at Object.Module._extensions..js (internal/modules/cjs/loader.js:789:10)
    at Module.load (internal/modules/cjs/loader.js:653:32)
    at tryModuleLoad (internal/modules/cjs/loader.js:593:12)
    at Function.Module._load (internal/modules/cjs/loader.js:585:3)
    at Module.require (internal/modules/cjs/loader.js:692:17)

It seems to be a permission issue, I know I could run sudo ./nodebb upgrade but I was told in the past to never run nodebb as root, so I am not sure why this time my usual steps are not working?

PitaJ

@dcook yeah it looks like at some point you executed a nodebb command as root. You can chown the files to your normal user.

dcook

@PitaJ that was the issue, not sure how that happened! I guess form now on I will do chown prior to running the upgrade command!

I did notice that I am getting some lines saying I must install peer dependencies?

And its also telling me to run: npm fund and npm audit fix as well, I ran those two commands but when I run the ./nodebb upgrade again after it says the same thing?

Can you advise how I fix those?

Bringing base dependencies up to date... started
npm WARN [email protected] requires a peer of moment-timezone@^0.4.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of nodebb-plugin-emoji@^2.0.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of textcomplete@^0.14.2 but none is installed. You must install peer dependencies yourself.

audited 3779 packages in 9.73s

6 packages are looking for funding
run npm fund for details

found 1 high severity vulnerability
run npm audit fix to fix them, or npm audit for details

PitaJ

@dcook I don't recommend you run any other npm commands unless you run into issues.

julian

@dcook Those are only warnings.

6 packages are looking for funding
run npm fund for details

The messages themselves will tell you what you need to know. If you wish to fund one of NodeBB's dependencies, you can, but it won't help your NodeBB run any faster, unfortunately

As for the high severity vulnerability, we're not aware of any at this time...

dcook

I just noticed that after upgrading the calendar is now blank and says: "Error the last argument must be of type function. Received type object"