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R language support for Atom-IDE

Home Page: https://atom.io/packages/ide-r

License: MIT License

JavaScript 100.00%
atom-ide language-server r

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atom-ide-r's Issues

Uncaught SyntaxError: Unexpected token C in JSON at position 9646

[Enter steps to reproduce:]

  1. ...
  2. ...

Atom: 1.40.1 x64
Electron: 3.1.10
OS: Microsoft Windows 10 Enterprise
Thrown From: ide-r package 0.1.8

Stack Trace

Uncaught SyntaxError: Unexpected token C in JSON at position 9646

At file:///C:/Users/mffranco/AppData/Local/atom/app-1.40.1/resources/app.asar/static/index.html:1

SyntaxError: Unexpected token C in JSON at position 9646
    at JSON.parse (<anonymous>)
    at SocketMessageReader.StreamMessageReader.onData (/packages/ide-r/node_modules/vscode-jsonrpc/lib/messageReader.js:219:29)
    at /packages/ide-r/node_modules/vscode-jsonrpc/lib/messageReader.js:185:19)
    at Socket.emit (events.js:182:13)
    at addChunk (_stream_readable.js:279:12)
    at readableAddChunk (_stream_readable.js:264:11)
    at Socket.Readable.push (_stream_readable.js:219:10)
    at TCP.onread (net.js:636:20)

Commands

     -0:10.1.0 hydrogen:run (input.hidden-input)
     -0:10.1.0 autocomplete-plus:cancel (atom-text-editor.editor.is-focused)
     -0:06.4.0 editor:move-to-end-of-word (input.hidden-input)

Non-Core Packages

atom-beautify 0.33.4 
atom-ide-ui 0.13.0 
atom-language-r 1.4.8 
Hydrogen 2.12.1 
hydrogen-launcher 1.2.2 
ide-r 0.1.8 
ksx-matrix 1.4.1 
ksx-matrix-ui 1.2.8 
rbox 0.5.0 
termination 0.7.4

No outline available on macOS

I got macOS with R version 3.4.1 (2017-06-30) -- "Single Candle" and when I open up outline on atom, it says that

No outline available
This is likely an error with the language package.

I have installed both atom-language-r and install.packages("languageserver").

Thoughts?!

Uncaught Error: spawn EACCES

Gettint the following error message immediately on Atom startup:

Atom: 1.30.0 x64
Electron: 2.0.5
OS: Mac OS X 10.13.6
Thrown From: ide-r package 0.1.8

Stack Trace

Uncaught Error: spawn EACCES

At internal/child_process.js:323

Error: spawn EACCES
    at _errnoException (util.js:1024:11)
    at ChildProcess.spawn (internal/child_process.js:323:11)
    at Object.exports.spawn (child_process.js:514:9)
    at RLanguageClient.spawnServer (/packages/ide-r/lib/main.js:41:29)
    at Server.server.listen (/packages/ide-r/lib/main.js:30:29)
    at Object.onceWrapper (events.js:313:30)
    at emitNone (events.js:106:13)
    at Server.emit (events.js:208:7)
    at emitListeningNT (net.js:1378:10)
    at _combinedTickCallback (internal/process/next_tick.js:135:11)
    at process._tickCallback (internal/process/next_tick.js:180:9)

Commands

Non-Core Packages

atom-clock 0.1.16 
atom-ide-ui 0.13.0 
atom-language-r 1.4.8 
Hydrogen 2.5.1 
hydrogen-launcher 1.2.2 
ide-python 1.0.0 
ide-r 0.1.8 
platformio-ide-terminal 2.8.4 
teletype 0.13.3

Uncaught SyntaxError: Unexpected token C in JSON at position 7518

Possibly related to #4

Steps to reproduce

  1. R version 3.5.0
  2. language-server 0.2.2
  3. Have a few files open, and hover mouse over a few functions for documenatation
  4. Error eventually thrown
  5. Subsequently, more errors thrown every time mouse triggers hoverover documentation:
Error: Header must provide a Content-Length property.
    at SocketMessageReader.StreamMessageReader.onData (C:\Users\xxxx\.atom\packages\ide-r\node_modules\vscode-jsonrpc\lib\messageReader.js:200:27)
    at Socket.<anonymous> (C:\Users\xxxx\.atom\packages\ide-r\node_modules\vscode-jsonrpc\lib\messageReader.js:185:19)
    at emitOne (events.js:96:13)
    at Socket.emit (events.js:191:7)
    at readableAddChunk (_stream_readable.js:178:18)
    at Socket.Readable.push (_stream_readable.js:136:10)
    at TCP.onread (net.js:560:20)

I can't seem to isolate any function documentation in particular that sets it off, but it looks like some function is screwing up the JSON output and causing all subsequent messages to be malformed.

Stack Trace

Uncaught SyntaxError: Unexpected token C in JSON at position 7518

At file:///C:/Users/xxxx/Atom/resources/app.asar/static/index.html:1

SyntaxError: Unexpected token C in JSON at position 7518
    at JSON.parse (<anonymous>)
    at SocketMessageReader.StreamMessageReader.onData (/packages/ide-r/node_modules/vscode-jsonrpc/lib/messageReader.js:219:29)
    at /packages/ide-r/node_modules/vscode-jsonrpc/lib/messageReader.js:185:19)
    at emitOne (events.js:96:13)
    at Socket.emit (events.js:191:7)
    at readableAddChunk (_stream_readable.js:178:18)
    at Socket.Readable.push (_stream_readable.js:136:10)
    at TCP.onread (net.js:560:20)

Commands

     -4:56.4.0 settings-view:open (input.hidden-input)
     -4:28.3.0 core:save (input.hidden-input)
  2x -2:18.3.0 core:backspace (input.hidden-input)
     -2:12.3.0 core:save (input.hidden-input)
     -1:35 core:copy (input.hidden-input)
     -1:25.4.0 core:paste (input.hidden-input)
     -1:22.2.0 editor:newline (input.hidden-input)
  4x -1:21.6.0 core:move-right (input.hidden-input)
  3x -1:19 core:backspace (input.hidden-input)
     -0:43.3.0 core:copy (input.hidden-input)
     -0:39 editor:newline (input.hidden-input)
     -0:38.5.0 core:move-up (input.hidden-input)
  7x -0:38.2.0 core:move-right (input.hidden-input)
     -0:36.6.0 core:paste (input.hidden-input)
  3x -0:27.9.0 core:backspace (input.hidden-input)
     -0:23.4.0 core:move-right (input.hidden-input)

Non-Core Packages

apex-syntax 0.2.0 
apex-ui 1.0.3 
atom-beautify 0.32.2 
atom-ide-ui 0.11.1 
atom-idle-autosave 0.3.0 
atom-material-syntax 1.0.8 
atom-material-syntax-dark 1.0.0 
atom-material-syntax-light 0.4.6 
atom-material-ui 2.1.1 
minimap-hide 0.3.0 
base-16-ocean-dark-ui-theme 1.7.2 
busy-signal 1.4.3 
city-lights-syntax 1.1.4 
city-lights-ui 1.2.0 
dark-flat-ui 1.2.4 
file-icons 2.1.20 
ide-python 0.9.2 
ide-r 0.1.6 
intentions 1.1.5 
language-cuda 0.1.0 
language-fortran 2.1.6 
language-latex 1.1.1 
language-lua 0.9.11 
language-r 0.4.2 
latex 0.50.0 
linter 2.2.0 
linter-lintr 1.1.4 
linter-ui-default 1.7.1 
material-palenight-syntax 1.5.7 
minimap 4.29.8 
outlander-syntax 2.0.0 
pdf-view 0.70.0 
slush-poppies 0.1.1 
unity-ui 2.1.11 
Zen 0.18.0

No data tooltip or function parameter autocomplete help for non-base R library functions

No data tooltip or function parameter autocomplete help appear for non-base R package functions. Sorry maybe I'm missing a setting but both work for base R functions so I'm guessing not.

If in my R code file I've e.g., library(edgeR) then in a line of code e.g. dge <- DGEList(...) when I hover over or mouse cursor stay on DGEList I don't get a popup data tooltip. And when I'm inside the parentheses it doesn't know or help with the available parameters, default values, etc.

Silent R core dumps caused by atom-ide-r or r-languageserver on Linux

I cannot tell what is causing it, but either atom-ide-r or r-languageserver, or both, are causing silent R core dumps when using Atom with these plugins on Linux. It didn't used to do this. I see the core dumps when I'm using Atom with an R file open under /var/lib/systemd/coredump. It happens when I have R files open within or outside a git repo and can have enough silent core dumps and restarts that Atom eventually give a message that the plugin reached the restart limit.

How do I figure out what is causing this?

[questions] menu and compilation

1.a. i don't see any menu neither command palette in atom once install ide-r. Is it normal?
1.b. I also don't see any new syntax in the atom list (such as R-IDE for sublime).
2. Is there a way to compile a Rmd file using the rmakdown::render command automatically as setted up in sublime IDE-R?

thanks

How to change the line length preference for warnings in Diagnostics?

It seems this package ignores the Atom preferences for preferred line length and max line length (in Settings/Editor), and I still get warnings from atom-ide-ui for all lines that exceed 80 characters despite setting the preference to 160 in Atom settings and all r-related packages (Rbox, Hydrogen, etc.).

screenshot from 2018-03-21 14 30 12

Is there a way to change that? My scripts are cluttered with line length warnings, and I don't want to hide warnings because they can be useful for other formatting issues.

Or is it something set independently from atom-ide-r, like in atom-ide-ui?

Cannot find languageserver in R_PROFILE_USER?

All of atom-ide-ui, ide-r, atom-language-r, R, and languageserver are installed. But Atom says "Unable to start the R language server".

I have ~/.Renviron with R_LIBS_USER=${R_USER}/.R/library, and languageserver is installed there. Can this be the cause of this problem? Does atom-ide-r require languageserver to be installed system-wide?

A few month ago I submitted a PR to linter-lintr to fix the similar issue (not merged yet, though):
AtomLinter/linter-lintr#123

Uncaught Error: Header must provide a Content-Length property.

[Enter steps to reproduce:]

  1. click warning popup from lintr
  2. edit

Atom: 1.40.1 x64
Electron: 3.1.10
OS: Microsoft Windows 7 Professional
Thrown From: ide-r package 0.1.8

Stack Trace

Uncaught Error: Header must provide a Content-Length property.

At C:\Users\stthein\.atom\packages\ide-r\node_modules\vscode-jsonrpc\lib\messageReader.js:200

Error: Header must provide a Content-Length property.
    at SocketMessageReader.StreamMessageReader.onData (/packages/ide-r/node_modules/vscode-jsonrpc/lib/messageReader.js:200:27)
    at /packages/ide-r/node_modules/vscode-jsonrpc/lib/messageReader.js:185:19)
    at Socket.emit (events.js:182:13)
    at addChunk (_stream_readable.js:279:12)
    at readableAddChunk (_stream_readable.js:264:11)
    at Socket.Readable.push (_stream_readable.js:219:10)
    at TCP.onread (net.js:636:20)

Commands

     -4:37.2.0 settings-view:open (input.hidden-input)
  2x -4:35.6.0 core:move-down (div.panels-item)
  5x -4:35 core:move-up (div.panels-item)
     -4:33.9.0 core:move-left (div.panels-item)
     -4:33.1.0 core:move-down (div.panels-item)
     -4:32.7.0 core:move-up (div.panels-item)
     -3:23.8.0 settings-view:open (input.hidden-input)
     -0:44.5.0 core:move-left (input.hidden-input)
     -0:43.8.0 core:delete (input.hidden-input)

Non-Core Packages

atom-ide-ui 0.13.0 
atom-language-r 1.4.8 
atom-material-syntax 1.0.8 
atom-material-ui 2.1.3 
Hydrogen 2.10.3 
ide-python 1.4.2 
ide-r 0.1.8 
language-stata 1.7.3 
teletype 0.13.4

Uncaught SyntaxError: Unexpected end of JSON input

[Enter steps to reproduce:]

  1. Clicked on a line that was marked for "warning".

Atom: 1.25.0 x64
Electron: 1.7.11
OS: 020-T47020HD
Thrown From: ide-r package 0.1.6

Stack Trace

Uncaught SyntaxError: Unexpected end of JSON input

At file:///C:/Users/*USERNAMEOMMITED*/AppData/Local/atom/app-1.25.0/resources/app.asar/static/index.html:1

SyntaxError: Unexpected end of JSON input
    at JSON.parse (<anonymous>)
    at SocketMessageReader.StreamMessageReader.onData (/packages/ide-r/node_modules/vscode-jsonrpc/lib/messageReader.js:219:29)
    at /packages/ide-r/node_modules/vscode-jsonrpc/lib/messageReader.js:185:19)
    at emitOne (events.js:96:13)
    at Socket.emit (events.js:191:7)
    at readableAddChunk (_stream_readable.js:178:18)
    at Socket.Readable.push (_stream_readable.js:136:10)
    at TCP.onread (net.js:560:20)

Commands

  2x -9:00.0 diagnostics:toggle-table (atom-workspace.workspace.scrollbars-visible-always.theme-one-dark-syntax.theme-one-dark-ui)
     -8:55.5.0 grammar-selector:show (atom-text-editor.editor.is-focused)
     -8:31.8.0 core:backspace (input.hidden-input)
     -2:32.1.0 diagnostics:toggle-table (atom-workspace.workspace.scrollbars-visible-always.theme-one-dark-syntax.theme-one-dark-ui)
     -2:16.6.0 encoding-selector:show (atom-text-editor.editor.is-focused)

Non-Core Packages

atom-ide-ui 0.9.4 
atom-language-r 1.4.0 
atom-material-syntax 1.0.8 
ide-r 0.1.6 
language-markdown 0.25.1

Uncaught SyntaxError: Unexpected token C in JSON at position 2126

[Enter steps to reproduce:]

  1. ...
  2. ...

Atom: 1.39.1 x64
Electron: 3.1.10
OS: Microsoft Windows 10 Enterprise
Thrown From: ide-r package 0.1.8

Stack Trace

Uncaught SyntaxError: Unexpected token C in JSON at position 2126

At file:///C:/Users/gcardozo/AppData/Local/atom/app-1.39.1/resources/app.asar/static/index.html:1

SyntaxError: Unexpected token C in JSON at position 2126
    at JSON.parse (<anonymous>)
    at SocketMessageReader.StreamMessageReader.onData (/packages/ide-r/node_modules/vscode-jsonrpc/lib/messageReader.js:219:29)
    at /packages/ide-r/node_modules/vscode-jsonrpc/lib/messageReader.js:185:19)
    at Socket.emit (events.js:182:13)
    at addChunk (_stream_readable.js:279:12)
    at readableAddChunk (_stream_readable.js:264:11)
    at Socket.Readable.push (_stream_readable.js:219:10)
    at TCP.onread (net.js:636:20)

Commands

     -2:14.4.0 tree-view:add-file (span.name.icon.jupyter-icon.dark-orange)
     -2:10.9.0 core:backspace (input.hidden-input)
     -2:03.2.0 core:confirm (input.hidden-input)
     -1:14.7.0 core:paste (input.hidden-input)
     -0:56.4.0 core:copy (input.hidden-input)
     -0:50.4.0 core:paste (input.hidden-input)
 10x -0:10.8.0 core:select-down (input.hidden-input)

Non-Core Packages

atom-beautify 0.33.4 
atom-ide-ui 0.13.0 
atom-language-r 1.4.8 
file-icons 2.1.33 
Hydrogen 2.10.3 
hydrogen-launcher 1.2.2 
ide-python 1.4.2 
ide-r 0.1.8 
kite 0.167.0 
multi-cursor 2.1.5 
scroll-through-time 0.3.1

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