Julia-1.0.app Permission denied

[ludwigwinkler]

Hi, I installed the plugin in PyCharm and Julia 1.0 and and set the Julia executable to "/Applications/Julia-1.0.app/Contents/Resources/julia/bin/julia".

Unfortunately I can't execute any Julia code as I get the following error:

Would anybody have an idea on what to do?

Thank you in advance. Cheers!

[ice1000]

Could you please show your project configuration? If you're not sure, close PyCharm and upload your workspace.xml here.

Don't worry, it's just some metadata of your project which helps us debug, it doesn't have much private information.

[ludwigwinkler]

Hi,

here you go. Thank you again for all the work!

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[ice1000]

@ludwigwinkler What about .idea/juliaConfig.xml?

[ice1000]

I didn't see anything wrong with the current workspace.xml, very weird.

[ghost]

Would it help if I set the DEBUG log options, using the Help option inside IntelliJ? If so, what settings should I use?

[ice1000]

@Andy-KNDJ No. Can I see your .idea/juliaConfig.xml? The error means that it's trying to run the .app file as an application but according to OP's workspace.xml there isn't a run config which tries to run the .app file. BTW his screenshot shows that he's trying to run a Test file, but I didn't see that in the workspace.xml

[ghost]

How's this:

 <?xml version="1.0" encoding="UTF-8"?>
  <project version="4">
    <component name="JuliaProjectSettings">
      <option name="exePath" value="/Applications/Julia-1.0.app" />
      <option name="version" value="Unknown" />
    </component>
  </project>

Curiously, this Julia exe does not exist. I did have Julia 1.0 installed at one stage, but migrated to JulaiPro. This works fine from the command line, as demonstrated below:

/usr/local/bin/julia
MacBook-Pro:~ Andy$ ls -alrt /usr/local/bin/julia
lrwxr-xr-x  1 Andy  staff  94  7 Oct 12:12 /usr/local/bin/julia -> /Applications/JuliaPro-0.6.4.1.app/Contents/Resources/julia/Contents/Resources/julia/bin/julia
MacBook-Pro:~ Andy$ julia
               _
   _       _ _(_)_     |  A fresh approach to technical computing
  (_)     | (_) (_)    |  Documentation: https://docs.julialang.org
   _ _   _| |_  __ _   |  Type "?help" for help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 0.6.4 (2018-07-09 19:09 UTC)
 _/ |\__'_|_|_|\__'_|  |  Official http://julialang.org/ release
|__/                   |  x86_64-apple-darwin14.5.0

julia> println("Hello world")
Hello world

julia>

From memory, I had exactly the same issue (Error=13) when I was running using Julia 1.0.

[ice1000]

<?xml version="1.0" encoding="UTF-8"?>
 <project version="4">
   <component name="JuliaProjectSettings">
     <option name="exePath" value="/Applications/Julia-1.0.app" />
     <option name="version" value="Unknown" />
   </component>
 </project>

Can you modify your settings in File | Settings | Languages & Frameworks | Julia? You can reset the Julia exe there.

[ice1000]

So this is just due to incorrect configuration? Hmm, seems we need a better way to notify users about invalid Julia config.

[ghost]

Hmmm the 'File | Settings | Languages & Frameworksdialog _already_ shows the Julia executable as/Applications/JuliaPro-0.6.4.1.app`. I tried using the file selection feature of the preferences dialog to select my JuliaPro installation and the juliaConfig was unchanged. Note also from my original bug report that the Julia executable in the error message is shown as the JuliaPro copy. I'm guessing that the plugin is getting that name from somewhere in the plugin config. Maybe the issue is that the exe in the plugin config does not match the exe in the julia config? I can manually edit the julia config if you think that might help?

[ice1000]

JuliaPro installation

Can you select your julia executable?

[ice1000]

By the way, when running your program, julia-intellij will use the "run configuration", which can be found here:

Click "edit configuration", change the julia exe for this run configuration:

[ice1000]

[ghost]

The Run... configuration for my program shows the JuliaPro instance, which is correct. However, this differs from the exe setting in my Julia config file.

[ice1000]

The Run... configuration for my program shows the JuliaPro instance, which is correct. However, this differs from the exe setting in my Julia config file.

The process is, we find your JuliaPro instance (xxx.app), run this command:

xxx.app --some-flags yourjuliafile.jl

Do you expect this to work? Can we use JuliaPro this way? I have no experience with JuliaPro so i'm not sure.

[ghost]

If you check my post here then you'll see how I have a symbolic link (named julia) that sits on my path. This points into the JuliaPro directory, to the actual julia executable - version 0.6.4.

If I work from the command line and type julia myjuliafile.jl then the fie runs just fine.

[ice1000]

Can you set your Julia executable to /usr/local/bin/julia?

[ghost]

@ice1000 - how do I set that? When I click on the '...' to the right of the executable selection option, I can't seem to find the /usr directory :-(

[ice1000]

You can either:

• Paste the directory in the input box
  • 
• Select this option
  • 

[ice1000]

This option.

[ghost]

Success :-) Setting the compiler to /usr/local/bin/julia fixed the problem for me! It would be nice if the plugin located the compiler underneath the OS X '.app' hierarchy.

It also works if I set the compiler to:

/Applications/JuliaPro-0.6.4.1.app/Contents/Resources/julia/Contents/Resources/julia/bin/julia

which is what the symbolic link at /usr/local/bin/julia is actually pointing to.

I guess the ideal in the OS X world be to allow developers to set the compiler to:

/Applications/JuliaPro-0.6.4.1.app (or /Applications/Julia-1.0.app, for example)

And then for the plugin to locate the actual julia compiler at runtime, by traversing down the '.app' director hierarchy until it found an executable file named 'julia'.

[ice1000]

So you didn't understand what does "Julia executable" mean at all. I have a thought: when you choose directory, we do a check for whether it's macOS and the selected directory is a "xxx.app". If so, we find the actually exe and choose it instead. This is a user experience issue, the plugin should guide the users.

[ghost]

That's pretty much what I meant. To the OS X user, the compiler will be taken to be the '.app' (even though I know that's not the actual compiler executable). As you say, it's a user experience issue, and I'm guessing that you want to make that as easy as possible. Alternatively, and as a less-good approach, you could warn if the user selects a 'compiler' that is not an executable file or is a directory. Either way, failing with a Permission Denied error doesn't feel right. And please don't think I'm being impolite - I think you guys are doing a great job, and you have my profound thanks!

[ice1000]

Long ago, we do have a check -- run --version with the selected exe and parse it. It's removed because Julia's breaking change :(

[ice1000]

https://github.com/ice1000/julia-intellij/blob/c5e592aa18d15341cb6acd3780dcad437a304c5c/src/org/ice1000/julia/lang/module/ui/ui-impl.kt#L46-L56 https://github.com/ice1000/julia-intellij/blob/c5e592aa18d15341cb6acd3780dcad437a304c5c/src/org/ice1000/julia/lang/module/utils.kt#L40-L57

And mostly important, https://github.com/ice1000/julia-intellij/blob/c5e592aa18d15341cb6acd3780dcad437a304c5c/src/org/ice1000/julia/lang/module/utils.kt#L137-L142

[ice1000]

OMG this file's git blame is interesting

[ghost]

Is the method findPathMac new code or old code? It looks pretty god to me, although I'm not familiar with Kotlin. However, I worry that it might break if JuliaPro is bien used. This matches the 'julia' test, but the julia executable is much deeper in the tree than a 'normal' julia installation.

The julia compiler under JuliaPro is at:

/Applications/JuliaPro-0.6.4.1.app/Contents/Resources/julia/Contents/Resources/julia/bin/julia

So a tree search for an executable named julia might work in both cases.

[ice1000]

Is the method findPathMac new code or old code?

It has been there since v0.1 I think

[ice1000]

Maybe we should have a priority: choose juliapro first, julia as an alternative

[ice1000]

@zxj5470

[ghost]

That's certainly an option, but I'd be inclined to look for the first match on the 'julia' string under /Applications, as at present. As I understand it, JuliaPro is just another distro of Julia. You already provide an option for users to manually select the julia compiler, so they can always explicitly select another version if they want.

[zxj5470]

New feature: just need to choose Julia-xxx.app folder in macOS. (?)

[ice1000]

@zxj5470 I'm happy with it.

[ghost]

fwiw, the following code snippet returns the Julia executable, underneath a Julia .app directory:

import java.io.File
import java.nio.file.Files
import java.nio.file.Path
import java.nio.file.attribute.BasicFileAttributes
import java.util.function.BiPredicate

/**
 * Matcher that locates a potential Julia .app directory
 */
val appMatcher = BiPredicate<Path, BasicFileAttributes> { path, basicFileAttributes ->
    basicFileAttributes.isDirectory() &&
            path.toFile().name.contains("julia", true) &&
            path.toFile().name.endsWith(".app")
}

/**
 * Returns a candidate Julia compiler
 */
fun findFile(): File {
    // hack so I can test stand-alone
    val appPath: Path = File("/Applications").toPath()

    val x: File = Files.find(appPath, 1, appMatcher).map {
        it.toFile().walkBottomUp()
                .filter { it.getName() == "julia" && Files.isRegularFile(it.toPath()) && Files.isExecutable(it.toPath()) }
    }.findFirst().get().first()

    return x
}

/**
 * Test the findFile function
 */
fun main(args: Array<String>) {
    println(findFile().toString())
}

It's my first bit of Kotlin code, so don't be too critical - lol ;-) e.g. Instead of the get, I think I should check for the null case, and (maybe) throw an exception.

[zxj5470]

Preview

There's a bug in PyCharm on account of disabled resize on New a Project.

[ice1000]

@Andy-KNDJ Don't worry, @zxj5470 will impl this

[ghost]

@Andy-KNDJ Don't worry, @zxj5470 will impl this

That's fine - I just wrote it for the fun of it :-)

I'm going to uninstall JuliaPro and migrate to Julia 1.0 (the latest version). tbh, I'd only gone back to the JuliaPro (0.6.4.1) release because i thought that the plugin might have issues with the latest version.

[ice1000]

What issue? Feel free to point out

[ghost]

What issue? Feel free to point out

I had this issue with V1.0 (i.e. the Permission Denied) and thought it might be because I was using the latest version of Julia. Turns out this was not the problem - no need to worry!

[ice1000]

Closed as fixed. You'll see update in 0.3.3

[ghost]

Brilliant!

[spockoyno]

I have a Julia "helloWorld" project in Intellij and another in PyCharm based on the same Julia 0.7 app installed on Mac OS. Works like a charm in Intellij, but unfortunately it's still an issue in PyCharm 2018.2: the same "permission denied" and "error 13". Is there a workaround for the PyCharm? (I couldn't find the option there to Select a Julia compiler there.)

PS. Huge thanks for the great plug-in -- much better than Atom, JuliaPro and IJulia that I've tried.

[ice1000]

@spockoyno It's fixed. Try the nightly build! It's on the README page.

[ice1000]

We plan to fix more bugs and release 0.3.3 soon.

[ice1000]

PS. Huge thanks for the great plug-in -- much better than Atom, JuliaPro and IJulia that I've tried.

Well, thanks very much. It's @zxj5470 creating new features recently, appreciate his work. I'm basically fixing some weird bugs randomly at the weekend. Julia's tooling is still mysterious, I still didn't find a nice way to integrate existing Julia tools since the REPL starts too slow, which drastically reduces user expr.

[spockoyno]

Thanks for doing a great job - I look forward to v. 0.3.3. My worst experience with JuliaPro + Julia 1.0 was not being able to install 50% of the packages that I needed. (Probably related to https://discourse.julialang.org/t/package-compatibility-caps/15301 )