I am trying to install Julia on Atom. What I made already is that I installed Julia in this folder :
E:\Program files\Users\Zeedo\AppData\Local\Julia-0.6.3
and I installed Atom. Then, I also installed language-Julia package.
Now, when I want to run a code, I get this error:
Julia could not be started.
We tried to launch Julia from:
julia
This path can be changed in the settings.
Details:
'"julia"' is not recognized as an internal or external command,
operable program or batch file.
So, I don't know where should I give the Julia address to the Atom.Or, if you know something that I am doing wrong, please let me know.
Thanks :)
Atom cannot run code by default, so that error message must be being thrown by a community package you've installed. Searching shows me the package is most likely atom-julia-client. And the error seems to be because it can't find the Julia binary it needs to run the program.
First, you should make sure you can run the julia command from the command line directly, which you can check by running julia --version. If this doesn't work, then you need to add the Julia binary to your path.
If the above didn't work, try go to Settings -> Packages -> julia-client. In here, the first setting is Julia Path, which is defaulted to julia (like in the error). Change this to an absolute path, directly to the binary (or to the folder containing the binary; try both if the first doesn't work).
FYI, the language-julia package just gives you syntax highlighting and snippets, and doesn't actually need any Julia stuff to work.
Related
I'm trying to install wholebrain by Daniel Fürth, following the instructions on the macosX install page (available here). I am running MacOS Big Sur 11.5.2, R 4.1.2, and RStudio 2021.09.1.
Unfortunately, the program is not straight-forward to install and requires significant developer tools to work correctly. I'm not a programmer and have almost no experience with coding, so I've been mucking through the instructions for two days now trying to get the install to work correctly and I'm firmly stuck on the final step.
In RS, when I run, devtools::install_github("tractatus/wholebrain", INSTALL_opts=c("--no-multiarch")) I get the following error message:
/bin/sh: pkg-config: command not found filter.cpp:9:10: fatal error: 'fftw3.h' file not found #include "fftw3.h" ^~~~~~~~~ 1 error generated. make: *** [filter.o] Error 1 ERROR: compilation failed for package ‘wholebrain’
I have been trying to figure out what this means for quite awhile now and I think I've narrowed it down to R is not reading the location of the fftw header file from where it was installed by Homebrew. (I could be totally wrong, again- not a programmer)
From what I understand, Homebrew always installs under opt/homebrew/cellar. And, in fact, in there is the compiled fftw program with the needed "fftw3.h" file. But for some reason, RStudio is not able to find and read the file in that location.
From random googling and reading of other posted issues, I think that RStudio may expect the file to be under usr/local/include. Can I just copy and paste the header file into that folder? Or will I be screwing something up if I do that? I am totally intimidated by fftw's description of manual compilation so I don't really want to attempt that. Is there a way to change where R is looking for that header file? I already set my wd to "/" so shouldn't R be able to access any folder on my computer?
I want to post an answer here for anyone who comes after me with the same issue. It came down to RStudio not recognizing the programs Homebrew had installed because it wasn't reading the file location where Homebrew saves them. Homebrew always installs programs in /opt/homebrew/... Here is what I had to do:
In RStudio, open your Renviron file using this command: usethis::edit_r_environ()
In the file that opens (which for me was totally blank), type: PATH=/opt/homebrew/bin:${PATH}, or whatever your particular path you want prepended to the Renviron path is.
Quit RStudio and, when prompted, save. Re-open RStudio and run Sys.getenv("PATH") to check. Your new path (in the example above, '/opt/homebrew/bin') should now be prepended to the list of paths that RStudio will use when looking for programs/files. For me this now looks like /opt/homebrew/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Library/Apple/usr/bin:/Applications/RStudio.app/Contents/MacOS/postback
Finally, I want to say thank you very much to Mark Setchell who really helped point me in the correct direction!
I am following the instructions here to install packages (I'm looking at the "Simple Installation") section: https://rstudio.github.io/reticulate/articles/python_packages.html
Here is my R code:
library(reticulate)
use_python(python="C:\\Users\\...\\AppData\\Local\\Programs\\Python\\Python39\\python.exe")
py_install("pandas")
However, I'm getting the following error:
Error: could not find a Python environment for
C:/Users/.../AppData/Local/Programs/Python/Python39/python.exe
How do I resolve this? I have used py_install() this way on another computer before, so I know it's possible and I would like to use it. However, I can't understand what I'm missing.
You might respond that I need to specify an environment when using py_install(), but the instructions in the link don't require that, and I know it can be done without specifying an environment every time. Do I need to somehow set a "default"?
EDIT: Just to clarify, I am on Windows.
You may not be connected to the proper environment. Depending on your OS, you will likely have to create a .Renviron file and direct R to look for it.
This post here, should help you diagnose the issue:
Unable to change Python path in reticulate
I've searched for tutorials to help configure the package in my PC, and I've found this one: https://www.youtube.com/watch?v=_fDhRL_LBdQ
I executed every part of the code interactively with the tutorial, but when I run ee_install() (after installing miniconda with py_discover_config() and other packages previously, such as reticulate), but it keeps me returning an error saying that anaconda is mandatory for the package since I'm a windows user.
Here is the error I get:
Error in ee_install_set_pyenv_env(py_env = py_env, py_path = python_path, : Windows users must install miniconda/anaconda to use rgee. The use of a Python environment is mandatory.
I've just installed Anaconda (full version with navigator) and I set a new python environment called "py2r" and tried to use the function ee_install_set_pyenv(), passing the path to the environment created through Anaconda Navigator (which has a python.exe) as paremeter to py_path and the name "py2r" as paremeter for py_env arg. And yet, it didn't work.
What am I missing?
In case you want to take a look at the code, I can provide it, but I don't think it's necessary because is a simple test script that follows as I described.
Thanks for your attention and congratulations for the library, it will be very usefull for me at work!
I fixed the ee_install() problems bypassing them and doing every passage manually. It will require no more then 10 mins and you will probably fix the installation problems. You can find and follow the manual installation with this tutorial:
https://www.youtube.com/watch?v=1-k6wNL2hlo
I tried to run a Python script from R with:
system('python script.py arg1 arg2')
And got an error:
ImportError: No module named pandas
This was a bit of a surprise since the script was working from the terminal as expected. Having encountered this type of issue before (with knitr, whence the engine.path chunk option), I know to check:
Sys.which('python')
# python
# "/usr/bin/python"
And compare it to the command line:
$ which python
# /Users/michael.chirico/anaconda2/bin/python
(i.e., the error arises because I have pandas installed for the anaconda distribution, though TBH I don't know why I have a different distribution)
Hence I can fix my issue by running:
system('/Users/michael.chirico/anaconda2/bin/python script.py arg1 arg2')
My question is two-fold:
How does R's system/Sys.which find a different python than my terminal?
How can I fix this besides writing out the full binary path each time?
I read ?Sys.which for some hints, but to no avail. In particular, ?Sys.which suggests Sys.which is using which:
This is an interface to the system command which
This is clearly (?) untrue; to be sure, I checked Sys.which('which') and which which to confirm both are pointing to /usr/bin/which (goaded on by this tidbit):
On a Unix-alike the full path to which (usually /usr/bin/which) is found when R is installed.
To the latter, on a whim I tried Sys.setenv(python = '/Users/michael.chirico/anaconda2/bin/python') to no avail.
As some of the comments hint, this is a problem that arises because the PATH environment variable is different for programs launched by Finder (or the Dock) than it is in the Terminal. There are ways to set the PATH for Dock-launched applications, but they aren't pretty. Here's a place to start looking if you want to go that route:
https://apple.stackexchange.com/questions/51677/how-to-set-path-for-finder-launched-applications
The other thing you can do, which is probably more straightforward, is tell R to set the PATH variable when it starts up, using Sys.setenv to add the path to your desired Python instance. You can do that for just one project, for your whole user account, or for the whole system, by placing the command in a .Rprofile file in the corresponding location. More information on how to do this here:
https://stat.ethz.ch/R-manual/R-devel/library/base/html/Startup.html
I installed Atom and uber-juno as instructed by Julia's homepage, but when I tried to start Julia in Atom, I was given the following error:
ERROR: LoadError: ArgumentError: Juno not found in path
in require at loading.jl:249
in include at boot.jl:261
in include_from_node1 at loading.jl:320
in process_options at client.jl:280
in _start at client.jl:378
while loading C:\Users\think\.atom\packages\julia-client\script\boot.jl, in expression starting on line 36
I think you are doing using Juno inside Atom. Juno.jl is a separate package for developing Juno plugins.
Fist save a new file with a .jl extension and type some Julia code (or open an existing .jl file) in Atom, then press SHIFT + ENTER with the cursor in the block of code that you want to evaluate, you should see the result, ie.
1 + 1 # type SHIFT + ENTER
A bubble notification will pop up with the value 2 (when you just start Atom you will see a spinning gear icon until Juno is ready to evaluate a block of code).
This isn't really a question for StackOverflow, it's a package/installation discussion. There was a new version tagged this morning which makes use of the new Juno.jl package where the front end stuff is held (this will be useful for package developers since it will allow them to extend Juno / add extra functionality for their packages which interact with Juno, adding only a light dependency). However, Juno.jl is not yet a registered package, leading to this mess.
One way to deal with this problem is to install the development version of the package:
Pkg.clone("https://github.com/JunoLab/Juno.jl")
However, this is not recommended for most users since you'll be at the bleeding edge (you may also need to do [Pkg.checkout(x) for x in ["Media", "Blink", "Atom"]] and use the dev install. So while this would fix this for right now, this will put you on the bleeding edge, a version which does not have a guarantee of stability. Thus, don't do this unless you're really familiar with Julia. (If you didn't see this error and immediately know to check Github for Juno.jl and use Pkg.clone, then you likely shouldn't be using this solution because you will get many random errors coming up all the time due to being on the development version!)
Otherwise, wait for the fix. This error is known, someone opened the issue here. The standard uber-juno install should be fixed up shortly.
If you want more help see the Juno Gitter or the Juno discussion board.
I just re-installed Atom and ran into the same problem. The problem comes from line 31 of ~/.atom/package/julia-client/script/boot.jl which is using Juno. Comment out this line and then Packages > Julia > Start Julia works.
The best solution is to uninstall and reinstall package julia-client and uber-juno.