I'm trying to customize the linter settings in VSCode for R but I'm a little confused.
I've checked just about every source available, from SO questions to the lintr package vingette, but I'm stumbling on an issue. It could be that since I'm not a programmer I'm just not understanding something basic but essential.
A question about line length linter 80 characters
Disable R-linting in VScode
How to change the line length preference for warnings in Diagnostics? #3
Specify linters in lintr::lint
lintr github page
Lint R code in Visual Studio
lintr v2.0.0
Using lintr
It seems like I need to create a .lintr file in the folder that my script is in. Or possibly make changes in the .lintr file in the lintr package ~lintr/R/ folder?
I guess I'm just confused on the .lintr file. I tried creating files called "lintr", ".lintr" and "ScriptName.lintr", then added the following line to it, as described in the above sources:
linters: with_defaults(line_length_linter=line_length_linter(120L))
Then I reopened the script but whatever I do, lintr continues to default to 80 spaces. I think I'm doing something wrong with the .lintr file but I'm not sure what. I also tried changing file called "lintr" in the lintr package directory, but I can't save the file because it has no extension type (though it appears to be in the Debian Control Field Format, whatever that is). Windows keeps giving me a prompt to save as "txt".
I'd appreciate any step-by-step instructions to get past this issue.
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'm using visual studio code to program in R and I have recently had trouble using the ?func and ??func command.
When typing something like ?rnorm, the message Couldn't show help for path: /library/stats/html/Normal.html shows up. The path is there and I'm sure R is in the path environment. This is really boggling me.
When I first installed R it was working absolutely fine in VSC but now it does not work. However the function works in the R shell. When I try to navigate to the R extension and click on "Help Topics by Package" it says help provider not available.
The packages/html files are there, but VSC doesn't want to access them.
Please advise what I can do to solve this.
I solved the same issue by checking my environmental variables. The steps I followed:
I added the bin installation file (C:\R\R-4.1.3\bin in my case, or C:\Program Files\R\R-4.1.3\bin) to the path in my user environmental variables. If you have an admin account, then you have to add the bin folder to the system environmental variables.
Check if you can start a R console from any terminal.
If that is positive, then in the Rpath settings for the R extension in vscode write r, or in the settings.json: "r.rpath.windows":"r"
Restart vscode. Check if the help pages are working.
Hope this helps ! Cheers.
This happened to me as well. I googled and tried different things and this works for me:
You need to provide the Rpath for the system you are using in the settings for the vscode R package. For example, for a windows machine, you need C:\Program Files\R\R-4.1.3\bin\x64\R.exe there if you installed the latest R using the default settings, and similarly for other systems.
Hope it helps!
I'm getting this error in VS Code:
Could not start the julia language server. Make sure the configuration setting julia.executablePath points to the julia binary.
In user settings I put
"julia.executablePath": "c:\\Program Files\\Julia\\Julia-0.5.0\\bin\\julia.exe"
which is a correct executable path.
Julia works without a problem in console and VS Code worked fine with older extension 0.4.2. I've tried reinstalling both the extension and VS Code, but it didn't help.
What am I doing wrong?
I had the same problem, just run Julia REPL and switch to pkg mode with ] and add LanguageServer package with add LanguageServer and restart vs code.
VS Code settings don't seem to always play nice with backslashes. Try instead single slashes, even on Windows:
"julia.executablePath": "c:/Program Files/Julia/Julia-0.5.0/bin/julia.exe"
It may, however, also be a problem with the blank in 'Program Files', in which case the legacy 8.3 filename convention could work:
"julia.executablePath": "c:/PROGRA~1/Julia/Julia-0.5.0/bin/julia.exe"
Note that you would typically have both 'C:\PROGRA~1' and 'C:\PROGRA~2' pointing to 'C:\Program Files' and 'C:\Program Files (x86)', respectively. Find the correct one from the console.
Have a look if the 'LanguageServer' package is actually installed/somehow uninstalled, this happened to me. After manually installing it, it was all fine and dandy again.
Indexing all the packages still takes ages, though.
https://github.com/JuliaEditorSupport/julia-vscode/issues/405
This can happen if the VS Code extension doesn't support the current version of Julia.
Also check that the path is pointing to the julia.exe executable inside the bin folder.
C:\Users\yourname\AppData\Local\Julia-0.5.0\bin\julia.exe
because there is also another one that doesn't work.
C:\Users\yourname\AppData\Local\Julia-0.5.0\julia.exe
Reinstalling Julia solved this for me, I tried the previous answers
It is probably due to a SysImage you have compiled and replaced the original sys.dll file with that. Try to check the path C:\Users\User\AppData\Local\Programs\Julia-1.7.3\lib\julia or any other path you have installed Julia and see if a sys.dll.backup exists there, together with a sys.dll file. Rename the sys.dll to sys.dll.old and rename the sys.dll.backup to sys.dll. Then restart julia or VS Code.
I'm trying to get PyQt5 working with WinPython. PyQt5 comes with a readme file for installation, and I have unsuccessfully tried a few combinations of what I thought the first part of the readme tells me to do.
I have:
Windows 7 Home Premium 64-bit
WinPython-64bit-2.7.9.1
Qt 5.4
PyQt-gpl-5.4
PyQt-gpl-5.4 is in the folder (only partially sure that this is where I should have put it)
C:\WinPython-64bit-2.7.9.1\python-2.7.9.amd64\Lib\site-packages\PyQt-gpl-5.4
My current attempt at getting everything working is: I'm trying to run the configure.py file in PyQt-gpl-5.4, but when I do so I consistently get the following error:
Error: PyQt5 requires Qt v5.0 or later. You seem to be using v4.8.6.
Make sure the correct version of qmake is on your PATH.
What I think is the required version of qmake being referred to is in the folder
C:\Qt\5.4\mingw491_32\bin
However, I have no idea how to fix the error by adding the qmake in this folder to PATH. My most recent attempt was to add the folder using Spyder's Tools->PYTHONPATH manager, but this made no difference. I also tried adding it using sys.path.append('C:\Qt\5.4\mingw491_32\bin'), but this didn't work either. I have since removed the folder name from both of these locations.
How do I get PyQt5 working with WinPython-64bit-2.7.9.1, or I think equivalently, how to I get the configure.py file in the PyQt-gpl-5.4 folder to run?
Thanks.
You definitely don't want the source code (i.e. PyQt-gpl-5.4) in the site-packages folder, because that's where the compiled modules will end up. Instead, it should just go in a temporary folder whilst you compile it.
When you run configure.py, you must take care to use the executable for the specific python that you are targeting. I do not know anything about WinPython, but for a normal python installation this means doing something like this:
C:\Python34\python configure.py
As a first step, before attempting to actually compile anything, it would be advisable to take at look at all the configuration options that are available, like this:
C:\Python34\python configure.py --help
(There's also the Installing PyQt5 section in the PyQt Docs).
This will tell you, for instance, that the simplest way to specify the Qt installation you are targeting would be something like this:
C:\Python34\python configure.py --qmake C:\Qt\5.4\mingw491_32\bin\qmake
EDIT:
Sorry, that last part is wrong: the --qmake option isn't available on Windows, so you have to add the directory containing the qmake executable to your PATH. This can be done with the following command:
set PATH=%PATH%;C:\Qt\5.4\mingw491_32\bin
On windows after running the grunt build command for creating brackets shell it gives done without errors but i dont see any .exe file generated..
What might be the problem???
Here are some possible solutions:
Are you following the full brackets-shell build instructions, including all prerequisites?
Make sure Brackets isn't running at the same time. The build will fail silently if the .exe file is currently in use (see bug).
Try with a fresh git clone of the repo. If your brackets-shell local copy has been around for a while, sometimes the build & deps folders can get in a bad state. (I'm assuming you haven't modified the source at all. If you have, try with an unmodified copy of the source first to make sure it builds correctly without any of your changes).
Check that python --version shows 2.7.x
Verbose build output would also be helpful in diagnosing issues like this, but unfortunately there's not yet an easy way to get that...
If you follow the instructions on bracket-shell's wiki page, the Windows executable should be created in the Release directory.