Like many others, I like writing my codes on several lines and I appreciate the auto-indent feature offered by RStudio. The issue suddenly started when the word undefined showed up in the code editor whenever I pressed Enter as I expected an automatic indentation. It is important to mention that this does not affect the proper running of the code.
my_fun <- function(xxx){
undefined
}
NB: Actually, when I copied and pasted the code here, undefined was not copied to! I had to manually add it. Here is another example.
library(magrittr)
mtcars %>%
undefinedhead()
Basically this is just RStudio telling you that you have not preset your tab spaces, but it is not actually dropping commands into your code.
You have the option of setting tabs to however many spaces you feel is appropriate and it allows teams to work with consistent spacing.
If you go to the main menu and click on Tools > Global Options and on the second tab in the left column click onCode . There you can set the spaces to meet your personal needs (or teams profile) and the undefined message will disappear.
This photgraph shows where you can find the preferences.
Related
I am using pycodestyle_magic as a linter in Jupyter. I am following the instructions at
https://github.com/mattijn/pycodestyle_magic
But I get error with 1-cell checking be it '%%pycodestyle' or '%%flake8'.
1st ERROR
# 1st CELL
%load_ext pycodestyle_magic
# 2nd CELL
%%pycodestyle
a=1
print(a)
2nd ERROR
# 1st CELL
%load_ext pycodestyle_magic
# 2nd CELL
%%flake8
a=1
print(a)
1st ERROR
I'm basing this on your image you posted for '1st error' and not the inaccurate code you posted:
Note that the error in your first error was saying line magic and not cell magic because it was not looking for cell magic anymore. You can see it will look for cell magic on the first line of a cell by putting in %%fake_magic as a first line and then 2 + 2 as a second line of cell. Running that you'll see UsageError: Cell magic %%fake_magic not found.
Hence, your first 'error' is that you are missing that the first line of the cell where you want to use cell magic becomes special. You cannot have something else on the first line where you want to use cell magic, even if it is commented out. In the image, you have #%%flake8 above %%pycodestyle. If you remove that line, it should work.
2nd ERROR
I'm basing this on your image you posted for '2nd ERROR' and not the inaccurate code you posted:
You've stumbled upon a bug currently involving flake8. (Maybe same or more bugs seem to prevent the %%flake8 magic from working at all for now, see comments.)
The solution/workaround is very similar to the '1st ERROR'. Remove the line you were trying to comment out because it being there is causing an issue.
The reasoning appears to be complex about the way the %%flake8 cell magic appears to work behind the scenes so that you cannot have comments in the code content at this time or it won't work. (And the second time it sees that comment symbol, it throws the error you see.) This bug has been reported here.
But the solution/work-around for now is straightforward. Remove the complexity you added, and see if it works.
In case of the %%flake8 magic, running the demo notebook as shown there doesn't work as shown, and so there is indeed a bug in the current version that was introduced by actually a bug in flake8 that the extension uses, see the specific comment here and the link to the underlying issue over at the flake8 repo. (In fact the extent that it doesn't work may be greater than the notebook reflects because as discussed in the comments, even cells without commented lines fail to report any formatting issues. The demo actually doesn't have any without and so I got distracted noting it only didn't show the buffer error for the first one in the demo notebook but since it had a commented line I thought it was still related.)The other way to workaround it at present is to install an older version of flake8 as pointed out here. The solution was merged though and should be available soon, and so just avoiding the triggering code in simple cases like yours is probably easier.
Note about the inaccurate code:
Post code for what gave you the issue, not what you think gave you the issue. Part of why you are asked to provide code as text the way you ran it, it is so those looking into it can run it the same way. Plus they don't have to type and can easily run it as you did. Beyond that, there's more reason behind it: you can try to see if what you observed originally matches what you are seeing now.
If you had run what you posted under the heading '1st ERROR' as the code block text, you would have seen it without the error you showed in your image. Usually you'd then discern the error/difference yourself. In other words, starball's comment was trying to point you to why you should be doing that, and sorted that 1st error out yourself. That would ultimately make your point about the fragile nature of %%flake8 magic have more impact because it isn't diluted by report of an error that isn't really an error. Plus, you may have realized what was necessary to avoid '2nd ERROR' because that code block works without error no matter how many times you run it.
Technical notes:
Anyone wishing to try out pycodestyle_magic with some of this code and the demo notebooks can click here to launch such a session served via the mybinder.org. service with most things necessary already set up. Once the session starts up in the classic Jupyter notebook interface, you need to do some further preparation to use pycodestyle_magic. As detailed here, you can install it with pip install flake8 pycodestyle_magic. So open a new notebook with the Python kernel backing it using New drop down on the upper right side and then choose the Python3 kernel. When it opens, make a cell that has %pip install flake8 pycodestyle_magic and run it. Then put %load_ext pycodestyle_magic as a cell and run that. You can now try the magic with code or pull the demo notebooks over and run those.
I'm wondering is it possible to customise R help files so that certain text is colour coded and easier to read. rdoc already does this except that it sends the output to the console. I would instead, like it to be sent to the help panel (i'm using Rstudio). Is there any workaround for this?
If we run ?lm normally, we can see the usual help file in the help panel on the right below but when you do it again after using rdoc in Rstudio we get the help file colour coded which is great but its sent to the console output (left side). Ideally, we would like it to remain on display in the help panel as we are running code. The way it is now - it disappears the minute you run something.
?lm
#devtools::install_github("mdequeljoe/rdoc")
library(rdoc)
options(rdoc.by_section = FALSE)
rdoc(lm)
I want to put the code into my .rprofile similar to #csgillespie .rprofile. Note, if you follow his code you can use ?lm instead of having to call rdoc(lm) directly to produce the colour coded console output.
I have a feeling this can't be done easily (if at all?) but interested to hear any suggestions.
Thanks
This is possible, but a little involved. You'll need your own css file defined to do it, though it would be possible to create a function that writes appropriate css.
As a proof of concept, I have used a copy of the "R.css" file defined inside every package's "/html" folder, and just changed the h2 color to red, with the file saved locally as "my.css".
Anyway, once you have the css file, this function will show the appropriate help file with the appropriate styling in your R viewer window:
help_css <- function(func, css_file)
{
pack <- sub("^.*:(.*)>$", "\\1", capture.output(environment(func)))
func <- deparse(substitute(func))
x <- readLines(paste0(find.package(pack), "/html/", func, ".html"))
x[3] <- paste("<style>",
paste(readLines(css_file), collapse = "\n"),
"</style>")
writeLines(x, file.path(tempdir(), "test.html"))
myViewer <- getOption("viewer")
myViewer(file.path(tempdir(), "test.html"))
}
So, for example, if I do:
help_css(lm, "my.css")
I get:
As of RStudio v1.2 you can style RStudio's integrated help pane by creating a custom user theme (essentially an .rstheme file).
I've given help pane styling a try in extending the rscodeio theme (without colored syntax highlighting, though). The latest CSS code is found here.
The help pane styling is currently only available in the optional Tomorrow Night Bright (rscodeio) editor theme.
To use it right away, you can either
install the current rscodeio master branch using remotes:
remotes::install_github("anthonynorth/rscodeio")
And then activating the editor theme named Tomorrow Night Bright (rscodeio) under Tools → Global Options… → Appearance → Editor theme. A first attempt of the help pane CSS code is included.
or – recommended – install my fork's interim-merge branch which contains all my latest work[1] overhauling the package, including a new apply_theme parameter to activate the desired editor theme right away:
remotes::install_github("salim-b/rscodeio#interim-merge")
rscodeio::install_themes(apply_theme = "Tomorrow Night Bright (rscodeio)")
[1]: This has also been proposed upstream a while ago (1, 2) but I haven't heard back from the author since.
The result looks as follows (example for ?pal::as_string):
Is there a way to write your own macro in R(studio). Many times in my code i need to comment out a line/piece of code, run it, and then comment it in again.
I know that a shortcut to comment in a line/piece of code is ctrl+shift+c, so I would like to create a shortcut e.g. ctrl+alt+c to comment in/out+run+comment in/out
You can create an Addins doing exactly what you want and assign a shortcut to it.
For exemple, that Addin is used to create upgraded shortcut for pipe.
To do what you want, a solution may be possible but require a few constrain.
Three, at least:
First, you need to select the code you want to comment
Secondly, in the same time you use the shortcut, the file should be saved.
Thirdly in your file, you can't have two time the same selected piece of code.
The commented code will be the input of the Addins.
The code is as simple as read your file, replace the code by commented code, then run the modified code.
It is different in what you want to achieve in the sense of in that case, it is more create a temporary copy of the code, comment the undesirable code, run the temporary modified code.
For shortcuts see here. Macros might be found here.
E.g. commenting in/out = Ctrl +Shift + C (Both)
If you want a to have a new shortcut, you have to ask RStudio. For an example, where it was already solved, see here. From the list of available shortcuts it is clear that "your" shortcut does not exist.
Running "%PSOURCE func" opens up a pane below that displays the source. Is there a way to change the behavior so that the source is directed to the corresponding output cell?
I asked a very similar question here (after yours - I should have checked in more detail). There is a quick hack there that works but should probably be improved, and a useful answer on its limitations.
Note that the point of my question was about displaying a single function from a file, appropriately highlighted: if you actually want to run it (as eg the %load magic would give you for the full file), you'll probably want to just use the inpect.getmembers functionality.
Does Rstudio have a mechanism to configure snippets of code, like Geany for example? For faster writing whole sections of user predefined frequent code.
It is not exactly the same as TAB completion already built in rstudio.
Example by mimicking geany snippets
While snippet definition is like line below:
fun = %cursor% <- function(x, ...)\s{\n\n}\n
the usage is like this:
fun<TAB> (like bash style completion)
# will end up in following insertion:
<- function(x, ...) {
}
so the user can then faster write the code by using her own snippets definition. And user can define ANY snippet of any size for completion by TAB.
It is not the Rstudio extract cmd, nieder Rstudio existing TAB context browser.
Code snippets are available in RStudio version 0.99.
https://support.rstudio.com/hc/en-us/articles/204463668-Code-Snippets
The "Extract Function" feature in RStudio may be what you're looking for. Scroll down to the Extract Function section and accompanying screenshot on this page of rstudio.com's documentation: http://www.rstudio.com/ide/docs/using/source
The text of the section reads, "RStudio can analyze a selection of code from within the source editor and automatically convert it into a re-usable function. Any 'free' variables within the selection (objects that are referenced but not created within the selection) are converted into function arguments."
Also see this screenshot: http://www.rstudio.com/images/screenshots/rstudio-code-transform.png
I do not know of such functionality. However, if you want to quickly want to implement functionality with small changes you could also achieve this using functions.
Ok, your question is now clear to me. To my knowledge, Rstudio currently does not have this kind of functionality. You could, however, post a request on their forum for this feature. They respond quite actively to these kinds of requests, so you could give it a try.