If I begin a line (i.e. a paragraph) in the details section of my .Rd file with \mjeqn a new line immediately follows the expression (anti-bonus points: the added new line seems to have wider line spacing than 'ordinary' new lines). How can I suppress this behavior when I want to start a line with inline mathy stuff using \mjeqn?
Sketched out example:
\mjeqn{foo^{bar}}{foo^bar} estimates bas.
Gives me something like the below when parsed (into html preview):
foo^bar
estimates bas.
I am just using mathjaxr, not roxygen2.
I don't know why that happens, but it looks like a bug, maybe in the R help rendering engine, maybe in the mathjaxr macro, or maybe in MathJax. A simple workaround is to put something invisible on the line ahead of the math, e.g.
\emph{}\mjeqn{foo^{bar}}{foo^bar} estimates bas.
Edited to add:
Digging into the rendering code, it seems the problem is that the \mjeqn macro expands into something that R ignores when trying to determine paragraphs, so it thinks the paragraph starts after that. Putting \emph{} ahead of it tells R that the paragraph has started and everything is fine. This has been incorporated into the package, so if you download the Github version, or wait for the next CRAN release, you won't need the workaround.
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.
Simple question about comment code aesthetics (color):
I recently noticed in someone's comment code that part of their comment color changed while using the # symbol. After experimenting with it, I noticed you also need to have an apostrophe (') right after the octothorp (#) as such:
#' #text
^--- This turned orange!
Since I'm a detailed commenter, I'd love to step things up if I could by adding color to my comments. I know part of the reason is my global IDE (RStudio) options, but I'd never seen anything change a comment's color before, so I was just curious:
Why does this occur? I've only seen # used when handling large, more-complex objects that need further specification => Ex. LargeObject#data$variable
Are there other symbols that trigger a color change? There's quotes of course (""), but quotes do not change color when they're commented out with an octothorp (#).
Also, on the image (bottom row), is there possibly a way to start and end a comment, followed by a command, all on one line? => Ex. #comment# print(summary(df))
The special highlighting you're seeing — words being highlighted after #' # — is specific to roxygen markup (a documentation-generation system for R). I don't know why that category doesn't seem to be listed/themeable (see #2).
The RStudio syntax highlighting colours are customizable (you can edit these themes visually), but based on what's documented at the link, there appears to be only one category for "comments".
This question has to do with the R parser, not the RStudio highlighting system. So the answer is "no"; everything from the first # on a line to the line break is considered a comment, no exceptions. In principle you could adjust the RStudio highlighting engine to recognize various delimiters within comments and display material following them differently, but you can't create in-line comments (as you could with /* */ in C) without modifying the R parser.
This issue is really strange, I want to read a csv file and after getting rid of all unnecessary parts my entire code boils down to this two-liner:
library(tidyverse)
read_csv('data1.csv')
If I knit the Rmd file, it works and a new webpage opens as usual:
However, if I run it either by (1) clicking the green play button; or (2) clicking Run -> Run All button:
Then it just doesn't work (In case you are wondering whether or not there is a third line of code, I make the scope of the screenshot larger). The code is so short that I have no idea what could possibly be wrong.
Following the comment from #user12728748, I changed
read_csv('data1.csv')
to
readr::read_csv('data1.csv')
and it works! But this is still odd since my understanding is that suppose there aren't namespace conflicts prepending namespace is not needed.
Loading readr explicitly, regardless of the order, does not work since it is loaded by tidyverse already:
Edit: I am using RStudio
Up till now, while commenting something, I was using % symbol. Alternatively, I am just using Ctrl+Shift+C shortcut, which results in commenting with % or %' (or # for chunks).
The problem is, even if I comment something, it still often causes compilation errors. Look at the part of screenshot below:
Lines 1 to 23 are fully commented and document starts at line 24. However, even if parts of the code are commented out and shouldn't affect it, they for some reason still results in errors.
If I move code from lines 24to32 at the very beginning of the file, it compiles without problems. I thought that maybe there can't be comments at the beginning of the file, but looks like it's not an issue, as trying things like moving \documentclass{article} at the very beginning still results in errors, even though there are less of them.
How can I comment lines, so they won't be calling compilation errors?
First, Make sure that all the lines you don't need are "correctely"commented.
Then, i think that you can't put commented code on the top of your document, also avoid to put commented code on your document it's a lousy code.
Whenever I compile my R code, I get a lot of extra white spaces that just clog up my worksheet.
Is there any way to suppress this, without changing the code to be on the same line using semicolons? I'm currently working in Sage Worksheets, on the cloud.
I've made some changes to slightly reduce whitespace in R mode for SageMathCloud (https://cloud.sagemath.com); restart your project to get this update. However, due to how Sage works they might not be sufficient. If you evaluate the following in a cell (in sage mode, or put %sage at the top), it will eliminate a lot of additional whitespace in %r mode.
def r_eval0(*args, **kwds):
return sage.interfaces.r.R.eval(sage.interfaces.r.r, *args, **kwds).strip().replace('\n\n','')
sage_salvus.r_eval0 = r_eval0