After running Doxygen on my C++ code, I built the pdf documentation like this :
pdflatex refman.tex
All page numbers in the table of contents in the resulting pdf file are ??. What could be the reason and how can it be fixed ?
UPDATE: Running pdflatex a second time fixes the table of contents...
It's not due to Doxygen but the way you generated the pdf with pdflatex.
You just have to recompile a second time with pdflatex to get the expected result.
I'm trying to create an RTF file to use in MS word of all the C++ files in my Visual Studio project. I'm using the most recent Doxygen and I set SOURCE_BROWSER to true, GENERATE_RTF to true, and RTF_SOURCE_CODE to true.
It says it will provide source code with syntax highlighting, but it just pastes all the code in Courier New font without any form of styling whatsoever. How can I get it to provide C++ syntax highlighting in its RTF output?
Indeed although stated in the documentation / Doxyfile the syntax highlighting was not implemented in doxygen.
I've just pushed a proposed patch to github (pull request 741, https://github.com/doxygen/doxygen/pull/741) that implements the syntax highlighting for RTF.
2018/06/10: The push request has been integrated in the master version on github.
If I run web2py with the -F option, it will generate a .prof file. How do I read the contents of this file? Hotshot doesn't appear to work (I tried RunSnakeRun as well).
Web2py uses cProfile; I found something that will load the cProfile generated file and spit out output to a webpage:
http://ymichael.com/2014/03/08/profiling-python-with-cprofile.html
pip install cprofilev, then run cprofilev on the .prof file. Enjoy!
snakeviz is a module/binary to view and generate cprofile .prof files. Recommended by the search engine. I really like its Sunburst plot.
https://jiffyclub.github.io/snakeviz/
I am using Fedora 18 on Virtual Box on my Windows XP desktop to learn Django. After going through the .txt documentation files, I discovered these files were written using restructuredText. I've been spending the last day or so trying to figure out how to convert the files into something readable (HTML, Latex, PDF, etc.). First thing I did, was install docutils (from source - download page) and used rst2html.py to convert the files to HTML to be readable.
When I used this tool, I was getting the Unknown interpreted text role "doc", Unknown interpreted text role "ref", Unknown interpreted text role "term" errors, and more when opening the docs/intro/index.txt, docs/intro/install.txt and docs/intro/tutorial01.txt files. I was able to find very little on Google describing the exact problem I was having so I tried to use a different option.
Naively thinking the errors were native to docutils I decided to search for another tool and found this page and installed restview. Well, I didn't realize restview used docutils so I ended up back at square one.
How do I get rid of these and other errors? Did I install docutils and restview correctly?
Please tell me if I need to add more info
You need to use Sphinx. This tool is used by the Django project and it defines additional reStructuredText constructs to complement those defined by docutils. Such as
http://sphinx-doc.org/markup/inline.html#role-doc
http://sphinx-doc.org/markup/inline.html#role-ref
http://sphinx-doc.org/markup/inline.html#role-term
I've previously asked about the commands for converting R Markdown to HTML.
What is a good way to convert R Markdown files to PDF documents?
A good solution would preserve as much as possible of the content (e.g., images, equations, html tables, etc.). The solution needs to be able to be run from the command-line. A good solution would also be cross-platform, and ideally minimise dependencies to make it easier to share makefiles and so forth.
Specifically, there are a lot of options:
Whether to convert RMD to MD to HTML to PDF; or RMD to MD to PDF; or RMD to PDF
If using the markdown package in R, which options to specify
Whether to use pandoc, a package built into R, or something else
Here's an example rmd file that presumably provides a reasonable test of any proposed solution. It was used as the basis for this blog post.
Updated Answer (10 Feb 2013)
rmarkdown package:
There is now an rmarkdown package available on github that interfaces with Pandoc.
It includes a render function. The documentation makes it pretty clear how to convert rmarkdown to pdf among a range of other formats. This includes including output formats in the rmarkdown file or running supplying an output format to the rend function. E.g.,
render("input.Rmd", "pdf_document")
Command-line:
When I run render from the command-line (e.g., using a makefile), I sometimes have issues with pandoc not being found. Presumably, it is not on the search path.
The following answer explains how to add pandoc to the R environment.
So for example, on my computer running OSX, where I have a copy of pandoc through RStudio, I can use the following:
Rscript -e "Sys.setenv(RSTUDIO_PANDOC='/Applications/RStudio.app/Contents/MacOS/pandoc');library(rmarkdown); library(utils); render('input.Rmd', 'pdf_document')"
Old Answer (circa 2012)
So, a number of people have suggested that Pandoc is the way to go. See notes below about the importance of having an up-to-date version of Pandoc.
Using Pandoc
I used the following command to convert R Markdown to HTML (i.e., a variant of this makefile), where RMDFILE is the name of the R Markdown file without the .rmd component (it also assumes that the extension is .rmd and not .Rmd).
RMDFILE=example-r-markdown
Rscript -e "require(knitr); require(markdown); knit('$RMDFILE.rmd', '$RMDFILE.md'); markdownToHTML('$RMDFILE.md', '$RMDFILE.html', options=c('use_xhml'))"
and then this command to convert to pdf
Pandoc -s example-r-markdown.html -o example-r-markdown.pdf
A few notes about this:
I removed the reference in the example file which exports plots to imgur to host images.
I removed a reference to an image that was hosted on imgur. Figures appear to need to be local.
The options in the markdownToHTML function meant that image references are to files and not to data stored in the HTML file (i.e., I removed 'base64_images' from the option list).
The resulting output looked like this. It has clearly made a very LaTeX style document in contrast to what I get if I print the HTML file to pdf from a browser.
Getting up-to-date version of Pandoc
As mentioned by #daroczig, it's important to have an up-to-date version of Pandoc in order to output pdfs. On Ubuntu as of 15th June 2012, I was stuck with version 1.8.1 of Pandoc in the package manager, but it seems from the change log that for pdf support you need at least version 1.9+ of Pandoc.
Thus, I installed caball-install.
And then ran:
cabal update
cabal install pandoc
Pandoc was installed in ~/.cabal/bin/pandoc
Thus, when I ran pandoc it was still seeing the old version.
See here for adding to the path.
I think you really need pandoc, which great software was designed and built just for this task :) Besides pdf, you could convert your md file to e.g. docx or odt among others.
Well, installing an up-to-date version of Pandoc might be challanging on Linux (as you would need the entire haskell-platform˙to build from the sources), but really easy on Windows/Mac with only a few megabytes of download.
If you have the brewed/knitted markdown file you can just call pandoc in e.g bash or with the system function within R. A POC demo of that latter is implemented in the Ṗandoc.convert function of my little package (which you must be terribly bored of as I try to point your attention there at every opportunity).
Right now (August 2014) You could use RStudio for converting R Markdown to PDF.
Basically, RStudio use pandoc to convert Rmd to PDF.
You could change metadata to:
Add table of contents
Change figure options
Change syntax highlighting style
Add LaTeX options
And many more...
For more details - http://rmarkdown.rstudio.com/pdf_document_format.html
For an option that looks more like what you get when you print from a browser, wkhtmltopdf provides one option.
On Ubuntu
sudo apt-get install wkhtmltopdf
And then the same command as for the pandoc example to get to the HTML:
RMDFILE=example-r-markdown
Rscript -e "require(knitr); require(markdown); knit('$RMDFILE.rmd', '$RMDFILE.md'); markdownToHTML('$RMDFILE.md', '$RMDFILE.html', options=c('use_xhml'))"
and then
wkhtmltopdf example-r-markdown.html example-r-markdown.pdf
The resulting file looked like this. It did not seem to handle the MathJax (this issue is discussed here), and the page breaks are ugly. However, in some cases, such a style might be preferred over a more LaTeX style presentation.
Only two steps:
Install the latest release "pandoc" from here:
https://github.com/jgm/pandoc/releases
Call the function pandoc in the library(knitr)
library(knitr)
pandoc('input.md', format = 'latex')
Thus, you can convert your "input.md" into "input.pdf".
I found using R studio the easiest way, but if wanting to control from the command line, then a simple R script can do the trick using rmarkdown render command (as mentioned above). Full script details here
#!/usr/bin/env R
# Render R markdown to PDF.
# Invoke with:
# > R -q -f make.R --args my_report.Rmd
# load packages
require(rmarkdown)
# require a parameter naming file to render
if (length(args) == 0) {
stop("Error: missing file operand", call. = TRUE)
} else {
# read report to render from command line
for (rmd in commandArgs(trailingOnly = TRUE)) {
# render Rmd to PDF
if ( grepl("\\.Rmd$", rmd) && file.exists(rmd)) {
render(rmd, pdf_document())
} else {
print(paste("Ignoring: ", rmd))
}
}
}
If you don't want to install anything you can output html. Then open the html file - it should open in a browser window, then right click to print. In the print window, select "save as pdf" in the bottom right hand corner if you're on a Mac. Voila!
Follow these simple steps :
1: In the Rmarkdown script run Knit(Ctrl+Shift+K)
2: Then after the html markdown is opened click Open in Browser(top left side) and
the html is opened in your web browser
3: Then use Ctrl+P and save as PDF .