I recently updated Doxygen, and found that latex has become very unhappy with the generated .tex files - many complaints about 'Undefined control sequence'. These were associated with instances of '\+' inserted seemingly at random into text. If I just brute force removed all instances of '\+' from the generated .tex files, pdflatex was able to finish successfully, and I got a reasonable looking document.
I then poked around a little in the Doxygen source, and found that util.cpp seemed to be responsible for emitting the '\+' sequence, and that it did so when a boolean called insideTabbing was not set. This seemed kind of odd to me, and as an experiment, changed the sense of the test wherever it was performed. When I run with the modified doxygen, the generated code seems to be fine.
So, is there some setting in my Doxyfile that I failed to use, and which would have prevented the behavior I've been seeing?
The comment about defining newcommand provided the answer to my problem. In my Doxygen configuration file, LATEX_HEADER is given a file name as a value. The contents of that file end up overriding/replacing some of the content that usually gets generated for refman.tex. Once I incorporated \newcommand{\+}{\discretionary{\mbox{\scriptsize$\hookleftarrow$}}{}{}} into my header file, pdflatex was able to run successfully to completion.
Related
I've been reading everywhere about the need to organize your R projects and also to use Rmarkdown.
I see an incoherence I can't solve.
Suppose I set for the following standard organization:
Project
data
raw-data
code
docs
out
reports
and also home of setwd().
Now I want to use Rmarkdown with my main project file called My_project.Rmd
I create it at the root project level, then I get at every knit rendition 2 directories created My_project_cache and My_project_files on to of every .hml file rendered that conflicts with the above structure.
This is very impractical.
I tried setting the options of output to avoid this, per this tip, but it fails on the cache directory, and I did not succeeded in setting Knit options to bypass it. And no-one seems to be bothered by this question making the solution look like a dead-end.
The other solution is to put My_project.Rmd directly in reports/ but it feels a little awkward and on top of that it breaks the above project structure by imposing ../ paths everywhere.
The third solution is to work with Rmd format, only at the end of a project, but this seems a little defeating the purpose of documenting everything neatly in the first place.
There may be a 4th solution using R Notebook feature, but it works until you decide to try to finalize your "final" document , which of course is never really final.
What am I missing here ?
For reference, I'm using RStudio on a Mac.
So, I'm not sure whether this has happened to anyone else, but I'm using Rmarkdown to create a beamer presentation. For whatever reason, there are some .Rmd files that are compiling, while others constantly go into "extended mode".
For instance, if I create a brand new .Rmd file, it will compile, but if I copy the contents of the document into another file (same exact thing), it goes into extended mode looking for pgf. Any understanding of why this might be the case?
Figured out that the problem was being caused by the auxiliary and intermediate files that are created once you try to compile the document. If you delete them, this should be resolved.
When my colleague and I run the same Rmd file on our respective computers they produce different .tex files. This is a problem, because the tex-file my computer produces doesn't compile. Apparently there is some invisible local setting that is different between our computers but what could it be? I updated all the Rpackages I use but to no avail.
The Rmd file starts with
output:
bookdown::pdf_document2:
keep_tex: yes
toc: false
And both of us compile it by simply hitting the knit-button in Rstudio.
Noticeable differences in the tex-files are:
extra linebreaks in different places
a line that is commented out in the rmd-file (<!-- blabla -->) appears in my tex-file, not in his, but some other out-commented lines appear in neither (as they should)
at the end of lines in tables there is a \strut inserted in my tex-file but not in his
Section heads read \hypertaget{blabla} in his file but not mine
For none of these difference I can find any place in the Rmd-file where any choice w.r.t to this is made - apparently some local settings file I am not aware of is used in the process??
Please let me know if you need more information.
EDIT: we found a partial answer and full solution, but I am still interested in what the underlying mechanism is. It turned out that I was using an older version of Rstudio. (It took me long to find that out because the check for updates tool in Rstudio kept telling me that I was using the newest version, but that is a separate issue.) Using the same version of Rstudio we get the same result.
The translation from Rmd to tex has multiple steps:
All the code chunks are extracted and executed via knitr, resulting in a md file.
The md file is translated to tex via pandoc.
For most people pandoc comes bundled with RStudio. So when you updated that, you got a more recent pandoc version. You can test for the used pandoc version with rmarkdown::pandoc_version().
I batch create the documents from the code by using doxygen. However, I lost code and I didn't lose the document. I want to convert the code back from the documents. Is there any option in doxygen to do this? Thank you very much.
By the way, the documents are all html files
Doxygen is a documentation generator; it's job is to go from code to documentation. As such, it has no functionality for reversing this process. Especially since the generated HTML can change from version to version.
Documentation conversion is also an inherently lossy process. Unless you outputted all of your source code into the documentation, you're not going to be able to reconstruct everything. The best you might do is rebuild most aspects of some headers, but even then, anything that goes undocumented (like header include files and such) won't be in the HTML.
I'd like to get scons to read a previous version number from a file, update a source file with a new version number and current date and then write the number back to the original file ready for the next build.
This needs to happen only when the target is out of date. IOW the version number doesn't change if no build takes place. The original file is source controlled and isn't a source file else it could trigger another build on check-in (due to CI). CLARIFICATION From scons' point of view the code will always be out of date due to the auto-generated source file but scons will only be run from a Continuous Integration job (Jenkins) when a SCM change is detected.
I've looked into AddPostMethod, but this seems to fire for all files within the list of source files.
Command and Builder methods use the VARIANT_DIR so I can't edit these files and then check them back in as they no longer map to the repo.
I'm hoping I'm just misunderstanding some of the finer details of scons else I'm running out of ideas!
Update
Thinking this through some more, Tom's comment is correct. Although I have two files, one version controlled text file (non-source code) and one non-source controlled source file there is no way to check one file in and prevent a continuous build/check-in cycle. Jenkins will see the new text file and spin off a build, and scons will see the new generated file. So unless I delete the generated file at some point, although this seems to go against the workflow of both tools.
Does anyone have any method for achieving this? It seems pretty straightforward. Ultimately I just want to generate build numbers each time a build is started.
From SCons User Guide section 8, Order-Only Dependencies, you can use the Requires method:
import time
# put whatever text you want in your version.c; this is just regular python
version_c_text = """
char *date = "%s";
""" % time.ctime(time.time())
open('version.c', 'w').write(version_c_text)
version_obj = Object('version.c')
hello = Program('hello.c',
LINKFLAGS = str(version_obj[0]))
Requires(hello, version_obj)
Two things to note: first you have to add the explicit Requires dependency. Second, you can't make version_obj a source of the Program builder, you have to cheat (here we pass it as a linkflag), otherwise you'll get an automatic full dependency on it.
This will update the version.c always, but won't rebuild just because version.c changed.