Changing working directory will impact the location of output

[etiennebr]

This is a problem with sweave as well, but when you change a directory
setwd("aplace")
this will output the figures and the .tex in ~ directory. It can even lead to having stuff really scattered.
setwd("here") plot(something) setwd("there") plot(something) ...
It can even bring LyX to crash.

[yihui]

This is expected. It is a bad idea to use setwd() in your code, and I do not see why it is necessary.

[etiennebr]

I see. I'm running tools from the command line which require to be in a
certain directory.

I could imagine another example, where sourcing files from different
projects where files are referred as "./data" for instance.

maybe this kind of operation could be enclosed in
`owd <- setwd("there")

make sure you don't produce a graph

setwd(owd)
#back to normal`

So, I understand this won't be possible in knitr. Thanks anyway for the
wonderful tool.

2011/12/5 Yihui Xie <
reply@reply.github.com

This is expected. It is a bad idea to use setwd() in your code, and I do
not see why it is necessary.

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#38 (comment)

[yihui]

You are right. It is a good practice to always restore the working directory after you are done with the computation.

I just did not realize why there could be a demand on setwd(). It is not impossible for knitr to allow you to setwd() (should be easy to remove this restriction). I will consider about it. Thanks for the feedback!

[hadley]

My two cents: you should not be changing working directories in the middle of a project. Changing working directory should almost never be done automatically - it's a UI operation because when you set a working directory, you're saying, I'm now working on this project.

[etiennebr]

While I understand your point, and with all the respect I have for your
opinion, I must say I do not see from your arguments if this should not be
done because it is not supported or because it is truly not a good practice.

Indeed, I could see a workaround like wraping these setwd() in a function :
system.cd <- function(wd, command, ...){ owd <- setwd(wd) system(command, ...) setwd(owd) }
However, on a practial point of view, this is changing the working
directory.

The root of the problem is a program I'm using which outputs files in the
directory from which it is launched. The other is not being able to specify
a working directory with system. What would be a good way of working with
this issue ? And would be portable on win and linux. My data is too big to
move it with my code, and this would be another malpractice :-) Would a
chess players call this a fork ?

Etienne

2011/12/6 hadley wickham <
reply@reply.github.com

My two cents: you should not be changing working directories in the middle
of a project. Changing working directory should almost never be done
automatically - it's a UI operation because when you set a working
directory, you're saying, I'm now working on this project.

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#38 (comment)

[hadley]

Ah oh, that makes sense. Using system is the one time you do actually need to change the working directory! (I wish it was an option)

I use the following function to run chunks of R code in an arbitrary working directory.

in_dir <- function(dir, code) {
  cur <- getwd()
  setwd(dir)
  on.exit(setwd(cur))

  force(code)
}

[yihui]

@etiennebr You can use setwd() freely in knitr now; it won't affect the paths of cache and figures even if you do not restore the working directory. That said, it is still recommended to restore it (e.g. use Hadley's function above); it is a safer practice.

[etiennebr]

I surrender to the ingenuity of in_dir! Thanks both of you.

[geneorama]

This working directory issue is challenging...

I have a project that is structured like this

MyProject
MyProject\Data
MyProject\KnitrReports
MyProject\KnitrReports\Report_1
MyProject\KnitrReports\Report_2
MyProject\Other_Things

If I run chunks in R Studio, then the working directory is "MyProject". I want / expect the working directory to be "MyProject".
However, when I knit the document, the working directory changes to the report directory.

I want to keep the reports separate so that I can manually manage the large cache folders, and just to keep things organized. This is an ongoing project with interdependent large sets of data, and I don't want to keep everything at the main project level.

I don't want to create an absolute path to the data, because I share the project on other machines. Plus, I think that's bad form anyway.

Right now I run setwd('../..') at the start of any chunk that loads data (which is nearly always one chunk at the top of any single script / report), and this seems to be working. However, I was confused about this and not sure how to handle it.

Any advice?

[etiennebr]

This one is kind of tricky, but I would say it is more related to RStudio
not running the script in the same working directory than in the session. I
can however understand why they took that decision.

I found this workaround, I experienced the same problem using
ProjectTemplate organisation.
if (basename(getwd()) == "src") setwd("..")

2012/7/24 Gene Leynes <
reply@reply.github.com

This working directory issue is challenging...

I have a project that is structured like this

My project
My project\Data
My project\KnitrReports
My project\KnitrReports\Report_1
My project\KnitrReports\Report_2
My project\Other_Things

If I run chunks in R Studio, then the working directory is "My Project".
I want / expect the working directory to be "My Project".
However, when I knit the document, the working directory changes to the
report directory.

I want to keep the reports separate so that I can manually manage the
large cache folders, and just to keep things organized. This is an ongoing
project with interdependent large sets of data, and I don't want to keep
everything at the main project level.

I don't want to create an absolute path to the data, because I share the
project on other machines. Plus, I think that's bad form anyway.

Right now I run setwd('../..') at the start of any chunk that loads data
(which is nearly always one chunk at the top of any single script / report).

Any advice?

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#38 (comment)

[geneorama]

Now this is just genius
'if (basename(getwd()) == "src") setwd("..")`