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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[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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[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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[geneorama]

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

[yihui]

You can use the package option root.dir to set the working directory, e.g. opts_knit$set(root.dir = '../Data/'); see http://yihui.name/knitr/options#package_options

Calling setwd() in the code chunks is a bad idea in general.

[geneorama]

Thanks! I tried that unsuccessfully, but I was doing it wrong.

[abnova]

I tried to set working directory to my project's home directory, using 'root.dir' option, but it didn't work properly. I used an absolute path to project's home directory, not a relative, as above. Is this a problem?

This is my report's R Markdown document: https://github.com/abnova/diss-floss/blob/master/analysis/eda-report.Rmd. And this is where I set the option: https://github.com/abnova/diss-floss/blob/master/config/knitr/knitr-setup-global.Rmd. Please take a look and advise.

UPDATE: I just tried using a relative path (root.dir='..') and it didn't work either. However, it got me thinking about what is the correct base directory to determine a relative one in a situation where a child document is located in a directory different than one of a parent document...

[paulboardman]

@abnova - rmarkdown set's the working directory to the location of the Rmd file (separately to knitr).

See the following line in render.R (part of the rmarkdown package): https://github.com/rstudio/rmarkdown/blob/28feca137762651c904e05ce119244fc41112fb4/R/render.R#L96

[abnova]

@paulboardman Thank you for the comment - I will take a look at that, when I'll get a chance (it's been a while since I was working on that code, but it's good to know nevertheless). Best regards!

[geneorama]

I've been using a function that I wrote to set the project directory
https://github.com/geneorama/geneorama/blob/master/R/set_project_dir.R

There's an example in this Rmd file:
https://github.com/geneorama/DataScienceForBusiness/blob/master/Lec3/Lecture_3.Rmd

I don't love my solution, but it works.

On Wed, Feb 25, 2015 at 2:50 PM, Aleksandr Blekh notifications@github.com
wrote:

@paulboardman https://github.com/paulboardman Thank you for the comment

• I will take a look at that, when I'll get a chance (it's been a while
  since I was working on that code, but it's good to know nevertheless). Best
  regards!

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[abnova]

@geneorama Thank you for the advice, Gene! Will take a look at that.

[geneorama]

Thanks, I would be really interested to hear if it works out for you, or if
you have any suggestions for a better coding practice.

On Thu, Feb 26, 2015 at 1:27 PM, Aleksandr Blekh notifications@github.com
wrote:

@geneorama https://github.com/geneorama Thank you for the advice, Gene!
Will take a look at that.

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[abnova]

@geneorama I would love to, but it'll be a while until I'll have a chance to get to my software again - currently I'm focusing my efforts on preparing for my Ph.D. dissertation defense (slides, talk, etc.).

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