[R-pkg-devel] nparACT package: "working directory was changed to...resetting"

[Duncan Murdoch]

On 19/12/2017 10:27 AM, Blume Christine wrote:
> Hi Duncan,
> 
> Thanks a lot! Good to see that you had a similar idea, I did just 
> that...in my example it looks like this, however, that does not help, 
> i.e. that is the code that is associated with the warning…
> 
> data(sleepstudy)
> 
> wd <- getwd()
> 
> name <- "sleepstudy_example"
> 
> newdir <- paste(wd,name, sep="/")
> 
> if (dir.exists(newdir)){
> 
> setwd(newdir)
> 
> write.table(sleepstudy, file = "sleepstudy.txt", row.names=FALSE, 
> col.names = FALSE)
> 
> r <- nparACT_flex_loop(newdir, SR = 4/60, minutes = 435)
> 
> } else {
> 
> dir.create(newdir)

This is probably a bad idea.  You're creating a subdirectory in the 
user's current working directory; you might not have file system 
permission to do that, and you probably don't have authorization from 
the user to do that.  I don't remember if CRAN checks for this, but I 
wouldn't be surprised if they do, or will in the future.

Since you need to write a file, you want to be sure that it's going to a 
place that is harmless and will succeed.  That's what tempdir() is for. 
At the end of your session it will be cleaned up, so you won't leave 
behind junk for the user.

So I would set newdir using

newdir <- file.path(tempdir(), name)

The other change I would make is to unconditionally use 
dir.create(newdir, showWarnings = FALSE).  You can be almost 100% sure 
that any error creating newdir will be just that it already exists, and 
since it's just somewhere in tempdir(), you don't really care about 
that.  This will simplify your example quite a bit.

Putting these two and my earlier suggestion together, your example becomes

data(sleepstudy)

name <- "sleepstudy_example"

newdir <- file.path(tempdir(),name)

dir.create(newdir, showWarnings = FALSE)

olddir <- setwd(newdir)

write.table(sleepstudy, file = "sleepstudy.txt", row.names=FALSE, 
col.names = FALSE)

r <- nparACT_flex_loop(newdir, SR = 4/60, minutes = 435)

setwd(olddir)

Duncan Murdoch



> 
> setwd(newdir)
> 
> write.table(sleepstudy, file = "sleepstudy.txt", row.names=FALSE, 
> col.names = FALSE)
> 
> r <- nparACT_flex_loop(newdir, SR = 4/60, minutes = 435)
> 
> }
> 
> setwd(wd)
> 
> }
> 
> Best,
> 
> Christine
> 
> -----Ursprüngliche Nachricht-----
> Von: Duncan Murdoch [mailto:murdoch.duncan at gmail.com]
> Gesendet: Dienstag, 19. Dezember 2017 16:19
> An: Blume Christine; r-package-devel at r-project.org
> Betreff: Re: [R-pkg-devel] nparACT package: "working directory was 
> changed to...resetting"
> 
> On 19/12/2017 9:42 AM, Blume Christine wrote:
> 
>  > Dear Community,
> 
>  >
> 
>  >
> 
>  >
> 
>  > For Fedora my package now gives a warning message when running the 
> example:
> 
>  >
> 
>  >
> 
>  >
> 
>  > "Warning: working directory was changed to 
> '/data/gannet/ripley/R/packages/tests-clang/nparACT.Rcheck/sleepstudy_example', 
> resetting"
> 
>  >
> 
>  >
> 
>  >
> 
>  > I do not really know how to approach/solve this, what has recently 
> been changed in R devel so this error message started appearing?
> 
> Previously you were allowed to change directory in an example.  Now 
> you're not.  This makes sense:  the user might not want to change the 
> working directory.
> 
> To fix this, just save the old directory, and restore it at the end of 
> your example.  For example,
> 
>     olddir <- setwd(tempdir())
> 
>     # Run the rest of the example code here
> 
>     setwd(olddir)
> 
> Duncan Murdoch
> 
>  >
> 
>  >
> 
>  >
> 
>  > The full message can be seen here:
> 
>  > https://CRAN.R-project.org/web/checks/check_results_nparACT.html
> 
>  >
> 
>  >
> 
>  >
> 
>  > Any help is appreciated and rewarded with gratitude.
> 
>  >
> 
>  >
> 
>  >
> 
>  > Best,
> 
>  >
> 
>  >
> 
>  >
> 
>  > Christine
> 
>  >
> 
>  >
> 
>  >
> 
>  >             [[alternative HTML version deleted]]
> 
>  >
> 
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> 
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