[R-pkg-devel] Detritus in temp directory - Note from submission of R package in CRAN

[Jeff Newmiller]

I agree that my example was not optimal, but I was trying to duplicate the existing behaviour with the exception of use of global variables.

On April 18, 2020 3:02:17 PM PDT, Duncan Murdoch <murdoch.duncan using gmail.com> wrote:
>On 18/04/2020 5:55 p.m., Jeff Newmiller wrote:
>> See below:
>> 
>> On Sat, 18 Apr 2020, David Andres Zamora Avila wrote:
>> 
>>> Thanks for your answers.
>>> This a part of my script where it creates files and saves it in
>anything
>>> path. I am not pretty secure how use file.path() or tempdir(). Can
>you give
>>> me more details about it, please?
>>>
>>> if (!exists("path_pet")){
>>>     path_pet <- getwd()
>>>   } else if (!exists("path_p")){
>>>     path_p <- getwd()
>>>   } else if (!exists("path_p") | !exists("path_pet")){
>>>     path_pet <- getwd()
>>>     path_p <- getwd()
>>>   }
>> 
>> The above code should not exist. You are making a package, so you are
>> putting it into a function and either looking for the existence of
>global
>> variables (side effects! requiring user to use special variable
>names!
>> this is not good!), or the "path_pet" and "path_p" variables were
>created
>> in your function and you should already know that they exist.
>> 
>> If we assume that "path_pet" and "path_p" are parameters to this
>package
>> function you are writing, like so:
>> 
>> myfunc <- function( x, y, ..., path_pet = getwd(), path_p = getwd() )
>{
>>     ...
>> }
>> 
>> then the user can let the default be the current working directory,
>or can
>> specify which directories the function should work in. Specifically,
>when
>> you are writing your examples or test code and pretending to be a
>user,
>> you can create a temporary directory and use it like so:
>
>I think your advice would probably pass the checks, but it's bad
>advice, 
>because it leaves the user vulnerable to having files wiped out by 
>myfunc().
>
>Functions shouldn't write to the current directory unless the user 
>explicitly asks for it.
>
>A better header would be
>
>myfunc <- function( x, y, ..., path_pet = temp.dir(), path_p = 
>temp.dir() ) {
>
>Then the user has to explicitly code "path_pet = getwd()" to wipe out 
>their own files.
>
>Duncan Murdoch
>
>> 
>> workingdir <- tempdir(TRUE)
>> result <- myfunc( A, B, path_pet = workingdir, path_p = workingdir )
>> 
>> which means you can then clean up after yourself with
>> 
>> unlink( workingdir, recursive = TRUE )
>> 
>> I don't think this question is really about R packages anymore... if
>you
>> still cannot read the help files to figure out your questions about
>how to
>> do manage temporary files then you should probably make a small
>> reproducible example(!!) and post a question on R-help.
>> 
>> (end of comments)
>> 
>>>   if (file_type == "raster"){
>>>     # ---- identify raster format and loading----
>>>     if (format == "GTiff"){
>>>
>>>       if( length(list.files(path_pet, pattern = ".tif")) == 0 |
>length(
>>> list.files(path_p, pattern = ".tif")) == 0){
>>>         stop("Not avaliable data of precipitation or
>evapotranspiration")
>>>       }
>>>       pet_files <- list.files(path_pet)
>>>       pet <- raster::stack(paste(path_pet, pet_files, sep = ""))
>>>       p_files <- list.files(path_p)
>>> Kind regards,
>>>
>>> David Zamora
>>>
>>> El jue., 16 abr. 2020 a las 17:12, Uwe Ligges (<
>>> ligges using statistik.tu-dortmund.de>) escribi?:
>>>
>>>>
>>>>
>>>> On 16.04.2020 20:09, Duncan Murdoch wrote:
>>>>> On 16/04/2020 1:11 p.m., David Andres Zamora Avila wrote:
>>>>>>    Hi,
>>>>>>
>>>>>> I submitted my package in CRAN and always appearance the next
>NOTE.
>>>>>>
>>>>>> Flavor: r-devel-linux-x86_64-debian-gcc
>>>>>> Check: for detritus in the temp directory, Result: NOTE
>>>>>>     Found the following files/directories:
>>>>>>       'RtmpcDoRWjr.nc'
>>>>>>
>>>>>> I have tried to solve it in several ways (like if(interactive()),
>but
>>>>>> I not
>>>>>> sure how can I solve it.
>>>>>
>>>>> How was the file created?  What the check wants is that you delete
>it
>>>>> when you are finished with it.  You can use the unlink() function
>to do
>>>>> that.
>>>>
>>>> Or better create it in tempdir(): I guess you used paste(tempdir(),
>...)
>>>> instead of file.path() and got afilename one level above tempdir()?
>>>>
>>>> Best,
>>>> Uwe Ligges
>>>>
>>>>
>>>>>
>>>>> Duncan Murdoch
>>>>>
>>>>> ______________________________________________
>>>>> R-package-devel using r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>>
>>>
>>>
>>> -- 
>>>
>>> David Zamora <https://sites.google.com/a/unal.edu.co/dazamoraa/>
>>> PhD Student, Universidad Nacional de Colombia, Bogot?
>>> phone: +571 3165000 ext 13406
>>> address: Av. NQS (Carrera 30) # 45-03, Hydraulics Lab (408-213)
>>> email: dazamoraa using unal.edu.co
>>>
>>> 	[[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-package-devel using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>
>> 
>>
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-- 
Sent from my phone. Please excuse my brevity.