[R-pkg-devel] File name error

[Uwe Ligges]

On 21.12.2017 18:22, Henrik Bengtsson wrote:
> Uwe/Kurt, is this 

You mean the new check? This is R.

> controlled by R itself or by the host system?  I
> suspect one of my R.filesets tests(*) fails (since a few days) because
> of this, but it might actually be a false positive.  I fail to
> reproduce it on Ubuntu 16.04 with:
> 
> * using R Under development (unstable) (2017-12-20 r73933)
> * using platform: x86_64-pc-linux-gnu (64-bit)
> 
> My test tries to verify that it can write to tempdir() using its
> *relative* path (if such is possible) - a test that effectively does:
> 
>> abs <- tempfile()
>> setwd(dirname(abs))
>> getwd()
> [1] "/tmp/Rtmpa9riPQ"
>> rel <- file.path("..", "..", abs)
>> rel <- gsub("//", "/", rel, fixed = TRUE)
>> rel
> [1] "../../tmp/Rtmpa9riPQ/file3251441e380d
>> cat("hello", file = res)

file = rel, I guess.


> 
> and fails in that last write on 'r-devel-linux-x86_64-debian-gcc'.  It
> could, of course, be a bug in my code that is now being revealed, but
> these tests been in place for many years, possibly more than a decade.
> 
> (*) https://cran.r-project.org/web/checks/check_results_R.filesets.html


Well, as this is also shown in R-release on Kurt's machines, I suspect 
this is either a problem where the directory you are working in is a 
link and the deriving the relative path fails or there is no space left 
in  tempdir() ...

In both cases, please ask Kurt who is on vacation, too.

Best,
Uwe






> Thxs,
> 
> Henrik
> 
> On Thu, Dec 21, 2017 at 2:21 AM, Uwe Ligges
> <ligges at statistik.tu-dortmund.de> wrote:
>> This is a new check:
>>
>> You must not write into the user's filespace without explicit agreement by
>> the user (by specifying path/name).
>>
>> Note that some users won't even have permissions to write into the package's
>> installation directory if that is set up site wide by an admin, for example.
>>
>> So please use tempdir() in the examples.
>>
>> Best,
>> Uwe Ligges
>>
>>
>>
>>
>>
>> On 21.12.2017 09:21, Blume Christine wrote:
>>>
>>> Hi Cathy,
>>>
>>> I also had troubles with debian (Fedora only gave warnings) and no
>>> problems with other systems. Mine was related to me writing a file (or
>>> rather trying to write) in a working directory other than tempdir (can be
>>> retrieved by tempdir()). I now write it to tempdir and then set the old
>>> working directory again at the end of the example. Perhaps that is somehow
>>> helpful for your case too?
>>>
>>> I can highly recommend to test your tar.gz file with the check() function
>>> of the rhub package. You can for example run check("pathtoyourpackage",
>>> platform = "debian-gcc-devel") or
>>> check_for_cran("pathtoyourpackage", platform = "debian-gcc-devel"), i.e.
>>> test your package on debian without troubles.
>>>
>>> Best,
>>> Christine
>>>
>>>
>>> -----Ursprüngliche Nachricht-----
>>> Von: R-package-devel [mailto:r-package-devel-bounces at r-project.org] Im
>>> Auftrag von Cathy Lee Gierke
>>> Gesendet: Donnerstag, 21. Dezember 2017 07:15
>>> An: R Package Development
>>> Betreff: [R-pkg-devel] File name error
>>>
>>> I am getting the following error from the auto-checks when trying to
>>> submit a package to CRAN:
>>> r-devel-linux-x86_64-debian-gcc
>>>
>>> <https://cran.r-project.org/web/checks/check_flavors.html#r-devel-linux-x86_64-debian-gcc>
>>> 3.0.0.2 3.63 56.71 60.34 ERROR
>>>
>>> <https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/CATkit-00check.html>
>>>
>>> Error in pdf(file = fileName4, width = 8, height = 10) :
>>>     cannot open file
>>>
>>> '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/CATkit/extdata/activity-stress-c57-2-part.txt--20Dec2017--03-51-46CAToutput.pdf'
>>>
>>> Since this works for ALL other flavors, I am assuming it may be some file
>>> name restrictions unique to debian-gcc???  I can't think what else would
>>> cause it to fail only in the OS.
>>>
>>> debian doesn't like "--"?
>>>
>>> Cathy Lee Gierke
>>>
>>>
>>> *“Darkness cannot drive out darkness: only light can do that. Hate cannot
>>> drive out hate: only love can do that.” * *“The arc of the moral universe is
>>> long, but it bends towards justice.”* *“Nothing in the world is more
>>> dangerous than sincere ignorance and conscientious stupidity.” *
>>> *“Never forget that everything Hitler did in Germany was legal.”   *
>>> *“Forgiveness is not an occasional act, it is a constant attitude.” *
>>> *“Injustice anywhere is a threat to justice everywhere.”  *
>>>
>>> ― Martin Luther King Jr.
>>>
>>> <http://www.goodreads.com/author/show/23924.Martin_Luther_King_Jr_>
>>>
>>>          [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
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>>
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