[R-pkg-devel] R Packages Never Finish Check

[Henrik Bengtsson]

I think R CMD check calls

res <- system2("du", "-k", TRUE, TRUE)

also on Windows, cf.
https://github.com/wch/r-source/blob/trunk/src/library/tools/R/check.R#L3859

It could be that you have a corrupt / different `du` tool on your
PATH.  As a first thing, try calling the above from within you package
directory.  You can also try it on the command line.   You should get
a list of sizes and paths.  If 'du' is doing something else, that
could be your answer.

As Peter says, it could also be that there's a link loop causing `du`
to never finish.  Now that link loop could either be in your package
source or in the temporary package source directory that R CMD check
sets up.  Troubleshooting the latter will be more tricky.

My $.02

Henrik

On Sat, Oct 1, 2016 at 3:02 AM, peter dalgaard <pdalgd at gmail.com> wrote:
>
>> On 30 Sep 2016, at 18:52 , Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
>>
>> On 30/09/2016 12:24 PM, Ortega, Cameron wrote:
>>> Hi,
>>>
>>> When I attempt to run Check on any package, the "checking installed package size..." Check never finishes. This is across multiple versions of R and RStudio, with every package I have attempted to run, including packages confirmed to pass Check quickly and with no issues for others.
>>>
>>> I have attempted to run Check using the following methods:
>>> -Check under the Build tab of RStudio
>>> -Running devtools::check() from the RStudio console
>>> -Running R CMD check from the command line
>>>
>>> Has anyone experienced Check failing to progress on any step, or have any ideas about what I should try next?
>>
>> I've never seen that, and I run R CMD check a lot, and devtools::check sometimes.  So you're probably stuck debugging it yourself.
>>
>> Do the usual debugging things:  simplify the process.  You're using devtools::check; see if the same thing happens in a terminal running R CMD check.  Depending on the answer to that, simplify the package down to almost nothing, and see if it still happens.
>>
>> If you're lucky, it will only happen in devtools::check, and then you can see what it is doing that's different than what R CMD check does.  If they both give the same problem, you might need to dive into the R sources to see what "* checking installed package size ..." really does, and try running code like that independently.
>>
>
> I think she said that she tried that...
>
> One more thing: when something "checks size" and loops forever, my suspicicion goes in the direction of the file system (link loops and such); perhaps try moving the build (or install) location? Also, our usual foe: virus checkers, could be involved.
>
> Peter D.
>
>> Duncan Murdoch
>>
>>>
>>>
>>> This is my session info:
>>> R version 3.3.1 (2016-06-21)
>>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>> Running under: Windows 7 x64 (build 7601) Service Pack 1
>>>
>>> locale:
>>> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252
>>> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>>> [5] LC_TIME=English_United States.1252
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> loaded via a namespace (and not attached):
>>> [1] tools_3.3.1
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> This is a print out from the RStudio Check:
>>> ==> devtools::check()
>>>
>>> Updating linkedata documentation
>>> Loading linkedata
>>> Writing NAMESPACE
>>> Writing linkedata.Rd
>>> Writing linke.Rd
>>> Setting env vars ---------------------------------------------------------------
>>> CFLAGS  : -Wall -pedantic
>>> CXXFLAGS: -Wall -pedantic
>>> Building linkedata -------------------------------------------------------------
>>> "C:/PROGRA~1/R/R-33~1.1/bin/x64/R" --no-site-file --no-environ --no-save  \
>>>   --no-restore --quiet CMD build  \
>>>   "C:\Users\caort\Documents\Subversion\rcode\lib\src\linkedata"  \
>>>   --no-resave-data --no-manual
>>>
>>> * checking for file 'C:\Users\caort\Documents\Subversion\rcode\lib\src\linkedata/DESCRIPTION' ... OK
>>> * preparing 'linkedata':
>>> * checking DESCRIPTION meta-information ... OK
>>> * checking for LF line-endings in source and make files
>>> * checking for empty or unneeded directories
>>> Removed empty directory 'linkedata/zipdta'
>>> * looking to see if a 'data/datalist' file should be added
>>> * building 'linkedata_0.1.0.tar.gz'
>>>
>>> Setting env vars ---------------------------------------------------------------
>>> _R_CHECK_CRAN_INCOMING_ : FALSE
>>> _R_CHECK_FORCE_SUGGESTS_: FALSE
>>> Checking linkedata -------------------------------------------------------------
>>> "C:/PROGRA~1/R/R-33~1.1/bin/x64/R" --no-site-file --no-environ --no-save  \
>>>   --no-restore --quiet CMD check  \
>>>   "C:\Users\caort\AppData\Local\Temp\Rtmp8EbYiM/linkedata_0.1.0.tar.gz"  \
>>>   --as-cran --timings --no-manual
>>>
>>> * using log directory 'C:/Users/caort/Documents/Subversion/rcode/lib/src/linkedata.Rcheck'
>>> * using R version 3.3.1 (2016-06-21)
>>> * using platform: x86_64-w64-mingw32 (64-bit)
>>> * using session charset: ISO8859-1
>>> * using options '--no-manual --as-cran'
>>> * checking for file 'linkedata/DESCRIPTION' ... OK
>>> * checking extension type ... Package
>>> * this is package 'linkedata' version '0.1.0'
>>> * checking package namespace information ... OK
>>> * checking package dependencies ... NOTE
>>> Package suggested but not available for checking: 'pvsolcalcs'
>>> * checking if this is a source package ... OK
>>> * checking if there is a namespace ... OK
>>> * checking for executable files ... OK
>>> * checking for hidden files and directories ... OK
>>> * checking for portable file names ... OK
>>> * checking whether package 'linkedata' can be installed ... OK
>>> * checking installed package size ...
>>>
>>>
>>>
>>>
>>>
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> --
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
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