[R-pkg-devel] Saving output of check()

[J C Nash]

I got several responses to my query. Henrik's does suggest "why", but I
am rather unhappy that R has this weakness. (See below for a sort of
workaround for Linux users.)

In particular, note that the check_built() function DOES return an object,
but it does NOT print().

In fact, putting alldep <- "embryogrowth" gives a result file

> Check the dependent packages
> Downloaded  /home/john/temp/wrkopt/dlpkg/embryogrowth_7.4.tar.gz 
> Results package: embryogrowth 
> 

while the bottom of the terminal file gives

> * checking data for non-ASCII characters ... OK
> * checking data for ASCII and uncompressed saves ... OK
> * checking examples ... OK
> * DONE
> 
> Status: OK
> 
> Results package: embryogrowth 
> R CMD check results
> 0 errors | 0 warnings | 0 notes
> 
>> 
>> sink()
>> 

Now the object cpkg.chk is still present, so I continued the exercise (terminal
copy here)

> 
>> ls()
> [1] "alldep"   "cpkg"     "cpkg.chk" "dd"       "dlname"   "ii"       "nall"    
>> sink("sinktest2.txt", split=TRUE)
>> cpkg.chk
> R CMD check results
> 0 errors | 0 warnings | 0 notes
> 
>> print(cpkg.chk)
> R CMD check results
> 0 errors | 0 warnings | 0 notes
> 
>> cat("note the above use just the object name as well as print()\n")
> note the above use just the object name as well as print()
>> sink()
>> 

but the file sinktest2.txt is just

> 
> note the above use just the object name as well as print()

Perhaps this isn't a bug, but it rather smells like one, especially the
failure to show the cpkg.chk.

Workaround for Linux: Run things via

R |& tee -a myteeoutput.txt

This will keep all the output (sink not needed). But it isn't quite as nice
for keeping the data.

I've also not managed to find a way to get the information out of the cpkg.chk
object. If someone knows how to do that, it would help.

Best, JN








On 2018-04-11 03:24 PM, Henrik Bengtsson wrote:
> R CMD check, which is used internally runs checks in standalone
> background R processes.  Output from these is not capturable/sinkable
> by the master R process.  The gist of what's happening is:
> 
>> sink("output.log")
>> system("echo hello")  ## not sinked/captured
> hello
>> sink()
>> readLines("output.log")
> character(0)
> 
> /Henrik
> 
> On Wed, Apr 11, 2018 at 11:05 AM, J C Nash <profjcnash at gmail.com> wrote:
>> Hi,
>>
>> In trying to test that an upgrade to my optimx package does not break other
>> packages, I wanted to loop over a list of all such packages in alldep, with
>> nall the length of this list.
>>
>> cat("Check the dependent packages\n")
>> for (ii in 1:nall){
>>   cpkg <- alldep[ii]
>>   dd <- "/home/john/temp/wrkopt/dlpkg"
>>   dlname <- download.packages(cpkg, destdir=dd )[[2]]
>>   cat("Downloaded ", dlname,"\n")
>>   cpkg.chk <- devtools::check_built(dlname)
>>   cat("Results package:",cpkg,"\n")
>>   print(cpkg.chk)
>> }
>>
>> Before running this, I did
>>
>> sink("dpkgcheck.txt", split=TRUE)
>>
>> and afterwards, I did sink().
>>
>> But ... none of the check output, nor the result of the final print, show
>> up in the output file dpkgcheck.txt.
>>
>> Have I totally misunderstood sink(), or is there a nasty bug?
>>
>> I've tried running in Rstudio and in the terminal. I'm running Linux Mint
>> 18.3 Sylvia.
>>
>> Linux john-j6-18 4.10.0-38-generic #42~16.04.1-Ubuntu SMP Tue Oct 10 16:32:20 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
>> john at john-j6-18 ~ $ R
>>
>> R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
>>
>>
>> J C Nash
>>
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