[R-pkg-devel] strange errors (non-ascii symbols) on win-builder R-devel

[Duncan Murdoch]

I think that is likely bad luck, in that your package was being 
evaluated at the same time as the new minpack.lm, and CRAN/winbuilder 
don't isolate the builds.  If you resubmit unchanged (I'd do this on 
winbuilder, not CRAN) you may get a more reasonable outcome.

Duncan Murdoch

On 24/01/2023 12:33 p.m., Maxim Nazarov wrote:
> Thank you, Tomas, for your insights!
> 
> I think I found the root cause of the problem - my package uses the `nlsLM` function from the `minpack.lm` package and coincidentally the new version of that package was submitted to CRAN recently.
> Looking at https://win-builder.r-project.org/incoming_pretest/minpack.lm_1.2-3_20230117_110122/reverseDependencies/changes.txt - we can see that this new version of minpack.lm is causing similar errors in many of its reverse dependencies.
> 
> In fact if I install that version from https://cran.r-project.org/incoming/archive/ I get the strange output when running a simple example from `nlsLM` even on linux:
> ```
> install.packages("https://cran.r-project.org/incoming/archive/minpack.lm_1.2-3.tar.gz")
> library(minpack.lm)
> DNase1 <- subset(DNase, Run == 1)
> capture.output(fm1DNase1 <- nlsLM(density ~ SSlogis(log(conc), Asym, xmid, scal), DNase1))
> ## produces "\xa8\002\x8c\003\x9bU"
> ```
> this seems to come from the C code, which I don't fully understand.
> 
> So I guess it is an unfortunate timing, and I just need to wait for the minpack.lm package to be fixed, but I'm wondering (philosophically) if it is correct that my package is checked against non-released (non-approved) version of minpack.lm and rejected because of its shortcomings?
> 
> Kind regards,
> Maxim Nazarov
> 
> 
> ----- Original Message -----
> From: "Tomas Kalibera" <tomas.kalibera using gmail.com>
> To: "Maxim Nazarov" <maxim.nazarov using openanalytics.eu>, "r-package-devel" <r-package-devel using r-project.org>
> Sent: Monday, 23 January, 2023 21:49:56
> Subject: Re: [R-pkg-devel] strange errors (non-ascii symbols) on win-builder R-devel
> 
> On 1/23/23 17:30, Maxim Nazarov wrote:
>> Hello all,
>>
>> I am submitting a minor update to one of my CRAN package (BIGL), and get strange errors on R-devel on win-builder - https://win-builder.r-project.org/incoming_pretest/BIGL_1.6.7_20230119_225109/Windows/00check.log and https://win-builder.r-project.org/o339zPAR6pWG/00check.log (different symbols)
>>
>> It shows strange output like "`1Y���hA�..." before tests and cryptic error-messages like "unable to translate '(<be><b1><a7>m' to a wide string"
>> I can also see similar output in examples - https://win-builder.r-project.org/o339zPAR6pWG/examples_and_tests/BIGL-Ex.Rout
> 
> These are errors and warnings in regex operations (grep, gsub) due to
> that the input data is not a valid string (validly encoded string).
> Because it is not valid, it cannot be converted to a wide string, which
> is needed for the regex operation, as this uses TRE.
> 
> So, you need to find out why the input strings are invalid. Common
> causes of such problems are that they are in a different encoding from
> the one told to R or to some other software on the way. Also the data
> may be corrupted.
> 
>> I don't get any isses on debian R-devel, on R-release on windows, and also can't reproduce the errors locally on a windows machine with R-devel, so I am a bit lost.
>> Would anyone have any idea of what goes wrong?
> 
> It should be fairly easy from the error output to find out which
> operations have failed in the vignette. Perhaps you could find out how
> their inputs were generated.
> 
> If you have a Windows machine with R running in UTF-8 as the native
> encoding, with recent R-devel, and the error is still not reproducible,
> try to confirm that the inputs for the failing operations are correct.
> 
> Best
> Tomas
> 
>>
>> Kind regards,
>> Maxim Nazarov
>>
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