[R-pkg-devel] Pre-test check fails with "non-standard things in check directory" on one platform

[Rainer M Krug]

Hi

I submitted an update of the dmdScheme package and got the response back from 
the pre-submission check that it failed on one platform with the Note:

* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ‘emeScheme’

(Links to the logs are here:

package dmdScheme_1.2.7.tar.gz does not pass the incoming checks automatically, 
please see the following pre-tests:
Windows: 

Status: OK
Debian: 

Status: 1 NOTE

)

This only occurs on the CRAN server and I can not reproduce it with rhub or 
locally on my Mac with 4.1.1.

I can currently not check the level version, as it seems to be not compiling 
for Mac. 

Could somebody give any guidance, how to fix this? Which one is the “check 
directory"? 

Thanks,

Rainer

--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

Orcid ID: -0002-7490-0066

Department of Evolutionary Biology and Environmental Studies
University of Zürich
Office Y34-J-74
Winterthurerstrasse 190
8075 Zürich
Switzerland

Office: +41 (0)44 635 47 64
Cell:   +41 (0)78 630 66 57
email:  rainer.k...@uzh.ch
rai...@krugs.de
Skype: RMkrug

PGP: 0x0F52F982

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Re: [R-pkg-devel] Pre-test check fails with "non-standard things in check directory" on one platform

[Duncan Murdoch]

On 02/09/2021 6:29 a.m., Rainer M Krug wrote:

Hi

I submitted an update of the dmdScheme package and got the response back from 
the pre-submission check that it failed on one platform with the Note:

* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
   ‘emeScheme’

(Links to the logs are here:

package dmdScheme_1.2.7.tar.gz does not pass the incoming checks automatically, 
please see the following pre-tests:
Windows: 

Status: OK
Debian: 

Status: 1 NOTE

)

This only occurs on the CRAN server and I can not reproduce it with rhub or 
locally on my Mac with 4.1.1.

I can currently not check the level version, as it seems to be not compiling 
for Mac.

Could somebody give any guidance, how to fix this? Which one is the “check 
directory"?


That's the one reported at the start of the log as the "log directory".

Fixing it is a little harder without more info.  That looks like a name 
that you would have created, given the name of your package.  You should 
look at your package source to figure out if there's an example or test 
that created it but didn't delete it.


Duncan Murdoch

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Re: [R-pkg-devel] Pre-test check fails with "non-standard things in check directory" on one platform

[Rainer M Krug]

> On 2 Sep 2021, at 14:02, Duncan Murdoch  wrote:
> 
> On 02/09/2021 6:29 a.m., Rainer M Krug wrote:
>> Hi
>> I submitted an update of the dmdScheme package and got the response back 
>> from the pre-submission check that it failed on one platform with the Note:
>> * checking for non-standard things in the check directory ... NOTE
>> Found the following files/directories:
>>   ‘emeScheme’
>> (Links to the logs are here:
>> package dmdScheme_1.2.7.tar.gz does not pass the incoming checks 
>> automatically, please see the following pre-tests:
>> Windows: 
>> 
>> Status: OK
>> Debian: 
>> 
>> Status: 1 NOTE
>> )
>> This only occurs on the CRAN server and I can not reproduce it with rhub or 
>> locally on my Mac with 4.1.1.
>> I can currently not check the level version, as it seems to be not compiling 
>> for Mac.
>> Could somebody give any guidance, how to fix this? Which one is the “check 
>> directory"?
> 
> That's the one reported at the start of the log as the "log directory".
> 
> Fixing it is a little harder without more info.  That looks like a name that 
> you would have created, given the name of your package.  You should look at 
> your package source to figure out if there's an example or test that created 
> it but didn't delete it.
> 

Thanks Duncan.


I will look at it and come back when I have further questions.

Rainer


> Duncan Murdoch

--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

Orcid ID: -0002-7490-0066

Department of Evolutionary Biology and Environmental Studies
University of Zürich
Office Y34-J-74
Winterthurerstrasse 190
8075 Zürich
Switzerland

Office: +41 (0)44 635 47 64
Cell:   +41 (0)78 630 66 57
email:  rainer.k...@uzh.ch
rai...@krugs.de
Skype: RMkrug

PGP: 0x0F52F982




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[R-pkg-devel] Unicode Name Warnings for Package Constant

[bill]

Hello,

 

In the janitor package, we want to optionally support conversion from
Unicode characters that visually map to mu or micro to the character "u".
For that, we were thinking to create an unexported character vector constant
with names of all the Unicode mu/micro characters and values of "u".  As a
work-around, I was able to fix the issue using setNames(), but it was a
non-intuitive fix, and I would prefer to just use create the named character
vector directly.

 

Is there a good way to prevent the warnings below?

 

When running the following (on Windows 10 with R 4.1.0) either during a
normal R session or while checking the package (via devtools::check()), we
get several warnings:

 

mu_to_u <-

  c(

"\u00b5"="u", "\u03bc"="u", "\u3382"="u", "\u338c"="u", "\u338d"="u",

"\u3395"="u", "\u339b"="u", "\u33b2"="u", "\u33b6"="u", "\u33bc"="u"

  )

 

  Warnings in file 'R/clean_names.R':

unable to translate '' to native encoding

unable to translate '' to native encoding

unable to translate '' to native encoding

unable to translate '' to native encoding

unable to translate '' to native encoding

unable to translate '' to native encoding

unable to translate '' to native encoding

unable to translate '' to native encoding

 

I tried wrapping this in suppressWarnings(), but the warnings still
occurred.

 

Thanks,

 

Bill


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Re: [R-pkg-devel] Unicode Name Warnings for Package Constant

[Duncan Murdoch]

On 02/09/2021 11:24 a.m., b...@denney.ws wrote:

Hello,

  


In the janitor package, we want to optionally support conversion from
Unicode characters that visually map to mu or micro to the character "u".
For that, we were thinking to create an unexported character vector constant
with names of all the Unicode mu/micro characters and values of "u".  As a
work-around, I was able to fix the issue using setNames(), but it was a
non-intuitive fix, and I would prefer to just use create the named character
vector directly.


I think the warning comes because on non-UTF8 platforms there are 
operations that will mess up names.  So using setNames() may fool the 
check, but it probably won't solve the problem.


On the other hand, I think all current platforms handle UTF8 data fine, 
so keeping the vector of characters as data should be fine.  Then the 
base chartr() function could do your translation for you.


To do the translation you want, you'd use something like

  original <- "45 \u00b5m"

chartr("\u00b5\u03bc\u3382\u338c\u338d\u3395\u339b\u33b2\u33b6\u33bc", 
"uu", original)


Duncan Murdoch


  


Is there a good way to prevent the warnings below?

  


When running the following (on Windows 10 with R 4.1.0) either during a
normal R session or while checking the package (via devtools::check()), we
get several warnings:

  


mu_to_u <-

   c(

 "\u00b5"="u", "\u03bc"="u", "\u3382"="u", "\u338c"="u", "\u338d"="u",

 "\u3395"="u", "\u339b"="u", "\u33b2"="u", "\u33b6"="u", "\u33bc"="u"

   )

  


   Warnings in file 'R/clean_names.R':

 unable to translate '' to native encoding

 unable to translate '' to native encoding

 unable to translate '' to native encoding

 unable to translate '' to native encoding

 unable to translate '' to native encoding

 unable to translate '' to native encoding

 unable to translate '' to native encoding

 unable to translate '' to native encoding

  


I tried wrapping this in suppressWarnings(), but the warnings still
occurred.

  


Thanks,

  


Bill


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Re: [R-pkg-devel] Unicode Name Warnings for Package Constant

[Tomas Kalibera]

In the current R releases, R symbol names are in the native encoding, 
which on Windows in R (the normal MSVCRT builds up to R 4.1) cannot be 
UTF-8 nor any other Unicode encoding. So you can't portably use such 
characters e.g. in names of vector elements or of bindings in an 
environment, so not even as keys in a hash map implemented using an 
environment.


This works in UCRT builds of Windows on recent Windows 10 (and on Unix 
and macOS for many years), but before that becomes the norm, it might be 
easiest to give up on this feature in your package. But, in principle, 
you can work with UTF-8 strings, sometimes (one needs to check the 
docs), but they cannot be R symbols. So you can do some operations e.g. 
with a vector like


c(mu = "\u00b5")

where the UTF-8 string is a value, not a name.

Best
Tomas


On 9/2/21 5:24 PM, b...@denney.ws wrote:

Hello,

  


In the janitor package, we want to optionally support conversion from
Unicode characters that visually map to mu or micro to the character "u".
For that, we were thinking to create an unexported character vector constant
with names of all the Unicode mu/micro characters and values of "u".  As a
work-around, I was able to fix the issue using setNames(), but it was a
non-intuitive fix, and I would prefer to just use create the named character
vector directly.

  


Is there a good way to prevent the warnings below?

  


When running the following (on Windows 10 with R 4.1.0) either during a
normal R session or while checking the package (via devtools::check()), we
get several warnings:

  


mu_to_u <-

   c(

 "\u00b5"="u", "\u03bc"="u", "\u3382"="u", "\u338c"="u", "\u338d"="u",

 "\u3395"="u", "\u339b"="u", "\u33b2"="u", "\u33b6"="u", "\u33bc"="u"

   )

  


   Warnings in file 'R/clean_names.R':

 unable to translate '' to native encoding

 unable to translate '' to native encoding

 unable to translate '' to native encoding

 unable to translate '' to native encoding

 unable to translate '' to native encoding

 unable to translate '' to native encoding

 unable to translate '' to native encoding

 unable to translate '' to native encoding

  


I tried wrapping this in suppressWarnings(), but the warnings still
occurred.

  


Thanks,

  


Bill


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