[R-pkg-devel] Spelling of PDB in Package Description

[Uwe Ligges]

On 14.09.2023 23:35, Leonard Mada wrote:
> Dear Uwe,
> 
> 
> I found out what is going on. There is an example:
> 
> ## Write the pdb object in file "Rpdb.pdb" into the current directory
> write.pdb(pdb, file = "Rpdb.pdb")
> 

In examples, you should write to tempdir(), if at all.

Best,
Uwe Ligges




> 
> The example was present in the previous version as well. So I did not 
> thought about it. I do not know how to handle this: although the example 
> should probably remain.
> 
> 
> Sincerely,
> 
> 
> Leonard
> 
> 
> On 9/15/2023 12:27 AM, Uwe Ligges wrote:
>> The spellng is fine and not a problem.
>>
>> For
>> * checking for non-standard things in the check directory ... NOTE
>> Found the following files/directories:
>>   ‘Rpdb.pdb’
>> You need to move this to ./inst or a subdirectory or, if data, 
>> consider ./extdata See Writing R Extensions.
>>
>> Best,
>> Uwe Ligges
>>
>>
>> On 14.09.2023 22:06, Avraham Adler wrote:
>>> Regarding PDB, in Rd format it’s best to wrap that in an \acronym{} 
>>> tag. See section 2.3 of 
>>> https://cran.r-project.org/doc/manuals/R-exts.html#Marking-text
>>>
>>> Avi
>>>
>>> Sent from my iPhone
>>>
>>>> On Sep 14, 2023, at 3:40 PM, Leonard Mada via R-package-devel 
>>>> <r-package-devel using r-project.org> wrote:
>>>>
>>>> Dear List Members,
>>>>
>>>> After resubmitting the updated version of the Rpdb package (2.3.1), 
>>>> the following Notes were generated:
>>>>
>>>> 1.) Spelling PDB
>>>> https://win-builder.r-project.org/incoming_pretest/Rpdb_2.3.1_20230914_173458/Windows/00check.log
>>>> https://win-builder.r-project.org/incoming_pretest/Rpdb_2.3.1_20230914_173458/Debian/00check.log
>>>>
>>>> The PDB stands for Protein Data Bank:
>>>> http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html
>>>>
>>>> It should be the correct spelling (and was the same in the previous 
>>>> versions of the package).
>>>>
>>>> 2.)  Small Sample PDB Files
>>>> * checking for non-standard things in the check directory ...
>>>> NOTE Found the following files/directories: ‘Rpdb.pdb’
>>>>
>>>> There is a directory with 3 very small sample pdb-files. The 
>>>> directory was also present in the previous version.
>>>>
>>>> How should I proceed? Or did I miss something?
>>>>
>>>>
>>>> Sincerely,
>>>>
>>>>
>>>> Leonard
>>>>
>>>> ______________________________________________
>>>> R-package-devel using r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>
>>>     [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-package-devel using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel