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

5 messages · Leonard Mada, Avraham Adler, Uwe Ligges

Original
Leonard Mada
# 
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
Avraham Adler
# 
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

  
  


  


      

    

    

      
      

        


  

        

      Uwe Ligges
    

    

      
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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:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Leonard Mada
    

    

      
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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")


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:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Uwe Ligges
    

    

      
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On 14.09.2023 23:35, Leonard Mada wrote:

            

      
      
      
    

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

Best,
Uwe Ligges