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[Bioc-devel] mosbi package: Suggested dependency not available

Hervé Pagès 
Hi Tim,

runibic has a compilation error on Mac because its native code uses 
OpenMP. However package code should not use OpenMP on Mac (see 
https://stat.ethz.ch/pipermail/r-sig-mac/2019-June/012995.html).

I just marked runibic as unsupported on Mac.

It seems that mosbi only uses runibic in one function, 
mosbi::run_unibic(), but that function is never called (the only place 
where I see a call to it is in the example section of its man page but 
the call is commented out). So the only reason that 'R CMD check' fails 
on Mac is because, by default, 'R CMD check' wants all the deps, even 
the suggested ones (i.e. soft deps), to be installed. To prevent this, I 
added a .BBSoptions file to mosbi, with the following line in it:

   CHECKprepend.mac: _R_CHECK_FORCE_SUGGESTS_=0

See for example the build report for piano 
https://bioconductor.org/checkResults/3.14/bioc-LATEST/piano/merida1-checksrc.html
for the effect that this will have on the exact command used during CHECK.

Cheers,
H.
On 21/10/2021 06:06, Kern, Lori wrote:

  
    

      
      
    

  


  


  


  
  

    

  

    
      
    
    
Thread (3 messages)

  

  

    
            
        Tim Daniel Rose
        
        mosbi package: Suggested dependency not available
      
      Oct 21
    
    
      
            
        Shepherd, Lori
        
        mosbi package: Suggested dependency not available
      
      Oct 21
    
    
      
            
        Hervé Pagès
        
        mosbi package: Suggested dependency not available
      
      Oct 21