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[Bioc-devel] R: R: R: Errors updating DaMiRseq package

Hervé Pagès 
It's better to discuss this on the bioc-devel list, Others might
benefit.

 >  I really did not know that latex2 was deprecated. I will modify
 >  the vignette ASAP.
 >
 >  Many thanks in advance.
 >
 >  Mattia

To troubleshoot this you can proceed in 2 steps:

   1) First generate the .tex file with 'R CMD Sweave DaMiRseq.Rnw'

   2) Then try to render it with 'pdflatex DaMiRseq.tex'

I did this on my laptop. Step 1) worked fine but step 2) produced the
same error as reported by our build system:

   ! LaTeX Error: Environment kframe undefined.

   See the LaTeX manual or LaTeX Companion for explanation.
   Type  H <return>  for immediate help.
    ...

   l.43 \begin{kframe}

So I opened the .tex file with an editor, and went to line 43 which is
where the LaTex error is happening. There I saw the deprecation warning
message right below line 43:

   \begin{kframe}

   {\ttfamily\noindent\color{warningcolor}{\#\# Warning: 'latex2' is 
deprecated.\\\#\# Use 'latex' instead.\\\#\# See help("{}Deprecated"{})}}

   \end{kframe}

Unfortunately you never got to see this message because you never got
to see the rendered version of the vignette. In the rendered version,
you wouldn't miss it because it would get displayed at the top of the
document and with special font and color.

Anyway, what's interesting here is that it's the LaTeX code for the
warning itself that seems to be causing the LaTeX error. If I remove
it, then step 2) works!

To reproduce all this, and like with any problem reported on the build
report for Bioc devel, you need to use Bioc devel and to make sure that
all your packages are up-to-date. In particular here, you want to make
sure that you have the latest devel version of BiocStyle (which is
2.5.38 at the moment).

Hope this helps,
H.
On 09/27/2017 09:49 AM, Herv? Pag?s wrote:

  
    

      
      
    

  


  


  


  
  

    

  

    
      
    
    
Thread (10 messages)

  

  

    
            
        Mattia Chiesa
        
        Errors updating DaMiRseq package
      
      Sep 22
    
    
      
            
        Turaga, Nitesh
        
        Errors updating DaMiRseq package
      
      Sep 22
    
    
      
            
        Mattia Chiesa
        
        R:  Errors updating DaMiRseq package
      
      Sep 23
    
    
      
            
        Martin Morgan
        
        R: Errors updating DaMiRseq package
      
      Sep 23
    
    
      
            
        Mattia Chiesa
        
        R:  R: Errors updating DaMiRseq package
      
      Sep 23
    
    
      
            
        Mattia Chiesa
        
        R:  R:  R: Errors updating DaMiRseq package
      
      Sep 26
    
    
      
            
        Hervé Pagès
        
        R:  R:  R: Errors updating DaMiRseq package
      
      Sep 27
    
    
      
            
        Hervé Pagès
        
        R:  R:  R: Errors updating DaMiRseq package
      
      Sep 27
    
    
      
            
        Andrzej Oleś
        
        R: R: R: Errors updating DaMiRseq package
      
      Sep 27
    
    
      
            
        Hervé Pagès
        
        R: R: R: Errors updating DaMiRseq package
      
      Sep 27