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[Bioc-devel] Unclear build failure ‘appending gaps’

6 messages · Michael Lawrence, Karl Stamm, Yue Zhao (Jason) +1 more

Karl Stamm
# 
My package rgsepd has failed build recently.

I don't understand the error message, and need some guidance. It says Error
building vignette, "appending gaps is not supported"

I can't find that statement anywhere in Google, so I don't know what it's
referring to.  Unfortunately, my package is an automation pipeline, so
there's one line of code that runs many others, and the line triggering the
error could represent any part of my pipeline.

I've checked the build on my end before uploading code changes, so I cant
reproduce the error. My build was okay until very recently, I have added a
CITATION file which is rather lengthy, and may be impacting the vignette
build?
Michael Lawrence
# 
This is due to some buggy changes to the internals of the S4Vectors
package. I should be able to fix these today.
On Sat, Mar 23, 2019 at 7:41 AM Karl Stamm <karl.stamm at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    
3 days later

    

      
      

        


  

        

      Karl Stamm
    

    

      
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That first error has resolved, and I have new errors on the build on
Windows and on OSX, while the Linux build goes fine.

I have build and check and test on OSX and Windows on my end and everything
works. There must be something different on the Bioc build servers I am not
matching up with. The OSX errors mention LateX commands, so that's not a
cross platform problem. Might be the build-server configuration.

I'm trying to get that red error sign off my build report, but I can't see
how to work on non-reproducible errors.

On Sat, Mar 23, 2019 at 10:21 AM Michael Lawrence <lawrence.michael at gene.com>
wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Yue Zhao (Jason)
    

    

      
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A new error showed up: logical subscript contains NAs


*--*

*Yue (Jason) Zhao*

PhD Candidate, Bioinformatics Program

Boston University

yuezh at bu.edu


On Sat, Mar 23, 2019 at 11:22 AM Michael Lawrence via Bioc-devel <

        
bioc-devel at r-project.org> wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Karl Stamm
    

    

      
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Is there a standard system loadout I should be matching? Something must be
different between my Windows build server and the bioconductor one.
I need to reproduce the error in order to debug it, but everything is
building fine locally.

        
On Tue, Mar 26, 2019 at 12:21 PM Yue Zhao (Jason) <yuezh at bu.edu> wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Shepherd, Lori
    

    

      
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The following will give you some info on the windows server:


http://bioconductor.org/checkResults/devel/bioc-LATEST/tokay2-NodeInfo.html


There have been some updates in other packages that should propagate on tomorrows build report.  I might suggest you wait to see if the package continues to have these ERRORs after then.


Cheers,



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263