Solutions for R Errors

System Errors

• I commonly experience errors running functions from the gtsummary package. These issues arise when running code within a virtualized Ubuntu OS. Functions that include many variables, from either tbl_uvregression(), tbl_regression(), or tbl_merge() will inevitably result in the following error:

  Error: C stack usage   7971348 is too close to the limit
  

  gtsummary produces a monster of nested code as seen in the traceback(). You can inspect the C stack usage in r using Cstack_info(). Unfortunately I don’t know of any way to modify this value within a running R session. Luckily it can be modified within the terminal using

  ulimit -s unlimited
  

  Then, within the current terminal, start an R session and run the desired code. I’m usually working in an R Markdown document which requires running

  rmarkdown::render(input = "./input.rmd", output_format = "html_document")
  

  Then R Markdown caching takes care of the rest and I can continue the normal document flow in other chunks. I don’t know of a way to start an rstudio session with the modified ulimit.

Building Packages

• While running R CMD check you may encounter checking PDF version of manual ... WARNING

  1. Determine why the latex build is failing. Open a terminal in the package folder and run

     R CMD Rd2pdf man/
     

     Look at the error messages and try to determine where the problem occurs.

  2. If you see the following:

     Converting Rd files to LaTeX 
     Creating pdf output from LaTeX ...
     Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
     Running 'texi2dvi' on 'Rd2.tex' failed.
     Messages:
     sh: 1: /usr/bin/texi2dvi: not found
     Output:
     
     Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
     Running 'texi2dvi' on 'Rd2.tex' failed.
     Messages:
     sh: 1: /usr/bin/texi2dvi: not found
     Output:
     
     Error in running tools::texi2pdf()
     

     then you need to install texi2dvi, which is located in the texinfo package. To install texinfo on Ubuntu use

     sudo apt-get install texinfo
     

     Note: do not install texinfo using TeX Live Manager. texi2dvi would not be placed into usr/bin/.

• While running R CMD check you may encounter no visible binding for global variable [object name]

  • Creating new objects inside your package using other package’s functions (data.table, dplyr, ggplot, etc) may produce this NOTE. See http://stackoverflow.com/a/12429344 for a nice discussion and solution. Use something like…

    #-----------------------------------------------------------------------------
    # To mitigate R CMD check producing NOTES
    # reference http://stackoverflow.com/a/12429344
    #-----------------------------------------------------------------------------
    globalVariables(c("object1", "object2"))
    

    outside of the package function at the bottom.

• The citation() function will produce a warning if the DESCRIPTION file does not include a date field. This can be ignored since submission to CRAN will automatically add the date field.