[Bioc-devel] installed, system.file(package="RCyjs") is "/Users/biocbuild/bbs-3.8-bioc/meat/RCyjs.buildbin-libdir/RCyjs"

My package RCyjs reads an html/js/css file when the constructor is called, then sends that file to the user?s browser.

The actual path to that file is calculated at global scope in RCyjs-class.R:

    cyjsBrowserFile <- system.file(package="RCyjs", "browserCode", "dist", "rcyjs.html?)

That file cannot be found at runtime.  Using

   options(error=recover)

I can trap that error, finding these two different interpretations of system.file(package=?RCyjs?):

    cyjsBrowserFile:
        "/Users/biocbuild/bbs-3.8-bioc/meat/RCyjs.buildbin-libdir/RCyjs/browserCode/dist/rcyjs.html?
     system.file(package="RCyjs")
       "/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RCyjs?

It appears that cyjsBrowserFile is assigned at the build system?s package construction time, not at the package load and use time.

Maybe this is new behavior?   Any suggestions on how to defer the calculation of system.file(package=?RCyjs?) till run time?

Thanks!

  - Paul

On Jun 29, 2018, at 4:11 PM, Martin Morgan <martin.morgan at roswellpark.org> wrote:



On 06/29/2018 06:44 PM, Paul Shannon wrote:

My package RCyjs reads an html/js/css file when the constructor is called, then sends that file to the user?s browser.
The actual path to that file is calculated at global scope in RCyjs-class.R:
   cyjsBrowserFile <- system.file(package="RCyjs", "browserCode", "dist", "rcyjs.html?)
That file cannot be found at runtime.  Using
  options(error=recover)
I can trap that error, finding these two different interpretations of system.file(package=?RCyjs?):
   cyjsBrowserFile:
       "/Users/biocbuild/bbs-3.8-bioc/meat/RCyjs.buildbin-libdir/RCyjs/browserCode/dist/rcyjs.html?
    system.file(package="RCyjs")
      "/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RCyjs?
It appears that cyjsBrowserFile is assigned at the build system?s package construction time, not at the package load and use time.
Maybe this is new behavior?   Any suggestions on how to defer the calculation of system.file(package=?RCyjs?) till run time?

you have the assignment at the 'top' level of your package R code

cyjsBrowserFile <- system.file(package="RCyjs", ...)

so that it gets evaluated when R source()s the file (approximately) to create the package. The correct paradigm would be to create the reference when the package is loaded, using .onLoad

cyjsBrowserFile <- NULL     # create symbol when built

.onLoad <- function(...) {
   cyjsBrowserFile <<- system.file(...  # assign symbol (using <<-) on load
}

Martin

Thanks!
 - Paul

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