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[R-pkg-devel] Issue with Biostrings-- can't find the base rgb function on r-devel

3 messages · Dalgleish, James (NIH/NCI) [V], Hugh Parsonage, Uwe Ligges

Original
Dalgleish, James (NIH/NCI) [V]
# 
Question:

NIPTeR is experiencing new warnings when loading Biostrings. I have the exact same warnings with my package, CNVScope.

It seems a little odd that the base function rgb cannot be found. What can cause a base package to not be found? I can't replicate this issue on either of my linux or windows machines or on winbuilder.

I have already asked the Bioconductor community, but didn't get a response (https://support.bioconductor.org/p/126878/).

Thanks,
James Dalgleish
Maintainer, CNVScope
NIH/NCI
Source: https://cran.r-project.org/web/checks/check_results_NIPTeR.html
Check Details
Version: 1.0.2
Check: whether the package can be unloaded cleanly
Result: WARN
    Error: package or namespace load failed for 'NIPTeR':
     .onLoad failed in loadNamespace() for 'Biostrings', details:
     call: rgb(1, 1, 1)
     error: could not find function "rgb"
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.2
Check: whether the namespace can be loaded with stated dependencies
Result: WARN
    Error: .onLoad failed in loadNamespace() for 'Biostrings', details:
     call: rgb(1, 1, 1)
     error: could not find function "rgb"
    Execution halted

    A namespace must be able to be loaded with just the base namespace
    loaded: otherwise if the namespace gets loaded by a saved object, the
    session will be unable to start.

    Probably some imports need to be declared in the NAMESPACE file.
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.2
Check: dependencies in R code
Result: NOTE
    Error: package or namespace load failed for 'NIPTeR':
     .onLoad failed in loadNamespace() for 'Biostrings', details:
     call: rgb(1, 1, 1)
     error: could not find function "rgb"
    Call sequence:
    6: stop(msg, call. = FALSE, domain = NA)
    5: value[[3L]](cond)
    4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    3: tryCatchList(expr, classes, parentenv, handlers)
    2: tryCatch({
     attr(package, "LibPath") <- which.lib.loc
     ns <- loadNamespace(package, lib.loc)
     env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
     }, error = function(e) {
     P <- if (!is.null(cc <- conditionCall(e)))
     paste(" in", deparse(cc)[1L])
     else ""
     msg <- gettextf("package or namespace load failed for %s%s:\n %s",
     sQuote(package), P, conditionMessage(e))
     if (logical.return)
     message(paste("Error:", msg), domain = NA)
     else stop(msg, call. = FALSE, domain = NA)
     })
    1: library(package, lib.loc = lib.loc, character.only = T
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.2
Check: R code for possible problems
Result: NOTE
    Error: .onLoad failed in loadNamespace() for 'Biostrings', details:
     call: rgb(1, 1, 1)
     error: could not find function "rgb"
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Hugh Parsonage
# 
rgb is from package grDevices not package base.

On Thu, 5 Dec 2019 at 2:48 pm, Dalgleish, James (NIH/NCI) [V] via
R-package-devel <r-package-devel at r-project.org> wrote:

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Uwe Ligges
    

    

      
      #
    

  


  

      
That was a bug in Biostrings that has been fixed in the meantime.

Best,
Uwe Ligges

        
On 05.12.2019 05:19, Hugh Parsonage wrote: