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

[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 using r-project.org> wrote:

> 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
>
>
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>
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