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

[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:
> 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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