Biostrings dependency cause new warnings on CRAN packages (base function rgb not found)
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Entering edit mode
@jamesdalgleish-14561
Last seen 3 days ago
United States

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

I would post sessionInfo(), but this occurs only on the check debian servers. It doesn't happen on windows 10 or Ubuntu (zero problems there). I realize that one response will probably be to ask it of someone else associated with CRAN (perfectly valid to ask), but I'm wondering if the Biostrings maintainer has seen this issue before or might be aware of it:

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
Biostrings • 836 views
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1
Entering edit mode
@martin-morgan-1513
Last seen 6 weeks ago
United States

This is an error in Biostrings that has since been addressed https://github.com/Bioconductor/Biostrings/commit/8d5a240c03cce6d0503956d6d99cae4d255c796f and is available now via BiocManager::install("Biostrings") when using BiocManager::version('3.11").

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