[R-pkg-devel] 'S4Vectors' Error - Bioconductor dependencies

[Martin Morgan]

I guess this is in R-4-0-0 alpha or R-devel, and is due to a change in the methods package. This is because a serialized object in S4Vectors needs to be re-created, and is likely because package(s) need to be updated. If this is your own machine, then you could make sure that

  BiocManager::valid()

returns TRUE and / or update all packages to the most recent available

  BiocManager::install(ask = FALSE)

I'm not sure about CRAN, but am confident that it will eventually clear itself up... (not much comfort, I know...)

Martin Morgan

On 3/31/20, 11:42 AM, "R-package-devel on behalf of Kelsey Chetnik" <r-package-devel-bounces using r-project.org on behalf of kchetnik73 using gmail.com> wrote:

    Hi,
    
    I am getting a dependencies error and I'm not sure how to solve it. This is
    the error:
    
    * installing *source* package 'MetaClean' ...
    ** using staged installation
    ** R
    ** data
    *** moving datasets to lazyload DB
    ** inst
    ** byte-compile and prepare package for lazy loading
    Error: .onLoad failed in loadNamespace() for 'S4Vectors', details:
      call: validObject(.Object)
      error: invalid class "LLint" object: superclass "integer_OR_LLint"
    not defined in the environment of the object's class
    Execution halted
    ERROR: lazy loading failed for package 'MetaClean'
    * removing 'd:/RCompile/CRANincoming/R-devel/lib/MetaClean'
    
    
    I think the issue is related to one of the bioconductor dependencies that I
    have (XCMS) not installing properly. I was told that I need to include
    biocViews: in my DESCRIPTION file, which I did, but the problem still
    persists. Could someone please take a look at my DESCRIPTION to let me know
    if there is something wrong / missing:
    
    Package: MetaClean
    Title: MetaClean for the Automatic Detection of Low Quality Peaks in
    Untargeted Metabolomics Data
    Version: 0.1.0
    Author: Kelsey Chetnik
    Maintainer: Kelsey Chetnik <kchetnik73 using gmail.com>
    Description: This package utilizes 12 peak quality metrics and 9 diverse
    machine learning algorithms to build a classifier for the automatic
      assessment of peak integration quality of peaks from untargeted
    metabolomics analyses.
    Depends: R (>= 3.5.0),
             MLmetrics
    biocViews:
    Imports:
        xcms,
        scmamp,
        caret,
        reshape2,
        knitr,
        ggplot2,
        plotrix,
        tools,
        utils,
        klaR,
        fastAdaboost,
        rpart,
        randomForest,
        kernlab,
        BiocStyle,
        methods,
        S4Vectors
    License: GPL-3
    Encoding: UTF-8
    LazyData: true
    RoxygenNote: 7.1.0
    VignetteBuilder: knitr
    
    I'm stuck because I'm able to compile and run the package on my machine
    (macOS) and a local windows machine without any ERRORS, WARNINGS, or NOTES
    but I keep getting this error when submitting to CRAN.
    
    Could someone please help me with this?
    
    Thanks,
    Kelsey
    
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