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-boun...@r-project.org on behalf of kchetni...@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 <kchetni...@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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