##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:corral.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings corral_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/corral.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘corral/DESCRIPTION’ ... OK
* this is package ‘corral’ version ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘corral’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘ggthemes:::check_pal_n’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
biplot_corral: no visible binding for global variable ‘Name’
plot_embedding: no visible binding for global variable ‘Xdim’
plot_embedding: no visible binding for global variable ‘Ydim’
scal_var: no visible binding for global variable ‘PC_ind’
scal_var: no visible binding for global variable ‘sv’
scal_var: no visible binding for global variable ‘Batch’
Undefined global functions or variables:
  Batch Name PC_ind Xdim Ydim sv
* checking Rd files ... NOTE
prepare_Rd: corral_preproc.Rd:41-43: Dropping empty section \details
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘corral-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: corral_mat
> ### Title: corral: Correspondence analysis on a single matrix
> ### Aliases: corral_mat corral_sce corral print.corral
> 
> ### ** Examples
> 
> mat <- matrix(sample(0:10, 5000, replace=TRUE), ncol=50)
> result <- corral_mat(mat)
Warning in irlba::irlba(mat, nv = ncomp, ...) :
  You're computing too large a percentage of total singular values, use a standard svd instead.
> result <- corral_mat(mat, method = 'irl', ncomp = 5)
> 
> library(DuoClustering2018)
> sce <- sce_full_Zhengmix4eq()[1:100,1:100]
see ?DuoClustering2018 and browseVignettes('DuoClustering2018') for documentation
loading from cache
require(“SpatialExperiment”)
> result_1 <- corral_sce(sce)
> result_2 <- corral_sce(sce, method = 'svd')
> result_3 <- corral_sce(sce, method = 'irl', ncomp = 30, whichmat = 'logcounts')
Error in SummarizedExperiment::assay(inp, whichmat) : 
  'assay(<SpatialExperiment>, i="character", ...)' invalid subscript 'i'
'logcounts' not in names(assays(<SpatialExperiment>))
Calls: corral_sce -> <Anonymous> -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/corral.Rcheck/00check.log’
for details.