##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cellscape.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cellscape_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/cellscape.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellscape/DESCRIPTION’ ... OK
* this is package ‘cellscape’ version ‘1.24.0’
* 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 ‘cellscape’ 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 R 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
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cellscape: no visible global function definition for ‘setNames’
cellscape: no visible global function definition for ‘melt’
cellscape: no visible global function definition for ‘na.omit’
cellscape: no visible global function definition for ‘combn’
cellscape: no visible binding for global variable ‘site’
cellscape: no visible binding for global variable ‘genotype’
cellscape: no visible binding for global variable ‘VAF’
cellscape: no visible global function definition for ‘n’
cellscape: no visible binding for global variable ‘n_gt’
cellscape: no visible binding for global variable ‘n’
cellscape: no visible binding for global variable ‘timepoint’
cellscape: no visible binding for global variable ‘single_cell_id’
getCNVHeatmapForEachSC: no visible binding for global variable
  ‘single_cell_id’
getCNVHeatmapForEachSC: no visible binding for global variable ‘px’
getCNVHeatmapForEachSC: no visible binding for global variable
  ‘px_width’
getCNVHeatmapForEachSC: no visible binding for global variable ‘chr’
getCNVHeatmapForEachSC: no visible binding for global variable
  ‘chrom_index’
getCNVHeatmapForEachSC: no visible binding for global variable
  ‘copy_number’
getCNVHeatmapForEachSC: no visible binding for global variable ‘sc_id’
getCNVHeatmapForEachSC: no visible binding for global variable
  ‘mode_cnv’
getCNVHeatmapForEachSC: no visible binding for global variable
  ‘cumsum_values’
getMutOrder: no visible global function definition for ‘dist’
getMutOrder: no visible global function definition for ‘hclust’
getMutOrder: no visible binding for global variable ‘site’
getMutOrder: no visible binding for global variable ‘VAF’
getMutOrder: no visible global function definition for ‘lm’
getMutOrder: no visible binding for global variable ‘na.omit’
getMutOrder: no visible global function definition for ‘coef’
getMutationsData: no visible binding for global variable
  ‘show_warnings’
getTargetedHeatmapForEachSC: no visible binding for global variable
  ‘single_cell_id’
getTargetedHeatmapForEachSC: no visible binding for global variable
  ‘chr’
getTargetedHeatmapForEachSC: no visible binding for global variable
  ‘coord’
Undefined global functions or variables:
  VAF chr chrom_index coef combn coord copy_number cumsum_values dist
  genotype hclust lm melt mode_cnv n n_gt na.omit px px_width sc_id
  setNames show_warnings single_cell_id site timepoint
Consider adding
  importFrom("stats", "coef", "dist", "hclust", "lm", "na.omit",
             "setNames")
  importFrom("utils", "combn")
to your NAMESPACE file.
* checking Rd files ... OK
* 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 ... WARNING
Duplicated \argument entries in documentation object 'dfs_tree':
  ‘chrom_bounds’ ‘ncols’ ‘chrom_bounds’ ‘cnv_data’ ‘chrom_bounds’
  ‘n_bp_per_pixel’ ‘mut_data’ ‘width’ ‘height’ ‘mutations’ ‘height’
  ‘width’ ‘clonal_prev’ ‘tree_edges’ ‘alpha’ ‘clonal_prev’ ‘tree_edges’
  ‘genotype_position’ ‘clone_colours’ ‘perturbations’ ‘mutations’
  ‘tree_edges’ ‘clonal_prev’ ‘clonal_prev’ ‘tree_edges’ ‘clone_colours’
  ‘mutations’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/cellscape.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cellscape
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘cellscape’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cellscape)