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### Running command:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:scMAGeCK.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings scMAGeCK_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/scMAGeCK.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scMAGeCK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scMAGeCK’ version ‘1.6.0’
* 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 ‘scMAGeCK’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
License components which are templates and need '+ file LICENSE':
  BSD_2_clause
* 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 ... WARNING
'::' or ':::' import not declared from: ‘purrr’
'library' or 'require' call to ‘utils’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot_gi_genes: warning in position_jitter(w = 0.1, h = 0): partial
  argument match of 'w' to 'width'
plot_gi_genes: warning in position_jitter(w = 0.1, h = 0): partial
  argument match of 'h' to 'height'
plot_single_genes: warning in position_jitter(w = 0.1, h = 0): partial
  argument match of 'w' to 'width'
plot_single_genes: warning in position_jitter(w = 0.1, h = 0): partial
  argument match of 'h' to 'height'
KO_eff: no visible global function definition for ‘capFirst’
KO_eff: no visible global function definition for ‘adjust’
KO_eff: no visible binding for global variable ‘padj’
KO_eff: no visible binding for global variable ‘lrsc’
KO_eff: no visible binding for global variable ‘logpadj’
dis_grna: no visible global function definition for ‘read.delim’
dis_grna: no visible binding for global variable ‘cell’
dis_grna: no visible binding for global variable ‘number_gRNA’
dis_grna: no visible binding for global variable ‘ncell’
featurePlot: no visible binding for global variable ‘plot.type’
featurePlot: no visible binding for global variable ‘cell’
featurePlot: no visible binding for global variable ‘number_gRNA’
featurePlot: no visible binding for global variable ‘ncell’
featurePlot: no visible binding for global variable ‘seurat_clusters’
featurePlot: no visible global function definition for ‘wilcox.test’
featurePlot: no visible binding for global variable ‘label’
featurePlot: no visible binding for global variable ‘genes’
featurePlot: no visible global function definition for
  ‘colorRampPalette’
featurePlot: no visible binding for global variable ‘UMAP_1’
featurePlot: no visible binding for global variable ‘UMAP_2’
featurePlot: no visible binding for global variable ‘level’
get_rank_tables: no visible global function definition for
  ‘getoriginalgseascore’
get_sc_signature: no visible binding for global variable ‘gs_c2_exps’
getsigmat: no visible global function definition for ‘capitalize’
plot_gi_genes: no visible binding for global variable ‘Type’
plot_gi_genes: no visible binding for global variable ‘Expression’
plot_single_genes: no visible binding for global variable ‘targetobj’
plot_single_genes: no visible binding for global variable ‘Type’
plot_single_genes: no visible binding for global variable ‘Expression’
pre_processRDS: no visible binding for global variable ‘cell’
scmageck_rra: no visible global function definition for ‘read.delim’
scmageck_rra: no visible global function definition for ‘capitalize’
sel_lr: no visible global function definition for ‘setNames’
sel_lr: no visible binding for global variable ‘sgRNA’
sel_lr: no visible binding for global variable ‘FDR’
sel_lr: no visible binding for global variable ‘padj’
sel_lr: no visible binding for global variable ‘genes’
sel_rra: no visible global function definition for ‘read.delim’
sel_rra: no visible binding for global variable ‘p.high’
sel_rra: no visible binding for global variable ‘p.low’
sel_rra: no visible binding for global variable ‘nscore’
sel_rra: no visible binding for global variable ‘pscore’
sel_rra: no visible binding for global variable ‘index’
sel_rra: no visible binding for global variable ‘markers’
sel_rra: no visible binding for global variable ‘FDR’
selectPlot: no visible binding for global variable ‘select.type’
selectPlot: no visible global function definition for ‘setNames’
selectPlot: no visible binding for global variable ‘sgRNA’
selectPlot: no visible binding for global variable ‘FDR’
selectPlot: no visible binding for global variable ‘padj’
selectPlot: no visible binding for global variable ‘genes’
selectPlot: no visible binding for global variable ‘p.high’
selectPlot: no visible binding for global variable ‘p.low’
selectPlot: no visible binding for global variable ‘sel_score1’
selectPlot: no visible binding for global variable ‘sel_score2’
selectPlot: no visible binding for global variable ‘index’
selectPlot: no visible binding for global variable ‘markers’
violin_plot: no visible global function definition for ‘read.delim’
violin_plot: no visible binding for global variable ‘seurat_clusters’
violin_plot: no visible global function definition for ‘wilcox.test’
violin_plot: no visible binding for global variable ‘label’
violin_plot: no visible binding for global variable ‘genes’
Undefined global functions or variables:
  Expression FDR Type UMAP_1 UMAP_2 adjust capFirst capitalize cell
  colorRampPalette genes getoriginalgseascore gs_c2_exps index label
  level logpadj lrsc markers ncell nscore number_gRNA p.high p.low padj
  plot.type pscore read.delim sel_score1 sel_score2 select.type
  setNames seurat_clusters sgRNA targetobj wilcox.test
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "setNames", "wilcox.test")
  importFrom("utils", "read.delim")
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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
featurePlot      107.630  0.740 108.370
pre_processRDS    87.432  0.196  87.630
selectPlot        19.559  0.056  19.615
scmageck-package  19.083  0.160  19.244
scmageck_lr       18.438  0.112  18.550
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/scMAGeCK.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL scMAGeCK
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘scMAGeCK’ ...
** 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 (scMAGeCK)