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### Running command:
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###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scMAGeCK.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings scMAGeCK_1.9.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/scMAGeCK.Rcheck'
* using R version 4.2.0 Patched (2022-04-24 r82246 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.9.0'
* 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 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      134.74  12.31  147.17
pre_processRDS    94.03  12.19  106.24
selectPlot        18.97   1.17   20.16
scmageck_lr       17.79   1.35   19.14
scmageck-package  17.53   1.21   18.75
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/scMAGeCK.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/scMAGeCK_1.9.0.tar.gz && rm -rf scMAGeCK.buildbin-libdir && mkdir scMAGeCK.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scMAGeCK.buildbin-libdir scMAGeCK_1.9.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL scMAGeCK_1.9.0.zip && rm scMAGeCK_1.9.0.tar.gz scMAGeCK_1.9.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3050k  100 3050k    0     0  9847k      0 --:--:-- --:--:-- --:--:-- 9870k
only one architecture so ignoring '--merge-multiarch'
* 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
* MD5 sums
packaged installation of 'scMAGeCK' as scMAGeCK_1.9.0.zip
* DONE (scMAGeCK)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'scMAGeCK' successfully unpacked and MD5 sums checked