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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:systemPipeShiny.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings systemPipeShiny_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/systemPipeShiny.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘systemPipeShiny/DESCRIPTION’ ... OK
* this is package ‘systemPipeShiny’ version ‘1.2.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘systemPipeShiny’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
core_topServer : module : <anonymous>: warning in eval(code, env =
  .GlobalEnv): partial argument match of 'env' to 'envir'
vs_rnaseq_normalServer : module: warning in read.delim(targetspath,
  comment = "#"): partial argument match of 'comment' to 'comment.char'
.validateGuide: no visible binding for global variable ‘guide_ui’
.validateGuide: no visible binding for global variable ‘guide_content’
.validateGuide : <anonymous>: no visible binding for global variable
  ‘guide_content’
admin_infoServer : timeDiffString: no visible binding for global
  variable ‘time_start’
admin_infoServer : getCPU: no visible binding for global variable ‘V2’
appLoadingTime: no visible binding for global variable ‘time_start’
core_topServer : module : <anonymous>: no visible global function
  definition for ‘dev.off’
core_topServer : module : <anonymous>: no visible binding for '<<-'
  assignment to ‘.cur_plot’
core_topServer : module : <anonymous>: no visible global function
  definition for ‘dev.cur’
core_topServer : module : <anonymous>: no visible binding for global
  variable ‘.cur_plot’
core_topServer : module : <anonymous>: no visible global function
  definition for ‘recordPlot’
core_topServer : module : <anonymous>: no visible global function
  definition for ‘png’
core_topServer : module : <anonymous>: no visible binding for global
  variable ‘.rs_dir’
core_topServer : module : <anonymous>: no visible binding for global
  variable ‘.plot_num’
core_topServer : module : <anonymous>: no visible global function
  definition for ‘replayPlot’
core_topServer : module : <anonymous>: no visible binding for '<<-'
  assignment to ‘.plot_num’
findTabInfo: no visible binding for global variable ‘tab_info’
parseGuide: no visible binding for global variable ‘guide_ui’
parseGuide: no visible binding for global variable ‘guide_content’
removeSpsTab: no visible binding for global variable ‘type’
removeSpsTab: no visible binding for global variable ‘tab_file_name’
vs_rnaseq_degServer : module: no visible binding for global variable
  ‘trans_table’
vs_rnaseq_degServer : module: no visible binding for global variable
  ‘Sample’
vs_rnaseq_degServer : module: no visible binding for global variable
  ‘log2FoldChange’
vs_rnaseq_degServer : module: no visible binding for global variable
  ‘padj’
vs_rnaseq_degServer : module: no visible binding for global variable
  ‘cmp’
vs_rnaseq_degServer : module: no visible binding for global variable
  ‘direction’
vs_rnaseq_degServer : module: no visible binding for global variable
  ‘pass_filter’
vs_rnaseq_degServer : module : <anonymous>: no visible binding for
  global variable ‘pass_filter’
vs_rnaseq_degServer : module : <anonymous>: no visible binding for
  global variable ‘cmp’
vs_rnaseq_degServer : module: no visible binding for global variable
  ‘baseMean’
vs_rnaseq_degServer : module: no visible global function definition for
  ‘png’
vs_rnaseq_degServer : module: no visible global function definition for
  ‘dev.off’
vs_rnaseq_glmServer : module: no visible binding for global variable
  ‘dim1’
vs_rnaseq_glmServer : module: no visible binding for global variable
  ‘dim2’
vs_rnaseq_heatmapServer : module: no visible global function definition
  for ‘png’
vs_rnaseq_heatmapServer : module: no visible global function definition
  for ‘dev.off’
vs_rnaseq_mdsServer : module: no visible binding for global variable
  ‘spsRNA_trans’
vs_rnaseq_mdsServer : module: no visible binding for global variable
  ‘X1’
vs_rnaseq_mdsServer : module: no visible binding for global variable
  ‘X2’
vs_rnaseq_normalServer : module: no visible binding for '<<-'
  assignment to ‘spsRNA_trans’
vs_rnaseq_normalServer : module: no visible binding for global variable
  ‘spsRNA_trans’
vs_rnaseq_normalServer : module: no visible binding for '<<-'
  assignment to ‘spsDEG’
vs_rnaseq_pcaServer : module: no visible binding for global variable
  ‘spsRNA_trans’
vs_rnaseq_pcaServer : module: no visible binding for global variable
  ‘PC1’
vs_rnaseq_pcaServer : module: no visible binding for global variable
  ‘PC2’
vs_rnaseq_tsneServer : module: no visible binding for global variable
  ‘dim1’
vs_rnaseq_tsneServer : module: no visible binding for global variable
  ‘dim2’
wf_runServer : module : <anonymous> : <anonymous>: no visible global
  function definition for ‘png’
wf_runServer : module : <anonymous> : <anonymous>: no visible binding
  for global variable ‘.rs_dir’
wf_runServer : module : <anonymous> : <anonymous>: no visible binding
  for global variable ‘.plot_num’
wf_runServer : module : <anonymous> : <anonymous>: no visible global
  function definition for ‘dev.cur’
wf_runServer : module : <anonymous> : <anonymous>: no visible global
  function definition for ‘dev.new’
wf_runServer : module : <anonymous> : <anonymous>: no visible global
  function definition for ‘dev.control’
wf_runServer : module : <anonymous> : <anonymous>: no visible binding
  for '<<-' assignment to ‘.plot_num’
wf_runServer : module : <anonymous>: no visible binding for '<<-'
  assignment to ‘.rs_dir’
wf_runServer : module : <anonymous>: no visible binding for '<<-'
  assignment to ‘.plot_num’
wf_runServer : module : <anonymous>: no visible binding for '<<-'
  assignment to ‘.cur_plot’
Undefined global functions or variables:
  .cur_plot .plot_num .rs_dir PC1 PC2 Sample V2 X1 X2 baseMean cmp
  dev.control dev.cur dev.new dev.off dim1 dim2 direction guide_content
  guide_ui log2FoldChange padj pass_filter png recordPlot replayPlot
  spsRNA_trans tab_file_name tab_info time_start trans_table type
Consider adding
  importFrom("grDevices", "dev.control", "dev.cur", "dev.new", "dev.off",
             "png", "recordPlot", "replayPlot")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/systemPipeShiny.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL systemPipeShiny
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘systemPipeShiny’ ...
** 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 (systemPipeShiny)

R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(systemPipeShiny)
Loading required package: shiny
Loading required package: spsUtil
Loading required package: spsComps
Loading required package: drawer
> test_check('systemPipeShiny')
[SPS-INFO] 2021-10-15 00:36:43 Created SPS encryption method container
[SPS-INFO] 2021-10-15 00:36:43 Default SPS-db found and is working
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install(c("DOT", "R.utils", "callr", "fs", "networkD3", "openssl", "pushbar", "readr", "rhandsontable", "shinyTree", "systemPipeR", "systemPipeRdata", "zip"))
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install(c("DESeq2", "Rtsne", "SummarizedExperiment", "UpSetR", "ape", "ggtree", "glmpca", "grid", "pheatmap", "systemPipeR", "tidyr"))
Error in getOption("encoding") : reached elapsed time limit
This Font Awesome icon ('warning') does not exist:
* if providing a custom `html_dependency` these `name` checks can 
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  be deactivated with `verify_fa = FALSE`
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* if providing a custom `html_dependency` these `name` checks can 
  be deactivated with `verify_fa = FALSE`
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* if providing a custom `html_dependency` these `name` checks can 
  be deactivated with `verify_fa = FALSE`
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* if providing a custom `html_dependency` these `name` checks can 
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[SPS-INFO] 2021-10-15 00:36:50 App starts ...

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* if providing a custom `html_dependency` these `name` checks can 
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* if providing a custom `html_dependency` these `name` checks can 
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Loading required package: shinyTree
create a new R6
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (2)
• Skip on checks (1)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 76 ]
> identical(Sys.getenv("NOT_CRAN"), "true")
[1] FALSE
> 
> proc.time()
   user  system elapsed 
 29.763   2.880  33.916