##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cbpManager.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings cbpManager_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/cbpManager.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cbpManager/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cbpManager' version '1.3.2'
* 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 whether package 'cbpManager' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See 'D:/biocbuild/bbs-3.15-bioc/meat/cbpManager.Rcheck/00install.out' for details.
* 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 ... WARNING
'::' or ':::' import not declared from: 'rlang'
Namespace in Imports field not imported from: 'markdown'
  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
cbpManager: no visible binding for '<<-' assignment to
  'cbpManager.options'
generateUIwidgets: no visible global function definition for
  'selectizeInput'
shinyAppServer: no visible binding for '<<-' assignment to 'study_dir'
shinyAppServer: no visible binding for '<<-' assignment to 'logDir'
shinyAppServer: no visible binding for '<<-' assignment to 'oncotree'
shinyAppServer: no visible binding for '<<-' assignment to
  'tumor_tissue_site'
shinyAppServer: no visible binding for '<<-' assignment to
  'cancer_type'
shinyAppServer: no visible binding for '<<-' assignment to
  'oncotree_code'
shinyAppServer: no visible binding for '<<-' assignment to
  'cancer_type_detailed'
Undefined global functions or variables:
  selectizeInput
* 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
Undocumented arguments in documentation object 'generateUIwidgets'
  'sampleIDs'

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 line endings in shell scripts ... 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 WARNINGs, 2 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/cbpManager.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL cbpManager
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'cbpManager' ...
** using non-staged installation via StagedInstall field
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cbpManager'
    finding HTML links ... done
    IsDate                                  html  
    ValidationDependencies                  html  
    addColumn_Server                        html  
    addColumn_UI                            html  
    addRowRc_Server                         html  
    addRowRc_UI                             html  
    addRow_Server                           html  
    addRow_UI                               html  
    cBioPortalToDataFrame                   html  
    cbpManager-pkg                          html  
    cbpManager                              html  
    check_input_dates                       html  
    convertDataFrame                        html  
    create_name                             html  
    deleteColumn_Server                     html  
    deleteColumn_UI                         html  
    deleteRowRc_Server                      html  
    deleteRowRc_UI                          html  
    deleteRow_Server                        html  
    deleteRow_UI                            html  
    editRowRc_Server                        html  
    editRowRc_UI                            html  
    editRow_Server                          html  
    editRow_UI                              html  
    fncols                                  html  
    generateOncotreeUIwidgets               html  
    generateUIwidgets                       html  
    getSampleIDs                            html  
    importPatientData                       html  
    saveResource_Server                     html  
    saveResource_UI                         html  
    saveTimeline_Server                     html  
    saveTimeline_UI                         html  
    setupConda_cbpManager                   html  
    shinyAppServer                          html  
    shinyAppUI                              html  
    updateOncotreeUIwidgets                 html  
    validateResourceDefinition              html  
    validateResourcePatient                 html  
    validateResourceSample                  html  
    validateResourceStudy                   html  
    writeLogfile                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cbpManager)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'iCheck' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'tripr' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(cbpManager)
Loading required package: shiny
Loading required package: shinydashboard

Attaching package: 'shinydashboard'

The following object is masked from 'package:graphics':

    box

> 
> test_check("cbpManager")
##---------------------------------------------------------------------------##
## Launching cbpManager
##---------------------------------------------------------------------------##
##---------------------------------------------------------------------------##
## Launching cbpManager
##---------------------------------------------------------------------------##
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 19 ]

== Skipped tests ===============================================================
* On CRAN (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 19 ]
> 
> proc.time()
   user  system elapsed 
   2.10    0.26    2.35