##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:adverSCarial.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings adverSCarial_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/adverSCarial.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘adverSCarial/DESCRIPTION’ ... OK
* this is package ‘adverSCarial’ version ‘1.0.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘adverSCarial’ 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
.advModificationsFunction: no visible global function definition for
  ‘is’
.advModificationsFunction : <anonymous>: no visible global function
  definition for ‘is’
.advModificationsNotFunction: no visible global function definition for
  ‘is’
.advModificationsNotFunction: no visible global function definition for
  ‘counts’
.advModificationsNotFunction : <anonymous>: no visible global function
  definition for ‘is’
.randWalkGetSeed: no visible global function definition for
  ‘SingleCellExperiment’
.randWalkGetSeed: no visible global function definition for ‘is’
.randWalkTryNewVector: no visible global function definition for
  ‘SingleCellExperiment’
.randWalkTryNewVector: no visible global function definition for ‘is’
MClassifier: no visible global function definition for ‘is’
MClassifier: no visible global function definition for ‘counts’
advChar: no visible global function definition for ‘new’
advGridMinChange: no visible global function definition for ‘is’
advGridMinChange: no visible global function definition for ‘counts’
advGridMinChange: no visible global function definition for
  ‘SingleCellExperiment’
advList: no visible global function definition for ‘new’
advMaxChange: no visible global function definition for ‘is’
advMaxChange: no visible global function definition for ‘counts’
advMaxChange: no visible global function definition for ‘new’
advModifications: no visible global function definition for ‘is’
advModifications: no visible global function definition for ‘counts’
advModifications: no visible global function definition for
  ‘SingleCellExperiment’
advRandWalkMinChange: no visible global function definition for ‘is’
advRandWalkMinChange: no visible global function definition for
  ‘counts’
advSingleGene: no visible global function definition for ‘is’
advSingleGene: no visible global function definition for ‘counts’
advSingleGene: no visible binding for '<<-' assignment to
  ‘lastResLength’
advSingleGene : <anonymous>: no visible binding for global variable
  ‘lastResLength’
advSingleGene : <anonymous>: no visible binding for '<<-' assignment to
  ‘lastResLength’
advSingleGene: no visible global function definition for ‘new’
matrixFromSCE: no visible global function definition for ‘is’
matrixFromSCE: no visible global function definition for ‘colData’
maxChangeOverview: no visible global function definition for ‘is’
maxChangeOverview: no visible global function definition for ‘counts’
predictWithNewValue: no visible global function definition for ‘is’
sceConvertToHGNC: no visible global function definition for ‘is’
sceConvertToHGNC: no visible global function definition for
  ‘SingleCellExperiment’
sceConvertToHGNC: no visible global function definition for ‘colData’
singleGeneOverview: no visible global function definition for ‘is’
singleGeneOverview: no visible global function definition for ‘counts’
Undefined global functions or variables:
  SingleCellExperiment colData counts is lastResLength new
Consider adding
  importFrom("methods", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
MClassifier      25.816  2.778  32.644
advChar           9.392  1.390  10.955
matrixFromSCE     8.878  1.108  10.555
sceConvertToHGNC  8.695  0.985  10.178
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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-3.18-bioc/meat/adverSCarial.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘adverSCarial’ ...
** 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 (adverSCarial)

R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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.

> BiocGenerics:::testPackage("adverSCarial")
Converting exprs object to a DelayedArray object
Running combination: 1 on 3
Running combination: 2 on 3
Running combination: 3 on 3
result length: 3
Converting exprs object to a DelayedArray object
Running first batch to determine walk seed: 1 on 3
Running first batch to determine walk seed: 2 on 3
Running first batch to determine walk seed: 3 on 3
No modified type, try with a higher firstBatch argument
Split number: 1/100
Split number: 2/100
Split number: 4/100
Split time: 0.000159978866577148
Split number: 8/100
Split time: 0.000220060348510742
Split number: 16/100
Split time: 0.000112056732177734
Split number: 32/100
Split time: 9.89437103271484e-05
Split number: 64/100
Split time: 9.89437103271484e-05
Split number: 100/100
Split time: 0.000136852264404297
result length: 3
result length: 3
Split number: 1/100
Split number: 2/100
Split number: 4/100
Split time: 0.000241994857788086
Split number: 8/100
Split time: 0.000149965286254883
Split number: 16/100
Split time: 0.000154018402099609
Split number: 32/100
Split time: 0.000257015228271484
Split number: 64/100
Split time: 0.000182867050170898
Split number: 100/100
Split time: 0.000188112258911133
Split number: 1/100
Split number: 2/100
Split number: 4/100
Split time: 0.000235080718994141
Split number: 8/100
Split time: 0.00014805793762207
Split number: 16/100
Split time: 0.000147104263305664
Split number: 32/100
Split time: 0.00014495849609375
Split number: 64/100
Split time: 0.000154972076416016
Split number: 100/100
Split time: 0.000207901000976562
Split number: 1/100
Split number: 2/100
Split number: 4/100
Split time: 0.000251054763793945
Split number: 8/100
Split time: 0.000158071517944336
Split number: 16/100
Split time: 0.00018000602722168
Split number: 32/100
Split time: 0.000169992446899414
Split number: 64/100
Split time: 0.000236988067626953
Split number: 100/100
Split time: 0.000189065933227539
Split number: 1/100
Split number: 2/100
Split number: 4/100
Split time: 0.000215053558349609
Split number: 8/100
Split time: 0.000116109848022461
Split number: 16/100
Split time: 0.000169038772583008
Split number: 32/100
Split time: 0.000188827514648438
Split number: 64/100
Split time: 0.000180959701538086
Split number: 100/100
Split time: 0.000208139419555664


RUNIT TEST PROTOCOL -- Sun Mar  3 18:52:36 2024 
*********************************************** 
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
adverSCarial RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  5.389   0.366   5.797