##############################################################################
##############################################################################
###
### 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/adverSCarial.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘adverSCarial/DESCRIPTION’ ... OK
* this is package ‘adverSCarial’ version ‘1.4.0’
* 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:
  vignettes/.RData
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 ‘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 code 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’
getDistantCouples: no visible global function definition for ‘combn’
getSignGenes : <anonymous>: no visible global function definition for
  ‘wilcox.test’
getSignGenes : <anonymous>: no visible global function definition for
  ‘t.test’
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 combn counts is lastResLength new t.test
  wilcox.test
Consider adding
  importFrom("methods", "is", "new")
  importFrom("stats", "t.test", "wilcox.test")
  importFrom("utils", "combn")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) advCGD.Rd:31-34: Lost braces
    31 | classifier = function(expr, clusters, target){
       |                                              ^
checkRd: (-1) advGridMinChange.Rd:34-37: Lost braces
    34 | classifier = function(expr, clusters, target){
       |                                              ^
checkRd: (-1) advMaxChange.Rd:39-42: Lost braces
    39 | classifier = function(expr, clusters, target){
       |                                              ^
checkRd: (-1) advRandWalkMinChange.Rd:36-39: Lost braces
    36 | classifier = function(expr, clusters, target){
       |                                              ^
checkRd: (-1) advSingleGene.Rd:43-46: Lost braces
    43 | classifier = function(expr, clusters, target){
       |                                              ^
checkRd: (-1) maxChangeOverview.Rd:35-38: Lost braces
    35 | classifier = function(expr, clusters, target){
       |                                              ^
checkRd: (-1) predictWithNewValue.Rd:36-39: Lost braces
    36 | classifier = function(expr, clusters, target){
       |                                              ^
checkRd: (-1) singleGeneOverview.Rd:37-40: Lost braces
    37 | classifier = function(expr, clusters, target){
       |                                              ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘advTraining’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'advMaxChange.Rd'
  ‘slot’

Undocumented arguments in Rd file 'advModifications.Rd'
  ‘slot’

Undocumented arguments in Rd file 'advSingleGene.Rd'
  ‘slot’

Undocumented arguments in Rd file 'predictWithNewValue.Rd'
  ‘slot’

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 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      22.180  1.751  26.439
matrixFromSCE     8.792  1.075  11.581
sceConvertToHGNC  8.647  0.952  11.367
advChar           5.884  0.880   6.835
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/adverSCarial.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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")
Running combination: 1 on 3
Running combination: 2 on 3
Running combination: 3 on 3
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
result length: 3
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
predictWithNewValue data.frame data.frame
Split number: 1/100
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: b
Split number: 2/100
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: b
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: b
Split number: 4/100
Split time: 0.000121831893920898
Split number: 8/100
Split time: 0.00013279914855957
Split number: 16/100
Split time: 0.000116109848022461
Split number: 32/100
Split time: 0.000114917755126953
Split number: 64/100
Split time: 0.000115871429443359
Split number: 100/100
Split time: 0.0001220703125
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
result length: 3
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
result length: 3
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
result length: 3
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
result length: 3
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
Split number: 1/100
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: b
Split number: 2/100
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: b
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: b
Split number: 4/100
Split time: 0.000127077102661133
Split number: 8/100
Split time: 0.000113010406494141
Split number: 16/100
Split time: 0.000123977661132812
Split number: 32/100
Split time: 0.000113964080810547
Split number: 64/100
Split time: 0.000107049942016602
Split number: 100/100
Split time: 0.000115871429443359
predictWithNewValue data.frame data.frame
Split number: 1/100
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: t
Split number: 2/100
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: t
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: t
Split number: 4/100
Split time: 0.000100851058959961
Split number: 8/100
Split time: 0.000108003616333008
Split number: 16/100
Split time: 0.000102996826171875
Split number: 32/100
Split time: 0.000105857849121094
Split number: 64/100
Split time: 0.000106096267700195
Split number: 100/100
Split time: 0.000113964080810547
predictWithNewValue data.frame data.frame
Split number: 1/100
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: b
Split number: 2/100
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: b
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: b
Split number: 4/100
Split time: 0.000106096267700195
Split number: 8/100
Split time: 0.000100135803222656
Split number: 16/100
Split time: 0.000108003616333008
Split number: 32/100
Split time: 9.79900360107422e-05
Split number: 64/100
Split time: 9.918212890625e-05
Split number: 100/100
Split time: 0.000103950500488281
predictWithNewValue data.frame data.frame
Split number: 1/100
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: t
Split number: 2/100
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: t
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: t
Split number: 4/100
Split time: 0.00010991096496582
Split number: 8/100
Split time: 0.000113964080810547
Split number: 16/100
Split time: 0.000104904174804688
Split number: 32/100
Split time: 0.000100135803222656
Split number: 64/100
Split time: 0.000101804733276367
Split number: 100/100
Split time: 0.000107049942016602


RUNIT TEST PROTOCOL -- Fri Jan 31 10:35:50 2025 
*********************************************** 
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 
  5.636   0.282   5.908