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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_1.3.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/adverSCarial.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-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 Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘adverSCarial/DESCRIPTION’ ... OK
* this is package ‘adverSCarial’ version ‘1.3.0’
* 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 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’
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 ... NOTE
checkRd: (-1) advGridMinChange.Rd:34-37: Lost braces
    34 | classifier = function(expr, clusters, target){
       |                                              ^
checkRd: (-1) advMaxChange.Rd:38-41: Lost braces
    38 | classifier = function(expr, clusters, target){
       |                                              ^
checkRd: (-1) advRandWalkMinChange.Rd:36-39: Lost braces
    36 | classifier = function(expr, clusters, target){
       |                                              ^
checkRd: (-1) advSingleGene.Rd:42-45: Lost braces
    42 | classifier = function(expr, clusters, target){
       |                                              ^
checkRd: (-1) maxChangeOverview.Rd:35-38: Lost braces
    35 | classifier = function(expr, clusters, target){
       |                                              ^
checkRd: (-1) predictWithNewValue.Rd:35-38: Lost braces
    35 | 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 ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'advGridMinChange.Rd':
advGridMinChange
  Code: function(exprs, clusters, target, classifier, genes,
                 modifications = list(c("perc1"), c("perc99")),
                 returnFirstFound = FALSE, argForClassif =
                 "data.frame", argForModif = "data.frame", verbose =
                 FALSE, iamsure = FALSE)
  Docs: function(exprs, clusters, target, classifier, genes,
                 modifications = list(c("perc1"), c("perc99")),
                 returnFirstFound = FALSE, argForClassif =
                 "DelayedMatrix", argForModif = "DelayedMatrix",
                 verbose = FALSE, iamsure = FALSE)
  Mismatches in argument default values:
    Name: 'argForClassif' Code: "data.frame" Docs: "DelayedMatrix"
    Name: 'argForModif' Code: "data.frame" Docs: "DelayedMatrix"

Codoc mismatches from Rd file 'advMaxChange.Rd':
advMaxChange
  Code: function(exprs, clusters, target, classifier, exclGenes = c(),
                 genes = c(), advMethod = "perc99", advFixedValue = 3,
                 advFct = NULL, maxSplitSize = 1, argForClassif =
                 "data.frame", argForModif = "data.frame", verbose =
                 FALSE)
  Docs: function(exprs, clusters, target, classifier, exclGenes = c(),
                 genes = c(), advMethod = "perc99", advFixedValue = 3,
                 advFct = NULL, maxSplitSize = 1, argForClassif =
                 "DelayedMatrix", argForModif = "data.frame", verbose =
                 FALSE)
  Mismatches in argument default values:
    Name: 'argForClassif' Code: "data.frame" Docs: "DelayedMatrix"

Codoc mismatches from Rd file 'advRandWalkMinChange.Rd':
advRandWalkMinChange
  Code: function(exprs, clusters, target, classifier, genes,
                 modifications = list(c("perc1"), c("perc99")),
                 firstBatch = 100, walkLength = 100, stepChangeRatio =
                 0.2, whileMaxCount = 10000, changeType = "any",
                 argForClassif = "data.frame", argForModif =
                 "data.frame", verbose = FALSE)
  Docs: function(exprs, clusters, target, classifier, genes,
                 modifications = list(c("perc1"), c("perc99")),
                 firstBatch = 100, walkLength = 100, stepChangeRatio =
                 0.2, whileMaxCount = 10000, changeType = "any",
                 argForClassif = "DelayedMatrix", argForModif =
                 "DelayedMatrix", verbose = FALSE)
  Mismatches in argument default values:
    Name: 'argForClassif' Code: "data.frame" Docs: "DelayedMatrix"
    Name: 'argForModif' Code: "data.frame" Docs: "DelayedMatrix"

Codoc mismatches from Rd file 'advSingleGene.Rd':
advSingleGene
  Code: function(exprs, clusters, target, classifier, exclGenes = c(),
                 genes = c(), advMethod = "perc99", advFixedValue = 3,
                 advFct = NULL, firstDichot = 100, maxSplitSize = 1,
                 returnFirstFound = FALSE, changeType = "any",
                 argForClassif = "data.frame", argForModif =
                 "data.frame", verbose = FALSE)
  Docs: function(exprs, clusters, target, classifier, exclGenes = c(),
                 genes = c(), advMethod = "perc99", advFixedValue = 3,
                 advFct = NULL, firstDichot = 100, maxSplitSize = 1,
                 returnFirstFound = FALSE, changeType = "any",
                 argForClassif = "DelayedMatrix", argForModif =
                 "data.frame", verbose = FALSE)
  Mismatches in argument default values:
    Name: 'argForClassif' Code: "data.frame" Docs: "DelayedMatrix"

Codoc mismatches from Rd file 'maxChangeOverview.Rd':
maxChangeOverview
  Code: function(exprs, clusters, classifier, exclGenes = c(), genes =
                 c(), modifications = list(c("perc1"), c("perc99")),
                 advMethod = "perc99", advFixedValue = 3, advFct =
                 NULL, maxSplitSize = 100, argForClassif =
                 "data.frame", argForModif = "data.frame", verbose =
                 FALSE)
  Docs: function(exprs, clusters, classifier, exclGenes = c(), genes =
                 c(), modifications = list(c("perc1"), c("perc99")),
                 advMethod = "perc99", advFixedValue = 3, advFct =
                 NULL, maxSplitSize = 100, argForClassif =
                 "DelayedMatrix", argForModif = "data.frame", verbose =
                 FALSE)
  Mismatches in argument default values:
    Name: 'argForClassif' Code: "data.frame" Docs: "DelayedMatrix"

Codoc mismatches from Rd file 'singleGeneOverview.Rd':
singleGeneOverview
  Code: function(exprs, clusters, classifier, exclGenes = c(), genes =
                 c(), modifications = list(c("perc1"), c("perc99")),
                 advMethod = "perc99", advFixedValue = 3, advFct =
                 NULL, firstDichot = 100, maxSplitSize = 100,
                 changeType = "any", argForClassif = "data.frame",
                 argForModif = "data.frame", verbose = FALSE)
  Docs: function(exprs, clusters, classifier, exclGenes = c(), genes =
                 c(), modifications = list(c("perc1"), c("perc99")),
                 advMethod = "perc99", advFixedValue = 3, advFct =
                 NULL, firstDichot = 100, maxSplitSize = 100,
                 changeType = "any", argForClassif = "DelayedMatrix",
                 argForModif = "data.frame", verbose = FALSE)
  Mismatches in argument default values:
    Name: 'argForClassif' Code: "data.frame" Docs: "DelayedMatrix"

* 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      39.279  4.658  54.871
advChar          20.782  2.521  24.771
sceConvertToHGNC 14.233  1.248  17.454
matrixFromSCE    12.336  1.381  15.655
* 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: 1 WARNING, 3 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-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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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
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
Split number: 1/100
Split number: 2/100
Split number: 4/100
Split time: 0.000484943389892578
Split number: 8/100
Split time: 0.00039219856262207
Split number: 16/100
Split time: 0.000395059585571289
Split number: 32/100
Split time: 0.0004119873046875
Split number: 64/100
Split time: 0.000444889068603516
Split number: 100/100
Split time: 0.000425100326538086
result length: 3
result length: 3
Split number: 1/100
Split number: 2/100
Split number: 4/100
Split time: 0.000406026840209961
Split number: 8/100
Split time: 0.000322103500366211
Split number: 16/100
Split time: 0.000635147094726562
Split number: 32/100
Split time: 0.000344038009643555
Split number: 64/100
Split time: 0.000348091125488281
Split number: 100/100
Split time: 0.000463962554931641
Split number: 1/100
Split number: 2/100
Split number: 4/100
Split time: 0.000391960144042969
Split number: 8/100
Split time: 0.000315189361572266
Split number: 16/100
Split time: 0.000345945358276367
Split number: 32/100
Split time: 0.000329971313476562
Split number: 64/100
Split time: 0.000340938568115234
Split number: 100/100
Split time: 0.000353097915649414
Split number: 1/100
Split number: 2/100
Split number: 4/100
Split time: 0.000396966934204102
Split number: 8/100
Split time: 0.000317096710205078
Split number: 16/100
Split time: 0.000323057174682617
Split number: 32/100
Split time: 0.000345945358276367
Split number: 64/100
Split time: 0.000341176986694336
Split number: 100/100
Split time: 0.000374078750610352
Split number: 1/100
Split number: 2/100
Split number: 4/100
Split time: 0.000404119491577148
Split number: 8/100
Split time: 0.000364780426025391
Split number: 16/100
Split time: 0.000325918197631836
Split number: 32/100
Split time: 0.000320911407470703
Split number: 64/100
Split time: 0.000360012054443359
Split number: 100/100
Split time: 0.000372171401977539


RUNIT TEST PROTOCOL -- Wed May  1 23:58:24 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 
 10.295   0.602  11.723