##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:adverSCarial.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings adverSCarial_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/adverSCarial.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘adverSCarial/DESCRIPTION’ ... OK
* this is package ‘adverSCarial’ version ‘1.6.0’
* 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 loading without being on the library search path ... 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      27.977  1.721  35.629
advChar          12.251  0.578  12.864
matrixFromSCE    10.056  1.278  16.441
sceConvertToHGNC  9.777  0.969  17.076
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/adverSCarial.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL adverSCarial
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘adverSCarial’ ...
** this is package ‘adverSCarial’ version ‘1.6.0’
** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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: 0.000421524047851562
Split number: 8/100
Split time: 0.000185728073120117
Split number: 16/100
Split time: 0.000166416168212891
Split number: 32/100
Split time: 0.000170707702636719
Split number: 64/100
Split time: 0.000174045562744141
Split number: 100/100
Split time: 0.000195503234863281
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: 0.000183343887329102
Split number: 8/100
Split time: 0.000165224075317383
Split number: 16/100
Split time: 0.000160455703735352
Split number: 32/100
Split time: 0.000167608261108398
Split number: 64/100
Split time: 0.00018763542175293
Split number: 100/100
Split time: 0.000173807144165039
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: 0.000205755233764648
Split number: 8/100
Split time: 0.000159978866577148
Split number: 16/100
Split time: 0.000158309936523438
Split number: 32/100
Split time: 0.000163078308105469
Split number: 64/100
Split time: 0.000188350677490234
Split number: 100/100
Split time: 0.000171899795532227
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: 0.000187397003173828
Split number: 8/100
Split time: 0.000160694122314453
Split number: 16/100
Split time: 0.000163793563842773
Split number: 32/100
Split time: 0.000159502029418945
Split number: 64/100
Split time: 0.000174522399902344
Split number: 100/100
Split time: 0.00017857551574707
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: 0.000186443328857422
Split number: 8/100
Split time: 0.000161409378051758
Split number: 16/100
Split time: 0.000156879425048828
Split number: 32/100
Split time: 0.0001983642578125
Split number: 64/100
Split time: 0.000165700912475586
Split number: 100/100
Split time: 0.000173091888427734


RUNIT TEST PROTOCOL -- Tue Oct  7 06:16:42 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 
  6.827   0.212   7.039