##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:adverSCarial.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings adverSCarial_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/adverSCarial.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 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’
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      20.197  1.284  22.056
matrixFromSCE     7.319  0.673   8.490
sceConvertToHGNC  7.295  0.693   8.454
advChar           7.184  0.336   7.520
* 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 ...
  ‘vign01_adverSCarial.Rmd’ using ‘UTF-8’... OK
  ‘vign02_overView_analysis.Rmd’ using ‘UTF-8’... OK
  ‘vign03_adapt_classifier.Rmd’ using ‘UTF-8’... OK
  ‘vign04_advRandWalkMinChange.Rmd’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/adverSCarial.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL adverSCarial
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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: 0.000143051147460938
Split number: 8/100
Split time: 0.000109434127807617
Split number: 16/100
Split time: 0.000102043151855469
Split number: 32/100
Split time: 9.60826873779297e-05
Split number: 64/100
Split time: 9.79900360107422e-05
Split number: 100/100
Split time: 0.000104188919067383
result length: 3
result length: 3
Split number: 1/100
Split number: 2/100
Split number: 4/100
Split time: 0.000149250030517578
Split number: 8/100
Split time: 0.000104904174804688
Split number: 16/100
Split time: 9.56058502197266e-05
Split number: 32/100
Split time: 9.34600830078125e-05
Split number: 64/100
Split time: 0.000102519989013672
Split number: 100/100
Split time: 9.39369201660156e-05
Split number: 1/100
Split number: 2/100
Split number: 4/100
Split time: 0.000141620635986328
Split number: 8/100
Split time: 0.000106096267700195
Split number: 16/100
Split time: 9.918212890625e-05
Split number: 32/100
Split time: 0.000104904174804688
Split number: 64/100
Split time: 0.000100612640380859
Split number: 100/100
Split time: 9.918212890625e-05
Split number: 1/100
Split number: 2/100
Split number: 4/100
Split time: 0.000136613845825195
Split number: 8/100
Split time: 0.000110626220703125
Split number: 16/100
Split time: 9.39369201660156e-05
Split number: 32/100
Split time: 9.48905944824219e-05
Split number: 64/100
Split time: 9.29832458496094e-05
Split number: 100/100
Split time: 9.79900360107422e-05
Split number: 1/100
Split number: 2/100
Split number: 4/100
Split time: 0.000139236450195312
Split number: 8/100
Split time: 9.70363616943359e-05
Split number: 16/100
Split time: 9.22679901123047e-05
Split number: 32/100
Split time: 9.39369201660156e-05
Split number: 64/100
Split time: 9.27448272705078e-05
Split number: 100/100
Split time: 9.44137573242188e-05


RUNIT TEST PROTOCOL -- Mon Apr 15 19:55:44 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 
  4.353   0.200   4.543