##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SimBu.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SimBu_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SimBu.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SimBu/DESCRIPTION’ ... OK
* this is package ‘SimBu’ version ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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:
  .BBSoptions
  .pre-commit-config.yaml
  .prettierignore
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 ‘SimBu’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/SimBu.Rcheck/00install.out’ for details.
* 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 ... OK
* 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 line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
setup_sfaira  12.939  3.482  25.540
simulate_bulk 11.575  0.695  12.285
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/SimBu.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘SimBu’ ...
** using non-staged installation via StagedInstall field
** 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
* DONE (SimBu)

R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
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.

> library(testthat)
> library(SimBu)
> 
> test_check("SimBu")
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:Matrix':

    expand, unname

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by 'spam'
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
Finished simulation.
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Using EPIC scaling factors.
Finished simulation.
Using EPIC scaling factors.
Finished simulation.
Using ABIS scaling factors.
Finished simulation.
Using quanTIseq scaling factors.
Finished simulation.
Using quanTIseq scaling factors.
Finished simulation.
Using custom scaling factors.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 31 ]
> 
> proc.time()
   user  system elapsed 
 62.778   2.402  65.302