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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:simPIC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings simPIC_1.5.3.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/simPIC.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘simPIC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘simPIC’ version ‘1.5.3’
* 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 ‘simPIC’ 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
simPICestimate 9.864  0.975  10.905
simPICcompare  4.989  0.185   5.199
* 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: OK

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘simPIC’ ...
** this is package ‘simPIC’ version ‘1.5.3’
** 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 (simPIC)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(simPIC)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
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 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

> 
> test_check("simPIC")
simPIC is:
updating parameters...
setting up SingleCellExperiment object...
Simulating library size...
Simulating peak mean...
using weibull distribution for simulating peak mean
Simulating true counts...
Done!!
simPIC is:
updating parameters...
setting up SingleCellExperiment object...
Simulating library size...
Simulating peak mean...
using weibull distribution for simulating peak mean
Simulating true counts...
Done!!

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

simPIC is:
estimating library size parameters...
estimating sparsity...
estimating peak mean parameters...
using weibull distribution for estimating peak mean
simPIC is:
estimating library size parameters...
estimating sparsity...
estimating peak mean parameters...
using weibull distribution for estimating peak mean
simPIC is:
estimating library size parameters...
estimating sparsity...
estimating peak mean parameters...
using gamma distribution for estimating peak mean
simPIC is:
estimating library size parameters...
estimating sparsity...
estimating peak mean parameters...
using weibull distribution for estimating peak mean
simPIC is:
estimating library size parameters...
estimating sparsity...
estimating peak mean parameters...
using weibull distribution for estimating peak mean
simPIC is:
updating parameters...
setting up SingleCellExperiment object...
Simulating library size...
Simulating peak mean...
using weibull distribution for simulating peak mean
Simulating true counts...
Done!!
simPIC is:
updating parameters...
setting up SingleCellExperiment object...
Simulating library size...
Simulating peak mean...
using weibull distribution for simulating peak mean
Simulating group DA
Simulating group (cell) means
Simulating BCV
Simulating true counts groups...
Done!!
simPIC is:
updating parameters...
setting up SingleCellExperiment object...
Simulating library size...
Simulating peak mean...
using weibull distribution for simulating peak mean
Simulating true counts...
Done!!
simPIC is:
updating parameters...
setting up SingleCellExperiment object...
Simulating library size...
Simulating peak mean...
using gamma distribution for simulating peak mean
Simulating true counts...
Done!!
simPIC is:
updating parameters...
setting up SingleCellExperiment object...
Simulating library size...
Simulating peak mean...
using lngamma distribution for simulating peak mean
Simulating true counts...
Done!!
simPIC is:
updating parameters...
setting up SingleCellExperiment object...
Simulating library size...
Simulating peak mean...
using pareto distribution for simulating peak mean
Simulating true counts...
Done!!
simPIC is:
updating parameters...
setting up SingleCellExperiment object...
Simulating library size...
Simulating peak mean...
using weibull distribution for simulating peak mean
Simulating true counts...
Done!!
[ FAIL 0 | WARN 17 | SKIP 0 | PASS 37 ]

[ FAIL 0 | WARN 17 | SKIP 0 | PASS 37 ]
> 
> proc.time()
   user  system elapsed 
 84.069   6.398  90.958