Package: splatter

Version: 1.7.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:splatter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings splatter_1.7.2.tar.gz

StartedAt: 2019-04-09 05:43:22 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 05:50:12 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 410.7 seconds

RetCode: 0

Status:  OK

CheckDir: splatter.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:splatter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings splatter_1.7.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/splatter.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘splatter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘splatter’ version ‘1.7.2’
* 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 ‘splatter’ 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 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 or elapsed time > 5s
                user system elapsed
BASiCSSimulate 5.611  0.357   5.968
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL splatter
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘splatter’ ...
** 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 (splatter)

R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> # setting R_TESTS to empty string because of
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> 
> library(testthat)
> library(splatter)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

> 
> test_check("splatter")
-----------------------------------------------------
MCMC sampler has been started: 20000 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 20000 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.324333
Average acceptance rate among mu[i]'s: 0.457085
Maximum acceptance rate among mu[i]'s: 0.612467
 
 
Minimum acceptance rate among delta[i]'s: 0.347933
Average acceptance rate among delta[i]'s: 0.447136
Maximum acceptance rate among delta[i]'s: 0.5156
 
 
Acceptance rate for phi (joint): 0.467667
 
 
Minimum acceptance rate among nu[j]'s: 0.396333
Average acceptance rate among nu[j]'s: 0.450798
Maximum acceptance rate among nu[j]'s: 0.489
 
 
Minimum acceptance rate among theta[k]'s: 0.4536
Average acceptance rate among theta[k]'s: 0.4536
Maximum acceptance rate among theta[k]'s: 0.4536
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 20000 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 20000 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.296667
Average acceptance rate among mu[i]'s: 0.441319
Maximum acceptance rate among mu[i]'s: 0.6038
 
 
Minimum acceptance rate among delta[i]'s: 0.369
Average acceptance rate among delta[i]'s: 0.449998
Maximum acceptance rate among delta[i]'s: 0.514267
 
 
Minimum acceptance rate among nu[jk]'s: 0.398133
Average acceptance rate among nu[jk]'s: 0.456478
Maximum acceptance rate among nu[jk]'s: 0.520733
 
 
Minimum acceptance rate among theta[k]'s: 0.451467
Average acceptance rate among theta[k]'s: 0.453867
Maximum acceptance rate among theta[k]'s: 0.456267
 
 
-----------------------------------------------------
 
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 140 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
134.450   7.798 145.796 

name	user	system	elapsed
BASiCSEstimate	0.000	0.001	0.001
BASiCSSimulate	5.611	0.357	5.968
addGeneLengths	0.357	0.002	0.359
compareSCEs	2.490	0.082	2.572
diffSCEs	2.025	0.008	2.033
getParam	0.001	0.000	0.001
getParams	0.001	0.001	0.000
listSims	0.016	0.002	0.017
lun2Estimate	0	0	0
lun2Simulate	0.256	0.027	0.284
lunEstimate	0.101	0.007	0.109
lunSimulate	0.935	0.030	0.965
makeCompPanel	0.000	0.000	0.001
makeDiffPanel	0	0	0
makeOverallPanel	0.001	0.000	0.001
mfaEstimate	0.245	0.019	0.266
mfaSimulate	1.200	0.136	1.336
newParams	0.002	0.001	0.002
phenoEstimate	0.111	0.008	0.118
phenoSimulate	0.993	0.099	1.094
scDDEstimate	0.000	0.000	0.001
scDDSimulate	0.000	0.000	0.001
setParam	0.014	0.001	0.015
setParams	0.034	0.003	0.037
simpleEstimate	0.501	0.020	0.522
simpleSimulate	0.995	0.012	1.008
sparseDCEstimate	2.516	0.822	3.339
sparseDCSimulate	0.498	0.123	0.621
splatEstimate	1.496	0.129	1.625
splatSimulate	1.385	0.129	1.514
summariseDiff	1.779	0.025	1.803
zinbEstimate	0.001	0.000	0.001
zinbSimulate	2.505	0.086	2.591