Multiple platform build/check report for BioC 3.7 - CHECK report for splatter on merida2

Package: splatter

Version: 1.4.3

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_1.4.3.tar.gz

StartedAt: 2018-10-17 00:13:17 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:18:38 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 320.5 seconds

RetCode: 0

Status: OK

CheckDir: splatter.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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_1.4.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/splatter.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.4.3’
* 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
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL splatter
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘splatter’ ...
** 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 (splatter)


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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, lengths, 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

> 
> 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: 0.209267
Average acceptance rate among mu[i]'s: 0.4614
Maximum acceptance rate among mu[i]'s: 0.6934
 
 
Minimum acceptance rate among delta[i]'s: 0.403067
Average acceptance rate among delta[i]'s: 0.453523
Maximum acceptance rate among delta[i]'s: 0.511
 
 
Acceptance rate for phi (joint): 0.466067
 
 
Minimum acceptance rate among nu[j]'s: 0.4108
Average acceptance rate among nu[j]'s: 0.444723
Maximum acceptance rate among nu[j]'s: 0.487133
 
 
Minimum acceptance rate among theta[k]'s: 0.4698
Average acceptance rate among theta[k]'s: 0.4698
Maximum acceptance rate among theta[k]'s: 0.4698
 
-----------------------------------------------------
 
-----------------------------------------------------
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: 0.295733
Average acceptance rate among mu[i]'s: 0.467299
Maximum acceptance rate among mu[i]'s: 0.627267
 
 
Minimum acceptance rate among delta[i]'s: 0.363733
Average acceptance rate among delta[i]'s: 0.450091
Maximum acceptance rate among delta[i]'s: 0.5202
 
 
Minimum acceptance rate among nu[jk]'s: 0.396933
Average acceptance rate among nu[jk]'s: 0.453417
Maximum acceptance rate among nu[jk]'s: 0.487067
 
 
Minimum acceptance rate among theta[k]'s: 0.4196
Average acceptance rate among theta[k]'s: 0.436567
Maximum acceptance rate among theta[k]'s: 0.453533
 
 
-----------------------------------------------------
 
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 140 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
115.590   3.652 120.798

name	user	system	elapsed
BASiCSEstimate	0.002	0.000	0.002
BASiCSSimulate	3.742	0.145	3.939
addGeneLengths	0.351	0.007	0.365
compareSCEs	1.343	0.055	1.417
diffSCEs	1.585	0.023	1.632
getParam	0.002	0.000	0.002
getParams	0.002	0.001	0.002
listSims	0.022	0.002	0.025
lun2Estimate	0.002	0.000	0.002
lun2Simulate	0.820	0.047	0.878
lunEstimate	0.083	0.005	0.090
lunSimulate	0.277	0.004	0.285
makeCompPanel	0.001	0.000	0.001
makeDiffPanel	0.001	0.000	0.001
makeOverallPanel	0.002	0.000	0.002
mfaEstimate	0.169	0.011	0.184
mfaSimulate	0.908	0.065	0.989
newParams	0.002	0.000	0.002
phenoEstimate	0.084	0.005	0.089
phenoSimulate	0.802	0.037	0.857
scDDEstimate	0.002	0.000	0.002
scDDSimulate	0.001	0.000	0.001
setParam	0.010	0.000	0.011
setParams	0.026	0.002	0.028
simpleEstimate	0.365	0.011	0.385
simpleSimulate	0.355	0.026	0.387
sparseDCEstimate	2.059	0.396	2.504
sparseDCSimulate	1.027	0.093	1.142
splatEstimate	1.333	0.048	1.397
splatSimulate	1.735	0.115	1.873
summariseDiff	1.587	0.026	1.642
zinbEstimate	0.002	0.000	0.002
zinbSimulate	1.863	0.041	1.935

CHECK report for splatter on merida2

Summary

Command output

Installation output

Tests output

Example timings