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CHECK report for splatter on machv2

This page was generated on 2020-10-17 11:59:41 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE splatter PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1715/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
splatter 1.12.0
Luke Zappia
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/splatter
Branch: RELEASE_3_11
Last Commit: 259b2df
Last Changed Date: 2020-04-27 15:04:52 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: splatter
Version: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2020-10-17 05:34:47 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:43:09 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 501.4 seconds
RetCode: 0
Status:  OK 
CheckDir: splatter.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/splatter.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.12.0’
* 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 ‘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 (user + system) or elapsed time > 5s
                   user system elapsed
scDDEstimate     28.307  0.404  28.749
kersplatEstimate  7.262  0.267   7.533
zinbEstimate      5.129  0.196   5.328
splatEstimate     5.044  0.133   5.180
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  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


Installation output

splatter.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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)

Tests output

splatter.Rcheck/tests/spelling.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
  0.326   0.076   0.374 

splatter.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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, 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, 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


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: 0.21
Average acceptance rate among mu[i]'s: 0.421265
Maximum acceptance rate among mu[i]'s: 0.5352
 
 
Minimum acceptance rate among delta[i]'s: 0.391267
Average acceptance rate among delta[i]'s: 0.4489
Maximum acceptance rate among delta[i]'s: 0.541733
 
 
Acceptance rate for phi (joint): 0.429067
 
 
Minimum acceptance rate among nu[j]'s: 0.384467
Average acceptance rate among nu[j]'s: 0.448498
Maximum acceptance rate among nu[j]'s: 0.499933
 
 
Minimum acceptance rate among theta[k]'s: 0.462667
Average acceptance rate among theta[k]'s: 0.462667
Maximum acceptance rate among theta[k]'s: 0.462667
 
-----------------------------------------------------
 
-----------------------------------------------------
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: 0.181267
Average acceptance rate among mu[i]'s: 0.444741
Maximum acceptance rate among mu[i]'s: 0.7594
 
 
Minimum acceptance rate among delta[i]'s: 0.375667
Average acceptance rate among delta[i]'s: 0.450051
Maximum acceptance rate among delta[i]'s: 0.5164
 
 
Minimum acceptance rate among nu[jk]'s: 0.4146
Average acceptance rate among nu[jk]'s: 0.530309
Maximum acceptance rate among nu[jk]'s: 0.637867
 
 
Minimum acceptance rate among theta[k]'s: 0.461733
Average acceptance rate among theta[k]'s: 0.462933
Maximum acceptance rate among theta[k]'s: 0.464133
 
 
-----------------------------------------------------
 
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 145 | SKIPPED: 0 | WARNINGS: 5 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
171.166   9.278 180.684 

Example timings

splatter.Rcheck/splatter-Ex.timings

nameusersystemelapsed
BASiCSEstimate0.0000.0000.001
BASiCSSimulate4.5200.1984.725
addGeneLengths0.4050.0060.412
compareSCEs4.2790.0784.360
diffSCEs3.3430.0083.353
getParam0.0000.0000.001
getParams0.0000.0000.001
kersplatEstimate7.2620.2677.533
kersplatSample1.8760.0811.957
kersplatSetup0.8690.0430.914
kersplatSimulate000
listSims0.0230.0030.027
lun2Estimate0.0000.0000.001
lun2Simulate0.3630.0130.376
lunEstimate0.4100.0050.415
lunSimulate0.3140.0150.330
makeCompPanel000
makeDiffPanel0.0000.0010.000
makeOverallPanel0.0010.0010.001
mfaEstimate0.1630.0110.174
mfaSimulate0.4610.0390.500
newParams0.0010.0010.002
phenoEstimate0.3740.0110.385
phenoSimulate0.8380.0340.872
scDDEstimate28.307 0.40428.749
scDDSimulate0.0010.0010.000
setParam0.0140.0010.015
setParams0.0320.0030.036
simpleEstimate0.4650.0050.471
simpleSimulate0.4400.0080.448
sparseDCEstimate1.2540.1091.366
sparseDCSimulate0.5430.0700.614
splatEstimate5.0440.1335.180
splatSimulate0.9050.0510.956
summariseDiff3.3410.0253.369
zinbEstimate5.1290.1965.328
zinbSimulate0.0660.0000.067