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CHECK report for splatter on malbec2

This page was generated on 2018-10-17 08:29:50 -0400 (Wed, 17 Oct 2018).

Package 1412/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
splatter 1.4.3
Luke Zappia
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/splatter
Branch: RELEASE_3_7
Last Commit: 9cca297
Last Changed Date: 2018-08-19 22:31:49 -0400 (Sun, 19 Aug 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: splatter
Version: 1.4.3
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:splatter.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings splatter_1.4.3.tar.gz
StartedAt: 2018-10-16 03:55:51 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 03:59:51 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 240.5 seconds
RetCode: 0
Status:  OK 
CheckDir: splatter.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:splatter.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings splatter_1.4.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/splatter.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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


Installation output

splatter.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL splatter
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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)

Tests output

splatter.Rcheck/tests/testthat.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
103.708   0.876 104.718 

Example timings

splatter.Rcheck/splatter-Ex.timings

nameusersystemelapsed
BASiCSEstimate0.0040.0000.000
BASiCSSimulate3.0680.0643.134
addGeneLengths0.2800.0200.302
compareSCEs0.9920.0201.014
diffSCEs1.5280.0001.528
getParam0.0000.0000.001
getParams0.0000.0000.001
listSims0.0200.0000.019
lun2Estimate0.0000.0000.001
lun2Simulate0.8200.0360.860
lunEstimate0.0560.0000.056
lunSimulate0.2280.0040.231
makeCompPanel0.0000.0000.001
makeDiffPanel000
makeOverallPanel0.0000.0000.001
mfaEstimate0.1160.0000.116
mfaSimulate0.7680.0000.765
newParams0.0000.0000.002
phenoEstimate0.0560.0000.055
phenoSimulate0.4960.0000.495
scDDEstimate0.0000.0000.001
scDDSimulate0.0000.0000.001
setParam0.0000.0040.007
setParams0.0120.0000.015
simpleEstimate0.2240.0000.226
simpleSimulate0.2520.0000.254
sparseDCEstimate1.2120.0001.218
sparseDCSimulate0.8040.0200.820
splatEstimate1.1760.0001.177
splatSimulate1.4920.0161.510
summariseDiff1.1200.0001.119
zinbEstimate0.0000.0000.001
zinbSimulate1.2600.0121.289