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CHECK report for splatter on malbec2

This page was generated on 2019-10-16 12:10:18 -0400 (Wed, 16 Oct 2019).

Package 1569/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
splatter 1.8.0
Luke Zappia
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/splatter
Branch: RELEASE_3_9
Last Commit: 0195bb5
Last Changed Date: 2019-05-02 11:54:05 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: splatter
Version: 1.8.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:splatter.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings splatter_1.8.0.tar.gz
StartedAt: 2019-10-16 05:12:19 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:17:47 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 328.1 seconds
RetCode: 0
Status:  OK 
CheckDir: splatter.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:splatter.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings splatter_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/splatter.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.8.0’
* 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
* 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:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL splatter
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
  0.227   0.036   0.251 

splatter.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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, 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

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 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
129.593   1.401 132.044 

Example timings

splatter.Rcheck/splatter-Ex.timings

nameusersystemelapsed
BASiCSEstimate000
BASiCSSimulate3.6030.0753.758
addGeneLengths0.2390.0040.243
compareSCEs1.1180.0321.150
diffSCEs1.2250.0001.225
getParam0.0010.0000.000
getParams000
listSims0.010.000.01
lun2Estimate000
lun2Simulate0.2500.0040.254
lunEstimate0.0520.0000.052
lunSimulate0.780.000.78
makeCompPanel000
makeDiffPanel000
makeOverallPanel000
mfaEstimate0.1700.0040.209
mfaSimulate1.1930.0081.201
newParams0.0020.0000.002
phenoEstimate0.1670.0000.167
phenoSimulate0.8750.0000.875
scDDEstimate000
scDDSimulate000
setParam0.0110.0000.010
setParams0.0260.0010.026
simpleEstimate0.3550.0080.499
simpleSimulate0.9820.0001.045
sparseDCEstimate1.6500.0231.773
sparseDCSimulate0.8990.0040.903
splatEstimate1.7360.0161.753
splatSimulate0.4860.0120.498
summariseDiff1.1060.0001.107
zinbEstimate0.0010.0000.001
zinbSimulate1.2420.0081.251