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This page was generated on 2021-10-22 12:05:12 -0400 (Fri, 22 Oct 2021).

CHECK results for splatter on merida1

To the developers/maintainers of the splatter package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/splatter.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1854/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
splatter 1.17.3  (landing page)
Luke Zappia
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/splatter
git_branch: master
git_last_commit: 4edfb8b
git_last_commit_date: 2021-10-07 08:13:30 -0400 (Thu, 07 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: splatter
Version: 1.17.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:splatter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings splatter_1.17.3.tar.gz
StartedAt: 2021-10-22 09:58:53 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 10:10:15 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 682.0 seconds
RetCode: 0
Status:   OK  
CheckDir: splatter.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:splatter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings splatter_1.17.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/splatter.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* 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 ‘1.17.3’
* 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     62.132  0.448  62.670
kersplatEstimate  6.916  0.254   7.185
BASiCSSimulate    6.151  0.276   6.441
mockEmpiricalSet  6.017  0.265   6.288
summariseDiff     6.118  0.051   6.176
mockBulkeQTL      5.857  0.305   6.174
diffSCEs          6.124  0.031   6.169
compareSCEs       5.812  0.135   5.960
splatEstimate     5.323  0.088   5.419
splatPopEstimate  5.240  0.105   5.355
zinbEstimate      4.955  0.136   5.106
* 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/Resources/bin/R CMD INSTALL splatter
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
Copyright (C) 2021 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 
  0.463   0.127   0.542 

splatter.Rcheck/tests/testthat.Rout


R version 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
Copyright (C) 2021 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: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

> 
> 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: 0.318933
Average acceptance rate among mu[i]'s: 0.442449
Maximum acceptance rate among mu[i]'s: 0.642267
 
 
Minimum acceptance rate among delta[i]'s: 0.3818
Average acceptance rate among delta[i]'s: 0.450307
Maximum acceptance rate among delta[i]'s: 0.525867
 
 
Acceptance rate for phi (joint): 0.407
 
 
Minimum acceptance rate among nu[j]'s: 0.392933
Average acceptance rate among nu[j]'s: 0.446416
Maximum acceptance rate among nu[j]'s: 0.5014
 
 
Minimum acceptance rate among theta[k]'s: 0.422333
Average acceptance rate among theta[k]'s: 0.422333
Maximum acceptance rate among theta[k]'s: 0.422333
 
-----------------------------------------------------
 
-----------------------------------------------------
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: 0.3176
Average acceptance rate among mu[i]'s: 0.459391
Maximum acceptance rate among mu[i]'s: 0.6118
 
 
Minimum acceptance rate among delta[i]'s: 0.381067
Average acceptance rate among delta[i]'s: 0.448929
Maximum acceptance rate among delta[i]'s: 0.522067
 
 
Minimum acceptance rate among nu[jk]'s: 0.376667
Average acceptance rate among nu[jk]'s: 0.4292
Maximum acceptance rate among nu[jk]'s: 0.470267
 
 
Minimum acceptance rate among theta[k]'s: 0.433533
Average acceptance rate among theta[k]'s: 0.4432
Maximum acceptance rate among theta[k]'s: 0.452867
 
 
-----------------------------------------------------
 
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 171 ]
> 
> proc.time()
   user  system elapsed 
267.392   8.958 276.704 

Example timings

splatter.Rcheck/splatter-Ex.timings

nameusersystemelapsed
BASiCSEstimate000
BASiCSSimulate6.1510.2766.441
addGeneLengths0.7840.0280.817
compareSCEs5.8120.1355.960
diffSCEs6.1240.0316.169
getParam0.0000.0000.001
getParams0.0010.0000.000
kersplatEstimate6.9160.2547.185
kersplatSample2.4710.1132.590
kersplatSetup0.2210.0210.242
kersplatSimulate000
listSims0.0280.0020.029
lun2Estimate000
lun2Simulate0.6280.0260.655
lunEstimate0.8950.0110.907
lunSimulate0.5810.0130.596
makeCompPanel0.0010.0010.000
makeDiffPanel000
makeOverallPanel000
mfaEstimate0.1470.0100.158
mfaSimulate1.3230.0551.380
minimiseSCE1.5480.0681.619
mockBulkMatrix0.0000.0000.001
mockBulkeQTL5.8570.3056.174
mockEmpiricalSet6.0170.2656.288
mockGFF0.0030.0000.003
mockVCF0.2120.0000.212
newParams0.0020.0000.003
phenoEstimate1.2660.0121.278
phenoSimulate1.0270.0621.090
scDDEstimate62.132 0.44862.670
scDDSimulate000
setParam0.0140.0010.015
setParams0.0250.0010.026
simpleEstimate0.9390.0060.945
simpleSimulate0.9850.0111.000
sparseDCEstimate1.6100.0821.698
sparseDCSimulate2.0090.0962.109
splatEstimate5.3230.0885.419
splatPopEstimate5.2400.1055.355
splatPopQuantNorm0.0430.0010.043
splatPopSimulate000
splatPopSimulateMeans000
splatPopSimulateSC000
splatSimulate1.4630.0381.503
summariseDiff6.1180.0516.176
zinbEstimate4.9550.1365.106
zinbSimulate0.4300.0140.444