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CHECK report for splatter on tokay1

This page was generated on 2018-04-12 13:29:17 -0400 (Thu, 12 Apr 2018).

Package 1333/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
splatter 1.2.2
Luke Zappia
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/splatter
Branch: RELEASE_3_6
Last Commit: 054eaf5
Last Changed Date: 2018-03-26 19:55:26 -0400 (Mon, 26 Mar 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: splatter
Version: 1.2.2
Command: rm -rf splatter.buildbin-libdir splatter.Rcheck && mkdir splatter.buildbin-libdir splatter.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=splatter.buildbin-libdir splatter_1.2.2.tar.gz >splatter.Rcheck\00install.out 2>&1 && cp splatter.Rcheck\00install.out splatter-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=splatter.buildbin-libdir --install="check:splatter-install.out" --force-multiarch --no-vignettes --timings splatter_1.2.2.tar.gz
StartedAt: 2018-04-12 03:21:55 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 03:29:48 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 473.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: splatter.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf splatter.buildbin-libdir splatter.Rcheck && mkdir splatter.buildbin-libdir splatter.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=splatter.buildbin-libdir splatter_1.2.2.tar.gz >splatter.Rcheck\00install.out 2>&1 && cp splatter.Rcheck\00install.out splatter-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=splatter.buildbin-libdir --install="check:splatter-install.out" --force-multiarch --no-vignettes --timings splatter_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/splatter.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'splatter/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'splatter' version '1.2.2'
* 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 whether package 'splatter' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/addFeatureStats.Rd:33: missing file link 'rowData'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/addGeneLengths.Rd:29: missing file link 'rowData'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/lun2Estimate.Rd:32: missing file link 'BiocParallelParam'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/lun2Estimate.Rd:34: missing file link 'SerialParam'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/scDDEstimate.Rd:30: missing file link 'BiocParallelParam'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/scDDEstimate.Rd:32: missing file link 'SerialParam'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/scDDSimulate.Rd:20: missing file link 'BiocParallelParam'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/scDDSimulate.Rd:22: missing file link 'SerialParam'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/splatSimulate.Rd:65: missing file link 'colData'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/splatSimulate.Rd:66: missing file link 'rowData'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/splatSimulate.Rd:67: missing file link 'assays'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/zinbEstimate.Rd:44: missing file link 'BiocParallelParam'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/zinbEstimate.Rd:46: missing file link 'SerialParam'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/splatter.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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 loading without being on the library search path ... OK
* loading checks for arch 'x64'
** 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/splatter.Rcheck/00check.log'
for details.

Installation output

splatter.Rcheck/00install.out


install for i386

* installing *source* package 'splatter' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'splatter'
    finding HTML links ... done
    BASiCSEstimate                          html  
    BASiCSParams                            html  
    BASiCSSimulate                          html  
    Lun2Params                              html  
    LunParams                               html  
    MFAParams                               html  
    Params                                  html  
    PhenoParams                             html  
    SCDDParams                              html  
    SimpleParams                            html  
    SplatParams                             html  
    ZINBParams                              html  
    addFeatureStats                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/addFeatureStats.Rd:33: missing file link 'rowData'
    addGeneLengths                          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/addGeneLengths.Rd:29: missing file link 'rowData'
    bridge                                  html  
    compareSCEs                             html  
    diffSCEs                                html  
    expandParams                            html  
    getLNormFactors                         html  
    getParam                                html  
    getParams                               html  
    getPathOrder                            html  
    listSims                                html  
    logistic                                html  
    lun2Estimate                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/lun2Estimate.Rd:32: missing file link 'BiocParallelParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/lun2Estimate.Rd:34: missing file link 'SerialParam'
    lun2Simulate                            html  
    lunEstimate                             html  
    lunSimulate                             html  
    makeCompPanel                           html  
    makeDiffPanel                           html  
    makeOverallPanel                        html  
    mfaEstimate                             html  
    mfaSimulate                             html  
    newParams                               html  
    phenoEstimate                           html  
    phenoSimulate                           html  
    rbindMatched                            html  
    scDDEstimate                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/scDDEstimate.Rd:30: missing file link 'BiocParallelParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/scDDEstimate.Rd:32: missing file link 'SerialParam'
    scDDSimulate                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/scDDSimulate.Rd:20: missing file link 'BiocParallelParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/scDDSimulate.Rd:22: missing file link 'SerialParam'
    setParam                                html  
    setParamUnchecked                       html  
    setParams                               html  
    setParamsUnchecked                      html  
    showPP                                  html  
    simpleEstimate                          html  
    simpleSimulate                          html  
    splatEstBCV                             html  
    splatEstDropout                         html  
    splatEstLib                             html  
    splatEstMean                            html  
    splatEstOutlier                         html  
    splatEstimate                           html  
    splatSimBCVMeans                        html  
    splatSimBatchCellMeans                  html  
    splatSimBatchEffects                    html  
    splatSimCellMeans                       html  
    splatSimDE                              html  
    splatSimDropout                         html  
    splatSimGeneMeans                       html  
    splatSimLibSizes                        html  
    splatSimTrueCounts                      html  
    splatSimulate                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/splatSimulate.Rd:65: missing file link 'colData'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/splatSimulate.Rd:66: missing file link 'rowData'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/splatSimulate.Rd:67: missing file link 'assays'
    splatter                                html  
    summariseDiff                           html  
    winsorize                               html  
    zinbEstimate                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/zinbEstimate.Rd:44: missing file link 'BiocParallelParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpoh4eIQ/R.INSTALL39e028d2c63/splatter/man/zinbEstimate.Rd:46: missing file link 'SerialParam'
    zinbSimulate                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'splatter' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'splatter' as splatter_1.2.2.zip
* DONE (splatter)
In R CMD INSTALL
In R CMD INSTALL

Tests output

splatter.Rcheck/tests_i386/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: scater
Loading required package: Biobase
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, cbind, colMeans, colSums, colnames, 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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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: 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 object is masked from 'package:base':

    apply


Attaching package: 'scater'

The following object is masked from 'package:S4Vectors':

    rename

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

    filter

> 
> test_check("splatter")
== testthat results  ===========================================================
OK: 58 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  89.60    1.06   90.85

splatter.Rcheck/tests_x64/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: scater
Loading required package: Biobase
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, cbind, colMeans, colSums, colnames, 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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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: 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 object is masked from 'package:base':

    apply


Attaching package: 'scater'

The following object is masked from 'package:S4Vectors':

    rename

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

    filter

> 
> test_check("splatter")
== testthat results  ===========================================================
OK: 58 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  76.50    0.78   77.37

Example timings

splatter.Rcheck/examples_i386/splatter-Ex.timings

nameusersystemelapsed
BASiCSEstimate000
BASiCSSimulate3.180.113.69
addGeneLengths0.670.000.68
compareSCEs1.070.031.09
diffSCEs0.560.000.56
getParam000
getParams000
listSims0.010.000.02
lun2Estimate000
lun2Simulate1.140.011.15
lunEstimate0.050.000.13
lunSimulate0.360.040.39
makeCompPanel000
makeDiffPanel000
makeOverallPanel000
mfaEstimate0.490.030.69
mfaSimulate0.570.030.61
newParams000
phenoEstimate0.130.000.34
phenoSimulate1.060.011.14
scDDEstimate000
scDDSimulate000
setParam000
setParams000
simpleEstimate0.380.010.39
simpleSimulate0.40.00.4
splatEstimate2.610.152.75
splatSimulate2.410.122.53
summariseDiff0.720.000.72
zinbEstimate000
zinbSimulate0.720.001.14

splatter.Rcheck/examples_x64/splatter-Ex.timings

nameusersystemelapsed
BASiCSEstimate000
BASiCSSimulate3.950.084.05
addGeneLengths0.800.030.83
compareSCEs1.370.001.52
diffSCEs0.740.000.73
getParam000
getParams000
listSims0.010.000.02
lun2Estimate000
lun2Simulate1.360.061.42
lunEstimate0.060.000.06
lunSimulate0.820.020.83
makeCompPanel000
makeDiffPanel000
makeOverallPanel000
mfaEstimate0.110.010.13
mfaSimulate1.040.031.07
newParams000
phenoEstimate0.100.020.11
phenoSimulate1.250.021.27
scDDEstimate000
scDDSimulate000
setParam0.010.000.01
setParams000
simpleEstimate0.640.060.71
simpleSimulate0.440.010.45
splatEstimate2.780.032.81
splatSimulate2.740.212.94
summariseDiff0.900.000.91
zinbEstimate000
zinbSimulate1.380.011.39