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CHECK report for singleCellTK on tokay2

This page was generated on 2019-10-16 12:41:16 -0400 (Wed, 16 Oct 2019).

Package 1532/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
singleCellTK 1.4.2
David Jenkins
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/singleCellTK
Branch: RELEASE_3_9
Last Commit: 0285e0c
Last Changed Date: 2019-08-04 13:29:24 -0400 (Sun, 04 Aug 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: singleCellTK
Version: 1.4.2
Command: set _R_CHECK_FORCE_SUGGESTS_=0&& C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:singleCellTK.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings singleCellTK_1.4.2.tar.gz
StartedAt: 2019-10-16 07:11:27 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 07:19:31 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 483.6 seconds
RetCode: 0
Status:  OK  
CheckDir: singleCellTK.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   set _R_CHECK_FORCE_SUGGESTS_=0&& C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:singleCellTK.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings singleCellTK_1.4.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/singleCellTK.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'singleCellTK/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'singleCellTK' version '1.4.2'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'singleCellTK' 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
* 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
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'shinythemes'
  All declared Imports should be used.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
gsvaSCE 5.79   0.47    6.35
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
DownsampleCells 5.08   0.27    5.35
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'spelling.R'
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/singleCellTK.Rcheck/00check.log'
for details.



Installation output

singleCellTK.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/singleCellTK_1.4.2.tar.gz && rm -rf singleCellTK.buildbin-libdir && mkdir singleCellTK.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=singleCellTK.buildbin-libdir singleCellTK_1.4.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL singleCellTK_1.4.2.zip && rm singleCellTK_1.4.2.tar.gz singleCellTK_1.4.2.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  424k  100  424k    0     0  6660k      0 --:--:-- --:--:-- --:--:-- 7443k

install for i386

* installing *source* package 'singleCellTK' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'singleCellTK'
    finding HTML links ... done
    ComBatSCE                               html  
    DownsampleCells                         html  
    DownsampleDepth                         html  
    MAST                                    html  
    SCtkExperiment-class                    html  
    SCtkExperiment                          html  
    alignSingleCellData                     html  
    calcEffectSizes                         html  
    convertGeneIDs                          html  
    createSCE                               html  
    distinctColors                          html  
    enrichRSCE                              html  
    filterSCData                            html  
    generateSimulatedData                   html  
    getBiomarker                            html  
    getClusterInputData                     html  
    getPCA                                  html  
    getTSNE                                 html  
    getUMAP                                 html  
    gsvaSCE                                 html  
    iterateSimulations                      html  
    mouseBrainSubsetSCE                     html  
    parseRsubreadLogs                       html  
    pcaVariances-set                        html  
    pcaVariances                            html  
    plotBatchVariance                       html  
    plotBiomarker                           html  
    plotDiffEx                              html  
    plotPCA                                 html  
    plotTSNE                                html  
    plotUMAP                                html  
    saveBiomarkerRes                        html  
    saveDiffExResults                       html  
    scDiffEx                                html  
    singleCellTK                            html  
    subDiffEx                               html  
    summarizeTable                          html  
    visPlot                                 html  
** 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

install for x64

* installing *source* package 'singleCellTK' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'singleCellTK' as singleCellTK_1.4.2.zip
* DONE (singleCellTK)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'singleCellTK' successfully unpacked and MD5 sums checked

Tests output

singleCellTK.Rcheck/tests_i386/spelling.Rout


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

> if (requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
   0.23    0.07    0.29 

singleCellTK.Rcheck/tests_x64/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-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.

> if (requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
   0.15    0.03    0.17 

singleCellTK.Rcheck/tests_i386/testthat.Rout


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

> library(testthat)
> library(singleCellTK)
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

Attaching package: 'IRanges'

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

    windows

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

Loading required package: SingleCellExperiment

Attaching package: 'singleCellTK'

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

    plotPCA

> 
> test_check("singleCellTK")
Estimating GSVA scores for 1 gene sets.
Computing observed enrichment scores
Estimating ECDFs with Gaussian kernels
Using parallel with 1 cores

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
Estimating GSVA scores for 1 gene sets.
Computing observed enrichment scores
Estimating ECDFs with Gaussian kernels
Using parallel with 1 cores

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
Estimating GSVA scores for 402 gene sets.
Computing observed enrichment scores
Estimating ECDFs with Gaussian kernels
Using parallel with 1 cores

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Standardizing Data across genes
Standardizing Data across genes
Using batch = 3 as a reference batch (this batch won't change)
Standardizing Data across genes
== testthat results  ===========================================================
[ OK: 78 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  61.06    3.37   64.40 

singleCellTK.Rcheck/tests_x64/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-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.

> library(testthat)
> library(singleCellTK)
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

Attaching package: 'IRanges'

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

    windows

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

Loading required package: SingleCellExperiment

Attaching package: 'singleCellTK'

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

    plotPCA

> 
> test_check("singleCellTK")
Estimating GSVA scores for 1 gene sets.
Computing observed enrichment scores
Estimating ECDFs with Gaussian kernels
Using parallel with 1 cores

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Estimating GSVA scores for 1 gene sets.
Computing observed enrichment scores
Estimating ECDFs with Gaussian kernels
Using parallel with 1 cores

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Estimating GSVA scores for 402 gene sets.
Computing observed enrichment scores
Estimating ECDFs with Gaussian kernels
Using parallel with 1 cores

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Standardizing Data across genes
Standardizing Data across genes
Using batch = 3 as a reference batch (this batch won't change)
Standardizing Data across genes
== testthat results  ===========================================================
[ OK: 78 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  62.20    2.14   64.32 

Example timings

singleCellTK.Rcheck/examples_i386/singleCellTK-Ex.timings

nameusersystemelapsed
ComBatSCE2.920.123.04
DownsampleCells3.790.334.11
DownsampleDepth0.810.120.94
MAST3.000.393.39
SCtkExperiment-class0.960.051.00
SCtkExperiment0.730.060.79
alignSingleCellData000
calcEffectSizes0.780.020.80
convertGeneIDs2.350.622.99
createSCE0.260.000.26
distinctColors0.020.000.02
enrichRSCE0.010.000.01
filterSCData1.140.001.14
generateSimulatedData0.300.040.33
getBiomarker0.020.000.02
getClusterInputData0.180.030.22
getPCA0.410.030.43
getTSNE0.500.050.55
getUMAP0.800.071.52
gsvaSCE5.790.476.35
iterateSimulations0.410.030.44
mouseBrainSubsetSCE0.020.000.02
pcaVariances-set0.390.030.42
pcaVariances0.180.040.22
plotBatchVariance2.690.072.76
plotBiomarker0.560.050.61
plotDiffEx1.220.141.36
plotPCA0.310.020.33
plotTSNE0.320.040.36
plotUMAP1.040.051.09
saveBiomarkerRes0.380.030.41
saveDiffExResults0.950.081.03
scDiffEx2.720.363.08
singleCellTK000
subDiffEx0.530.030.56
summarizeTable0.160.020.17
visPlot4.590.014.61

singleCellTK.Rcheck/examples_x64/singleCellTK-Ex.timings

nameusersystemelapsed
ComBatSCE4.710.234.94
DownsampleCells5.080.275.35
DownsampleDepth0.710.080.80
MAST4.230.184.42
SCtkExperiment-class0.550.020.56
SCtkExperiment1.470.031.50
alignSingleCellData000
calcEffectSizes1.670.091.76
convertGeneIDs3.330.814.14
createSCE0.180.070.25
distinctColors000
enrichRSCE000
filterSCData0.460.010.47
generateSimulatedData0.290.050.34
getBiomarker0.020.000.02
getClusterInputData0.280.000.28
getPCA0.360.090.45
getTSNE1.640.031.67
getUMAP0.960.102.62
gsvaSCE3.790.374.16
iterateSimulations1.150.051.20
mouseBrainSubsetSCE0.000.010.02
pcaVariances-set0.240.020.25
pcaVariances0.110.030.14
plotBatchVariance1.780.091.87
plotBiomarker0.470.000.47
plotDiffEx2.110.132.24
plotPCA0.280.030.30
plotTSNE0.320.020.34
plotUMAP0.50.00.5
saveBiomarkerRes1.240.001.24
saveDiffExResults0.260.010.28
scDiffEx4.040.064.09
singleCellTK000
subDiffEx0.420.070.49
summarizeTable0.120.010.14
visPlot3.690.023.70