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CHECK report for CATALYST on tokay2

This page was generated on 2020-10-17 11:56:12 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CATALYST PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 234/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CATALYST 1.12.2
Helena L. Crowell
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/CATALYST
Branch: RELEASE_3_11
Last Commit: 3846718
Last Changed Date: 2020-07-02 09:14:54 -0400 (Thu, 02 Jul 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CATALYST
Version: 1.12.2
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CATALYST.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CATALYST_1.12.2.tar.gz
StartedAt: 2020-10-17 02:16:52 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:42:57 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 1565.6 seconds
RetCode: 0
Status:  OK  
CheckDir: CATALYST.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CATALYST.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CATALYST_1.12.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/CATALYST.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CATALYST/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CATALYST' version '1.12.2'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'CATALYST' 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 ... 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 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 (user + system) or elapsed time > 5s
                  user system elapsed
plotPbExprs      18.94   0.04   18.99
plotDR           18.07   0.06   21.92
plotDiffHeatmap  14.71   0.02   15.07
plotExprHeatmap  13.55   0.05   13.76
plotMultiHeatmap 12.62   0.06   12.67
plotClusterExprs 10.70   0.04   11.40
plotFreqHeatmap  10.63   0.00   10.63
sce2fcs           9.76   0.19    9.95
mergeClusters     9.76   0.05    9.82
plotCodes         8.91   0.08   10.35
pbMDS             8.47   0.05    8.51
plotAbundances    7.95   0.00    7.96
SCE-accessors     6.97   0.32    7.61
extractClusters   6.86   0.02    6.88
runDR             6.83   0.00    6.83
plotExprs         6.61   0.11    6.75
plotYields        5.99   0.03    6.01
plotMahal         5.78   0.06    5.84
cluster           5.75   0.00    5.75
clrDR             5.52   0.20    5.72
filterSCE         5.53   0.06    5.59
plotScatter       5.14   0.10    5.23
plotSpillmat      5.07   0.08    5.16
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
plotDR           21.21   0.04   21.25
plotMultiHeatmap 15.11   0.06   15.17
plotClusterExprs 12.94   0.11   13.06
plotPbExprs      12.78   0.01   12.82
plotDiffHeatmap  12.45   0.08   12.54
plotExprHeatmap  11.50   0.02   11.51
plotCodes        10.78   0.04   10.83
sce2fcs          10.34   0.12   10.47
plotAbundances   10.12   0.05   10.19
pbMDS             9.67   0.03    9.77
SCE-accessors     9.27   0.23    9.50
mergeClusters     8.40   0.00    8.40
plotMahal         8.28   0.04    8.32
clrDR             7.97   0.05    9.22
filterSCE         7.95   0.06    8.01
adaptSpillmat     7.70   0.09    9.26
plotFreqHeatmap   7.58   0.04    7.62
runDR             6.68   0.00    6.67
cluster           6.62   0.01    7.48
extractClusters   6.49   0.02    6.50
plotExprs         6.27   0.11    6.38
estCutoffs        6.06   0.04    6.11
compCytof         6.02   0.05    7.89
applyCutoffs      5.25   0.10    5.83
plotYields        5.24   0.03    5.26
* 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: OK


Installation output

CATALYST.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/CATALYST_1.12.2.tar.gz && rm -rf CATALYST.buildbin-libdir && mkdir CATALYST.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CATALYST.buildbin-libdir CATALYST_1.12.2.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL CATALYST_1.12.2.zip && rm CATALYST_1.12.2.tar.gz CATALYST_1.12.2.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 3591k  100 3591k    0     0  38.0M      0 --:--:-- --:--:-- --:--:-- 41.2M

install for i386

* installing *source* package 'CATALYST' ...
** 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 'CATALYST'
    finding HTML links ... done
    SCE-accessors                           html  
    finding level-2 HTML links ... done

    adaptSpillmat                           html  
    applyCutoffs                            html  
    assignPrelim                            html  
    clrDR                                   html  
    cluster                                 html  
    compCytof                               html  
    computeSpillmat                         html  
    data                                    html  
    estCutoffs                              html  
    extractClusters                         html  
    filterSCE                               html  
    guessPanel                              html  
    mergeClusters                           html  
    normCytof                               html  
    pbMDS                                   html  
    plotAbundances                          html  
    plotClusterExprs                        html  
    plotClusterHeatmap                      html  
    plotCodes                               html  
    plotCounts                              html  
    plotDR                                  html  
    plotDiffHeatmap                         html  
    plotEvents                              html  
    plotExprHeatmap                         html  
    plotExprs                               html  
    plotFreqHeatmap                         html  
    plotMahal                               html  
    plotMultiHeatmap                        html  
    plotNRS                                 html  
    plotPbExprs                             html  
    plotScatter                             html  
    plotSpillmat                            html  
    plotYields                              html  
    prepData                                html  
    runDR                                   html  
    sce2fcs                                 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 'CATALYST' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CATALYST' as CATALYST_1.12.2.zip
* DONE (CATALYST)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'CATALYST' successfully unpacked and MD5 sums checked

Tests output

CATALYST.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(CATALYST)
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

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


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("CATALYST")
== testthat results  ===========================================================
[ OK: 732 | SKIPPED: 0 | WARNINGS: 37 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 178.48    3.56  184.18 

CATALYST.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(CATALYST)
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

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


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("CATALYST")
== testthat results  ===========================================================
[ OK: 732 | SKIPPED: 0 | WARNINGS: 37 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 185.04    1.68  186.73 

Example timings

CATALYST.Rcheck/examples_i386/CATALYST-Ex.timings

nameusersystemelapsed
SCE-accessors6.970.327.61
adaptSpillmat3.950.054.01
applyCutoffs3.440.203.64
assignPrelim1.450.041.48
clrDR5.520.205.72
cluster5.750.005.75
compCytof4.960.045.00
computeSpillmat4.890.034.92
data0.030.010.05
estCutoffs4.390.034.42
extractClusters6.860.026.88
filterSCE5.530.065.59
guessPanel0.070.000.06
mergeClusters9.760.059.82
normCytof3.080.013.09
pbMDS8.470.058.51
plotAbundances7.950.007.96
plotClusterExprs10.70 0.0411.40
plotCodes 8.91 0.0810.35
plotCounts1.410.001.90
plotDR18.07 0.0621.92
plotDiffHeatmap14.71 0.0215.07
plotEvents3.20.03.2
plotExprHeatmap13.55 0.0513.76
plotExprs6.610.116.75
plotFreqHeatmap10.63 0.0010.63
plotMahal5.780.065.84
plotMultiHeatmap12.62 0.0612.67
plotNRS1.740.021.75
plotPbExprs18.94 0.0418.99
plotScatter5.140.105.23
plotSpillmat5.070.085.16
plotYields5.990.036.01
prepData2.640.012.66
runDR6.830.006.83
sce2fcs9.760.199.95

CATALYST.Rcheck/examples_x64/CATALYST-Ex.timings

nameusersystemelapsed
SCE-accessors9.270.239.50
adaptSpillmat7.700.099.26
applyCutoffs5.250.105.83
assignPrelim2.530.003.03
clrDR7.970.059.22
cluster6.620.017.48
compCytof6.020.057.89
computeSpillmat4.610.034.64
data0.010.050.07
estCutoffs6.060.046.11
extractClusters6.490.026.50
filterSCE7.950.068.01
guessPanel0.050.000.05
mergeClusters8.40.08.4
normCytof3.650.053.69
pbMDS9.670.039.77
plotAbundances10.12 0.0510.19
plotClusterExprs12.94 0.1113.06
plotCodes10.78 0.0410.83
plotCounts1.790.001.79
plotDR21.21 0.0421.25
plotDiffHeatmap12.45 0.0812.54
plotEvents2.590.002.59
plotExprHeatmap11.50 0.0211.51
plotExprs6.270.116.38
plotFreqHeatmap7.580.047.62
plotMahal8.280.048.32
plotMultiHeatmap15.11 0.0615.17
plotNRS1.340.001.34
plotPbExprs12.78 0.0112.82
plotScatter4.820.024.82
plotSpillmat4.510.084.60
plotYields5.240.035.26
prepData1.570.001.58
runDR6.680.006.67
sce2fcs10.34 0.1210.47