Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-22 15:05:11 -0400 (Wed, 22 Sep 2021).

CHECK results for clusterExperiment on tokay2

To the developers/maintainers of the clusterExperiment package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/clusterExperiment.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 330/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clusterExperiment 2.12.0  (landing page)
Elizabeth Purdom
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/clusterExperiment
git_branch: RELEASE_3_13
git_last_commit: 3dc45a6
git_last_commit_date: 2021-05-19 12:21:34 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    TIMEOUT    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    TIMEOUT    OK  

Summary

Package: clusterExperiment
Version: 2.12.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clusterExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings clusterExperiment_2.12.0.tar.gz
StartedAt: 2021-09-21 20:51:32 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 21:31:48 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 2416.1 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: clusterExperiment.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clusterExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings clusterExperiment_2.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/clusterExperiment.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'clusterExperiment/DESCRIPTION' ... OK
* this is package 'clusterExperiment' version '2.12.0'
* 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 whether package 'clusterExperiment' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   3.6Mb
    libs   2.1Mb
* 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 ... NOTE
Foreign function calls to a different package:
  .C(ape::node_depth, ...)
  .C(ape::node_depth_edgelength, ...)
  .C(ape::node_height, ...)
  .C(ape::node_height_clado, ...)
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* 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 ... WARNING
Output for data("rsecFluidigm", package = "clusterExperiment"):
  Search path was changed
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/clusterExperiment/libs/i386/clusterExperiment.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/clusterExperiment/libs/x64/clusterExperiment.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
plotClusters              21.75   0.07   21.82
plotBarplot               20.96   0.07   21.03
plotHeatmap               19.47   0.13   19.60
clusterMany               18.54   0.06   18.61
plotClustersWorkflow      17.56   0.05   17.63
getClusterManyParams      12.08   0.03   12.11
workflowClusters          11.22   0.00   11.22
clusterContrasts           9.80   0.28   10.16
makeConsensus              9.45   0.03    9.49
assignUnassigned           8.47   0.14    8.61
plotReducedDims            6.76   0.03    6.79
plotClustersTable          6.75   0.01    6.76
mergeClusters              5.89   0.00    5.89
ClusterExperiment-methods  5.00   0.58    5.57
plotFeatureBoxplot         5.29   0.03    5.33
plotFeatureScatter         5.27   0.04    5.31
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
plotClusters              26.32   0.10   26.42
clusterMany               23.01   0.08   23.09
plotHeatmap               22.39   0.05   22.43
plotBarplot               22.13   0.03   22.15
plotClustersWorkflow      21.09   0.10   21.19
getClusterManyParams      13.83   0.03   13.86
workflowClusters          12.70   0.03   12.74
clusterContrasts          11.72   0.04   11.75
makeConsensus              9.58   0.04    9.61
assignUnassigned           9.54   0.01    9.57
plotClustersTable          7.94   0.01    7.96
plotFeatureBoxplot         7.34   0.01    7.36
mergeClusters              7.22   0.00    7.22
ClusterExperiment-methods  6.70   0.16    6.86
plotReducedDims            6.62   0.02    6.64
plotFeatureScatter         6.33   0.03    6.36
getBestFeatures            6.31   0.02    6.34
plotDendrogram             5.82   0.00    5.81
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat_a-c.R'
  Running 'testthat_d-i.R'
  Running 'testthat_j-z.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat_a-c.R'

Installation output

clusterExperiment.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/clusterExperiment_2.12.0.tar.gz && rm -rf clusterExperiment.buildbin-libdir && mkdir clusterExperiment.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clusterExperiment.buildbin-libdir clusterExperiment_2.12.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL clusterExperiment_2.12.0.zip && rm clusterExperiment_2.12.0.tar.gz clusterExperiment_2.12.0.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
 12 4097k   12  507k    0     0  1235k      0  0:00:03 --:--:--  0:00:03 1234k
 70 4097k   70 2883k    0     0  2078k      0  0:00:01  0:00:01 --:--:-- 2078k
100 4097k  100 4097k    0     0  2251k      0  0:00:01  0:00:01 --:--:-- 2251k

install for i386

* installing *source* package 'clusterExperiment' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c search_pairs.cpp -o search_pairs.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c subsampleLoop.cpp -o subsampleLoop.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o clusterExperiment.dll tmp.def RcppExports.o search_pairs.o subsampleLoop.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/clusterExperiment.buildbin-libdir/00LOCK-clusterExperiment/00new/clusterExperiment/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
** help
*** installing help indices
  converting help for package 'clusterExperiment'
    finding HTML links ... done
    ClusterExperiment-class                 html  
    ClusterExperiment-methods               html  
    ClusterFunction-class                   html  
    ClusterFunction-methods                 html  
    RSEC                                    html  
    addClusterings                          html  
    assignUnassigned                        html  
    builtInClusteringFunctions              html  
    clusterContrasts                        html  
    finding level-2 HTML links ... done

    clusterDendrogram                       html  
    clusterExperiment-deprecated            html  
    clusterMany                             html  
    clusterSingle                           html  
    fluidigmData                            html  
    getBestFeatures                         html  
    getClusterIndex                         html  
    getClusterManyParams                    html  
    mainClustering                          html  
    makeConsensus                           html  
    makeDendrogram                          html  
    mergeClusters                           html  
    numericalAsCharacter                    html  
    plotBarplot                             html  
    plotClusters                            html  
    plotClustersTable                       html  
    plotClustersWorkflow                    html  
    plotContrastHeatmap                     html  
    plotDendrogram                          html  
    plotFeatureBoxplot                      html  
    plotFeatureScatter                      html  
    plotHeatmap                             html  
    plotReducedDims                         html  
    plottingFunctions                       html  
    reduceFunctions                         html  
    renameClusters                          html  
    rsecFluidigm                            html  
    search_pairs                            html  
    seqCluster                              html  
    simData                                 html  
    subsampleClustering                     html  
    subset                                  html  
    transformData                           html  
    updateObject                            html  
    workflowClusters                        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 'clusterExperiment' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c search_pairs.cpp -o search_pairs.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c subsampleLoop.cpp -o subsampleLoop.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o clusterExperiment.dll tmp.def RcppExports.o search_pairs.o subsampleLoop.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/clusterExperiment.buildbin-libdir/clusterExperiment/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clusterExperiment' as clusterExperiment_2.12.0.zip
* DONE (clusterExperiment)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'clusterExperiment' successfully unpacked and MD5 sums checked

Tests output

clusterExperiment.Rcheck/tests_i386/testthat_a-c.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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)
> test_check("clusterExperiment",filter = "^[A-Ca-c]")
Loading required package: clusterExperiment
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
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.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

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
3 parameter combinations, 0 use sequential method, 0 use subsampling method
Running Clustering on Parameter Combinations...
done.
3 parameter combinations, 0 use sequential method, 0 use subsampling method
Running Clustering on Parameter Combinations...
done.
3 parameter combinations, 0 use sequential method, 0 use subsampling method
Running Clustering on Parameter Combinations...
done.
3 parameter combinations, 0 use sequential method, 0 use subsampling method
Running Clustering on Parameter Combinations...
done.
== Skipped tests ===============================================================
* On Windows (3)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 815 ]
> 
> proc.time()
   user  system elapsed 
 501.85    4.50  507.20 

clusterExperiment.Rcheck/tests_x64/testthat_a-c.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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)
> test_check("clusterExperiment",filter = "^[A-Ca-c]")
Loading required package: clusterExperiment
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
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.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

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
3 parameter combinations, 0 use sequential method, 0 use subsampling method
Running Clustering on Parameter Combinations...
done.
3 parameter combinations, 0 use sequential method, 0 use subsampling method
Running Clustering on Parameter Combinations...
done.
3 parameter combinations, 0 use sequential method, 0 use subsampling method
Running Clustering on Parameter Combinations...
done.
3 parameter combinations, 0 use sequential method, 0 use subsampling method
Running Clustering on Parameter Combinations...
done.

clusterExperiment.Rcheck/tests_i386/testthat_d-i.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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)
> test_check("clusterExperiment",filter = "^[D-Id-i]")
Loading required package: clusterExperiment
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
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.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

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 415 ]
> 
> proc.time()
   user  system elapsed 
 303.37    2.78  306.18 

clusterExperiment.Rcheck/tests_i386/testthat_j-z.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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)
> test_check("clusterExperiment",filter = "^[J-Zj-z]")
Loading required package: clusterExperiment
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
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.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

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
== Skipped tests ===============================================================
* On Bioconductor (1)
* On Windows (4)

[ FAIL 0 | WARN 0 | SKIP 5 | PASS 326 ]
> 
> proc.time()
   user  system elapsed 
 224.35    2.46  226.82 

Example timings

clusterExperiment.Rcheck/examples_i386/clusterExperiment-Ex.timings

nameusersystemelapsed
ClusterExperiment-class0.420.050.47
ClusterExperiment-methods5.000.585.57
ClusterFunction-class000
addClusterings1.780.031.81
assignUnassigned8.470.148.61
builtInClusteringFunctions000
clusterContrasts 9.80 0.2810.16
clusterDendrogram0.50.00.5
clusterMany18.54 0.0618.61
clusterSingle0.570.000.56
fluidigmData000
getBestFeatures4.850.064.92
getClusterIndex0.740.020.75
getClusterManyParams12.08 0.0312.11
mainClustering2.060.032.09
makeConsensus9.450.039.49
makeDendrogram3.110.073.17
mergeClusters5.890.005.89
numericalAsCharacter000
plotBarplot20.96 0.0721.03
plotClusters21.75 0.0721.82
plotClustersTable6.750.016.76
plotClustersWorkflow17.56 0.0517.63
plotContrastHeatmap4.400.014.42
plotDendrogram4.210.044.23
plotFeatureBoxplot5.290.035.33
plotFeatureScatter5.270.045.31
plotHeatmap19.47 0.1319.60
plotReducedDims6.760.036.79
plottingFunctions2.490.162.64
reduceFunctions0.890.000.89
renameClusters0.730.000.74
rsecFluidigm000
seqCluster000
simData000
subsampleClustering000
subset1.080.011.10
transformData0.260.000.26
workflowClusters11.22 0.0011.22

clusterExperiment.Rcheck/examples_x64/clusterExperiment-Ex.timings

nameusersystemelapsed
ClusterExperiment-class0.560.000.56
ClusterExperiment-methods6.700.166.86
ClusterFunction-class0.020.000.02
addClusterings1.880.001.87
assignUnassigned9.540.019.57
builtInClusteringFunctions000
clusterContrasts11.72 0.0411.75
clusterDendrogram0.830.010.84
clusterMany23.01 0.0823.09
clusterSingle0.680.010.69
fluidigmData000
getBestFeatures6.310.026.34
getClusterIndex0.810.010.83
getClusterManyParams13.83 0.0313.86
mainClustering1.640.031.67
makeConsensus9.580.049.61
makeDendrogram3.440.013.45
mergeClusters7.220.007.22
numericalAsCharacter000
plotBarplot22.13 0.0322.15
plotClusters26.32 0.1026.42
plotClustersTable7.940.017.96
plotClustersWorkflow21.09 0.1021.19
plotContrastHeatmap505
plotDendrogram5.820.005.81
plotFeatureBoxplot7.340.017.36
plotFeatureScatter6.330.036.36
plotHeatmap22.39 0.0522.43
plotReducedDims6.620.026.64
plottingFunctions2.580.002.58
reduceFunctions0.970.031.00
renameClusters0.800.030.83
rsecFluidigm0.010.000.02
seqCluster000
simData000
subsampleClustering000
subset1.290.031.31
transformData0.340.000.34
workflowClusters12.70 0.0312.74