Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2024-12-24 11:41 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 367/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clusterExperiment 2.27.0  (landing page)
Elizabeth Purdom
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/clusterExperiment
git_branch: devel
git_last_commit: 3bb82fb
git_last_commit_date: 2024-10-29 10:12:11 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for clusterExperiment on palomino7

To the developers/maintainers of the clusterExperiment package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: clusterExperiment
Version: 2.27.0
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:clusterExperiment.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings clusterExperiment_2.27.0.tar.gz
StartedAt: 2024-12-23 23:18:17 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 23:34:35 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 978.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: clusterExperiment.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:clusterExperiment.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings clusterExperiment_2.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/clusterExperiment.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'clusterExperiment/DESCRIPTION' ... OK
* this is package 'clusterExperiment' version '2.27.0'
* 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 ... 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 'clusterExperiment' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
  installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   3.6Mb
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... 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 ... NOTE
checkRd: (-1) ClusterExperiment-class.Rd:177-180: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ClusterExperiment-class.Rd:181-182: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ClusterFunction-class.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ClusterFunction-class.Rd:71-77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ClusterFunction-class.Rd:78-84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ClusterFunction-class.Rd:85-94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ClusterFunction-class.Rd:95-97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ClusterFunction-class.Rd:98-99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ClusterFunction-class.Rd:104-105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ClusterFunction-class.Rd:106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ClusterFunction-class.Rd:107-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builtInClusteringFunctions.Rd:60-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builtInClusteringFunctions.Rd:64-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builtInClusteringFunctions.Rd:74-77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builtInClusteringFunctions.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builtInClusteringFunctions.Rd:79-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builtInClusteringFunctions.Rd:93-96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builtInClusteringFunctions.Rd:97-105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builtInClusteringFunctions.Rd:106-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clusterContrasts.Rd:55-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) clusterContrasts.Rd:60-61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) clusterDendrogram.Rd:125-132: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clusterDendrogram.Rd:133-150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clusterDendrogram.Rd:137-138: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clusterDendrogram.Rd:139-142: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clusterDendrogram.Rd:143-147: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clusterDendrogram.Rd:148-150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clusterDendrogram.Rd:154-158: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clusterDendrogram.Rd:159-172: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clusterDendrogram.Rd:163-165: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clusterDendrogram.Rd:166-168: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clusterDendrogram.Rd:169-170: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clusterMany.Rd:210-213: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) clusterMany.Rd:214-215: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) clusterMany.Rd:216-217: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) clusterMany.Rd:218-219: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) clusterSingle.Rd:177-191: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clusterSingle.Rd:192-197: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clusterSingle.Rd:198-203: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clusterSingle.Rd:205-213: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clusterSingle.Rd:215-233: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clusterSingle.Rd:140: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) clusterSingle.Rd:141-142: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) clusterSingle.Rd:143: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getBestFeatures.Rd:99-100: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getBestFeatures.Rd:102-103: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getBestFeatures.Rd:105-106: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getBestFeatures.Rd:108-111: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getBestFeatures.Rd:113-117: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getBestFeatures.Rd:119-120: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getBestFeatures.Rd:122-123: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getClusterIndex.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getClusterIndex.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getClusterIndex.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getClusterIndex.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getClusterIndex.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mainClustering.Rd:107-108: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mainClustering.Rd:109-114: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mainClustering.Rd:115-117: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mainClustering.Rd:118-119: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mainClustering.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mainClustering.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) makeConsensus.Rd:84-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) makeConsensus.Rd:87-89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) makeConsensus.Rd:89-92: Lost braces
    89 |  out of those not '-1'} \item{\code{noUnassignedCorrection}{ a vector of 
       |                                                            ^
checkRd: (-1) mergeClusters.Rd:186-188: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mergeClusters.Rd:189-190: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mergeClusters.Rd:191-195: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mergeClusters.Rd:196-205: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mergeClusters.Rd:206-208: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mergeClusters.Rd:209-211: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mergeClusters.Rd:223: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mergeClusters.Rd:224-225: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mergeClusters.Rd:226-227: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mergeClusters.Rd:228-230: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mergeClusters.Rd:231-233: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotClusters.Rd:169-172: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotClusters.Rd:174-177: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotClusters.Rd:179-183: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotClusters.Rd:185-189: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotClusters.Rd:191-192: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotDendrogram.Rd:91: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotDendrogram.Rd:92-93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotHeatmap.Rd:294-295: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHeatmap.Rd:296-299: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHeatmap.Rd:299-302: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHeatmap.Rd:302: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHeatmap.Rd:303: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHeatmap.Rd:304-307: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHeatmap.Rd:218-219: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotHeatmap.Rd:220-221: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotHeatmap.Rd:222-223: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotHeatmap.Rd:224-225: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plottingFunctions.Rd:144-145: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plottingFunctions.Rd:146-150: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plottingFunctions.Rd:151-154: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plottingFunctions.Rd:155-161: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plottingFunctions.Rd:162-167: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plottingFunctions.Rd:173-174: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plottingFunctions.Rd:175-176: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plottingFunctions.Rd:177-178: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) reduceFunctions.Rd:191-192: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) reduceFunctions.Rd:193-194: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) seqCluster.Rd:80-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) seqCluster.Rd:85-88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) seqCluster.Rd:90-91: Lost braces in \itemize; \value handles \item{}{} directly
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  clusterContrasts.Rd: makeContrasts
  clusterSingle.Rd: SingleCellExperiment
  getBestFeatures.Rd: topTable
  mainClustering.Rd: SingleCellExperiment
  mergeClusters.Rd: plot.phylo, locfdr
  plotClustersTable.Rd: NMF
  plotDendrogram.Rd: phydataplot, ape, plot.phylo
  reduceFunctions.Rd: SingleCellExperiment
  seqCluster.Rd: SingleCellExperiment
  subsampleClustering.Rd: SingleCellExperiment
  subset.Rd: SingleCellExperiment
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'renameClusters.Rd'
  'object'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/clusterExperiment/libs/x64/clusterExperiment.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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 nor [v]sprintf. 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
mergeClusters   6.03   0.20    6.23
getBestFeatures 6.01   0.12    6.27
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat_a-c.R'
  Running 'testthat_d-i.R'
  Running 'testthat_j-z.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 6 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/clusterExperiment.Rcheck/00check.log'
for details.


Installation output

clusterExperiment.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL clusterExperiment
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'clusterExperiment' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
using C++11
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c search_pairs.cpp -o search_pairs.o
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c subsampleLoop.cpp -o subsampleLoop.o
g++ -shared -s -static-libgcc -o clusterExperiment.dll tmp.def RcppExports.o search_pairs.o subsampleLoop.o -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lRlapack -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-clusterExperiment/00new/clusterExperiment/libs/x64
** 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'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (clusterExperiment)

Tests output

clusterExperiment.Rcheck/tests/testthat_a-c.Rout


R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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 0 | SKIP 4 | PASS 748 ]

══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On Windows (4): 'test-clusterMany.R:254:2', 'test-clusterMany.R:310:2',
  'test-clusterSingle.R:388:2', 'test-clusterSingle.R:1083:2'

[ FAIL 0 | WARN 0 | SKIP 4 | PASS 748 ]
> 
> proc.time()
   user  system elapsed 
 184.81    4.40  189.92 

clusterExperiment.Rcheck/tests/testthat_d-i.Rout


R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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 2 | PASS 392 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On Windows (2): 'test-getBestFeatures.R:180:2', 'test-heatmaps.R:65:2'

[ FAIL 0 | WARN 2 | SKIP 2 | PASS 392 ]
> 
> proc.time()
   user  system elapsed 
 165.39    3.62  169.23 

clusterExperiment.Rcheck/tests/testthat_j-z.Rout


R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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 0 | SKIP 4 | PASS 336 ]

══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On Windows (4): 'test-RSEC.R:41:2', 'test-RSEC.R:57:2',
  'test-otherPlots.R:241:2', 'test-subsampleClustering.R:26:5'

[ FAIL 0 | WARN 0 | SKIP 4 | PASS 336 ]
> 
> proc.time()
   user  system elapsed 
 137.73    3.43  141.34 

Example timings

clusterExperiment.Rcheck/clusterExperiment-Ex.timings

nameusersystemelapsed
ClusterExperiment-class0.410.000.40
ClusterExperiment-methods2.620.232.89
ClusterFunction-class0.010.000.01
addClusterings1.080.051.13
assignUnassigned000
builtInClusteringFunctions000
clusterContrasts000
clusterDendrogram0.820.060.89
clusterMany000
clusterSingle0.320.020.33
fluidigmData000
getBestFeatures6.010.126.27
getClusterIndex0.600.080.67
getClusterManyParams000
mainClustering2.000.112.10
makeConsensus000
makeDendrogram2.750.132.88
mergeClusters6.030.206.23
numericalAsCharacter000
plotBarplot000
plotClusters000
plotClustersTable3.890.224.12
plotClustersWorkflow000
plotContrastHeatmap3.700.113.83
plotDendrogram3.470.063.53
plotFeatureBoxplot2.910.123.04
plotFeatureScatter2.510.052.56
plotHeatmap000
plotReducedDims3.640.053.69
plottingFunctions1.160.051.20
reduceFunctions0.610.010.62
renameClusters0.310.020.33
rsecFluidigm000
seqCluster000
simData000
subsampleClustering000
subset0.670.070.75
transformData0.160.000.16
workflowClusters000