Elizabeth Purdom
| Snapshot Date: 2025-01-03 13:40 -0500 (Fri, 03 Jan 2025) |
| 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) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-04 11:43 -0500 (Sat, 04 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4756 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4475 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4435 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4390 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4383 |
| 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 368/2275 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| clusterExperiment 2.27.0 (landing page) Elizabeth Purdom
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. |
| Package: clusterExperiment |
| Version: 2.27.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:clusterExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings clusterExperiment_2.27.0.tar.gz |
| StartedAt: 2025-01-03 19:37:37 -0500 (Fri, 03 Jan 2025) |
| EndedAt: 2025-01-03 19:51:39 -0500 (Fri, 03 Jan 2025) |
| EllapsedTime: 842.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: clusterExperiment.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:clusterExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings clusterExperiment_2.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/clusterExperiment.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* 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 ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘clusterExperiment’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
installed size is 5.6Mb
sub-directories of 1Mb or more:
R 1.4Mb
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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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
‘/Users/biocbuild/bbs-3.21-bioc/meat/clusterExperiment.Rcheck/00check.log’
for details.
clusterExperiment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL clusterExperiment ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘clusterExperiment’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c search_pairs.cpp -o search_pairs.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c subsampleLoop.cpp -o subsampleLoop.o clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o clusterExperiment.so RcppExports.o search_pairs.o subsampleLoop.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-clusterExperiment/00new/clusterExperiment/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (clusterExperiment)
clusterExperiment.Rcheck/tests/testthat_a-c.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
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> 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
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 3 | PASS 750 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On Mac (3): 'test-clusterMany.R:255:2', 'test-clusterMany.R:311:2',
'test-clusterSingle.R:389:2'
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 750 ]
>
> proc.time()
user system elapsed
160.375 3.863 165.287
clusterExperiment.Rcheck/tests/testthat_d-i.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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
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 Mac (2): 'test-getBestFeatures.R:181:2', 'test-heatmaps.R:66:2'
[ FAIL 0 | WARN 2 | SKIP 2 | PASS 392 ]
>
> proc.time()
user system elapsed
141.440 2.448 144.639
clusterExperiment.Rcheck/tests/testthat_j-z.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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
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 3 | PASS 338 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On Mac (3): 'test-RSEC.R:42:2', 'test-RSEC.R:58:2', 'test-otherPlots.R:242:2'
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 338 ]
>
> proc.time()
user system elapsed
103.665 2.738 106.875
clusterExperiment.Rcheck/clusterExperiment-Ex.timings
| name | user | system | elapsed | |
| ClusterExperiment-class | 0.283 | 0.008 | 0.292 | |
| ClusterExperiment-methods | 2.879 | 0.120 | 3.020 | |
| ClusterFunction-class | 0.012 | 0.001 | 0.012 | |
| addClusterings | 0.773 | 0.013 | 0.789 | |
| assignUnassigned | 0.001 | 0.000 | 0.000 | |
| builtInClusteringFunctions | 0.001 | 0.000 | 0.002 | |
| clusterContrasts | 0.001 | 0.000 | 0.001 | |
| clusterDendrogram | 1.944 | 0.023 | 1.975 | |
| clusterMany | 0 | 0 | 0 | |
| clusterSingle | 0.248 | 0.006 | 0.257 | |
| fluidigmData | 0 | 0 | 0 | |
| getBestFeatures | 3.544 | 0.123 | 3.695 | |
| getClusterIndex | 0.987 | 0.016 | 1.010 | |
| getClusterManyParams | 0.000 | 0.001 | 0.001 | |
| mainClustering | 2.635 | 0.076 | 2.728 | |
| makeConsensus | 0.000 | 0.000 | 0.001 | |
| makeDendrogram | 1.921 | 0.053 | 1.985 | |
| mergeClusters | 4.146 | 0.058 | 4.231 | |
| numericalAsCharacter | 0.000 | 0.000 | 0.001 | |
| plotBarplot | 0.000 | 0.001 | 0.000 | |
| plotClusters | 0.000 | 0.001 | 0.001 | |
| plotClustersTable | 3.191 | 0.055 | 3.267 | |
| plotClustersWorkflow | 0 | 0 | 0 | |
| plotContrastHeatmap | 2.736 | 0.049 | 2.807 | |
| plotDendrogram | 2.406 | 0.029 | 2.445 | |
| plotFeatureBoxplot | 2.378 | 0.032 | 2.428 | |
| plotFeatureScatter | 2.012 | 0.030 | 2.054 | |
| plotHeatmap | 0.001 | 0.001 | 0.001 | |
| plotReducedDims | 2.604 | 0.038 | 2.657 | |
| plottingFunctions | 0.715 | 0.014 | 0.735 | |
| reduceFunctions | 0.463 | 0.014 | 0.480 | |
| renameClusters | 0.281 | 0.011 | 0.294 | |
| rsecFluidigm | 0.000 | 0.000 | 0.002 | |
| seqCluster | 0.000 | 0.000 | 0.001 | |
| simData | 0.000 | 0.001 | 0.002 | |
| subsampleClustering | 0.000 | 0.001 | 0.001 | |
| subset | 1.189 | 0.023 | 1.220 | |
| transformData | 0.136 | 0.002 | 0.139 | |
| workflowClusters | 0.000 | 0.000 | 0.001 | |