Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:38:57 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
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 370/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
clusterExperiment 2.23.0 (landing page) Elizabeth Purdom
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | 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: 2.23.0 |
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_2.23.0.tar.gz |
StartedAt: 2024-03-27 20:14:58 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 20:33:27 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 1109.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: clusterExperiment.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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_2.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/clusterExperiment.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘clusterExperiment/DESCRIPTION’ ... OK * this is package ‘clusterExperiment’ version ‘2.23.0’ * 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 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 ... NOTE 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:175-178: Lost braces in \itemize; meant \describe ? checkRd: (-1) ClusterExperiment-class.Rd:179-180: 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 ... 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 is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotReducedDims 5.310 0.071 5.472 plotClustersTable 5.190 0.079 5.338 mergeClusters 4.948 0.099 5.130 * 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: 1 WARNING, 6 NOTEs See ‘/Users/biocbuild/bbs-3.19-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/4.4-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 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++11 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c search_pairs.cpp -o search_pairs.o clang++ -arch x86_64 -std=gnu++11 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c subsampleLoop.cpp -o subsampleLoop.o clang++ -arch x86_64 -std=gnu++11 -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/4.4-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) (2024-03-18 r86148) -- "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 = "^[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 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, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, 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 274.751 5.740 285.108
clusterExperiment.Rcheck/tests/testthat_d-i.Rout
R Under development (unstable) (2024-03-18 r86148) -- "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 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, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, 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 186.128 3.548 191.354
clusterExperiment.Rcheck/tests/testthat_j-z.Rout
R Under development (unstable) (2024-03-18 r86148) -- "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 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, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, 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 339 ] ══ 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 339 ] > > proc.time() user system elapsed 158.262 3.703 163.634
clusterExperiment.Rcheck/clusterExperiment-Ex.timings
name | user | system | elapsed | |
ClusterExperiment-class | 0.440 | 0.012 | 0.464 | |
ClusterExperiment-methods | 3.232 | 0.131 | 3.409 | |
ClusterFunction-class | 0.011 | 0.001 | 0.012 | |
addClusterings | 1.316 | 0.057 | 1.394 | |
assignUnassigned | 0 | 0 | 0 | |
builtInClusteringFunctions | 0.002 | 0.000 | 0.001 | |
clusterContrasts | 0 | 0 | 0 | |
clusterDendrogram | 2.085 | 0.054 | 2.167 | |
clusterMany | 0.001 | 0.000 | 0.001 | |
clusterSingle | 0.487 | 0.008 | 0.498 | |
fluidigmData | 0 | 0 | 0 | |
getBestFeatures | 4.434 | 0.144 | 4.649 | |
getClusterIndex | 1.095 | 0.024 | 1.131 | |
getClusterManyParams | 0 | 0 | 0 | |
mainClustering | 1.932 | 0.072 | 2.033 | |
makeConsensus | 0.000 | 0.001 | 0.001 | |
makeDendrogram | 3.591 | 0.084 | 3.748 | |
mergeClusters | 4.948 | 0.099 | 5.130 | |
numericalAsCharacter | 0.001 | 0.001 | 0.001 | |
plotBarplot | 0 | 0 | 0 | |
plotClusters | 0.000 | 0.000 | 0.001 | |
plotClustersTable | 5.190 | 0.079 | 5.338 | |
plotClustersWorkflow | 0.000 | 0.001 | 0.000 | |
plotContrastHeatmap | 3.389 | 0.070 | 3.507 | |
plotDendrogram | 3.494 | 0.054 | 3.603 | |
plotFeatureBoxplot | 4.864 | 0.068 | 4.995 | |
plotFeatureScatter | 4.374 | 0.060 | 4.488 | |
plotHeatmap | 0.001 | 0.000 | 0.001 | |
plotReducedDims | 5.310 | 0.071 | 5.472 | |
plottingFunctions | 1.056 | 0.024 | 1.098 | |
reduceFunctions | 0.860 | 0.023 | 0.908 | |
renameClusters | 0.488 | 0.010 | 0.503 | |
rsecFluidigm | 0.001 | 0.000 | 0.001 | |
seqCluster | 0 | 0 | 0 | |
simData | 0.001 | 0.001 | 0.000 | |
subsampleClustering | 0 | 0 | 0 | |
subset | 1.352 | 0.028 | 1.395 | |
transformData | 0.243 | 0.002 | 0.247 | |
workflowClusters | 0 | 0 | 0 | |