############################################################################## ############################################################################## ### ### 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_2.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/clusterExperiment.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘clusterExperiment/DESCRIPTION’ ... OK * this is package ‘clusterExperiment’ version ‘2.25.0’ * 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: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 ... OK * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotReducedDims 10.951 0.188 13.921 plotClustersTable 10.939 0.110 12.838 mergeClusters 10.746 0.123 12.749 plotFeatureBoxplot 9.289 0.081 11.128 getBestFeatures 8.412 0.294 11.215 plotFeatureScatter 8.150 0.080 9.775 plotContrastHeatmap 7.362 0.091 8.693 plotDendrogram 7.201 0.078 8.769 ClusterExperiment-methods 5.679 0.316 7.258 makeDendrogram 5.353 0.059 6.466 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat_a-c.R’ Running ‘testthat_d-i.R’ Running ‘testthat_j-z.R’