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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:clusterExperiment.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings clusterExperiment_2.26.0.tar.gz
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* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/clusterExperiment.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘clusterExperiment/DESCRIPTION’ ... OK
* this is package ‘clusterExperiment’ version ‘2.26.0’
* 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: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   3.6Mb
    libs   2.0Mb
* 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 loading without being on the library search path ... 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
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 6 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/clusterExperiment.Rcheck/00check.log’
for details.