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### Running command:
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###   /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
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/clusterExperiment.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-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 Ventura 13.7.1
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 15.0.0 (clang-1500.1.0.2.5)’
* 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.