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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_2.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/clusterExperiment.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clusterExperiment/DESCRIPTION’ ... OK
* this is package ‘clusterExperiment’ version ‘2.14.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘clusterExperiment’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    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 R 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 ... OK
* 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
plotClusters              39.428  0.176  39.646
clusterMany               35.737  0.119  35.886
plotBarplot               35.581  0.105  35.857
plotHeatmap               34.461  0.304  34.891
plotClustersWorkflow      33.139  0.089  33.251
getClusterManyParams      22.582  0.099  22.700
workflowClusters          19.177  0.058  19.247
clusterContrasts          18.919  0.159  19.092
assignUnassigned          15.326  0.105  15.438
makeConsensus             14.561  0.048  14.619
plotClustersTable         13.109  0.042  13.159
plotReducedDims           11.235  0.034  11.305
mergeClusters             10.703  0.059  10.789
ClusterExperiment-methods 10.068  0.159  10.237
plotFeatureBoxplot         9.474  0.030   9.511
plotFeatureScatter         9.274  0.034   9.318
plotDendrogram             7.162  0.035   7.202
plotContrastHeatmap        6.986  0.058   7.049
getBestFeatures            7.004  0.033   7.042
makeDendrogram             5.881  0.022   5.909
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat_a-c.R’
  Running ‘testthat_d-i.R’