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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CATALYST_1.32.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CATALYST.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CATALYST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CATALYST’ version ‘1.32.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 24 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CATALYST’ can be installed ... OK
* checking installed package size ... OK
* 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 ... OK
* checking R code for possible problems ... NOTE
plotExprs: no visible binding for global variable ‘ndensity’
Undefined global functions or variables:
  ndensity
* checking Rd files ... NOTE
checkRd: (-1) plotDiffHeatmap.Rd:87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotDiffHeatmap.Rd:88: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SCE-accessors.Rd: SingleCellExperiment, FlowSOM, ConsensusClusterPlus
  cluster.Rd: ggplot
  compCytof.Rd: flowFrame
  data.Rd: flowSet, flowFrame
  plotClusterExprs.Rd: ggplot
  plotCounts.Rd: ggplot
  plotExprs.Rd: ggplot
  plotPbExprs.Rd: SingleCellExperiment
  prepData.Rd: read.FCS
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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
plotPbExprs      23.836  0.901  24.799
plotMultiHeatmap 19.512  0.100  19.650
plotDiffHeatmap  18.486  0.088  18.618
plotDR           16.987  0.071  17.104
sce2fcs          14.096  0.156  14.288
plotExprHeatmap  13.140  0.036  13.205
pbMDS            11.648  0.092  11.765
plotAbundances   11.253  0.032  11.311
plotCodes        10.690  0.056  10.771
plotClusterExprs 10.593  0.032  10.657
clrDR             9.943  0.147  10.112
mergeClusters     9.954  0.111  10.096
plotFreqHeatmap   9.433  0.064   9.519
SCE-accessors     9.256  0.212   9.494
plotMahal         8.753  0.064   8.838
filterSCE         8.202  0.055   8.278
cluster           8.096  0.059   8.173
plotSpillmat      7.570  0.220   7.808
compCytof         7.645  0.036   7.699
extractClusters   6.832  0.020   6.869
estCutoffs        6.545  0.072   6.632
computeSpillmat   6.508  0.092   6.615
plotScatter       6.372  0.199   6.594
runDR             6.371  0.175   6.562
plotYields        6.253  0.112   6.380
plotExprs         6.284  0.044   6.343
adaptSpillmat     5.607  0.044   5.664
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/CATALYST.Rcheck/00check.log’
for details.