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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_1.31.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CATALYST.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CATALYST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CATALYST’ version ‘1.31.2’
* 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 ... OK
* 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      18.749  0.124  18.914
plotMultiHeatmap 18.216  0.087  18.342
plotDiffHeatmap  16.237  0.111  16.440
plotDR           14.695  0.183  14.920
plotExprHeatmap  13.763  0.086  13.893
sce2fcs          13.205  0.068  13.308
plotClusterExprs 10.500  0.091  10.639
SCE-accessors     9.427  0.256   9.709
plotFreqHeatmap   9.476  0.096   9.595
plotAbundances    9.393  0.136   9.554
pbMDS             9.032  0.275   9.339
plotCodes         9.122  0.101   9.251
clrDR             8.730  0.303   9.058
mergeClusters     8.402  0.111   8.546
plotMahal         8.412  0.011   8.444
filterSCE         7.667  0.148   7.834
compCytof         7.445  0.324   7.797
cluster           7.406  0.163   7.588
plotSpillmat      7.301  0.084   7.402
extractClusters   6.397  0.123   6.541
estCutoffs        6.189  0.199   6.411
runDR             6.039  0.031   6.081
adaptSpillmat     5.653  0.140   5.809
plotYields        5.693  0.028   5.735
plotScatter       5.593  0.032   5.638
computeSpillmat   5.420  0.168   5.602
plotExprs         5.077  0.044   5.135
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/CATALYST.Rcheck/00check.log’
for details.