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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_1.29.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/CATALYST.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (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 ‘1.29.1’
* 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 ‘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 ... 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 ... 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      18.916  0.084  19.038
plotMultiHeatmap 18.199  0.064  18.303
plotDiffHeatmap  16.411  0.052  16.505
plotDR           16.143  0.148  16.325
sce2fcs          14.921  0.055  15.010
plotExprHeatmap  13.944  0.051  14.024
plotClusterExprs 10.767  0.080  10.881
mergeClusters     9.659  0.036   9.721
plotAbundances    9.527  0.159   9.707
plotFreqHeatmap   9.479  0.088   9.592
pbMDS             9.447  0.076   9.539
plotCodes         9.361  0.036   9.417
clrDR             9.028  0.176   9.230
SCE-accessors     8.746  0.284   9.051
filterSCE         7.954  0.064   8.033
cluster           7.636  0.168   7.820
compCytof         7.670  0.035   7.722
plotMahal         7.426  0.032   7.476
extractClusters   7.206  0.060   7.281
computeSpillmat   6.579  0.152   6.745
runDR             6.145  0.052   6.203
plotSpillmat      6.143  0.036   6.192
estCutoffs        5.996  0.036   6.045
adaptSpillmat     5.854  0.115   5.982
plotYields        5.861  0.012   5.886
plotScatter       5.623  0.056   5.689
plotExprs         4.988  0.040   5.039
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/CATALYST.Rcheck/00check.log’
for details.