##############################################################################
##############################################################################
###
### Running command:
###
###   /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
###
##############################################################################
##############################################################################


* 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      18.785  0.124  18.951
plotMultiHeatmap 18.112  0.028  18.176
plotDiffHeatmap  15.951  0.032  16.053
sce2fcs          15.275  0.028  15.340
plotDR           14.830  0.096  14.963
plotExprHeatmap  13.480  0.056  13.564
plotClusterExprs 10.423  0.040  10.493
SCE-accessors     9.590  0.224   9.840
plotFreqHeatmap   9.552  0.079   9.653
pbMDS             9.454  0.136   9.612
mergeClusters     9.415  0.076   9.519
plotCodes         9.069  0.036   9.127
clrDR             8.764  0.072   8.864
plotAbundances    8.571  0.091   8.684
filterSCE         7.884  0.012   7.915
extractClusters   7.438  0.092   7.549
compCytof         7.433  0.052   7.503
plotMahal         7.370  0.000   7.386
cluster           6.488  0.024   6.528
computeSpillmat   6.253  0.143   6.410
plotSpillmat      6.059  0.048   6.120
runDR             5.953  0.011   5.976
plotYields        5.788  0.040   5.840
adaptSpillmat     5.571  0.107   5.692
plotScatter       5.351  0.028   5.390
estCutoffs        5.235  0.044   5.293
* 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.