Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-09-26 12:03 -0400 (Fri, 26 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4831
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4619
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4563
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 281/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CATALYST 1.33.1  (landing page)
Helena L. Crowell
Snapshot Date: 2025-09-25 13:45 -0400 (Thu, 25 Sep 2025)
git_url: https://git.bioconductor.org/packages/CATALYST
git_branch: devel
git_last_commit: 0262c36
git_last_commit_date: 2025-07-13 09:49:24 -0400 (Sun, 13 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for CATALYST on nebbiolo2

To the developers/maintainers of the CATALYST package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CATALYST.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: CATALYST
Version: 1.33.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings CATALYST_1.33.1.tar.gz
StartedAt: 2025-09-25 21:52:26 -0400 (Thu, 25 Sep 2025)
EndedAt: 2025-09-25 22:08:59 -0400 (Thu, 25 Sep 2025)
EllapsedTime: 993.4 seconds
RetCode: 0
Status:   OK  
CheckDir: CATALYST.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings CATALYST_1.33.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/CATALYST.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘CATALYST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CATALYST’ version ‘1.33.1’
* 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      20.129  0.037  21.026
plotMultiHeatmap 16.936  0.007  17.482
plotDR           16.110  0.095  16.867
plotDiffHeatmap  14.803  0.106  16.535
plotExprHeatmap  13.969  0.136  14.774
sce2fcs          12.885  0.102  14.099
pbMDS            10.256  0.185  10.527
plotClusterExprs  9.934  0.065  10.710
plotAbundances    9.569  0.130   9.994
plotFreqHeatmap   9.625  0.041   9.955
clrDR             9.151  0.182   9.585
SCE-accessors     8.035  0.974   9.761
mergeClusters     8.491  0.034  10.123
plotCodes         8.131  0.005   8.571
filterSCE         7.407  0.032   7.658
plotMahal         7.343  0.021   8.855
cluster           6.676  0.196   7.211
compCytof         6.796  0.027   7.051
extractClusters   6.104  0.212   6.582
plotExprs         6.247  0.063   6.356
runDR             5.734  0.073   6.065
plotScatter       5.597  0.034   5.993
plotYields        5.511  0.045   5.752
plotSpillmat      5.383  0.027   5.874
computeSpillmat   5.269  0.028   5.455
estCutoffs        5.110  0.045   5.269
adaptSpillmat     4.761  0.108   5.072
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/CATALYST.Rcheck/00check.log’
for details.


Installation output

CATALYST.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL CATALYST
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘CATALYST’ ...
** this is package ‘CATALYST’ version ‘1.33.1’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CATALYST)

Tests output

CATALYST.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(CATALYST)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> 
> test_check("CATALYST")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 746 ]
> 
> proc.time()
   user  system elapsed 
206.183   6.101 222.654 

Example timings

CATALYST.Rcheck/CATALYST-Ex.timings

nameusersystemelapsed
SCE-accessors8.0350.9749.761
adaptSpillmat4.7610.1085.072
applyCutoffs3.7990.0223.923
assignPrelim2.3070.0012.377
clrDR9.1510.1829.585
cluster6.6760.1967.211
compCytof6.7960.0277.051
computeSpillmat5.2690.0285.455
data0.0030.0070.010
estCutoffs5.1100.0455.269
extractClusters6.1040.2126.582
filterSCE7.4070.0327.658
guessPanel0.0310.0020.034
mergeClusters 8.491 0.03410.123
normCytof3.6250.0103.776
pbMDS10.256 0.18510.527
plotAbundances9.5690.1309.994
plotClusterExprs 9.934 0.06510.710
plotCodes8.1310.0058.571
plotCounts2.2560.0022.259
plotDR16.110 0.09516.867
plotDiffHeatmap14.803 0.10616.535
plotEvents2.5740.0242.759
plotExprHeatmap13.969 0.13614.774
plotExprs6.2470.0636.356
plotFreqHeatmap9.6250.0419.955
plotMahal7.3430.0218.855
plotMultiHeatmap16.936 0.00717.482
plotNRS2.2560.0032.389
plotPbExprs20.129 0.03721.026
plotScatter5.5970.0345.993
plotSpillmat5.3830.0275.874
plotYields5.5110.0455.752
prepData3.1160.1033.220
runDR5.7340.0736.065
sce2fcs12.885 0.10214.099