Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-10-03 12:07 -0400 (Fri, 03 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4845
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4632
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4577
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 282/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CATALYST 1.33.1  (landing page)
Helena L. Crowell
Snapshot Date: 2025-10-02 13:45 -0400 (Thu, 02 Oct 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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: CATALYST
Version: 1.33.1
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_1.33.1.tar.gz
StartedAt: 2025-10-03 05:24:43 -0000 (Fri, 03 Oct 2025)
EndedAt: 2025-10-03 05:38:20 -0000 (Fri, 03 Oct 2025)
EllapsedTime: 816.8 seconds
RetCode: 0
Status:   OK  
CheckDir: CATALYST.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.33.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/CATALYST.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 ‘1.33.1’
* 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      22.067  0.044  22.170
plotMultiHeatmap 19.572  0.079  19.708
plotDiffHeatmap  16.620  0.040  16.754
plotDR           16.245  0.087  16.388
plotExprHeatmap  14.541  0.128  14.709
sce2fcs          13.224  0.052  13.315
plotClusterExprs 10.383  0.040  10.464
plotFreqHeatmap   9.786  0.056   9.870
plotAbundances    9.468  0.060   9.559
plotCodes         9.412  0.024   9.465
pbMDS             9.327  0.092   9.447
clrDR             8.940  0.071   9.038
SCE-accessors     8.381  0.164   8.574
plotMahal         8.457  0.008   8.490
mergeClusters     8.221  0.024   8.276
cluster           7.402  0.052   7.476
compCytof         7.427  0.020   7.469
extractClusters   6.598  0.008   6.626
filterSCE         6.463  0.036   6.518
computeSpillmat   6.200  0.128   6.345
plotScatter       6.145  0.100   6.260
plotExprs         6.172  0.024   6.215
plotSpillmat      6.176  0.008   6.201
plotYields        5.961  0.028   6.006
adaptSpillmat     5.477  0.084   5.577
runDR             5.206  0.000   5.220
estCutoffs        5.041  0.044   5.096
* 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-3.22-bioc/meat/CATALYST.Rcheck/00check.log’
for details.


Installation output

CATALYST.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL CATALYST
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
236.305   3.200 240.198 

Example timings

CATALYST.Rcheck/CATALYST-Ex.timings

nameusersystemelapsed
SCE-accessors8.3810.1648.574
adaptSpillmat5.4770.0845.577
applyCutoffs4.2040.0444.261
assignPrelim2.1850.0122.203
clrDR8.9400.0719.038
cluster7.4020.0527.476
compCytof7.4270.0207.469
computeSpillmat6.2000.1286.345
data0.0080.0000.008
estCutoffs5.0410.0445.096
extractClusters6.5980.0086.626
filterSCE6.4630.0366.518
guessPanel0.0320.0000.031
mergeClusters8.2210.0248.276
normCytof3.4380.0193.469
pbMDS9.3270.0929.447
plotAbundances9.4680.0609.559
plotClusterExprs10.383 0.04010.464
plotCodes9.4120.0249.465
plotCounts2.0770.0042.088
plotDR16.245 0.08716.388
plotDiffHeatmap16.620 0.04016.754
plotEvents2.8360.0002.844
plotExprHeatmap14.541 0.12814.709
plotExprs6.1720.0246.215
plotFreqHeatmap9.7860.0569.870
plotMahal8.4570.0088.490
plotMultiHeatmap19.572 0.07919.708
plotNRS2.3770.0002.384
plotPbExprs22.067 0.04422.170
plotScatter6.1450.1006.260
plotSpillmat6.1760.0086.201
plotYields5.9610.0286.006
prepData2.9720.0363.016
runDR5.2060.0005.220
sce2fcs13.224 0.05213.315