| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:37 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 280/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CATALYST 1.32.1 (landing page) Helena L. Crowell
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| Package: CATALYST |
| Version: 1.32.1 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings CATALYST_1.32.1.tar.gz |
| StartedAt: 2025-10-15 21:27:04 -0400 (Wed, 15 Oct 2025) |
| EndedAt: 2025-10-15 21:39:11 -0400 (Wed, 15 Oct 2025) |
| EllapsedTime: 726.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CATALYST.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings CATALYST_1.32.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CATALYST.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.32.1’
* 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 14.104 0.042 14.098
plotMultiHeatmap 12.829 0.077 12.833
plotDR 12.337 0.078 12.417
plotDiffHeatmap 10.699 0.041 10.716
plotExprHeatmap 9.245 0.057 9.270
sce2fcs 8.761 0.036 8.797
mergeClusters 6.963 0.038 6.995
plotAbundances 6.581 0.062 6.643
plotCodes 6.591 0.027 6.624
pbMDS 6.461 0.039 6.479
plotClusterExprs 6.347 0.080 6.421
clrDR 6.061 0.091 6.152
SCE-accessors 5.894 0.080 5.976
plotFreqHeatmap 5.799 0.054 5.854
runDR 5.574 0.001 5.576
plotMahal 5.486 0.068 5.555
filterSCE 5.001 0.021 5.022
* 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-3.21-bioc/meat/CATALYST.Rcheck/00check.log’
for details.
CATALYST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL CATALYST ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘CATALYST’ ... ** this is package ‘CATALYST’ version ‘1.32.1’ ** 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)
CATALYST.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "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: GenomeInfoDb
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
160.697 2.414 162.341
CATALYST.Rcheck/CATALYST-Ex.timings
| name | user | system | elapsed | |
| SCE-accessors | 5.894 | 0.080 | 5.976 | |
| adaptSpillmat | 3.298 | 0.047 | 3.344 | |
| applyCutoffs | 2.593 | 0.046 | 2.641 | |
| assignPrelim | 1.343 | 0.002 | 1.346 | |
| clrDR | 6.061 | 0.091 | 6.152 | |
| cluster | 4.784 | 0.049 | 4.833 | |
| compCytof | 4.907 | 0.063 | 4.970 | |
| computeSpillmat | 3.890 | 0.027 | 3.918 | |
| data | 0.005 | 0.002 | 0.007 | |
| estCutoffs | 3.374 | 0.080 | 3.454 | |
| extractClusters | 4.598 | 0.010 | 4.609 | |
| filterSCE | 5.001 | 0.021 | 5.022 | |
| guessPanel | 0.020 | 0.004 | 0.024 | |
| mergeClusters | 6.963 | 0.038 | 6.995 | |
| normCytof | 2.360 | 0.017 | 2.377 | |
| pbMDS | 6.461 | 0.039 | 6.479 | |
| plotAbundances | 6.581 | 0.062 | 6.643 | |
| plotClusterExprs | 6.347 | 0.080 | 6.421 | |
| plotCodes | 6.591 | 0.027 | 6.624 | |
| plotCounts | 1.284 | 0.002 | 1.285 | |
| plotDR | 12.337 | 0.078 | 12.417 | |
| plotDiffHeatmap | 10.699 | 0.041 | 10.716 | |
| plotEvents | 1.770 | 0.024 | 1.794 | |
| plotExprHeatmap | 9.245 | 0.057 | 9.270 | |
| plotExprs | 3.865 | 0.024 | 3.889 | |
| plotFreqHeatmap | 5.799 | 0.054 | 5.854 | |
| plotMahal | 5.486 | 0.068 | 5.555 | |
| plotMultiHeatmap | 12.829 | 0.077 | 12.833 | |
| plotNRS | 1.487 | 0.005 | 1.492 | |
| plotPbExprs | 14.104 | 0.042 | 14.098 | |
| plotScatter | 4.472 | 0.026 | 4.500 | |
| plotSpillmat | 4.298 | 0.018 | 4.316 | |
| plotYields | 4.714 | 0.020 | 4.734 | |
| prepData | 1.369 | 0.007 | 1.377 | |
| runDR | 5.574 | 0.001 | 5.576 | |
| sce2fcs | 8.761 | 0.036 | 8.797 | |