Build/check report for BioC 3.23 - CHECK results for Cardinal on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4428
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*

CHECK results for Cardinal on nebbiolo1

To the developers/maintainers of the Cardinal package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Cardinal.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: Cardinal

Version: 3.13.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings Cardinal_3.13.0.tar.gz

StartedAt: 2025-10-30 20:16:10 -0400 (Thu, 30 Oct 2025)

EndedAt: 2025-10-30 20:30:18 -0400 (Thu, 30 Oct 2025)

EllapsedTime: 847.3 seconds

RetCode: 0

Status: OK

CheckDir: Cardinal.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings Cardinal_3.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/Cardinal.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘Cardinal/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Cardinal’ version ‘3.13.0’
* 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 ‘Cardinal’ 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 whether startup messages can be suppressed ... 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Cardinal-package.Rd: bplapply, simple_logger
  MSImagingArrays-class.Rd: ImzMeta-class, ProcessingStep-class
  MSImagingExperiment-class.Rd: ImzMeta-class, ProcessingStep-class
  MeansTest.Rd: lme, chunkApply, bplapply
  ResultsList-class.Rd: SimpleList-class
  SpatialCV.Rd: chunkApply, bplapply, cv_do
  SpatialDGMM.Rd: chunkApply, bplapply
  SpatialFastmap.Rd: chunkApply, bplapply
  SpatialKMeans.Rd: chunkApply, bplapply
  SpatialPCA.Rd: chunkApply, bplapply, irlba
  SpatialPLS.Rd: chunkApply, bplapply
  SpatialResults-class.Rd: DataFrame-class
  SpatialShrunkenCentroids.Rd: chunkApply, bplapply
  SpectraArrays-class.Rd: SimpleList-class
  SpectralImagingArrays-class.Rd: ProcessingStep-class
  SpectralImagingData-class.Rd: ProcessingStep-class
  SpectralImagingExperiment-class.Rd: DataFrame-class,
    ProcessingStep-class
  XDataFrame-class.Rd: DataFrame-class, DataFrame
  colocalized.Rd: chunkApply, bplapply
  estimateDomain.Rd: chunkApply, bplapply, chunkLapply
  findNeighbors.Rd: sparse_mat-class
  normalize.Rd: rescale_sum, rescale_rms, rescale_ref
  peakAlign.Rd: chunkApply, bplapply
  peakPick.Rd: estnoise_diff, estnoise_sd, estnoise_mad,
    estnoise_quant, estnoise_filt, findpeaks_cwt
  peakProcess.Rd: chunkApply, bplapply
  plot-image.Rd: enhance, filt2, plot_image
  plot-spectra.Rd: downsample, plot_signal
  process.Rd: chunkApply, bplapply
  readMSIData.Rd: matter, chunkApply, bplapply
  recalibrate.Rd: warp1_loc, warp1_dtw, warp1_cow
  reduceBaseline.Rd: estbase_loc, estbase_hull, estbase_snip,
    estbase_med
  simulateSpectra.Rd: chunkApply, bplapply
  smooth.Rd: filt1_gauss, filt1_bi, filt1_adapt, filt1_diff,
    filt1_guide, filt1_pag, filt1_sg, filt1_ma
  spatialDists.Rd: chunkApply, bplapply
  spatialWeights.Rd: chunkApply, bplapply, sparse_mat-class
  spectrapply.Rd: chunkApply, bplapply
  summarize.Rd: chunkApply, bplapply
  writeMSIData.Rd: chunkApply, bplapply
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
MeansTest  13.792  0.374  14.166
plot-image  5.087  0.087   5.175
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/Cardinal.Rcheck/00check.log’
for details.

Installation output

Cardinal.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL Cardinal
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘Cardinal’ ...
** this is package ‘Cardinal’ version ‘3.13.0’
** using staged installation
** R
** 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 (Cardinal)

Tests output

Cardinal.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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(Cardinal)
Loading required package: BiocParallel
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: ProtGenerics

Attaching package: 'ProtGenerics'

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

    smooth

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

> 
> test_check("Cardinal")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 782 ]
> 
> proc.time()
   user  system elapsed 
225.339   4.371 228.022

Example timings

Cardinal.Rcheck/Cardinal-Ex.timings

name	user	system	elapsed
MSImagingArrays-class	0.154	0.005	0.159
MSImagingExperiment-class	0.111	0.000	0.112
MassDataFrame-class	0.026	0.001	0.027
MeansTest	13.792	0.374	14.166
PositionDataFrame-class	0.050	0.001	0.050
SpatialDGMM	2.890	0.013	2.904
SpatialFastmap	2.239	0.039	2.278
SpatialKMeans	2.336	0.042	2.377
SpatialNMF	2.223	0.026	2.250
SpatialPCA	2.181	0.031	2.213
SpatialPLS	2.236	0.044	2.280
SpatialShrunkenCentroids	2.999	0.018	3.018
SpectraArrays-class	0.007	0.001	0.008
SpectralImagingArrays-class	0.065	0.000	0.065
SpectralImagingExperiment-class	0.068	0.001	0.069
XDataFrame-class	0.017	0.000	0.016
bin	0.560	0.001	0.562
colocalized	2.603	0.041	2.645
features	2.038	0.010	2.048
findNeighbors	0.051	0.003	0.055
normalize	0.467	0.001	0.469
peakAlign	0.665	0.001	0.665
peakPick	0.734	0.000	0.733
peakProcess	0.660	0.002	0.662
pixels	1.984	0.003	1.987
plot-image	5.087	0.087	5.175
plot-spectra	0.663	0.007	0.670
process	0.640	0.001	0.644
recalibrate	0.686	0.000	0.687
reduceBaseline	0.605	0.000	0.605
simulateSpectra	2.325	0.020	2.345
sliceImage	2.021	0.003	2.025
smooth	0.596	0.001	0.598
spatialDists	2.154	0.016	2.169
spatialWeights	2.238	0.033	2.272
spectrapply	2.017	0.001	2.018
subset	2.244	0.045	2.290
summarize	2.362	0.020	2.387