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This page was generated on 2025-10-06 11:37 -0400 (Mon, 06 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4832
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4613
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4554
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4585
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 275/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Cardinal 3.10.0  (landing page)
Kylie Ariel Bemis
Snapshot Date: 2025-10-02 13:40 -0400 (Thu, 02 Oct 2025)
git_url: https://git.bioconductor.org/packages/Cardinal
git_branch: RELEASE_3_21
git_last_commit: 07d9273
git_last_commit_date: 2025-04-15 10:37:46 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


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: 3.10.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Cardinal_3.10.0.tar.gz
StartedAt: 2025-10-05 21:27:42 -0400 (Sun, 05 Oct 2025)
EndedAt: 2025-10-05 21:40:32 -0400 (Sun, 05 Oct 2025)
EllapsedTime: 770.1 seconds
RetCode: 0
Status:   OK  
CheckDir: Cardinal.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Cardinal_3.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Cardinal.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 ‘Cardinal/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Cardinal’ version ‘3.10.0’
* 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  13.398  0.397  13.798
plot-image  5.054  0.079   5.134
* 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-3.21-bioc/meat/Cardinal.Rcheck/00check.log’
for details.


Installation output

Cardinal.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL Cardinal
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘Cardinal’ ...
** this is package ‘Cardinal’ version ‘3.10.0’
** 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 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(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 756 ]
> 
> proc.time()
   user  system elapsed 
178.954   5.595 182.814 

Example timings

Cardinal.Rcheck/Cardinal-Ex.timings

nameusersystemelapsed
MSImagingArrays-class0.1540.0120.167
MSImagingExperiment-class0.1180.0170.135
MassDataFrame-class0.0240.0000.026
MeansTest13.398 0.39713.798
PositionDataFrame-class0.0570.0020.060
SpatialDGMM2.6470.0102.658
SpatialFastmap2.1520.0392.192
SpatialKMeans2.2950.0522.348
SpatialNMF2.1580.0152.175
SpatialPCA2.1750.0082.184
SpatialPLS2.1180.0012.120
SpatialShrunkenCentroids2.8620.0042.867
SpectraArrays-class0.0080.0000.008
SpectralImagingArrays-class0.0600.0010.062
SpectralImagingExperiment-class0.0620.0000.063
XDataFrame-class0.0140.0000.015
bin0.8540.0430.896
colocalized2.1950.0122.208
features2.0140.0362.050
findNeighbors0.0500.0020.052
normalize0.4540.0020.456
peakAlign0.6090.0030.613
peakPick0.7180.0010.719
peakProcess0.6360.0030.639
pixels1.9500.0011.953
plot-image5.0540.0795.134
plot-spectra0.6560.0050.661
process0.6230.0040.626
recalibrate0.7230.0000.723
reduceBaseline0.6000.0000.599
simulateSpectra2.3720.0162.395
sliceImage2.0340.0052.040
smooth0.5940.0000.594
spatialDists2.2030.0092.212
spatialWeights2.1860.0322.218
spectrapply2.0230.0042.027
subset2.2520.0042.256
summarize2.2020.0022.203