##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Cardinal_3.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Cardinal.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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  17.069  0.204  17.364
plot-image  6.207  0.045   6.289
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/Cardinal.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Cardinal
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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)

R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
211.546   6.664 217.908