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### Running command:
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###   /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_3.9.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Cardinal.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘Cardinal/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Cardinal’ version ‘3.9.0’
* 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 12.663  0.388  13.055
* 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.