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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mariner.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mariner_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/mariner.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mariner/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mariner’ version ‘1.0.0’
* package encoding: UTF-8
* 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 ‘mariner’ 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 R 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘plotgardener:::check_page’ ‘plotgardener:::convert_page’
  ‘plotgardener:::current_viewports’ ‘plotgardener:::defaultUnits’
  ‘plotgardener:::pgEnv’
  See the note in ?`:::` about the use of this operator.
* 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 ... OK
* 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
CountMatrix-class         17.841  2.227  29.540
adjustEnrichment          15.901  1.797  23.894
aggPairMcols              10.635  2.348  17.830
calcLoopEnrichment         9.896  1.740  16.375
aggHicMatrices             8.557  1.685  14.962
changePixelRes             8.473  1.009  14.664
selectPixel                7.695  0.669  13.211
pullHicMatrices            7.685  0.477  12.753
pullHicPixels              6.734  0.401  11.360
mergePairs                 5.915  0.583   9.544
counts                     5.992  0.490  10.799
getPairClusters            4.912  0.313   8.412
path                       4.811  0.345   7.709
MergedGInteractions-class  4.377  0.479  10.435
sources                    4.459  0.378   7.842
selectionMethod            4.298  0.242   7.578
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.17-bioc/meat/mariner.Rcheck/00check.log’
for details.