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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gCrisprTools_2.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/gCrisprTools.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gCrisprTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gCrisprTools’ version ‘2.10.0’
* 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 ‘gCrisprTools’ 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘RobustRankAggreg’
  All declared Imports should be used.
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'ct.targetSetEnrichment.Rd':
  ‘pvalue.cutoff’ ‘organism’ ‘db.cut’ ‘species’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
ct.GREATdb             37.618  2.510  45.983
ct.makeReport          34.406  3.940  45.290
ct.guideCDF            16.287 11.905  31.312
ct.compareContrasts    23.451  1.423  28.517
ct.contrastBarchart    21.773  0.196  24.647
ct.makeContrastReport  17.647  3.057  24.594
ct.upSet               18.606  1.362  23.408
ct.seas                16.099  1.392  21.584
ct.rankSimple          13.436  0.146  15.682
ct.stackGuides          8.791  2.660  12.588
ct.GCbias               8.147  0.686  10.288
ct.seasPrep             7.615  0.797   9.680
ct.makeQCReport         7.147  0.748   9.437
ct.PRC                  6.129  0.904   7.802
ct.CAT                  5.858  0.352   7.840
ct.preprocessFit        5.062  0.090   6.069
ct.signalSummary        4.866  0.114   5.794
ct.simpleResult         4.635  0.335   5.685
ct.normalizeGuides      4.531  0.429   5.668
ct.ROC                  4.704  0.046   5.406
ct.targetSetEnrichment  4.535  0.117   5.698
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘unit.tests.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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/gCrisprTools.Rcheck/00check.log’
for details.