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### Running command:
###
###   /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_2.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/gCrisprTools.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 ‘2.12.0’
* 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            36.648  2.328  40.865
ct.makeReport         33.523  3.441  39.972
ct.guideCDF           17.325 11.982  31.176
ct.compareContrasts   23.327  1.417  28.424
ct.contrastBarchart   21.622  0.123  23.191
ct.upSet              18.108  1.276  19.979
ct.makeContrastReport 16.326  2.511  20.858
ct.seas               15.967  1.493  19.575
ct.rankSimple         12.918  0.058  13.517
ct.stackGuides         8.604  2.259  11.259
ct.GCbias              8.091  0.632   9.367
ct.seasPrep            7.472  0.750   8.906
ct.makeQCReport        7.076  0.639   8.541
ct.PRC                 6.010  0.784   6.951
ct.CAT                 5.775  0.330   6.508
ct.simpleResult        4.651  0.334   5.374
ct.preprocessFit       4.901  0.079   5.167
ct.signalSummary       4.745  0.112   5.171
ct.normalizeGuides     4.485  0.362   5.147
ct.ROC                 4.686  0.045   5.469
* 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-3.20-bioc/meat/gCrisprTools.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gCrisprTools
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘gCrisprTools’ ...
** using staged installation
** R
** data
** 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 (gCrisprTools)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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.

> #require("BiocGenerics", quietly = TRUE)
> BiocGenerics:::testPackage("gCrisprTools")


RUNIT TEST PROTOCOL -- Tue Dec 31 04:07:41 2024 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
gCrisprTools RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 15.910   0.868  19.280