Package: gCrisprTools

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gCrisprTools_1.14.0.tar.gz

StartedAt: 2020-04-15 02:28:22 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:34:49 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 387.2 seconds

RetCode: 0

Status:  OK

CheckDir: gCrisprTools.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gCrisprTools_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/gCrisprTools.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gCrisprTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gCrisprTools’ version ‘1.14.0’
* 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 ‘gCrisprTools’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
* 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 ... 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 ... 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 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 or elapsed time > 5s
                              user system elapsed
ct.makeReport               43.796  4.071  47.405
ct.PantherPathwayEnrichment 33.420  5.095  63.362
ct.guideCDF                 18.387  4.553  23.036
ct.makeContrastReport       19.266  1.914  21.198
ct.makeQCReport             10.507  1.142  11.015
ct.stackGuides               5.890  1.028   6.940
ct.GCbias                    5.498  0.359   5.888
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘unit.tests.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-3.10-bioc/meat/gCrisprTools.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL gCrisprTools
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

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 -- Wed Apr 15 02:34:43 2020 
*********************************************** 
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 
  4.801   0.309   5.123 

name	user	system	elapsed
aln	0.004	0.002	0.006
ann	0.110	0.006	0.117
ct.DirectionalTests	0.542	0.171	0.714
ct.GCbias	5.498	0.359	5.888
ct.PRC	1.221	0.045	1.278
ct.PantherPathwayEnrichment	33.420	5.095	63.362
ct.ROC	0.178	0.009	0.186
ct.RRAaPvals	0.447	0.035	0.488
ct.RRAalpha	0.290	0.011	0.304
ct.alignmentChart	0.004	0.001	0.005
ct.alphaBeta	0.007	0.001	0.008
ct.ecdf	0.001	0.000	0.001
ct.filterReads	0.382	0.091	0.477
ct.gRNARankByReplicate	0.465	0.046	0.514
ct.generateResults	0.699	0.036	0.743
ct.guideCDF	18.387	4.553	23.036
ct.inputCheck	0.106	0.005	0.112
ct.makeContrastReport	19.266	1.914	21.198
ct.makeQCReport	10.507	1.142	11.015
ct.makeReport	43.796	4.071	47.405
ct.normalizeBySlope	1.189	0.111	1.311
ct.normalizeGuides	3.487	0.404	3.931
ct.normalizeMedians	0.741	0.066	0.813
ct.normalizeNTC	0.939	0.083	1.029
ct.normalizeSpline	1.047	0.110	1.162
ct.prepareAnnotation	0.682	0.110	0.796
ct.preprocessFit	2.888	0.069	2.969
ct.rawCountDensities	0.176	0.013	0.191
ct.resultCheck	0.110	0.007	0.116
ct.stackGuides	5.890	1.028	6.940
ct.targetSetEnrichment	0.148	0.006	0.154
ct.topTargets	0.505	0.016	0.525
ct.viewControls	0.349	0.038	0.390
ct.viewGuides	0.368	0.015	0.384
es	0.057	0.002	0.059
essential.genes	0.002	0.001	0.003
fit	0.157	0.004	0.161
resultsDF	0.106	0.003	0.110