Package: gCrisprTools

Version: 1.12.0

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_1.12.0.tar.gz

StartedAt: 2019-10-16 02:58:49 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:07:03 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 494.3 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_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/gCrisprTools.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.12.0’
* 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.PantherPathwayEnrichment 150.690  8.368 161.062
ct.makeReport                53.380  8.073  60.951
ct.guideCDF                  20.996 13.360  34.363
ct.makeContrastReport        22.968  4.183  27.260
ct.makeQCReport              12.004  1.761  12.992
ct.stackGuides                7.458  2.113   9.571
ct.GCbias                     5.841  0.650   6.500
* 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-3.9-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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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")
PANTHER.db version 1.0.4


RUNIT TEST PROTOCOL -- Wed Oct 16 03:06:56 2019 
*********************************************** 
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 
  5.959   0.725   6.635 

name	user	system	elapsed
aln	0.005	0.004	0.009
ann	0.144	0.014	0.159
ct.DirectionalTests	0.801	0.425	1.228
ct.GCbias	5.841	0.650	6.500
ct.PRC	1.196	0.059	1.261
ct.PantherPathwayEnrichment	150.690	8.368	161.062
ct.ROC	0.228	0.067	0.296
ct.RRAaPvals	0.503	0.147	0.650
ct.RRAalpha	0.363	0.135	0.497
ct.alignmentChart	0.008	0.002	0.011
ct.alphaBeta	0.017	0.001	0.018
ct.ecdf	0.002	0.001	0.002
ct.filterReads	0.391	0.132	0.523
ct.gRNARankByReplicate	0.580	0.224	0.806
ct.generateResults	0.823	0.183	1.006
ct.guideCDF	20.996	13.360	34.363
ct.inputCheck	0.138	0.018	0.156
ct.makeContrastReport	22.968	4.183	27.260
ct.makeQCReport	12.004	1.761	12.992
ct.makeReport	53.380	8.073	60.951
ct.normalizeBySlope	1.149	0.169	1.320
ct.normalizeGuides	3.326	0.590	3.936
ct.normalizeMedians	0.649	0.097	0.752
ct.normalizeNTC	1.080	0.397	1.477
ct.normalizeSpline	0.991	0.171	1.164
ct.prepareAnnotation	0.674	0.078	0.757
ct.preprocessFit	3.996	0.093	4.090
ct.rawCountDensities	0.185	0.025	0.210
ct.resultCheck	0.165	0.018	0.184
ct.stackGuides	7.458	2.113	9.571
ct.targetSetEnrichment	0.139	0.021	0.159
ct.topTargets	0.573	0.065	0.639
ct.viewControls	0.558	0.436	0.993
ct.viewGuides	0.482	0.036	0.518
es	0.054	0.009	0.063
essential.genes	0.002	0.001	0.004
fit	0.169	0.013	0.181
resultsDF	0.119	0.011	0.129