Package: gCrisprTools

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gCrisprTools_1.6.0.tar.gz

StartedAt: 2018-04-12 04:02:13 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 04:08:04 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 351.9 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 --no-vignettes --timings gCrisprTools_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/gCrisprTools.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.6.0’
* 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  9.4Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    1.4Mb
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
ct.PantherPathwayEnrichment 103.490  3.368 112.253
ct.makeReport                39.331  3.257  43.571
ct.guideCDF                  14.328  7.355  22.100
ct.makeContrastReport        17.764  1.782  20.133
ct.makeQCReport              10.776  0.542  11.481
ct.stackGuides                5.405  0.899   6.449
ct.GCbias                     5.408  0.289   5.792
* 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-3.6-bioc/meat/gCrisprTools.Rcheck/00check.log’
for details.

* installing *source* package ‘gCrisprTools’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gCrisprTools)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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 -- Thu Apr 12 04:07:58 2018 
*********************************************** 
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 
  3.839   0.161   4.081 

name	user	system	elapsed
aln	0.004	0.001	0.005
ann	0.089	0.005	0.095
ct.DirectionalTests	0.509	0.170	0.694
ct.GCbias	5.408	0.289	5.792
ct.PRC	1.027	0.024	1.080
ct.PantherPathwayEnrichment	103.490	3.368	112.253
ct.ROC	0.220	0.039	0.260
ct.RRAaPvals	0.440	0.111	0.554
ct.RRAalpha	0.318	0.073	0.392
ct.alignmentChart	0.007	0.001	0.008
ct.alphaBeta	0.012	0.002	0.013
ct.ecdf	0.002	0.000	0.002
ct.filterReads	0.353	0.092	0.451
ct.gRNARankByReplicate	0.418	0.097	0.520
ct.generateResults	0.841	0.169	1.032
ct.guideCDF	14.328	7.355	22.100
ct.inputCheck	0.075	0.006	0.081
ct.makeContrastReport	17.764	1.782	20.133
ct.makeQCReport	10.776	0.542	11.481
ct.makeReport	39.331	3.257	43.571
ct.normalizeBySlope	1.002	0.078	1.096
ct.normalizeGuides	2.897	0.281	3.247
ct.normalizeMedians	0.737	0.185	0.945
ct.normalizeNTC	0.840	0.062	0.930
ct.normalizeSpline	0.963	0.084	1.069
ct.prepareAnnotation	0.574	0.039	0.641
ct.preprocessFit	2.750	0.076	2.882
ct.rawCountDensities	0.138	0.011	0.151
ct.resultCheck	0.121	0.008	0.132
ct.stackGuides	5.405	0.899	6.449
ct.targetSetEnrichment	0.130	0.010	0.143
ct.topTargets	0.438	0.036	0.488
ct.viewControls	0.282	0.042	0.327
ct.viewGuides	0.349	0.027	0.383
es	0.092	0.010	0.104
essential.genes	0.002	0.001	0.003
fit	0.200	0.012	0.212
resultsDF	0.110	0.010	0.121