Package: gCrisprTools

Version: 1.6.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings gCrisprTools_1.6.0.tar.gz

StartedAt: 2018-04-11 23:39:29 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 23:45:27 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 358.5 seconds

RetCode: 0

Status:  OK

CheckDir: gCrisprTools.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings gCrisprTools_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/gCrisprTools.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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  9.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    1.1Mb
* 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 86.228  2.044  93.128
ct.guideCDF                 29.444  0.152  29.614
ct.makeReport               21.568  0.644  22.237
ct.makeContrastReport       11.932  0.816  13.017
ct.makeQCReport              7.820  0.340   8.176
ct.GCbias                    6.716  0.104   6.827
* 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
  ‘/home/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-pc-linux-gnu (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 Apr 11 23:45:24 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 
  3.152   0.084   3.237 

name	user	system	elapsed
aln	0.004	0.000	0.004
ann	0.080	0.004	0.083
ct.DirectionalTests	0.296	0.064	0.358
ct.GCbias	6.716	0.104	6.827
ct.PRC	0.944	0.012	0.956
ct.PantherPathwayEnrichment	86.228	2.044	93.128
ct.ROC	0.184	0.004	0.190
ct.RRAaPvals	0.352	0.016	0.368
ct.RRAalpha	0.276	0.004	0.280
ct.alignmentChart	0.000	0.004	0.004
ct.alphaBeta	0.004	0.004	0.016
ct.ecdf	0.000	0.000	0.001
ct.filterReads	0.244	0.040	0.283
ct.gRNARankByReplicate	0.436	0.028	0.464
ct.generateResults	1.044	0.028	1.075
ct.guideCDF	29.444	0.152	29.614
ct.inputCheck	0.084	0.000	0.081
ct.makeContrastReport	11.932	0.816	13.017
ct.makeQCReport	7.820	0.340	8.176
ct.makeReport	21.568	0.644	22.237
ct.normalizeBySlope	1.228	0.036	1.267
ct.normalizeGuides	3.804	0.164	3.975
ct.normalizeMedians	0.804	0.028	0.833
ct.normalizeNTC	0.988	0.028	1.019
ct.normalizeSpline	1.080	0.044	1.123
ct.prepareAnnotation	0.524	0.024	0.549
ct.preprocessFit	2.080	0.164	2.247
ct.rawCountDensities	0.120	0.004	0.126
ct.resultCheck	0.096	0.004	0.102
ct.stackGuides	4.944	0.044	5.000
ct.targetSetEnrichment	0.132	0.000	0.131
ct.topTargets	0.4	0.0	0.4
ct.viewControls	0.236	0.000	0.238
ct.viewGuides	0.312	0.004	0.316
es	0.072	0.000	0.074
essential.genes	0.000	0.000	0.002
fit	0.208	0.000	0.210
resultsDF	0.100	0.008	0.110