Package: gCrisprTools

Version: 1.14.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings gCrisprTools_1.14.0.tar.gz

StartedAt: 2020-04-15 04:07:46 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:13:52 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 365.8 seconds

RetCode: 0

Status:  OK

CheckDir: gCrisprTools.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings gCrisprTools_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/gCrisprTools.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.14.0’
* 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  8.2Mb
  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               26.356  0.240  27.024
ct.PantherPathwayEnrichment 24.820  0.500  34.206
ct.guideCDF                 18.832  0.016  18.885
ct.makeContrastReport       12.568  0.284  13.021
ct.GCbias                    8.752  0.124   8.914
ct.makeQCReport              7.208  0.300   7.538
ct.stackGuides               5.944  0.012   5.987
ct.normalizeGuides           4.976  0.104   5.092
* 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-3.10-bioc/meat/gCrisprTools.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL gCrisprTools
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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-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")


RUNIT TEST PROTOCOL -- Wed Apr 15 04:13:49 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 
  5.148   0.156   5.370 

name	user	system	elapsed
aln	0.000	0.004	0.002
ann	0.084	0.000	0.085
ct.DirectionalTests	0.476	0.104	0.597
ct.GCbias	8.752	0.124	8.914
ct.PRC	1.004	0.008	1.013
ct.PantherPathwayEnrichment	24.820	0.500	34.206
ct.ROC	0.164	0.000	0.165
ct.RRAaPvals	0.504	0.028	0.534
ct.RRAalpha	0.368	0.008	0.378
ct.alignmentChart	0.004	0.000	0.005
ct.alphaBeta	0.004	0.004	0.009
ct.ecdf	0.004	0.000	0.001
ct.filterReads	0.500	0.004	0.507
ct.gRNARankByReplicate	0.828	0.028	0.854
ct.generateResults	0.996	0.012	1.010
ct.guideCDF	18.832	0.016	18.885
ct.inputCheck	0.140	0.008	0.148
ct.makeContrastReport	12.568	0.284	13.021
ct.makeQCReport	7.208	0.300	7.538
ct.makeReport	26.356	0.240	27.024
ct.normalizeBySlope	1.644	0.056	1.702
ct.normalizeGuides	4.976	0.104	5.092
ct.normalizeMedians	1.056	0.008	1.071
ct.normalizeNTC	1.308	0.016	1.332
ct.normalizeSpline	1.508	0.020	1.531
ct.prepareAnnotation	0.988	0.084	1.079
ct.preprocessFit	3.128	0.020	3.159
ct.rawCountDensities	0.208	0.000	0.208
ct.resultCheck	0.168	0.004	0.174
ct.stackGuides	5.944	0.012	5.987
ct.targetSetEnrichment	0.180	0.008	0.188
ct.topTargets	0.596	0.004	0.604
ct.viewControls	0.380	0.008	0.393
ct.viewGuides	0.524	0.004	0.557
es	0.128	0.004	0.133
essential.genes	0.004	0.000	0.002
fit	0.228	0.004	0.241
resultsDF	0.112	0.004	0.115