BioC 3.5: CHECK report for gCrisprTools on veracruz2

Package: gCrisprTools

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gCrisprTools_1.4.0.tar.gz

StartedAt: 2017-10-18 03:50:57 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 03:55:50 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 292.9 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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/gCrisprTools.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.4.0’
* 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 49.865  1.222  54.328
ct.makeReport               40.311  3.542  45.131
ct.guideCDF                 15.584  7.683  24.992
ct.makeContrastReport       19.275  1.681  21.958
ct.makeQCReport             11.355  0.612  12.150
ct.stackGuides               5.768  0.955   6.896
ct.GCbias                    5.494  0.271   5.940
* 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-3.5-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)

name	user	system	elapsed
aln	0.004	0.001	0.005
ann	0.102	0.006	0.115
ct.DirectionalTests	0.449	0.146	0.614
ct.GCbias	5.494	0.271	5.940
ct.PRC	1.042	0.028	1.096
ct.PantherPathwayEnrichment	49.865	1.222	54.328
ct.ROC	0.210	0.009	0.225
ct.RRAaPvals	0.373	0.023	0.407
ct.RRAalpha	0.276	0.014	0.299
ct.alignmentChart	0.004	0.001	0.006
ct.alphaBeta	0.008	0.001	0.010
ct.ecdf	0.001	0.000	0.001
ct.filterReads	0.323	0.040	0.399
ct.gRNARankByReplicate	0.388	0.039	0.441
ct.generateResults	0.710	0.096	0.839
ct.guideCDF	15.584	7.683	24.992
ct.inputCheck	0.098	0.007	0.106
ct.makeContrastReport	19.275	1.681	21.958
ct.makeQCReport	11.355	0.612	12.150
ct.makeReport	40.311	3.542	45.131
ct.normalizeBySlope	1.043	0.076	1.132
ct.normalizeGuides	3.006	0.340	3.460
ct.normalizeMedians	0.671	0.063	0.759
ct.normalizeNTC	0.854	0.069	0.958
ct.normalizeSpline	1.064	0.125	1.229
ct.prepareAnnotation	0.600	0.044	0.663
ct.preprocessFit	2.891	0.064	3.041
ct.rawCountDensities	0.140	0.011	0.156
ct.resultCheck	0.115	0.010	0.127
ct.stackGuides	5.768	0.955	6.896
ct.targetSetEnrichment	0.135	0.007	0.147
ct.topTargets	0.443	0.025	0.481
ct.viewControls	0.348	0.078	0.440
ct.viewGuides	0.368	0.018	0.395
es	0.091	0.005	0.100
essential.genes	0.002	0.001	0.003
fit	0.211	0.009	0.225
resultsDF	0.122	0.006	0.130