BioC 3.4: CHECK report for gCrisprTools on zin1

Package: gCrisprTools

Version: 0.99.92

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings gCrisprTools_0.99.92.tar.gz

StartedAt: 2016-09-20 06:46:28 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 06:49:53 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 204.8 seconds

RetCode: 0

Status:  OK

CheckDir: gCrisprTools.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings gCrisprTools_0.99.92.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/gCrisprTools.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘0.99.92’
* 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  6.9Mb
  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 30.116  1.016  31.775
ct.makeReport               21.516  0.156  21.678
ct.RRAaPvals                15.884  2.296  11.551
ct.makeQCReport             13.920  0.168  14.097
ct.guideCDF                 12.200  0.076  12.274
ct.makeContrastReport        9.428  0.200   9.814
ct.generateResults           3.456  3.112   2.588
ct.GCbias                    6.076  0.068   6.172
* 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-3.4-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	0.000	0.003
ann	0.076	0.008	0.084
ct.DirectionalTests	0.348	0.076	0.425
ct.GCbias	6.076	0.068	6.172
ct.PRC	0.872	0.008	0.878
ct.PantherPathwayEnrichment	30.116	1.016	31.775
ct.ROC	0.148	0.016	0.164
ct.RRAaPvals	15.884	2.296	11.551
ct.RRAalpha	0.320	0.000	0.322
ct.RRAalphaBatch	4.064	0.056	4.118
ct.alignmentChart	0.004	0.000	0.004
ct.alphaBeta	0.008	0.000	0.007
ct.ecdf	0	0	0
ct.filterReads	0.296	0.000	0.296
ct.gRNARankByReplicate	0.476	0.012	0.485
ct.generateResults	3.456	3.112	2.588
ct.guideCDF	12.200	0.076	12.274
ct.inputCheck	0.084	0.000	0.082
ct.makeContrastReport	9.428	0.200	9.814
ct.makeQCReport	13.920	0.168	14.097
ct.makeReport	21.516	0.156	21.678
ct.normalizeBySlope	1.120	0.016	1.144
ct.normalizeGuides	3.520	0.084	3.604
ct.normalizeMedians	0.768	0.012	0.781
ct.normalizeNTC	0.900	0.020	0.928
ct.normalizeSpline	1.076	0.020	1.096
ct.prepareAnnotation	0.560	0.024	0.586
ct.preprocessFit	2.824	0.024	2.848
ct.rawCountDensities	0.136	0.000	0.143
ct.resultCheck	0.104	0.000	0.106
ct.stackGuides	4.32	0.02	4.34
ct.targetSetEnrichment	0.116	0.000	0.117
ct.topTargets	0.412	0.012	0.422
ct.viewControls	0.252	0.000	0.251
ct.viewGuides	0.332	0.000	0.329
es	0.044	0.004	0.050
essential.genes	0.000	0.000	0.002
fit	0.164	0.000	0.161
resultsDF	0.108	0.000	0.110