BioC 3.4: CHECK report for gCrisprTools on morelia

Package: gCrisprTools

Version: 0.99.92

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gCrisprTools_0.99.92.tar.gz

StartedAt: 2016-09-20 06:50:28 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 06:55:01 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 272.2 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_0.99.92.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/gCrisprTools.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘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  7.1Mb
  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.makeReport               33.918  3.285  37.088
ct.PantherPathwayEnrichment 30.957  0.873  34.004
ct.RRAaPvals                24.662  5.645  16.155
ct.makeQCReport             22.095  1.607  23.591
ct.guideCDF                 12.690  6.609  19.305
ct.makeContrastReport       13.252  1.566  14.968
ct.generateResults           6.403  2.352   2.620
ct.RRAalphaBatch             5.441  0.381   5.825
* 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-3.4-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	0.001	0.005
ann	0.096	0.007	0.105
ct.DirectionalTests	0.354	0.090	0.445
ct.GCbias	4.374	0.185	4.586
ct.PRC	1.075	0.027	1.149
ct.PantherPathwayEnrichment	30.957	0.873	34.004
ct.ROC	0.134	0.010	0.144
ct.RRAaPvals	24.662	5.645	16.155
ct.RRAalpha	0.676	0.077	0.753
ct.RRAalphaBatch	5.441	0.381	5.825
ct.alignmentChart	0.004	0.001	0.011
ct.alphaBeta	0.006	0.000	0.007
ct.ecdf	0.001	0.000	0.001
ct.filterReads	0.339	0.150	0.495
ct.gRNARankByReplicate	0.386	0.037	0.456
ct.generateResults	6.403	2.352	2.620
ct.guideCDF	12.690	6.609	19.305
ct.inputCheck	0.117	0.008	0.125
ct.makeContrastReport	13.252	1.566	14.968
ct.makeQCReport	22.095	1.607	23.591
ct.makeReport	33.918	3.285	37.088
ct.normalizeBySlope	1.044	0.089	1.134
ct.normalizeGuides	3.157	0.371	3.604
ct.normalizeMedians	0.553	0.050	0.629
ct.normalizeNTC	0.810	0.067	0.895
ct.normalizeSpline	0.951	0.122	1.131
ct.prepareAnnotation	0.728	0.046	0.793
ct.preprocessFit	2.683	0.047	2.729
ct.rawCountDensities	0.114	0.009	0.124
ct.resultCheck	0.093	0.005	0.098
ct.stackGuides	3.996	0.948	4.946
ct.targetSetEnrichment	0.104	0.008	0.111
ct.topTargets	0.347	0.022	0.369
ct.viewControls	0.281	0.032	0.314
ct.viewGuides	0.307	0.018	0.325
es	0.043	0.005	0.049
essential.genes	0.002	0.001	0.002
fit	0.175	0.009	0.185
resultsDF	0.151	0.008	0.159