BioC 3.5: CHECK report for gCrisprTools on oaxaca

Package: gCrisprTools

Version: 1.2.70

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gCrisprTools_1.2.70.tar.gz

StartedAt: 2017-03-04 03:11:10 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 03:16:29 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 319.3 seconds

RetCode: 0

Status:  OK

CheckDir: gCrisprTools.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gCrisprTools_1.2.70.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/gCrisprTools.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.2.70’
* 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 58.022  1.169  60.963
ct.makeReport               37.689  3.149  41.200
ct.makeContrastReport       19.875  1.844  21.750
ct.guideCDF                 14.243  5.876  20.127
ct.makeQCReport              9.925  0.543  12.590
ct.RRAaPvals                 5.573  1.337   4.358
ct.GCbias                    5.373  0.228   5.631
* 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	0.003	0.001	0.004
ann	0.093	0.010	0.102
ct.DirectionalTests	0.402	0.117	0.518
ct.GCbias	5.373	0.228	5.631
ct.PRC	1.262	0.033	1.326
ct.PantherPathwayEnrichment	58.022	1.169	60.963
ct.ROC	0.267	0.013	0.280
ct.RRAaPvals	5.573	1.337	4.358
ct.RRAalpha	0.348	0.024	0.374
ct.RRAalphaBatch	1.530	0.138	1.670
ct.alignmentChart	0.004	0.001	0.005
ct.alphaBeta	0.010	0.001	0.037
ct.ecdf	0.001	0.000	0.001
ct.filterReads	0.507	0.042	0.550
ct.gRNARankByReplicate	0.551	0.058	0.611
ct.generateResults	1.882	0.844	1.079
ct.guideCDF	14.243	5.876	20.127
ct.inputCheck	0.123	0.009	0.133
ct.makeContrastReport	19.875	1.844	21.750
ct.makeQCReport	9.925	0.543	12.590
ct.makeReport	37.689	3.149	41.200
ct.normalizeBySlope	0.849	0.063	1.002
ct.normalizeGuides	2.570	0.277	2.992
ct.normalizeMedians	0.529	0.048	0.598
ct.normalizeNTC	0.676	0.053	0.750
ct.normalizeSpline	0.869	0.097	0.985
ct.prepareAnnotation	0.530	0.036	0.584
ct.preprocessFit	2.381	0.051	2.430
ct.rawCountDensities	0.109	0.008	0.587
ct.resultCheck	0.096	0.006	0.101
ct.stackGuides	3.967	0.864	4.960
ct.targetSetEnrichment	0.106	0.007	0.114
ct.topTargets	0.342	0.020	0.362
ct.viewControls	0.246	0.035	0.282
ct.viewGuides	0.330	0.044	0.373
es	0.071	0.005	0.076
essential.genes	0.001	0.001	0.002
fit	0.184	0.007	0.191
resultsDF	0.095	0.006	0.101