BioC 3.5: CHECK report for gCrisprTools on toluca2

Package: gCrisprTools

Version: 1.2.72

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gCrisprTools_1.2.72.tar.gz

StartedAt: 2017-04-23 04:09:38 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 04:14:49 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 310.5 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_1.2.72.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/gCrisprTools.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.2.72’
* 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.makeReport               47.518  3.762  52.121
ct.PantherPathwayEnrichment 42.548  1.194  45.852
ct.makeContrastReport       23.174  1.911  27.161
ct.guideCDF                 15.671  6.075  22.569
ct.makeQCReport             11.845  0.564  12.644
ct.stackGuides               6.266  1.312   7.649
ct.GCbias                    5.958  0.345   6.368
* 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	0.111	0.015	0.127
ct.DirectionalTests	0.504	0.147	0.653
ct.GCbias	5.958	0.345	6.368
ct.PRC	1.297	0.067	1.381
ct.PantherPathwayEnrichment	42.548	1.194	45.852
ct.ROC	0.260	0.017	0.331
ct.RRAaPvals	1.078	0.204	1.433
ct.RRAalpha	0.319	0.015	0.337
ct.alignmentChart	0.005	0.000	0.005
ct.alphaBeta	0.008	0.001	0.009
ct.ecdf	0.001	0.000	0.001
ct.filterReads	0.502	0.047	0.555
ct.gRNARankByReplicate	0.534	0.052	0.658
ct.generateResults	0.817	0.099	1.020
ct.guideCDF	15.671	6.075	22.569
ct.inputCheck	0.111	0.007	0.123
ct.makeContrastReport	23.174	1.911	27.161
ct.makeQCReport	11.845	0.564	12.644
ct.makeReport	47.518	3.762	52.121
ct.normalizeBySlope	1.208	0.095	1.308
ct.normalizeGuides	3.676	0.391	4.158
ct.normalizeMedians	0.783	0.116	0.907
ct.normalizeNTC	0.950	0.074	1.032
ct.normalizeSpline	1.189	0.113	1.313
ct.prepareAnnotation	0.799	0.061	0.867
ct.preprocessFit	3.735	0.087	3.853
ct.rawCountDensities	0.164	0.013	0.179
ct.resultCheck	0.137	0.008	0.146
ct.stackGuides	6.266	1.312	7.649
ct.targetSetEnrichment	0.150	0.011	0.164
ct.topTargets	0.495	0.029	0.536
ct.viewControls	0.373	0.041	0.418
ct.viewGuides	0.469	0.057	0.535
es	0.105	0.005	0.110
essential.genes	0.003	0.001	0.003
fit	0.259	0.009	0.272
resultsDF	0.139	0.006	0.146