BioC 3.4: CHECK report for gCrisprTools on malbec1

Package: gCrisprTools

Version: 1.0.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings gCrisprTools_1.0.0.tar.gz

StartedAt: 2017-04-14 22:39:27 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 22:42:58 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 211.2 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_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/gCrisprTools.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.0.0’
* 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  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 32.732  0.268  33.640
ct.RRAaPvals                23.320  4.572  10.905
ct.makeReport               19.988  0.116  20.119
ct.makeQCReport             12.632  0.100  12.751
ct.guideCDF                 10.772  0.028  10.804
ct.makeContrastReport        8.876  0.156   9.053
ct.GCbias                    6.728  0.068   6.799
ct.generateResults           3.484  1.772   1.912
ct.RRAalphaBatch             5.176  0.072   5.253
* 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	0.000	0.000	0.002
ann	0.084	0.008	0.091
ct.DirectionalTests	0.292	0.068	0.359
ct.GCbias	6.728	0.068	6.799
ct.PRC	0.928	0.008	0.938
ct.PantherPathwayEnrichment	32.732	0.268	33.640
ct.ROC	0.140	0.008	0.146
ct.RRAaPvals	23.320	4.572	10.905
ct.RRAalpha	0.496	0.012	0.507
ct.RRAalphaBatch	5.176	0.072	5.253
ct.alignmentChart	0.004	0.000	0.004
ct.alphaBeta	0.004	0.000	0.007
ct.ecdf	0.000	0.000	0.001
ct.filterReads	0.276	0.000	0.275
ct.gRNARankByReplicate	0.452	0.000	0.454
ct.generateResults	3.484	1.772	1.912
ct.guideCDF	10.772	0.028	10.804
ct.inputCheck	0.08	0.00	0.08
ct.makeContrastReport	8.876	0.156	9.053
ct.makeQCReport	12.632	0.100	12.751
ct.makeReport	19.988	0.116	20.119
ct.normalizeBySlope	1.452	0.016	1.469
ct.normalizeGuides	3.992	0.052	4.049
ct.normalizeMedians	0.776	0.012	0.789
ct.normalizeNTC	1.000	0.008	1.006
ct.normalizeSpline	1.148	0.008	1.157
ct.prepareAnnotation	0.560	0.012	0.575
ct.preprocessFit	2.380	0.020	2.404
ct.rawCountDensities	0.128	0.000	0.129
ct.resultCheck	0.100	0.004	0.103
ct.stackGuides	4.192	0.008	4.203
ct.targetSetEnrichment	0.112	0.000	0.114
ct.topTargets	0.376	0.000	0.375
ct.viewControls	0.236	0.000	0.235
ct.viewGuides	0.304	0.000	0.302
es	0.052	0.000	0.051
essential.genes	0.004	0.000	0.001
fit	0.152	0.004	0.159
resultsDF	0.108	0.000	0.109