BioC 3.5: CHECK report for gCrisprTools on malbec2

Package: gCrisprTools

Version: 1.4.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings gCrisprTools_1.4.0.tar.gz

StartedAt: 2017-08-15 23:12:56 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 23:16:33 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 216.9 seconds

RetCode: 0

Status:  OK

CheckDir: gCrisprTools.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings gCrisprTools_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/gCrisprTools.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.4.0’
* 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  9.2Mb
  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 32.060  1.768  35.672
ct.makeReport               20.704  0.200  20.925
ct.makeContrastReport       11.864  0.260  12.698
ct.guideCDF                 10.832  0.072  10.915
ct.makeQCReport              6.916  0.148   7.075
ct.GCbias                    6.416  0.168   6.593
* 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
  ‘/home/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	0.000	0.003
ann	0.080	0.004	0.085
ct.DirectionalTests	0.304	0.044	0.349
ct.GCbias	6.416	0.168	6.593
ct.PRC	1.144	0.040	1.187
ct.PantherPathwayEnrichment	32.060	1.768	35.672
ct.ROC	0.184	0.000	0.185
ct.RRAaPvals	0.936	0.016	0.951
ct.RRAalpha	0.296	0.000	0.294
ct.alignmentChart	0.004	0.000	0.003
ct.alphaBeta	0.008	0.000	0.094
ct.ecdf	0.000	0.000	0.001
ct.filterReads	0.456	0.000	0.456
ct.gRNARankByReplicate	0.696	0.016	0.715
ct.generateResults	0.588	0.000	0.587
ct.guideCDF	10.832	0.072	10.915
ct.inputCheck	0.080	0.004	0.088
ct.makeContrastReport	11.864	0.260	12.698
ct.makeQCReport	6.916	0.148	7.075
ct.makeReport	20.704	0.200	20.925
ct.normalizeBySlope	1.072	0.052	1.124
ct.normalizeGuides	3.412	0.080	3.492
ct.normalizeMedians	0.832	0.012	0.843
ct.normalizeNTC	1.092	0.016	1.109
ct.normalizeSpline	1.156	0.016	1.175
ct.prepareAnnotation	0.552	0.004	0.556
ct.preprocessFit	2.136	0.028	2.166
ct.rawCountDensities	0.148	0.000	0.145
ct.resultCheck	0.112	0.000	0.112
ct.stackGuides	4.748	0.024	4.772
ct.targetSetEnrichment	0.116	0.000	0.116
ct.topTargets	0.380	0.000	0.382
ct.viewControls	0.288	0.000	0.290
ct.viewGuides	0.320	0.004	0.320
es	0.068	0.004	0.072
essential.genes	0.000	0.000	0.001
fit	0.200	0.000	0.204
resultsDF	0.164	0.004	0.169