BioC 3.6: CHECK report for gCrisprTools on malbec1

Package: gCrisprTools

Version: 1.5.5

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings gCrisprTools_1.5.5.tar.gz

StartedAt: 2017-08-15 23:21:05 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 23:24:24 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 198.3 seconds

RetCode: 0

Status:  OK

CheckDir: gCrisprTools.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings gCrisprTools_1.5.5.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-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 ‘1.5.5’
* 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 31.648  1.676  34.315
ct.makeReport               19.624  0.196  19.829
ct.makeContrastReport       12.044  0.304  16.623
ct.guideCDF                 10.536  0.112  10.652
ct.makeQCReport              7.260  0.208   7.478
ct.GCbias                    6.304  0.132   6.439
* 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-3.6-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	0.004	0.004
ann	0.076	0.016	0.092
ct.DirectionalTests	0.304	0.064	0.367
ct.GCbias	6.304	0.132	6.439
ct.PRC	0.940	0.012	0.953
ct.PantherPathwayEnrichment	31.648	1.676	34.315
ct.ROC	0.188	0.000	0.188
ct.RRAaPvals	0.936	0.008	0.944
ct.RRAalpha	0.26	0.00	0.26
ct.alignmentChart	0.004	0.000	0.004
ct.alphaBeta	0.012	0.000	0.023
ct.ecdf	0.000	0.000	0.001
ct.filterReads	0.276	0.020	0.295
ct.gRNARankByReplicate	0.456	0.000	0.456
ct.generateResults	0.556	0.004	0.561
ct.guideCDF	10.536	0.112	10.652
ct.inputCheck	0.096	0.000	0.099
ct.makeContrastReport	12.044	0.304	16.623
ct.makeQCReport	7.260	0.208	7.478
ct.makeReport	19.624	0.196	19.829
ct.normalizeBySlope	1.068	0.052	1.120
ct.normalizeGuides	3.380	0.068	3.450
ct.normalizeMedians	0.784	0.012	0.796
ct.normalizeNTC	0.904	0.012	0.918
ct.normalizeSpline	1.056	0.028	1.086
ct.prepareAnnotation	0.560	0.000	0.557
ct.preprocessFit	2.168	0.016	2.185
ct.rawCountDensities	0.140	0.004	0.142
ct.resultCheck	0.116	0.000	0.115
ct.stackGuides	4.380	0.004	4.386
ct.targetSetEnrichment	0.116	0.000	0.116
ct.topTargets	0.38	0.00	0.38
ct.viewControls	0.236	0.004	0.239
ct.viewGuides	0.312	0.000	0.310
es	0.072	0.000	0.073
essential.genes	0.004	0.000	0.001
fit	0.192	0.004	0.197
resultsDF	0.104	0.000	0.105