BioC 3.0: CHECK report for Rqc on oaxaca

Package: Rqc

Version: 1.0.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Rqc_1.0.4.tar.gz

StartedAt: 2015-04-10 03:03:19 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 03:08:19 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 300.2 seconds

RetCode: 0

Status:  OK

CheckDir: Rqc.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 --no-multiarch Rqc_1.0.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/Rqc.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rqc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rqc’ version ‘1.0.4’
* 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 ‘Rqc’ can be installed ... [21s/21s] OK
* checking installed package size ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [114s/85s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
rqc                    16.100  2.641  13.710
rqcReport              14.130  2.766  13.083
Rqc-package            12.665  1.496  14.111
rqcCycleQualityBoxCalc  6.157  1.886   5.281
rqcCycleQualityBoxPlot  5.598  1.252   4.841
rqcCycleQualityPlot     4.663  1.496   3.050
* 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

* installing *source* package ‘Rqc’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rqc)

name	user	system	elapsed
Rqc-package	12.665	1.496	14.111
rqc	16.100	2.641	13.710
rqcCycleAverageQualityCalc	2.128	1.002	1.229
rqcCycleAverageQualityPlot	1.430	0.855	1.305
rqcCycleBaseCallsCalc	0.466	0.140	1.352
rqcCycleBaseCallsLinePlot	1.511	0.818	1.426
rqcCycleBaseCallsPlot	1.662	0.842	1.550
rqcCycleGCCalc	1.278	0.824	1.216
rqcCycleGCPlot	1.347	0.827	1.233
rqcCycleQualityBoxCalc	6.157	1.886	5.281
rqcCycleQualityBoxPlot	5.598	1.252	4.841
rqcCycleQualityCalc	3.471	1.078	3.413
rqcCycleQualityPlot	4.663	1.496	3.050
rqcQA	2.246	1.037	1.283
rqcReadQualityCalc	1.345	0.871	1.244
rqcReadQualityPlot	1.393	0.868	1.285
rqcReadWidthCalc	0.300	0.123	1.254
rqcReadWidthPlot	1.333	0.831	1.218
rqcReport	14.130	2.766	13.083