BioC 3.0: CHECK report for Rqc on zin1

Package: Rqc

Version: 1.0.4

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings Rqc_1.0.4.tar.gz

StartedAt: 2015-04-10 04:00:29 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 04:04:47 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 258.1 seconds

RetCode: 0

Status:  OK

CheckDir: Rqc.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings Rqc_1.0.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/Rqc.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (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 ... [19s/19s] 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 ... [87s/65s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
rqc                    11.656  1.292   9.713
rqcReport              10.164  1.076   8.634
Rqc-package             9.625  0.652   9.970
rqcCycleQualityBoxCalc  5.324  0.612   4.089
rqcCycleQualityBoxPlot  4.764  0.492   4.303
* 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	9.625	0.652	9.970
rqc	11.656	1.292	9.713
rqcCycleAverageQualityCalc	1.988	0.316	0.903
rqcCycleAverageQualityPlot	2.256	0.448	1.171
rqcCycleBaseCallsCalc	1.296	0.260	1.468
rqcCycleBaseCallsLinePlot	1.040	0.216	1.204
rqcCycleBaseCallsPlot	1.896	0.324	1.388
rqcCycleGCCalc	2.344	0.564	1.107
rqcCycleGCPlot	1.657	0.360	1.130
rqcCycleQualityBoxCalc	5.324	0.612	4.089
rqcCycleQualityBoxPlot	4.764	0.492	4.303
rqcCycleQualityCalc	3.117	0.524	2.342
rqcCycleQualityPlot	3.164	0.544	2.284
rqcQA	2.348	0.544	0.895
rqcReadQualityCalc	1.680	0.364	1.120
rqcReadQualityPlot	1.684	0.376	1.142
rqcReadWidthCalc	0.925	0.208	1.195
rqcReadWidthPlot	1.172	0.200	1.115
rqcReport	10.164	1.076	8.634