BioC 3.1: CHECK report for Rqc on morelia

Package: Rqc

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rqc_1.2.0.tar.gz

StartedAt: 2015-10-09 05:54:44 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 05:58:40 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 236.4 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 Rqc_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/Rqc.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.2.0’
* 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 ‘Rqc’ can be installed ... [12s/12s] 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 ... [158s/111s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
Rqc-package            16.498  1.770  16.896
rqc                    14.565  1.768  14.208
rqcReport              13.264  1.455  12.668
rqcCycleQualityBoxPlot  5.400  0.971   4.674
rqcCycleQualityBoxCalc  5.113  0.997   4.496
rqcCycleQualityCalc     4.234  1.030   3.584
* 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: OK

* installing *source* package ‘Rqc’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (Rqc)

name	user	system	elapsed
Rqc-package	16.498	1.770	16.896
perCycleBasecall	2.770	0.809	1.940
perCycleQuality	2.891	0.925	2.287
perFileInformation	0.014	0.015	1.637
perReadQuality	2.724	0.807	1.892
perReadWidth	0.013	0.010	1.536
rqc	14.565	1.768	14.208
rqcCycleAverageQualityCalc	1.472	0.472	1.995
rqcCycleAverageQualityPcaCalc	2.673	0.865	1.876
rqcCycleAverageQualityPcaPlot	2.595	0.773	1.931
rqcCycleAverageQualityPlot	2.734	0.806	1.926
rqcCycleBaseCallsCalc	1.810	0.584	2.386
rqcCycleBaseCallsLinePlot	2.934	0.978	2.187
rqcCycleBaseCallsPlot	2.881	0.823	2.108
rqcCycleGCCalc	2.688	0.892	2.051
rqcCycleGCPlot	2.740	1.018	2.040
rqcCycleQualityBoxCalc	5.113	0.997	4.496
rqcCycleQualityBoxPlot	5.400	0.971	4.674
rqcCycleQualityCalc	4.234	1.030	3.584
rqcCycleQualityPlot	2.756	0.706	3.441
rqcQA	2.618	0.881	1.936
rqcReadQualityBoxCalc	2.889	0.809	2.164
rqcReadQualityBoxPlot	2.703	0.876	1.996
rqcReadQualityCalc	2.582	0.981	1.932
rqcReadQualityPlot	1.398	0.595	1.964
rqcReadWidthCalc	1.428	0.688	2.074
rqcReadWidthPlot	2.730	1.022	2.195
rqcReport	13.264	1.455	12.668
stats4trim	2.851	1.080	2.256