BioC 3.1: CHECK report for Rqc on zin2

Package: Rqc

Version: 1.2.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings Rqc_1.2.0.tar.gz

StartedAt: 2015-10-09 05:09:33 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 05:13:09 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 216.1 seconds

RetCode: 0

Status:  OK

CheckDir: Rqc.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings Rqc_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/Rqc.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-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 ‘1.2.0’
* 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 ... [11s/11s] 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 ... [148s/105s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
rqc                    18.509  1.563  14.732
Rqc-package            16.183  1.203  15.365
rqcReport              14.264  1.006  14.788
rqcCycleQualityBoxCalc  5.751  0.356   4.544
rqcCycleQualityBoxPlot  5.679  0.421   4.452
* 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	16.183	1.203	15.365
perCycleBasecall	2.875	0.313	1.921
perCycleQuality	3.007	0.357	1.833
perFileInformation	0.010	0.016	1.538
perReadQuality	4.455	0.471	1.815
perReadWidth	0.014	0.012	1.483
rqc	18.509	1.563	14.732
rqcCycleAverageQualityCalc	2.879	0.368	1.705
rqcCycleAverageQualityPcaCalc	2.762	0.362	1.556
rqcCycleAverageQualityPcaPlot	2.921	0.325	1.711
rqcCycleAverageQualityPlot	3.185	0.393	2.022
rqcCycleBaseCallsCalc	3.075	0.345	1.850
rqcCycleBaseCallsLinePlot	3.003	0.355	1.796
rqcCycleBaseCallsPlot	3.220	0.414	2.040
rqcCycleGCCalc	3.091	0.443	1.804
rqcCycleGCPlot	2.926	0.368	1.696
rqcCycleQualityBoxCalc	5.751	0.356	4.544
rqcCycleQualityBoxPlot	5.679	0.421	4.452
rqcCycleQualityCalc	4.361	0.315	3.102
rqcCycleQualityPlot	4.312	0.390	3.140
rqcQA	2.852	0.329	1.647
rqcReadQualityBoxCalc	3.034	0.373	1.805
rqcReadQualityBoxPlot	2.887	0.317	1.673
rqcReadQualityCalc	2.956	0.380	1.713
rqcReadQualityPlot	2.840	0.375	1.667
rqcReadWidthCalc	2.956	0.323	1.674
rqcReadWidthPlot	2.949	0.347	1.662
rqcReport	14.264	1.006	14.788
stats4trim	3.081	0.309	2.140