BioC 3.2: CHECK report for Rqc on oaxaca

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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_1.4.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/Rqc.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.4.2’
* 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 ... [36s/40s] 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [89s/88s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
Rqc-package 20.793  1.613  22.286
rqc         19.782  1.365  21.623
rqcReport   16.925  0.395  16.936
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [16s/18s]
 [17s/18s] 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: OK

* installing *source* package ‘Rqc’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RRDNA.cpp -o RRDNA.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Rqc.so RRDNA.o RcppExports.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/Rqc.Rcheck/Rqc/libs
** 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	20.793	1.613	22.286
RqcResultSet-class	0.040	0.001	0.104
checkpoint	0.004	0.001	0.004
detectFileFormat	0.006	0.000	0.026
fromRRDNA	0.002	0.001	0.002
matdist	0.001	0.000	0.001
rqc	19.782	1.365	21.623
rqcCycleAverageQualityPcaPlot	0.350	0.002	0.352
rqcCycleAverageQualityPlot	0.740	0.001	0.742
rqcCycleBaseCallsPlot	0.624	0.002	0.675
rqcCycleGCPlot	0.327	0.003	0.330
rqcCycleQualityBoxPlot	3.794	0.008	3.866
rqcCycleQualityPlot	1.683	0.014	1.698
rqcFileHeatmap	0.051	0.001	0.054
rqcGroupCycleAverageQualityPlot	0.409	0.002	0.418
rqcQA	0.302	0.001	0.304
rqcReadFrequencyPlot	0.293	0.002	0.295
rqcReadQualityBoxPlot	0.362	0.001	0.364
rqcReadQualityPlot	0.267	0.001	0.268
rqcReadWidthPlot	0.311	0.002	0.371
rqcReport	16.925	0.395	16.936
rqcShinyReport	0.003	0.000	0.003
stats4trim	0.222	0.003	0.225
subsetByGroup	1.490	0.040	1.532
toRRDNA	0.002	0.000	0.002

BioC 3.2: CHECK report for Rqc on oaxaca

Summary

Command output