BioC 3.5: 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_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Rqc.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.9.0’
* 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 ... 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 ... NOTE
.ui.Rqc: no visible global function definition for 'packageVersion'
rqc: no visible global function definition for 'browseURL'
rqcCycleAverageQualityPcaCalc: no visible global function definition
  for 'prcomp'
rqcFileHeatmap: no visible global function definition for 'hclust'
stats4trim : <anonymous>: no visible global function definition for
  'head'
Undefined global functions or variables:
  browseURL hclust head packageVersion prcomp
Consider adding
  importFrom("stats", "hclust", "prcomp")
  importFrom("utils", "browseURL", "head", "packageVersion")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
Rqc-package 17.742  0.466  18.667
rqc         16.974  0.459  16.333
rqcReport   15.565  0.411  14.902
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/Rqc.Rcheck/00check.log’
for details.

* installing *source* package ‘Rqc’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c RRDNA.cpp -o RRDNA.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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-3.5-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	17.742	0.466	18.667
RqcResultSet-class	0.036	0.001	0.038
checkpoint	0.004	0.001	0.004
detectFileFormat	0.004	0.000	0.005
fromRRDNA	0.001	0.000	0.001
matdist	0.001	0.000	0.000
rqc	16.974	0.459	16.333
rqcCycleAverageQualityPcaPlot	0.269	0.000	0.269
rqcCycleAverageQualityPlot	0.297	0.001	0.298
rqcCycleBaseCallsPlot	0.586	0.009	0.595
rqcCycleGCPlot	0.259	0.002	0.262
rqcCycleQualityBoxPlot	3.204	0.009	3.216
rqcCycleQualityPlot	1.042	0.007	1.049
rqcFileHeatmap	0.201	0.001	0.206
rqcGroupCycleAverageQualityPlot	0.523	0.003	0.525
rqcQA	0.241	0.001	0.243
rqcReadFrequencyPlot	0.325	0.002	0.327
rqcReadQualityBoxPlot	0.289	0.001	0.290
rqcReadQualityPlot	0.272	0.001	0.273
rqcReadWidthPlot	0.444	0.002	0.445
rqcReport	15.565	0.411	14.902
rqcShinyReport	0.005	0.001	0.005
stats4trim	0.112	0.004	0.115
subsetByGroup	0.485	0.037	0.523
subsetByPair	0.006	0.000	0.006
toRRDNA	0.001	0.001	0.002

BioC 3.5: CHECK report for Rqc on oaxaca

Summary

Command output