BioC 3.6: CHECK report for Rqc on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Rqc_1.11.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/Rqc.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.11.0’
* 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 18.404  1.744  19.095
rqc         14.884  1.868  15.556
rqcReport   12.156  1.648  12.849
* 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
  ‘/home/biocbuild/bbs-3.6-bioc/meat/Rqc.Rcheck/00check.log’
for details.

* installing *source* package ‘Rqc’ ...
** libs
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RRDNA.cpp -o RRDNA.o
RRDNA.cpp: In function ‘Rcpp::StringVector toRRDNA(Rcpp::StringVector)’:
RRDNA.cpp:51:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (j = 0; j < dna.size(); j+=3)
                           ^
RRDNA.cpp: In function ‘Rcpp::StringVector fromRRDNA(Rcpp::StringVector)’:
RRDNA.cpp:102:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(j = 1; j < rrdna.size(); ++j) {
                      ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o Rqc.so RRDNA.o RcppExports.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-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	18.404	1.744	19.095
RqcResultSet-class	0.028	0.004	0.030
checkpoint	0.004	0.000	0.003
detectFileFormat	0.004	0.000	0.003
fromRRDNA	0.000	0.000	0.001
matdist	0.004	0.000	0.000
rqc	14.884	1.868	15.556
rqcCycleAverageQualityPcaPlot	0.284	0.024	0.308
rqcCycleAverageQualityPlot	0.308	0.004	0.313
rqcCycleBaseCallsPlot	0.520	0.004	0.522
rqcCycleGCPlot	0.248	0.000	0.248
rqcCycleQualityBoxPlot	3.092	0.024	3.117
rqcCycleQualityPlot	0.880	0.004	0.888
rqcFileHeatmap	0.184	0.004	0.190
rqcGroupCycleAverageQualityPlot	0.328	0.000	0.326
rqcQA	0.204	0.000	0.205
rqcReadFrequencyPlot	0.188	0.004	0.191
rqcReadQualityBoxPlot	0.256	0.000	0.253
rqcReadQualityPlot	0.192	0.000	0.192
rqcReadWidthPlot	0.272	0.000	0.271
rqcReport	12.156	1.648	12.849
rqcShinyReport	0.000	0.004	0.005
stats4trim	0.100	0.008	0.109
subsetByGroup	1.168	0.088	1.257
subsetByPair	0.008	0.000	0.006
toRRDNA	0.000	0.000	0.001

BioC 3.6: CHECK report for Rqc on malbec1

Summary

Command output