BioC 3.2: CHECK report for Rqc on zin1

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Rqc_1.4.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/Rqc.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.4.2’
* 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 ... [29s/29s] 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 ... [75s/68s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
Rqc-package 18.250  1.922  17.236
rqc         18.056  2.084  16.879
rqcReport   13.744  1.359  13.962
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [13s/13s]
 [13s/13s] 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
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c RRDNA.cpp -o RRDNA.o
RRDNA.cpp: In function ‘Rcpp::StringVector toRRDNA(Rcpp::StringVector)’:
RRDNA.cpp:51:38: 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:102:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(j = 1; j < rrdna.size(); ++j) {
                                   ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o Rqc.so RRDNA.o RcppExports.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/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	18.250	1.922	17.236
RqcResultSet-class	0.029	0.004	0.033
checkpoint	0.003	0.000	0.003
detectFileFormat	0.003	0.000	0.003
fromRRDNA	0.001	0.000	0.001
matdist	0.001	0.000	0.001
rqc	18.056	2.084	16.879
rqcCycleAverageQualityPcaPlot	0.276	0.020	0.296
rqcCycleAverageQualityPlot	0.288	0.012	0.300
rqcCycleBaseCallsPlot	0.487	0.000	0.486
rqcCycleGCPlot	0.254	0.004	0.257
rqcCycleQualityBoxPlot	2.649	0.004	2.660
rqcCycleQualityPlot	1.664	0.024	1.688
rqcFileHeatmap	0.039	0.004	0.044
rqcGroupCycleAverageQualityPlot	0.309	0.000	0.313
rqcQA	0.195	0.000	0.195
rqcReadFrequencyPlot	0.189	0.000	0.189
rqcReadQualityBoxPlot	0.268	0.000	0.268
rqcReadQualityPlot	0.202	0.000	0.201
rqcReadWidthPlot	0.224	0.000	0.225
rqcReport	13.744	1.359	13.962
rqcShinyReport	0.002	0.000	0.003
stats4trim	0.197	0.020	0.217
subsetByGroup	1.375	0.036	1.338
toRRDNA	0.001	0.000	0.002

BioC 3.2: CHECK report for Rqc on zin1

Summary

Command output