BioC 3.2: CHECK report for Rqc on linux1.bioconductor.org

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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_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-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 ‘1.4.0’
* 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 ... [27s/27s] 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 ... [79s/73s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
Rqc-package 20.025  1.881  19.279
rqc         18.016  2.158  17.193
rqcReport   14.855  1.360  15.277
* 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	20.025	1.881	19.279
RqcResultSet-class	0.561	0.032	0.593
checkpoint	0.003	0.000	0.003
detectFileFormat	0.005	0.000	0.005
fromRRDNA	0.001	0.004	0.002
matdist	0.000	0.000	0.001
rqc	18.016	2.158	17.193
rqcCycleAverageQualityPcaPlot	0.807	0.012	0.822
rqcCycleAverageQualityPlot	0.305	0.004	0.311
rqcCycleBaseCallsPlot	0.413	0.000	0.413
rqcCycleGCPlot	0.208	0.000	0.208
rqcCycleQualityBoxPlot	2.477	0.000	2.477
rqcCycleQualityPlot	1.603	0.004	1.607
rqcFileHeatmap	0.033	0.004	0.037
rqcGroupCycleAverageQualityPlot	0.288	0.000	0.288
rqcQA	0.179	0.000	0.179
rqcReadFrequencyPlot	0.165	0.000	0.165
rqcReadQualityBoxPlot	0.228	0.000	0.228
rqcReadQualityPlot	0.177	0.000	0.177
rqcReadWidthPlot	0.137	0.000	0.140
rqcReport	14.855	1.360	15.277
rqcShinyReport	0.004	0.000	0.004
stats4trim	0.756	0.044	0.802
subsetByGroup	1.675	0.007	1.563
toRRDNA	0.002	0.000	0.002

BioC 3.2: CHECK report for Rqc on linux1.bioconductor.org

Summary

Command output