BioC 3.3: CHECK report for Rqc on linux2.bioconductor.org

Package: Rqc

Version: 1.5.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Rqc_1.5.0.tar.gz

StartedAt: 2015-10-27 07:43:56 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 07:48:43 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 287.0 seconds

RetCode: 0

Status:  OK

CheckDir: Rqc.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Rqc_1.5.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/Rqc.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.5.0’
* 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 ... [81s/74s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
Rqc-package 20.359  1.864  19.587
rqc         18.703  2.154  17.803
rqcReport   13.963  1.279  14.363
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [11s/10s]
 [11s/11s] 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-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c RRDNA.cpp -o RRDNA.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o Rqc.so RRDNA.o RcppExports.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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	20.359	1.864	19.587
RqcResultSet-class	0.028	0.000	0.029
checkpoint	0.002	0.000	0.002
detectFileFormat	0.003	0.000	0.003
fromRRDNA	0.001	0.000	0.001
matdist	0	0	0
rqc	18.703	2.154	17.803
rqcCycleAverageQualityPcaPlot	0.788	0.036	0.830
rqcCycleAverageQualityPlot	0.439	0.000	0.441
rqcCycleBaseCallsPlot	0.696	0.000	0.698
rqcCycleGCPlot	0.231	0.004	0.236
rqcCycleQualityBoxPlot	3.684	0.000	3.683
rqcCycleQualityPlot	2.011	0.000	2.011
rqcFileHeatmap	0.071	0.000	0.071
rqcGroupCycleAverageQualityPlot	0.448	0.000	0.448
rqcQA	0.215	0.000	0.214
rqcReadFrequencyPlot	0.499	0.004	0.504
rqcReadQualityBoxPlot	0.317	0.000	0.317
rqcReadQualityPlot	0.28	0.00	0.28
rqcReadWidthPlot	0.225	0.000	0.225
rqcReport	13.963	1.279	14.363
rqcShinyReport	0.004	0.000	0.004
stats4trim	0.716	0.036	0.753
subsetByGroup	1.560	0.008	1.459
toRRDNA	0.002	0.000	0.002