BioC 3.4: CHECK report for QDNAseq on malbec1

Package: QDNAseq

Version: 1.10.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings QDNAseq_1.10.0.tar.gz

StartedAt: 2017-04-15 00:37:25 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:40:07 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 161.9 seconds

RetCode: 0

Status:  OK

CheckDir: QDNAseq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings QDNAseq_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/QDNAseq.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘QDNAseq/DESCRIPTION’ ... OK
* this is package ‘QDNAseq’ version ‘1.10.0’
* 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 ‘QDNAseq’ 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
callBins      13.860  0.040  13.909
frequencyPlot 13.572  0.008  13.588
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘QDNAseq,reproducibility.R’
  Running ‘QDNAseq.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: OK

* installing *source* package ‘QDNAseq’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (QDNAseq)

name	user	system	elapsed
addPhenodata	0.140	0.004	0.146
applyFilters	0.412	0.004	0.416
binReadCounts	0	0	0
callBins	13.860	0.040	13.909
compareToReference	0.944	0.000	0.944
correctBins	0.676	0.004	0.679
createBins	0	0	0
estimateCorrection	0.632	0.004	0.637
exportBins	0.000	0.000	0.001
frequencyPlot	13.572	0.008	13.588
getBinAnnotations	0.000	0.000	0.001
highlightFilters	0.428	0.000	0.430
isobarPlot	0.656	0.008	0.664
makeCgh	0.816	0.000	0.813
noisePlot	0.848	0.000	0.849
normalizeBins	0.684	0.000	0.684
normalizeSegmentedBins	4.832	0.000	4.832
plot	1.008	0.000	1.010
poolRuns	0.132	0.000	0.130
segmentBins	4.468	0.004	4.473
smoothOutlierBins	0.960	0.004	0.965