BioC 3.5: CHECK report for QDNAseq on oaxaca

Package: QDNAseq

Version: 1.11.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings QDNAseq_1.11.0.tar.gz

StartedAt: 2017-03-04 07:31:42 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 07:35:12 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 210.3 seconds

RetCode: 0

Status:  OK

CheckDir: QDNAseq.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings QDNAseq_1.11.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/QDNAseq.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘QDNAseq/DESCRIPTION’ ... OK
* this is package ‘QDNAseq’ 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 ‘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 sizes of PDF files under ‘inst/doc’ ... 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
frequencyPlot          15.236  0.237  15.479
callBins               14.606  0.220  14.831
normalizeSegmentedBins  6.020  0.118   6.140
segmentBins             5.689  0.086   5.779
* 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	0.122	0.010	0.132
applyFilters	0.174	0.011	0.185
binReadCounts	0	0	0
callBins	14.606	0.220	14.831
compareToReference	1.413	0.063	1.477
correctBins	0.700	0.034	0.735
createBins	0.001	0.000	0.001
estimateCorrection	0.669	0.031	0.701
exportBins	0.001	0.001	0.001
frequencyPlot	15.236	0.237	15.479
getBinAnnotations	0	0	0
highlightFilters	0.651	0.055	0.722
isobarPlot	0.613	0.023	0.646
makeCgh	0.867	0.059	0.926
noisePlot	0.886	0.045	0.932
normalizeBins	0.588	0.035	0.623
normalizeSegmentedBins	6.020	0.118	6.140
plot	1.246	0.072	1.319
poolRuns	0.234	0.015	0.249
segmentBins	5.689	0.086	5.779
smoothOutlierBins	0.659	0.047	0.705