BioC 3.4: CHECK report for QDNAseq on morelia

Package: QDNAseq

Version: 1.9.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings QDNAseq_1.9.1.tar.gz

StartedAt: 2016-09-20 11:38:49 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 11:41:45 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 176.4 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_1.9.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/QDNAseq.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.9.1’
* 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          13.343  0.183  13.534
callBins               12.982  0.172  13.163
normalizeSegmentedBins  5.583  0.100   5.688
segmentBins             5.132  0.073   5.208
* 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	0.130	0.012	0.142
applyFilters	0.406	0.013	0.419
binReadCounts	0.000	0.000	0.001
callBins	12.982	0.172	13.163
compareToReference	1.115	0.061	1.177
correctBins	0.759	0.035	0.794
createBins	0.001	0.000	0.001
estimateCorrection	0.735	0.029	0.765
exportBins	0	0	0
frequencyPlot	13.343	0.183	13.534
getBinAnnotations	0.000	0.000	0.001
highlightFilters	0.552	0.062	0.630
isobarPlot	0.562	0.022	0.599
makeCgh	1.138	0.051	1.190
noisePlot	0.789	0.045	0.836
normalizeBins	1.018	0.039	1.057
normalizeSegmentedBins	5.583	0.100	5.688
plot	1.115	0.059	1.175
poolRuns	0.153	0.011	0.164
segmentBins	5.132	0.073	5.208
smoothOutlierBins	0.658	0.042	0.700