BioC 3.5: CHECK report for QDNAseq on toluca2

Package: QDNAseq

Version: 1.11.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings QDNAseq_1.11.2.tar.gz

StartedAt: 2017-04-23 08:23:09 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 08:26:49 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 220.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: QDNAseq.Rcheck

Warnings: 1

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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_1.11.2.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 r72187)
* 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 ‘1.11.2’
* 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 ... WARNING
Undocumented code objects:
  ‘exportVCF’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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          15.344  0.241  15.697
callBins               15.020  0.234  15.408
normalizeSegmentedBins  5.928  0.124   6.090
segmentBins             5.643  0.084   5.752
* 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: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/QDNAseq.Rcheck/00check.log’
for details.

* 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	0.180	0.015	0.195
applyFilters	0.265	0.015	0.283
binReadCounts	0.001	0.000	0.001
callBins	15.020	0.234	15.408
compareToReference	1.393	0.068	1.468
correctBins	0.801	0.040	0.849
createBins	0.001	0.000	0.001
estimateCorrection	0.757	0.038	0.795
exportBins	0.000	0.000	0.001
frequencyPlot	15.344	0.241	15.697
getBinAnnotations	0	0	0
highlightFilters	0.692	0.060	0.762
isobarPlot	0.677	0.031	0.712
makeCgh	1.033	0.068	1.110
noisePlot	0.976	0.043	1.029
normalizeBins	0.859	0.050	0.918
normalizeSegmentedBins	5.928	0.124	6.090
plot	1.234	0.064	1.312
poolRuns	0.211	0.016	0.230
segmentBins	5.643	0.084	5.752
smoothOutlierBins	0.890	0.054	0.945