BioC 3.3: CHECK report for QDNAseq on morelia

Package: QDNAseq

Version: 1.7.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings QDNAseq_1.7.5.tar.gz

StartedAt: 2016-04-21 06:24:36 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 06:27:16 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 159.7 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_1.7.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/QDNAseq.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.7.5’
* 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 ... [9s/9s] 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 ... NOTE
estimateCorrection,QDNAseqReadCounts : calculateFits: no visible global
  function definition for ‘formula’
Undefined global functions or variables:
  formula
Consider adding
  importFrom("stats", "formula")
to your NAMESPACE file.
* 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 ... [47s/47s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
frequencyPlot          12.173  0.122  12.300
callBins               11.983  0.099  12.083
normalizeSegmentedBins  5.207  0.067   5.278
segmentBins             5.119  0.060   5.182
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘QDNAseq,reproducibility.R’ [6s/6s]
  Running ‘QDNAseq.R’ [12s/12s]
 [18s/18s] 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-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	0.127	0.010	0.137
applyFilters	0.386	0.011	0.396
binReadCounts	0.001	0.000	0.001
callBins	11.983	0.099	12.083
compareToReference	0.809	0.043	0.851
correctBins	0.706	0.035	0.740
createBins	0.001	0.000	0.001
estimateCorrection	0.703	0.028	0.732
exportBins	0	0	0
frequencyPlot	12.173	0.122	12.300
getBinAnnotations	0.001	0.000	0.001
highlightFilters	0.503	0.038	0.555
isobarPlot	0.539	0.024	0.579
makeCgh	0.832	0.039	0.872
noisePlot	0.784	0.035	0.823
normalizeBins	0.738	0.030	0.768
normalizeSegmentedBins	5.207	0.067	5.278
plot	0.716	0.038	0.755
poolRuns	0.154	0.011	0.166
segmentBins	5.119	0.060	5.182
smoothOutlierBins	0.605	0.033	0.637