BioC 3.2: CHECK report for QDNAseq on oaxaca

Package: QDNAseq

Version: 1.6.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings QDNAseq_1.6.1.tar.gz

StartedAt: 2016-04-23 03:21:38 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 03:25:10 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 211.9 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_1.6.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/QDNAseq.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.6.1’
* 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 ... [12s/14s] 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 ... NOTE
Unexported object imported by a ':::' call: ‘Biobase:::.showAnnotatedDataFrame’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘log2adhoc’ ‘sqrtadhoc’
* 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 ... [54s/56s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
frequencyPlot          13.991  0.157  14.361
callBins               13.616  0.143  14.466
normalizeSegmentedBins  5.865  0.080   5.948
segmentBins             5.266  0.057   5.325
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘QDNAseq,reproducibility.R’ [8s/8s]
  Running ‘QDNAseq.R’ [14s/15s]
 [22s/24s] 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-3.2-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	0.208	0.011	0.220
applyFilters	0.419	0.009	0.429
binReadCounts	0	0	0
callBins	13.616	0.143	14.466
compareToReference	1.140	0.052	1.192
correctBins	0.849	0.041	0.892
createBins	0.001	0.000	0.001
estimateCorrection	0.814	0.040	0.854
exportBins	0.000	0.000	0.001
frequencyPlot	13.991	0.157	14.361
getBinAnnotations	0.001	0.001	0.001
highlightFilters	0.495	0.046	0.549
isobarPlot	0.907	0.031	0.961
makeCgh	0.936	0.054	0.990
noisePlot	0.743	0.036	0.780
normalizeBins	0.763	0.034	0.797
normalizeSegmentedBins	5.865	0.080	5.948
plot	0.871	0.051	0.924
poolRuns	0.160	0.009	0.170
segmentBins	5.266	0.057	5.325
smoothOutlierBins	0.831	0.039	0.870