BioC 3.1: CHECK report for QDNAseq on petty

Package: QDNAseq

Version: 1.4.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings QDNAseq_1.4.2.tar.gz

StartedAt: 2015-10-09 01:18:28 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:23:43 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 314.8 seconds

RetCode: 0

Status:  OK

CheckDir: QDNAseq.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings QDNAseq_1.4.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/QDNAseq.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘QDNAseq/DESCRIPTION’ ... OK
* this is package ‘QDNAseq’ version ‘1.4.2’
* 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 ... [18s/18s] 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 loading without being on the library search path ... 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 ... [87s/88s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
callBins               23.871  0.214  24.129
frequencyPlot          22.244  0.253  22.651
normalizeSegmentedBins  8.926  0.116   9.048
segmentBins             8.142  0.081   9.060
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘QDNAseq,reproducibility.R’ [12s/12s]
  Running ‘QDNAseq.R’ [20s/20s]
 [32s/33s] 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-3.1-bioc/meat/QDNAseq.Rcheck/00check.log’
for details.

* installing *source* package ‘QDNAseq’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (QDNAseq)

name	user	system	elapsed
addPhenodata	0.238	0.021	0.260
applyFilters	0.700	0.019	0.719
binReadCounts	0.001	0.000	0.000
callBins	23.871	0.214	24.129
compareToReference	1.882	0.088	1.973
correctBins	1.230	0.062	1.294
createBins	0.000	0.000	0.001
estimateCorrection	0.984	0.047	1.031
exportBins	0.001	0.001	0.001
frequencyPlot	22.244	0.253	22.651
getBinAnnotations	0.001	0.000	0.002
highlightFilters	0.667	0.076	0.752
isobarPlot	1.390	0.043	1.456
makeCgh	1.351	0.082	1.432
noisePlot	1.123	0.059	1.185
normalizeBins	1.398	0.067	1.468
normalizeSegmentedBins	8.926	0.116	9.048
plot	1.601	0.098	1.701
poolRuns	0.226	0.014	0.240
segmentBins	8.142	0.081	9.060
smoothOutlierBins	1.547	0.074	1.621