BioC 3.0: CHECK report for QDNAseq on oaxaca

Package: QDNAseq

Version: 1.2.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch QDNAseq_1.2.4.tar.gz

StartedAt: 2015-04-10 02:27:18 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 02:32:15 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 297.2 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 --no-multiarch QDNAseq_1.2.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/QDNAseq.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.2.4’
* 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 ... NOTE
createBins: no visible global function definition for ‘organism’
* 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 ... [69s/70s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
callBins               17.429  0.155  17.690
frequencyPlot          16.527  0.166  16.738
normalizeSegmentedBins  6.554  0.080   6.707
segmentBins             6.110  0.070   6.212
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘QDNAseq,reproducibility.R’ [12s/12s]
  Running ‘QDNAseq.R’ [18s/19s]
 [31s/31s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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	0.198	0.018	0.216
applyFilters	0.750	0.016	0.787
binReadCounts	0.000	0.000	0.001
callBins	17.429	0.155	17.690
compareToReference	1.452	0.060	1.517
correctBins	1.127	0.043	1.171
createBins	0.000	0.000	0.001
estimateCorrection	1.009	0.042	1.053
exportBins	0.001	0.000	0.001
frequencyPlot	16.527	0.166	16.738
getBinAnnotations	0.001	0.000	0.001
highlightFilters	0.812	0.054	0.877
isobarPlot	0.881	0.028	0.920
makeCgh	1.390	0.060	1.459
noisePlot	1.222	0.050	1.306
normalizeBins	1.123	0.044	1.176
normalizeSegmentedBins	6.554	0.080	6.707
plot	1.680	0.072	1.793
poolRuns	0.194	0.014	0.208
segmentBins	6.110	0.070	6.212
smoothOutlierBins	1.419	0.058	1.500