BioC 3.3: CHECK report for QDNAseq on morelia

Package: QDNAseq

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings QDNAseq_1.7.0.tar.gz

StartedAt: 2015-10-22 09:58:27 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 10:01:12 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 164.4 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_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/QDNAseq.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.7.0’
* 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 ... [8s/8s] 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 ... [48s/48s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
callBins      12.918  0.130  13.057
frequencyPlot 11.486  0.131  11.621
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘QDNAseq,reproducibility.R’ [6s/6s]
  Running ‘QDNAseq.R’ [11s/11s]
 [16s/16s] 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	0.182	0.013	0.194
applyFilters	0.456	0.011	0.468
binReadCounts	0.000	0.000	0.001
callBins	12.918	0.130	13.057
compareToReference	1.128	0.055	1.185
correctBins	0.888	0.033	0.922
createBins	0.001	0.000	0.001
estimateCorrection	0.738	0.036	0.775
exportBins	0.000	0.000	0.001
frequencyPlot	11.486	0.131	11.621
getBinAnnotations	0.001	0.000	0.000
highlightFilters	0.539	0.037	0.583
isobarPlot	0.736	0.027	0.798
makeCgh	0.719	0.039	0.758
noisePlot	0.587	0.030	0.618
normalizeBins	0.887	0.030	0.917
normalizeSegmentedBins	4.731	0.050	4.781
plot	0.726	0.035	0.763
poolRuns	0.193	0.010	0.204
segmentBins	4.737	0.042	4.781
smoothOutlierBins	0.735	0.033	0.768