BioC 3.4: CHECK report for QDNAseq on zin1

Package: QDNAseq

Version: 1.9.1

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings QDNAseq_1.9.1.tar.gz

StartedAt: 2016-09-20 11:00:11 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 11:02:54 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 163.3 seconds

RetCode: 0

Status:  OK

CheckDir: QDNAseq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings QDNAseq_1.9.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/QDNAseq.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘QDNAseq/DESCRIPTION’ ... OK
* this is package ‘QDNAseq’ version ‘1.9.1’
* 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 ... 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
callBins               14.120  0.028  14.153
frequencyPlot          14.076  0.004  14.085
normalizeSegmentedBins  6.344  0.000   6.438
segmentBins             6.100  0.160   6.276
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘QDNAseq,reproducibility.R’
  Running ‘QDNAseq.R’
 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: OK

* 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	0.144	0.004	0.148
applyFilters	0.396	0.004	0.399
binReadCounts	0	0	0
callBins	14.120	0.028	14.153
compareToReference	0.992	0.000	1.003
correctBins	0.756	0.008	0.777
createBins	0.004	0.000	0.000
estimateCorrection	0.704	0.192	0.896
exportBins	0.000	0.000	0.001
frequencyPlot	14.076	0.004	14.085
getBinAnnotations	0.000	0.000	0.001
highlightFilters	0.620	0.004	0.622
isobarPlot	0.556	0.008	0.563
makeCgh	1.068	0.000	1.073
noisePlot	0.708	0.000	0.707
normalizeBins	0.784	0.004	0.788
normalizeSegmentedBins	6.344	0.000	6.438
plot	0.912	0.000	0.919
poolRuns	0.132	0.176	0.308
segmentBins	6.100	0.160	6.276
smoothOutlierBins	1.012	0.096	1.107