BioC 3.3: CHECK report for rCGH on oaxaca

Package: rCGH

Version: 1.2.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rCGH_1.2.2.tar.gz

StartedAt: 2016-10-13 05:31:53 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 05:39:18 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 445.1 seconds

RetCode: 0

Status:  OK

CheckDir: rCGH.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 rCGH_1.2.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/rCGH.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rCGH/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rCGH’ version ‘1.2.2’
* 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 ‘rCGH’ 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 loading without being on the library search path ... 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
byGeneTable  18.170  0.284  18.580
multiplot    15.964  0.158  16.132
plotProfile  15.325  0.152  15.499
rCGH-package 13.308  0.112  13.471
plotLOH      12.794  0.089  12.938
recenter     12.597  0.066  12.692
view         12.547  0.062  12.624
segmentCGH   12.159  0.066  12.241
plotDensity  11.611  0.062  11.701
EMnormalize  11.596  0.067  11.674
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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 ‘rCGH’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rCGH)

name	user	system	elapsed
AllAccessors	1.562	0.023	1.590
EMnormalize	11.596	0.067	11.674
adjustSignal	4.449	0.023	4.476
byGeneTable	18.170	0.284	18.580
hg18	0.005	0.001	0.006
hg19	0.004	0.001	0.005
hg38	0.005	0.001	0.006
multiplot	15.964	0.158	16.132
plotDensity	11.611	0.062	11.701
plotLOH	12.794	0.089	12.938
plotProfile	15.325	0.152	15.499
rCGH-Agilent-class	0.001	0.000	0.002
rCGH-SNP6-class	0.001	0.000	0.001
rCGH-class	0.001	0.000	0.001
rCGH-cytoScan-class	0.002	0.000	0.001
rCGH-generic-class	0.001	0.001	0.002
rCGH-package	13.308	0.112	13.471
readAffyCytoScan	0.858	0.005	0.864
readAffySNP6	0.903	0.007	0.911
readAgilent	1.242	0.016	1.259
readGeneric	0.015	0.000	0.015
recenter	12.597	0.066	12.692
segmentCGH	12.159	0.066	12.241
setInfo	0.858	0.005	0.865
view	12.547	0.062	12.624