BioC 3.6: CHECK report for rCGH on veracruz1

Package: rCGH

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rCGH_1.7.0.tar.gz

StartedAt: 2017-08-16 07:26:14 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 07:32:29 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 374.4 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_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/rCGH.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.7.0’
* 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 ‘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
multiplot    11.777  0.162  12.290
byGeneTable  11.695  0.176  12.197
plotProfile  10.274  0.130  10.715
recenter      7.515  0.041   7.765
rCGH-package  7.199  0.047   7.498
EMnormalize   7.072  0.043   7.345
plotLOH       6.929  0.047   7.204
plotDensity   6.549  0.039   6.748
view          6.023  0.021   6.220
segmentCGH    5.793  0.023   5.992
adjustSignal  5.502  0.042   5.716
* 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	0.959	0.020	1.005
EMnormalize	7.072	0.043	7.345
adjustSignal	5.502	0.042	5.716
byGeneTable	11.695	0.176	12.197
hg18	0.005	0.001	0.006
hg19	0.003	0.001	0.003
hg38	0.004	0.001	0.006
multiplot	11.777	0.162	12.290
plotDensity	6.549	0.039	6.748
plotLOH	6.929	0.047	7.204
plotProfile	10.274	0.130	10.715
rCGH-Agilent-class	0.001	0.000	0.001
rCGH-SNP6-class	0.001	0.000	0.001
rCGH-class	0.001	0.000	0.001
rCGH-cytoScan-class	0.001	0.000	0.001
rCGH-generic-class	0.001	0.001	0.001
rCGH-oncoScan-class	0.001	0.000	0.001
rCGH-package	7.199	0.047	7.498
readAffyCytoScan	0.628	0.004	0.645
readAffyOncoScan	0.034	0.001	0.035
readAffySNP6	0.668	0.007	0.687
readAgilent	1.219	0.013	1.255
readGeneric	0.012	0.001	0.013
recenter	7.515	0.041	7.765
segmentCGH	5.793	0.023	5.992
setInfo	0.636	0.003	0.658
view	6.023	0.021	6.220