BioC 3.5: CHECK report for rCGH on veracruz2

Package: rCGH

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rCGH_1.6.0.tar.gz

StartedAt: 2017-10-18 07:57:16 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 08:04:00 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 403.5 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_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/rCGH.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.6.0’
* 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
byGeneTable  13.173  0.249  13.891
multiplot    12.497  0.199  13.119
plotProfile  10.686  0.169  11.260
rCGH-package  7.577  0.078   7.877
plotLOH       7.379  0.074   7.685
EMnormalize   7.338  0.067   7.679
plotDensity   6.899  0.061   7.159
recenter      6.883  0.063   7.197
view          6.208  0.042   6.454
segmentCGH    6.122  0.047   6.329
adjustSignal  5.832  0.082   6.131
* 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	1.017	0.027	1.069
EMnormalize	7.338	0.067	7.679
adjustSignal	5.832	0.082	6.131
byGeneTable	13.173	0.249	13.891
hg18	0.003	0.001	0.005
hg19	0.004	0.001	0.004
hg38	0.004	0.001	0.006
multiplot	12.497	0.199	13.119
plotDensity	6.899	0.061	7.159
plotLOH	7.379	0.074	7.685
plotProfile	10.686	0.169	11.260
rCGH-Agilent-class	0.002	0.000	0.002
rCGH-SNP6-class	0.001	0.000	0.001
rCGH-class	0.001	0.000	0.001
rCGH-cytoScan-class	0.001	0.000	0.001
rCGH-generic-class	0.000	0.000	0.001
rCGH-oncoScan-class	0.001	0.000	0.001
rCGH-package	7.577	0.078	7.877
readAffyCytoScan	0.619	0.005	0.631
readAffyOncoScan	0.033	0.001	0.035
readAffySNP6	0.653	0.007	0.678
readAgilent	1.170	0.013	1.226
readGeneric	0.011	0.001	0.012
recenter	6.883	0.063	7.197
segmentCGH	6.122	0.047	6.329
setInfo	0.655	0.004	0.673
view	6.208	0.042	6.454