BioC 3.5: CHECK report for rCGH on toluca2

Package: rCGH

Version: 1.5.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rCGH_1.5.1.tar.gz

StartedAt: 2017-04-23 08:41:44 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 08:49:06 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 442.0 seconds

RetCode: 0

Status:  OK

CheckDir: rCGH.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rCGH_1.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/rCGH.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.5.1’
* 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 ‘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  15.713  0.254  16.205
multiplot    15.314  0.244  15.684
plotProfile  12.355  0.187  12.721
rCGH-package  8.909  0.070   9.055
plotDensity   8.130  0.064   8.294
plotLOH       8.091  0.066   8.213
EMnormalize   7.825  0.050   7.941
recenter      7.610  0.049   7.719
segmentCGH    6.838  0.029   6.910
view          6.749  0.035   6.792
adjustSignal  6.480  0.051   6.550
* 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	1.204	0.027	1.239
EMnormalize	7.825	0.050	7.941
adjustSignal	6.480	0.051	6.550
byGeneTable	15.713	0.254	16.205
hg18	0.005	0.000	0.005
hg19	0.004	0.000	0.005
hg38	0.004	0.001	0.005
multiplot	15.314	0.244	15.684
plotDensity	8.130	0.064	8.294
plotLOH	8.091	0.066	8.213
plotProfile	12.355	0.187	12.721
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	0.001	0.000	0.001
rCGH-oncoScan-class	0.001	0.000	0.001
rCGH-package	8.909	0.070	9.055
readAffyCytoScan	0.757	0.005	0.764
readAffyOncoScan	0.036	0.001	0.037
readAffySNP6	0.806	0.004	0.811
readAgilent	1.289	0.007	1.299
readGeneric	0.013	0.000	0.014
recenter	7.610	0.049	7.719
segmentCGH	6.838	0.029	6.910
setInfo	0.778	0.003	0.782
view	6.749	0.035	6.792