BioC 3.5: CHECK report for rCGH on oaxaca

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: 2017-03-04 07:47:53 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 07:54:42 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 408.9 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 r72177)
* 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
multiplot    14.249  0.188  14.453
byGeneTable  14.094  0.240  14.473
plotProfile  10.871  0.140  11.040
rCGH-package  8.366  0.064   8.468
recenter      7.809  0.048   7.865
view          7.167  0.028   7.201
EMnormalize   7.116  0.048   7.168
plotDensity   7.096  0.055   7.245
segmentCGH    6.767  0.026   6.796
plotLOH       6.304  0.076   6.383
* 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	0.994	0.025	1.020
EMnormalize	7.116	0.048	7.168
adjustSignal	4.227	0.056	4.283
byGeneTable	14.094	0.240	14.473
hg18	0.003	0.000	0.003
hg19	0.003	0.001	0.004
hg38	0.003	0.001	0.003
multiplot	14.249	0.188	14.453
plotDensity	7.096	0.055	7.245
plotLOH	6.304	0.076	6.383
plotProfile	10.871	0.140	11.040
rCGH-Agilent-class	0.002	0.000	0.002
rCGH-SNP6-class	0.002	0.001	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	0.000
rCGH-package	8.366	0.064	8.468
readAffyCytoScan	0.669	0.004	0.673
readAffyOncoScan	0.027	0.001	0.028
readAffySNP6	0.797	0.006	0.802
readAgilent	1.455	0.013	1.475
readGeneric	0.015	0.000	0.016
recenter	7.809	0.048	7.865
segmentCGH	6.767	0.026	6.796
setInfo	0.871	0.004	0.877
view	7.167	0.028	7.201