BioC 3.6: CHECK report for DMRScan on veracruz1

Package: DMRScan

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DMRScan_1.1.0.tar.gz

StartedAt: 2017-08-16 02:20:56 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:27:05 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 369.1 seconds

RetCode: 0

Status:  OK

CheckDir: DMRScan.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DMRScan_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/DMRScan.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 ‘DMRScan/DESCRIPTION’ ... OK
* this is package ‘DMRScan’ version ‘1.1.0’
* 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 ‘DMRScan’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
DMRScan_slidingWindow 78.755  1.981  83.443
DMRScan_package       78.085  2.053  82.409
makeCpGgenes          63.651  1.769  69.258
makeCpGregions        62.040  1.752  65.850
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/DMRScan.Rcheck/00check.log’
for details.

* installing *source* package ‘DMRScan’ ...
** 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 (DMRScan)

name	user	system	elapsed
DMRScan.methylationData	0.583	0.028	0.639
DMRScan.phenotypes	0.002	0.000	0.003
DMRScan_package	78.085	2.053	82.409
DMRScan_slidingWindow	78.755	1.981	83.443
Region-class_init	0.001	0.000	0.002
RegionList-class_init	0.002	0.000	0.001
Rt-methods	0.001	0.000	0.000
St-methods	0	0	0
estimateThreshold	0.062	0.000	0.065
getRegions	0.000	0.000	0.001
makeCpGgenes	63.651	1.769	69.258
makeCpGregions	62.040	1.752	65.850
nCpG	0.001	0.000	0.000
pVal	0.001	0.001	0.001
pos	0.002	0.000	0.002
setRegion	0.002	0.000	0.002
tVal	0.001	0.000	0.001