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BioC 3.5: CHECK report for DMRScan on malbec2

This page was generated on 2017-10-18 14:18:20 -0400 (Wed, 18 Oct 2017).

Package 358/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DMRScan 1.0.0
Christian M Page
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/DMRScan
Branch: RELEASE_3_5
Last Commit: 5042a5e
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DMRScan
Version: 1.0.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings DMRScan_1.0.0.tar.gz
StartedAt: 2017-10-17 22:45:27 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 22:50:41 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 314.6 seconds
RetCode: 0
Status:  OK 
CheckDir: DMRScan.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings DMRScan_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/DMRScan.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DMRScan/DESCRIPTION’ ... OK
* this is package ‘DMRScan’ version ‘1.0.0’
* 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 72.456  0.032  72.585
DMRScan_package       63.752  0.112  63.941
makeCpGgenes          59.760  0.108  59.946
makeCpGregions        55.692  0.016  55.772
* 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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/DMRScan.Rcheck/00check.log’
for details.


DMRScan.Rcheck/00install.out:

* 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)

DMRScan.Rcheck/DMRScan-Ex.timings:

nameusersystemelapsed
DMRScan.methylationData0.5640.1280.690
DMRScan.phenotypes0.0040.0000.004
DMRScan_package63.752 0.11263.941
DMRScan_slidingWindow72.456 0.03272.585
Region-class_init0.0000.0000.001
RegionList-class_init000
Rt-methods000
St-methods000
estimateThreshold0.0440.0000.042
getRegions000
makeCpGgenes59.760 0.10859.946
makeCpGregions55.692 0.01655.772
nCpG0.0000.0000.001
pVal0.0000.0000.002
pos0.0040.0000.002
setRegion0.0040.0000.001
tVal0.0000.0000.001