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CHECK report for dmrseq on malbec2

This page was generated on 2019-04-09 11:50:06 -0400 (Tue, 09 Apr 2019).

Package 443/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dmrseq 1.3.11
Keegan Korthauer
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/dmrseq
Branch: master
Last Commit: d11b75b
Last Changed Date: 2019-04-08 11:44:36 -0400 (Mon, 08 Apr 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]YES, new version is higher than in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK YES, new version is higher than in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK YES, new version is higher than in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: dmrseq
Version: 1.3.11
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:dmrseq.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings dmrseq_1.3.11.tar.gz
StartedAt: 2019-04-09 00:08:26 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:14:30 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 363.0 seconds
RetCode: 0
Status:  OK 
CheckDir: dmrseq.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:dmrseq.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings dmrseq_1.3.11.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/dmrseq.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dmrseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dmrseq’ version ‘1.3.11’
* 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 ‘dmrseq’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
* 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 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 ... NOTE
plotDMRs: warning in rank(as.numeric(rowSums(cov.unique)), ties =
  "first"): partial argument match of 'ties' to 'ties.method'
plotEmpiricalDistribution: no visible binding for global variable ‘wt’
Undefined global functions or variables:
  wt
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
dmrseq   34.533  8.527  19.179
getAnnot 16.596  0.617  19.668
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/dmrseq.Rcheck/00check.log’
for details.



Installation output

dmrseq.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL dmrseq
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘dmrseq’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (dmrseq)

Tests output


Example timings

dmrseq.Rcheck/dmrseq-Ex.timings

nameusersystemelapsed
BS.chr211.7170.0871.805
annot.chr210.0010.0000.002
dmrs.ex0.0010.0000.001
dmrseq34.533 8.52719.179
getAnnot16.596 0.61719.668
meanDiff1.2770.0361.314
plotDMRs0.7980.0280.826
plotEmpiricalDistribution3.2480.1323.380
simDMRs1.8860.0441.930