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CHECK report for dmrseq on malbec1

This page was generated on 2019-04-16 11:53:19 -0400 (Tue, 16 Apr 2019).

Package 424/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dmrseq 1.2.5
Keegan Korthauer
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/dmrseq
Branch: RELEASE_3_8
Last Commit: 467248f
Last Changed Date: 2019-03-25 10:06:09 -0400 (Mon, 25 Mar 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: dmrseq
Version: 1.2.5
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:dmrseq.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings dmrseq_1.2.5.tar.gz
StartedAt: 2019-04-15 23:33:43 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:39:26 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 342.7 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-3.8-bioc/R/bin/R CMD check --install=check:dmrseq.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings dmrseq_1.2.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/dmrseq.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.2.5’
* 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   43.336  8.388  23.483
getAnnot 15.552  0.656  18.830
* 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-3.8-bioc/meat/dmrseq.Rcheck/00check.log’
for details.



Installation output

dmrseq.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL dmrseq
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘dmrseq’ ...
** 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
* DONE (dmrseq)

Tests output


Example timings

dmrseq.Rcheck/dmrseq-Ex.timings

nameusersystemelapsed
BS.chr211.9040.0601.965
annot.chr210.0000.0000.002
dmrs.ex0.0000.0000.002
dmrseq43.336 8.38823.483
getAnnot15.552 0.65618.830
meanDiff0.9080.0080.918
plotDMRs1.1320.0281.169
plotEmpiricalDistribution4.1800.1684.360
simDMRs3.3840.0563.448