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CHECK report for dmrseq on machv2

This page was generated on 2020-10-17 11:58:24 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE dmrseq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 492/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dmrseq 1.8.0
Keegan Korthauer
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/dmrseq
Branch: RELEASE_3_11
Last Commit: 4ff63a9
Last Changed Date: 2020-04-27 15:14:15 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: dmrseq
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:dmrseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings dmrseq_1.8.0.tar.gz
StartedAt: 2020-10-17 00:38:56 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 00:48:22 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 565.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: dmrseq.Rcheck
Warnings: 1

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:dmrseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings dmrseq_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/dmrseq.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.8.0’
* 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 ‘dmrseq’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.0Mb
* 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 ... WARNING
Found the following significant warnings:

  Warning: 'GenomicRangesList' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
dmrseq   44.943  9.078  23.002
getAnnot 32.381  2.292  37.312
simDMRs   5.155  0.140   5.302
* 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 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/dmrseq.Rcheck/00check.log’
for details.



Installation output

dmrseq.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL dmrseq
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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.chr211.3810.0891.471
annot.chr210.0020.0030.005
dmrs.ex0.0020.0030.005
dmrseq44.943 9.07823.002
getAnnot32.381 2.29237.312
meanDiff0.5990.0410.642
plotDMRs1.4320.0341.468
plotEmpiricalDistribution3.5610.3593.926
simDMRs5.1550.1405.302