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CHECK report for DMRcaller on machv2

This page was generated on 2020-10-17 11:58:23 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE DMRcaller PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 488/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DMRcaller 1.20.0
Nicolae Radu Zabet
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/DMRcaller
Branch: RELEASE_3_11
Last Commit: 60b08b5
Last Changed Date: 2020-04-27 14:48:00 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: DMRcaller
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DMRcaller.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DMRcaller_1.20.0.tar.gz
StartedAt: 2020-10-17 00:36:49 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 00:44:33 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 464.3 seconds
RetCode: 0
Status:  OK 
CheckDir: DMRcaller.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DMRcaller.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DMRcaller_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/DMRcaller.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 ‘DMRcaller/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DMRcaller’ version ‘1.20.0’
* 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 ‘DMRcaller’ can be installed ... OK
* checking installed package size ... OK
* 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
extractGC: no visible global function definition for ‘getSeq’
extractGC: no visible global function definition for ‘seqlevels’
Undefined global functions or variables:
  getSeq seqlevels
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
mergeDMRsIteratively 19.256  0.094  19.369
computeDMRs          18.463  0.125  18.602
readBismarkPool       7.052  0.290   7.402
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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-3.11-bioc/meat/DMRcaller.Rcheck/00check.log’
for details.



Installation output

DMRcaller.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DMRcaller
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘DMRcaller’ ...
** using staged installation
** R
** data
** 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 (DMRcaller)

Tests output

DMRcaller.Rcheck/tests/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("DMRcaller")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Parameters checking ...
Extract methylation in the corresponding context 
Computing DMRs 
Merge adjacent DMRs
Merge DMRs iteratively
Filter DMRs 
Parameters checking ...
Extract methylation in the corresponding context 
Computing DMRs at  Chr1:1..4976 
Calculating interpolations...
Identifying DMRs...
Analysed reads inside DMRs
Merge DMRs iteratively
Filter DMRs 
Parameters checking ...
Extract methylation in the corresponding context 
Computing DMRs at  Chr1:1..4976 
Selecting data...
Identifying DMRs...
Validating objects 
Finding overlaps 
Joining objects 
Parameters checking ...
Extract methylation in the corresponding context 
Computing DMRs at  Chr1:1..4976 
Count inside each bin...
Filter the bins...
Identifying DMRs...
Merge adjacent DMRs
Merge DMRs iteratively
Filter DMRs 
Parameters checking ...
Merge DMRs iteratively ...


RUNIT TEST PROTOCOL -- Sat Oct 17 00:44:23 2020 
*********************************************** 
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
DMRcaller RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 
Warning message:
In fisher.test(matrix(unlist(x), nrow = 2, byrow = TRUE), alternative = alternative) :
  'x' has been rounded to integer: Mean relative difference: 0.002857143
> 
> proc.time()
   user  system elapsed 
228.262   0.919 229.634 

Example timings

DMRcaller.Rcheck/DMRcaller-Ex.timings

nameusersystemelapsed
DMRcaller0.0020.0040.006
analyseReadsInsideRegionsForCondition1.2950.0661.362
computeDMRs18.463 0.12518.602
computeDMRsReplicates0.0010.0010.001
computeMethylationDataCoverage0.6730.0640.738
computeMethylationDataSpatialCorrelation0.6380.0500.687
computeMethylationProfile1.8180.0821.899
computeOverlapProfile3.2100.0213.232
extractGC0.0000.0000.001
filterDMRs3.0680.0883.159
getWholeChromosomes0.6250.0280.655
joinReplicates0.0000.0000.001
mergeDMRsIteratively19.256 0.09419.369
plotLocalMethylationProfile1.6750.0821.757
plotMethylationDataCoverage1.4780.0781.561
plotMethylationDataSpatialCorrelation0.0010.0000.001
plotMethylationProfile1.5550.0361.595
plotMethylationProfileFromData3.3190.0913.413
plotOverlapProfile3.4260.0193.448
poolMethylationDatasets1.1900.0521.244
poolTwoMethylationDatasets1.1130.0651.179
readBismark3.0400.1073.161
readBismarkPool7.0520.2907.402
saveBismark1.9680.0502.028