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This page was generated on 2021-09-20 15:05:40 -0400 (Mon, 20 Sep 2021).

CHECK results for DMRcaller on machv2

To the developers/maintainers of the DMRcaller package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DMRcaller.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 516/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DMRcaller 1.24.0  (landing page)
Nicolae Radu Zabet
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/DMRcaller
git_branch: RELEASE_3_13
git_last_commit: 828312c
git_last_commit_date: 2021-05-19 12:12:36 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DMRcaller
Version: 1.24.0
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_1.24.0.tar.gz
StartedAt: 2021-09-19 18:25:14 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 18:32:32 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 438.3 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_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/DMRcaller.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.24.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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
computeDMRs          26.358  0.195  31.727
mergeDMRsIteratively 26.012  0.100  26.136
readBismarkPool       6.789  0.293   7.106
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-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
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.max, which.min


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

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 -- Sun Sep 19 18:32:24 2021 
*********************************************** 
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 
205.044   0.785 205.965 

Example timings

DMRcaller.Rcheck/DMRcaller-Ex.timings

nameusersystemelapsed
DMRcaller0.0010.0040.014
analyseReadsInsideRegionsForCondition1.4190.0561.715
computeDMRs26.358 0.19531.727
computeDMRsReplicates000
computeMethylationDataCoverage0.6290.0360.665
computeMethylationDataSpatialCorrelation0.7570.0370.795
computeMethylationProfile2.0360.0702.108
computeOverlapProfile2.6590.0092.670
extractGC000
filterDMRs3.9750.0454.022
getWholeChromosomes0.3090.0090.319
joinReplicates0.0000.0000.001
mergeDMRsIteratively26.012 0.10026.136
plotLocalMethylationProfile2.1880.1142.303
plotMethylationDataCoverage1.1850.0471.233
plotMethylationDataSpatialCorrelation000
plotMethylationProfile2.0310.0392.071
plotMethylationProfileFromData4.7970.1184.919
plotOverlapProfile3.7890.0173.806
poolMethylationDatasets1.2760.0611.340
poolTwoMethylationDatasets0.9650.0531.018
readBismark2.8860.1323.027
readBismarkPool6.7890.2937.106
saveBismark1.7330.0701.869