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This page was generated on 2025-10-18 12:04 -0400 (Sat, 18 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 603/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DMRcaller 1.41.2  (landing page)
Nicolae Radu Zabet
Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 Oct 2025)
git_url: https://git.bioconductor.org/packages/DMRcaller
git_branch: devel
git_last_commit: 066119e
git_last_commit_date: 2025-10-17 09:51:50 -0400 (Fri, 17 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for DMRcaller on lconway

To the developers/maintainers of the DMRcaller package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: DMRcaller
Version: 1.41.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DMRcaller.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DMRcaller_1.41.2.tar.gz
StartedAt: 2025-10-17 21:42:21 -0400 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 21:53:25 -0400 (Fri, 17 Oct 2025)
EllapsedTime: 664.7 seconds
RetCode: 0
Status:   OK  
CheckDir: DMRcaller.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DMRcaller.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DMRcaller_1.41.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/DMRcaller.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DMRcaller/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DMRcaller’ version ‘1.41.2’
* package encoding: UTF-8
* 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 ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘GenomicRanges’ ‘S4Vectors’ ‘IRanges’ ‘betareg’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘GenomeInfoDb’ ‘Seqinfo’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.validateModif: no visible global function definition for ‘seqlengths’
extractGC: no visible global function definition for ‘seqlevels’
readONTbam: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg38’
readONTbam: no visible global function definition for ‘seqlengths’
selectCytosine: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg38’
selectCytosine : <anonymous>: no visible global function definition for
  ‘seqlengths’
selectCytosine : <anonymous>: no visible global function definition for
  ‘seqlevels<-’
selectCytosine : <anonymous>: no visible global function definition for
  ‘seqlengths<-’
selectCytosine: no visible global function definition for ‘seqlevels<-’
selectCytosine: no visible global function definition for ‘seqlevels’
Undefined global functions or variables:
  BSgenome.Hsapiens.UCSC.hg38 seqlengths seqlengths<- seqlevels
  seqlevels<-
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  analyseReadsInsideRegionsForCondition.Rd: GRanges
  computeDMRs.Rd: GRanges
  computeMethylationDataCoverage.Rd: GRanges
  computeMethylationProfile.Rd: GRanges
  computeOverlapProfile.Rd: GRanges
  computeVMDs.Rd: GRanges
  extractGC.Rd: GRanges
  filterDMRs.Rd: GRanges
  filterVMDs.Rd: GRanges
  getWholeChromosomes.Rd: GRanges
  mergeDMRsIteratively.Rd: GRanges
  plotLocalMethylationProfile.Rd: GRanges, GRangesList
  plotMethylationDataCoverage.Rd: GRanges
  plotMethylationProfile.Rd: GRanges
  plotMethylationProfileFromData.Rd: GRanges
  plotOverlapProfile.Rd: GRanges
  poolMethylationDatasets.Rd: GRangesList, GRanges
  poolTwoMethylationDatasets.Rd: GRanges
  readBismark.Rd: GRanges
  readBismarkPool.Rd: GRanges
  saveBismark.Rd: GRanges
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 (user + system) or elapsed time > 5s
                       user system elapsed
computePMDs          82.098  0.547  84.997
filterVMDs           29.677  0.206  30.952
mergeDMRsIteratively 11.757  0.169  12.526
computeDMRs          11.550  0.168  11.798
readBismarkPool       5.045  0.539   6.886
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/DMRcaller.Rcheck/00check.log’
for details.


Installation output

DMRcaller.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DMRcaller
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘DMRcaller’ ...
** this is package ‘DMRcaller’ version ‘1.41.2’
** 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

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, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min


Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Parameters checking ...
Using user-specified core count: 1
Current parallel setting, BPPARAM: 
class: SerialParam
  bpisup: FALSE; bpnworkers: 1; bptasks: 2147483647; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bpRNGseed: ; bptimeout: NA; bpprogressbar: TRUE
  bpexportglobals: FALSE; bpexportvariables: FALSE; bpforceGC: FALSE
  bpfallback: FALSE
  bplogdir: NA
  bpresultdir: NA
Extract methylation in the corresponding context 
Loading required namespace: GenomeInfoDb
Computing DMRs 
Merge adjacent DMRs
Merge DMRs iteratively
Filter DMRs 
Parameters checking ...
Current parallel setting, BPPARAM: 
class: SerialParam
  bpisup: FALSE; bpnworkers: 1; bptasks: 2147483647; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bpRNGseed: ; bptimeout: NA; bpprogressbar: TRUE
  bpexportglobals: FALSE; bpexportvariables: FALSE; bpforceGC: FALSE
  bpfallback: FALSE
  bplogdir: NA
  bpresultdir: NA
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 ...
Current parallel setting, BPPARAM: 
class: SerialParam
  bpisup: FALSE; bpnworkers: 1; bptasks: 2147483647; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bpRNGseed: ; bptimeout: NA; bpprogressbar: TRUE
  bpexportglobals: FALSE; bpexportvariables: FALSE; bpforceGC: FALSE
  bpfallback: FALSE
  bplogdir: NA
  bpresultdir: NA
Extract methylation in the corresponding context 
Computing DMRs at  Chr1:1..4976 
Selecting data...
Identifying DMRs...
Validating objects 
Finding overlaps 
Joining objects 
Parameters checking ...
Using user-specified core count: 1
Current parallel setting, BPPARAM: 
class: SerialParam
  bpisup: FALSE; bpnworkers: 1; bptasks: 2147483647; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bpRNGseed: ; bptimeout: NA; bpprogressbar: TRUE
  bpexportglobals: FALSE; bpexportvariables: FALSE; bpforceGC: FALSE
  bpfallback: FALSE
  bplogdir: NA
  bpresultdir: NA
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 ...
Current parallel setting, BPPARAM: 
class: SerialParam
  bpisup: FALSE; bpnworkers: 1; bptasks: 2147483647; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bpRNGseed: ; bptimeout: NA; bpprogressbar: TRUE
  bpexportglobals: FALSE; bpexportvariables: FALSE; bpforceGC: FALSE
  bpfallback: FALSE
  bplogdir: NA
  bpresultdir: NA
Merge DMRs iteratively ...
Loading required package: GenomeInfoDb
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: BiocIO
Loading required package: rtracklayer
Parameters checking ...
Parameters checking ...
Select the Cytosine Positions in the specified BSgenome ...
Current parallel setting, BPPARAM: 
class: SerialParam
  bpisup: FALSE; bpnworkers: 1; bptasks: 2147483647; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bpRNGseed: ; bptimeout: NA; bpprogressbar: TRUE
  bpexportglobals: FALSE; bpexportvariables: FALSE; bpforceGC: FALSE
  bpfallback: FALSE
  bplogdir: NA
  bpresultdir: NA
[readONTbam] Generating index file for BAM ...
[readONTbam] Loading BAM ...
Step 1 (scanBam): 0.15 sec
[readONTbam] Filtering invalid or empty reads ...
Step 2 (filter): 0.32 sec
[readONTbam] Generating cytosine position list and indel_info ...
[readONTbam] Start Decoding MM/ML ...

  |                                                                            
  |                                                                      |   0%[readONTbam] Decoding MM/ML: 20% (1/5 reads)

  |                                                                            
  |==============                                                        |  20%[readONTbam] Decoding MM/ML: 40% (2/5 reads)

  |                                                                            
  |============================                                          |  40%[readONTbam] Decoding MM/ML: 60% (3/5 reads)

  |                                                                            
  |==========================================                            |  60%[readONTbam] Decoding MM/ML: 80% (4/5 reads)

  |                                                                            
  |========================================================              |  80%[readONTbam] Decoding MM/ML: 100% (5/5 reads)

  |                                                                            
  |======================================================================| 100%

Step 3 (decode Bam file): 8.45 sec
[readONTbam] Calculating overlaps with reference cytosines ...
Step 4 (coverage): 4.11 sec
[readONTbam] Annotating high-confidence modified reads ...
Step 5 (ONT_Cm & readsM meta-column): 1.38 sec
[readONTbam] Annotating unmodified (covered) reads & Calculating coverage per position...
Step 6 (ONT_C & readsN meta-column): 1.18 sec
[readONTbam] Done. Returning annotated GRanges.
Total: 15.59 sec


RUNIT TEST PROTOCOL -- Fri Oct 17 21:53:09 2025 
*********************************************** 
Number of test functions: 7 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
DMRcaller RUnit Tests - 7 test functions, 0 errors, 0 failures
Number of test functions: 7 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
188.230   3.835 193.563 

Example timings

DMRcaller.Rcheck/DMRcaller-Ex.timings

nameusersystemelapsed
DMRcaller0.0010.0030.004
analyseReadsInsideRegionsForCondition1.0470.0452.350
analyseReadsInsideRegionsForConditionPMD0.7050.0401.665
computeCoMethylatedPositions000
computeCoMethylatedRegions0.4270.0140.447
computeDMRs11.550 0.16811.798
computeDMRsReplicates0.0000.0010.001
computeMethylationDataCoverage0.4210.0660.720
computeMethylationDataSpatialCorrelation1.2000.0481.261
computeMethylationProfile1.2190.0551.280
computeOverlapProfile1.6050.0421.702
computePMDs82.098 0.54784.997
computeVMDs0.0000.0010.001
extractGC000
filterDMRs1.8060.0751.893
filterPMDs2.0450.0552.114
filterVMDs29.677 0.20630.952
filterVMRsONT0.0000.0000.001
getWholeChromosomes0.1230.0150.587
joinReplicates0.5070.1241.473
mergeDMRsIteratively11.757 0.16912.526
mergePMDsIteratively4.7260.0454.814
plotLocalMethylationProfile1.9470.1312.134
plotMethylationDataCoverage0.9050.0911.008
plotMethylationDataSpatialCorrelation0.9400.0851.034
plotMethylationProfile1.1540.0451.229
plotMethylationProfileFromData3.3250.1463.506
plotOverlapProfile1.9760.0242.014
poolMethylationDatasets0.5480.0840.661
poolTwoMethylationDatasets0.5030.0360.549
readBismark2.0160.2162.343
readBismarkPool5.0450.5396.886
readONTbam0.0000.0010.000
saveBismark1.4370.0861.663
selectCytosine0.0000.0010.001