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###
### 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_1.42.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/DMRcaller.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DMRcaller/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DMRcaller’ version ‘1.42.0’
* 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                    86.412  0.693 143.759
filterVMDs                     30.455  0.239  48.028
computeDMRs                    11.677  0.214  20.926
mergeDMRsIteratively           11.024  0.118  17.429
readBismarkPool                 4.580  0.326   7.609
mergePMDsIteratively            4.430  0.039   6.982
plotMethylationProfileFromData  3.483  0.120   5.541
* 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.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DMRcaller
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘DMRcaller’ ...
** this is package ‘DMRcaller’ version ‘1.42.0’
** 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)

R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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): 2.06 sec
[readONTbam] Filtering invalid or empty reads ...
Step 2 (filter): 0.51 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): 10.33 sec
[readONTbam] Calculating overlaps with reference cytosines ...
Step 4 (coverage): 7.81 sec
[readONTbam] Annotating high-confidence modified reads ...
Step 5 (ONT_Cm & readsM meta-column): 2.44 sec
[readONTbam] Annotating unmodified (covered) reads & Calculating coverage per position...
Step 6 (ONT_C & readsN meta-column): 2.50 sec
[readONTbam] Done. Returning annotated GRanges.
Total: 25.65 sec


RUNIT TEST PROTOCOL -- Wed Nov 26 01:54:41 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 
There were 36 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
187.943   3.408 295.858