Nicolae Radu Zabet
| Snapshot Date: 2025-12-18 13:45 -0500 (Thu, 18 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/DMRcaller |
| git_branch: RELEASE_3_22 |
| git_last_commit: ba466d4 |
| git_last_commit_date: 2025-10-29 10:25:12 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-22 12:04 -0500 (Mon, 22 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4883 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 606/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DMRcaller 1.42.0 (landing page) Nicolae Radu Zabet
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| Package: DMRcaller |
| Version: 1.42.0 |
| 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 |
| StartedAt: 2025-12-19 03:29:52 -0500 (Fri, 19 Dec 2025) |
| EndedAt: 2025-12-19 03:52:37 -0500 (Fri, 19 Dec 2025) |
| EllapsedTime: 1365.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DMRcaller.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/DMRcaller.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘1.42.0’
* 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 185.615 0.781 198.292
filterVMDs 84.267 0.364 94.773
mergeDMRsIteratively 23.818 0.141 27.248
computeDMRs 23.415 0.325 25.581
mergePMDsIteratively 9.298 0.044 9.558
readBismarkPool 8.901 0.381 10.139
plotMethylationProfileFromData 5.418 0.111 5.643
* 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.
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 ‘1.42.0’ ** 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)
DMRcaller.Rcheck/tests/runTests.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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): 0.27 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): 18.23 sec
[readONTbam] Calculating overlaps with reference cytosines ...
Step 4 (coverage): 4.74 sec
[readONTbam] Annotating high-confidence modified reads ...
Step 5 (ONT_Cm & readsM meta-column): 1.98 sec
[readONTbam] Annotating unmodified (covered) reads & Calculating coverage per position...
Step 6 (ONT_C & readsN meta-column): 1.66 sec
[readONTbam] Done. Returning annotated GRanges.
Total: 27.38 sec
RUNIT TEST PROTOCOL -- Fri Dec 19 03:52:20 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
446.341 5.121 469.979
DMRcaller.Rcheck/DMRcaller-Ex.timings
| name | user | system | elapsed | |
| DMRcaller | 0.003 | 0.010 | 0.014 | |
| analyseReadsInsideRegionsForCondition | 1.791 | 0.068 | 2.151 | |
| analyseReadsInsideRegionsForConditionPMD | 1.452 | 0.096 | 1.662 | |
| computeCoMethylatedPositions | 0.000 | 0.001 | 0.002 | |
| computeCoMethylatedRegions | 0.793 | 0.023 | 0.863 | |
| computeDMRs | 23.415 | 0.325 | 25.581 | |
| computeDMRsReplicates | 0.001 | 0.002 | 0.002 | |
| computeMethylationDataCoverage | 0.714 | 0.045 | 0.806 | |
| computeMethylationDataSpatialCorrelation | 1.596 | 0.079 | 1.775 | |
| computeMethylationProfile | 2.246 | 0.066 | 2.484 | |
| computeOverlapProfile | 3.588 | 0.108 | 4.037 | |
| computePMDs | 185.615 | 0.781 | 198.292 | |
| computeVMDs | 0.001 | 0.001 | 0.002 | |
| extractGC | 0.000 | 0.001 | 0.001 | |
| filterDMRs | 3.716 | 0.062 | 4.116 | |
| filterPMDs | 4.202 | 0.039 | 4.587 | |
| filterVMDs | 84.267 | 0.364 | 94.773 | |
| filterVMRsONT | 0.000 | 0.002 | 0.002 | |
| getWholeChromosomes | 0.263 | 0.012 | 0.308 | |
| joinReplicates | 1.604 | 0.084 | 1.910 | |
| mergeDMRsIteratively | 23.818 | 0.141 | 27.248 | |
| mergePMDsIteratively | 9.298 | 0.044 | 9.558 | |
| plotLocalMethylationProfile | 2.621 | 0.111 | 2.965 | |
| plotMethylationDataCoverage | 1.420 | 0.075 | 1.607 | |
| plotMethylationDataSpatialCorrelation | 2.197 | 0.089 | 2.335 | |
| plotMethylationProfile | 2.275 | 0.037 | 2.395 | |
| plotMethylationProfileFromData | 5.418 | 0.111 | 5.643 | |
| plotOverlapProfile | 3.834 | 0.047 | 3.899 | |
| poolMethylationDatasets | 0.750 | 0.057 | 0.810 | |
| poolTwoMethylationDatasets | 1.573 | 0.098 | 1.679 | |
| readBismark | 3.364 | 0.187 | 3.635 | |
| readBismarkPool | 8.901 | 0.381 | 10.139 | |
| readONTbam | 0.000 | 0.001 | 0.001 | |
| saveBismark | 2.300 | 0.114 | 2.949 | |
| selectCytosine | 0.000 | 0.001 | 0.001 | |