Nicolae Radu Zabet
| Snapshot Date: 2025-10-31 13:45 -0400 (Fri, 31 Oct 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 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-01 12:02 -0400 (Sat, 01 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:DMRcaller.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings DMRcaller_1.42.0.tar.gz |
| StartedAt: 2025-10-31 23:13:39 -0400 (Fri, 31 Oct 2025) |
| EndedAt: 2025-10-31 23:24:39 -0400 (Fri, 31 Oct 2025) |
| EllapsedTime: 659.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DMRcaller.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:DMRcaller.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings DMRcaller_1.42.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/DMRcaller.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 74.942 0.183 75.182
filterVMDs 27.697 0.232 27.928
computeDMRs 10.245 0.174 10.419
mergeDMRsIteratively 9.547 0.088 9.635
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/DMRcaller.Rcheck/00check.log’
for details.
DMRcaller.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL DMRcaller ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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): 0.93 sec
[readONTbam] Filtering invalid or empty reads ...
Step 2 (filter): 0.22 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): 6.20 sec
[readONTbam] Calculating overlaps with reference cytosines ...
Step 4 (coverage): 3.94 sec
[readONTbam] Annotating high-confidence modified reads ...
Step 5 (ONT_Cm & readsM meta-column): 2.13 sec
[readONTbam] Annotating unmodified (covered) reads & Calculating coverage per position...
Step 6 (ONT_C & readsN meta-column): 0.76 sec
[readONTbam] Done. Returning annotated GRanges.
Total: 14.18 sec
RUNIT TEST PROTOCOL -- Fri Oct 31 23:22:49 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
158.492 2.847 161.381
DMRcaller.Rcheck/DMRcaller-Ex.timings
| name | user | system | elapsed | |
| DMRcaller | 0.001 | 0.000 | 0.001 | |
| analyseReadsInsideRegionsForCondition | 1.302 | 0.050 | 1.352 | |
| analyseReadsInsideRegionsForConditionPMD | 0.716 | 0.005 | 0.722 | |
| computeCoMethylatedPositions | 0 | 0 | 0 | |
| computeCoMethylatedRegions | 0.372 | 0.029 | 0.401 | |
| computeDMRs | 10.245 | 0.174 | 10.419 | |
| computeDMRsReplicates | 0 | 0 | 0 | |
| computeMethylationDataCoverage | 0.464 | 0.036 | 0.500 | |
| computeMethylationDataSpatialCorrelation | 1.303 | 0.118 | 1.421 | |
| computeMethylationProfile | 1.044 | 0.040 | 1.085 | |
| computeOverlapProfile | 1.467 | 0.010 | 1.477 | |
| computePMDs | 74.942 | 0.183 | 75.182 | |
| computeVMDs | 0 | 0 | 0 | |
| extractGC | 0 | 0 | 0 | |
| filterDMRs | 1.587 | 0.037 | 1.624 | |
| filterPMDs | 1.729 | 0.003 | 1.733 | |
| filterVMDs | 27.697 | 0.232 | 27.928 | |
| filterVMRsONT | 0 | 0 | 0 | |
| getWholeChromosomes | 0.191 | 0.017 | 0.208 | |
| joinReplicates | 0.521 | 0.037 | 0.558 | |
| mergeDMRsIteratively | 9.547 | 0.088 | 9.635 | |
| mergePMDsIteratively | 3.867 | 0.049 | 3.916 | |
| plotLocalMethylationProfile | 1.601 | 0.145 | 1.746 | |
| plotMethylationDataCoverage | 0.753 | 0.060 | 0.812 | |
| plotMethylationDataSpatialCorrelation | 0.791 | 0.026 | 0.817 | |
| plotMethylationProfile | 1.013 | 0.014 | 1.028 | |
| plotMethylationProfileFromData | 2.667 | 0.006 | 2.673 | |
| plotOverlapProfile | 1.626 | 0.014 | 1.640 | |
| poolMethylationDatasets | 0.520 | 0.012 | 0.532 | |
| poolTwoMethylationDatasets | 1.279 | 0.014 | 1.293 | |
| readBismark | 1.310 | 0.025 | 1.336 | |
| readBismarkPool | 2.861 | 0.040 | 2.901 | |
| readONTbam | 0 | 0 | 0 | |
| saveBismark | 0.801 | 0.016 | 0.832 | |
| selectCytosine | 0 | 0 | 0 | |