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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_1.41.2.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 ‘1.41.2’
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘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’
findUnmodCoverageCpp: no visible binding for global variable
  ‘_DMRcaller_findUnmodCoverageCpp’
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 _DMRcaller_findUnmodCoverageCpp
  seqlengths seqlengths<- seqlevels 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘DMRcaller-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: analyseReadsInsideRegionsForConditionPMD
> ### Title: Analyse reads inside regions for condition
> ### Aliases: analyseReadsInsideRegionsForConditionPMD
> 
> ### ** Examples
> 
> 
> # load the ONT methylation data
> data(ontSampleGRangesList)
>  
> #load the PMDs in CG context. These PMDs were computed with minGap = 200.
> data(PMDsNoiseFilterCG)
> 
> #retrive the number of reads in CG context in GM18501
> PMDsNoiseFilterCGreadsCG <- analyseReadsInsideRegionsForConditionPMD(
+                              PMDsNoiseFilterCG[1:10], 
+                              ontSampleGRangesList[["GM18501"]], context = "CG", 
+                              label = "GM18501")
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 levels in corresponding context ...
Compute reads inside each region ...
Loading required namespace: GenomeInfoDb
Failed with error:  ‘there is no package called ‘GenomeInfoDb’’
Error in .requirePackage(package) : 
  unable to load required package ‘GenomeInfoDb’
Calls: analyseReadsInsideRegionsForConditionPMD ... vapply -> FUN -> is -> getClassDef -> .requirePackage
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
   
  1 Test Suite : 
  DMRcaller RUnit Tests - 1 test function, 1 error, 0 failures
  ERROR in /tmp/Rtmpa8AlyF/RLIBS_c027761ecdd5f/DMRcaller/unitTests/test_DMRcaller.R: Error while sourcing  /tmp/Rtmpa8AlyF/RLIBS_c027761ecdd5f/DMRcaller/unitTests/test_DMRcaller.R : Error in library(BSgenome.Hsapiens.UCSC.hg38) : 
    there is no package called 'BSgenome.Hsapiens.UCSC.hg38'
  
  Test files with failing tests
  
     test_DMRcaller.R 
       /tmp/Rtmpa8AlyF/RLIBS_c027761ecdd5f/DMRcaller/unitTests/test_DMRcaller.R 
  
  
  Error in BiocGenerics:::testPackage("DMRcaller") : 
    unit tests failed for package DMRcaller
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘DMRcaller.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'GenomeInfoDb''

Quitting from DMRcaller.Rmd:553-578 [computingBiologicalReplicates]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'i' in selecting a method for function '[': error in evaluating the argument 'x' in selecting a method for function 'from': unable to load required package 'GenomeInfoDb'
---
Backtrace:
     ▆
  1. ├─DMRcaller::computeDMRsReplicates(...)
  2. │ └─DMRcaller:::.computeDMRsReplicatesBins(...)
  3. │   ├─...[]
  4. │   ├─S4Vectors::queryHits(...)
  5. │   │ └─S4Vectors::from(x, ...)
  6. │   ├─IRanges::findOverlaps(localContextMethylationData, regions)
  7. │   └─GenomicRanges::findOverlaps(localContextMethylationData, regions)
  8. │     └─GenomicRanges (local) .local(query, subject, maxgap, minoverlap, type, select, ...)
  9. │       └─GenomicRanges:::findOverlaps_GNCList(...)
 10. │         ├─base::merge(seqinfo(query), seqinfo(subject))
 11. │         └─Seqinfo::merge(seqinfo(query), seqinfo(subject))
 12. │           └─Seqinfo:::.merge_Seqinfo_objects(x, y, ...)
 13. │             └─base::vapply(args, function(arg) is(arg, class(x)), logical(1))
 14. │               └─Seqinfo (local) FUN(X[[i]], ...)
 15. │                 └─methods::is(arg, class(x))
 16. │                   └─methods::getClassDef(...)
 17. │                     └─methods:::.requirePackage(package)
 18. │                       └─base::stop(...)
 19. ├─base::.handleSimpleError(...)
 20. │ └─base (local) h(simpleError(msg, call))
 21. └─base::.handleSimpleError(...)
 22.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'DMRcaller.Rmd' failed with diagnostics:
error in evaluating the argument 'i' in selecting a method for function '[': error in evaluating the argument 'x' in selecting a method for function 'from': unable to load required package 'GenomeInfoDb'
--- failed re-building ‘DMRcaller.Rmd’

SUMMARY: processing the following file failed:
  ‘DMRcaller.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/DMRcaller.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL DMRcaller
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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)

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

Error in library(BSgenome.Hsapiens.UCSC.hg38) : 
  there is no package called 'BSgenome.Hsapiens.UCSC.hg38'


RUNIT TEST PROTOCOL -- Fri Oct  3 23:22:20 2025 
*********************************************** 
Number of test functions: 1 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
DMRcaller RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in /tmp/Rtmpa8AlyF/RLIBS_c027761ecdd5f/DMRcaller/unitTests/test_DMRcaller.R: Error while sourcing  /tmp/Rtmpa8AlyF/RLIBS_c027761ecdd5f/DMRcaller/unitTests/test_DMRcaller.R : Error in library(BSgenome.Hsapiens.UCSC.hg38) : 
  there is no package called 'BSgenome.Hsapiens.UCSC.hg38'

Test files with failing tests

   test_DMRcaller.R 
     /tmp/Rtmpa8AlyF/RLIBS_c027761ecdd5f/DMRcaller/unitTests/test_DMRcaller.R 


Error in BiocGenerics:::testPackage("DMRcaller") : 
  unit tests failed for package DMRcaller
Execution halted