Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-03 12:03 -0400 (Fri, 03 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4845 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4632 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4577 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
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 600/2337 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DMRcaller 1.41.2 (landing page) Nicolae Radu Zabet
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
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: 1.41.2 |
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 |
StartedAt: 2025-10-02 23:18:27 -0400 (Thu, 02 Oct 2025) |
EndedAt: 2025-10-02 23:23:34 -0400 (Thu, 02 Oct 2025) |
EllapsedTime: 307.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: DMRcaller.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * 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/RtmpfPo3Ma/RLIBS_1f08077e9bdb90/DMRcaller/unitTests/test_DMRcaller.R: Error while sourcing /tmp/RtmpfPo3Ma/RLIBS_1f08077e9bdb90/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/RtmpfPo3Ma/RLIBS_1f08077e9bdb90/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.
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 ‘1.41.2’ ** 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)
DMRcaller.Rcheck/tests/runTests.Rout.fail
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 -- Thu Oct 2 23:22:24 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/RtmpfPo3Ma/RLIBS_1f08077e9bdb90/DMRcaller/unitTests/test_DMRcaller.R: Error while sourcing /tmp/RtmpfPo3Ma/RLIBS_1f08077e9bdb90/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/RtmpfPo3Ma/RLIBS_1f08077e9bdb90/DMRcaller/unitTests/test_DMRcaller.R Error in BiocGenerics:::testPackage("DMRcaller") : unit tests failed for package DMRcaller Execution halted
DMRcaller.Rcheck/DMRcaller-Ex.timings
name | user | system | elapsed | |
DMRcaller | 0.002 | 0.000 | 0.001 | |
analyseReadsInsideRegionsForCondition | 1.285 | 0.037 | 1.322 | |