Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-16 12:03 -0400 (Sat, 16 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4596 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4538 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
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 1252/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MethylSeekR 1.49.0 (landing page) Lukas Burger
| 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 | ERROR | skipped | ||||||||||
To the developers/maintainers of the MethylSeekR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MethylSeekR.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: MethylSeekR |
Version: 1.49.0 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MethylSeekR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MethylSeekR_1.49.0.tar.gz |
StartedAt: 2025-08-16 00:05:46 -0400 (Sat, 16 Aug 2025) |
EndedAt: 2025-08-16 00:10:40 -0400 (Sat, 16 Aug 2025) |
EllapsedTime: 293.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: MethylSeekR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MethylSeekR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MethylSeekR_1.49.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MethylSeekR.Rcheck’ * using R version 4.5.1 (2025-06-13) * 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 ‘MethylSeekR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MethylSeekR’ version ‘1.49.0’ * 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 ‘MethylSeekR’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘parallel’ 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 Namespace in Imports field not imported from: ‘geneplotter’ All declared Imports should be used. Package in Depends field not imported from: ‘rtracklayer’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE PMDviterbiSegmentation : <anonymous>: no visible global function definition for ‘values’ PMDviterbiSegmentation : <anonymous>: no visible global function definition for ‘predict’ PMDviterbiSegmentation : <anonymous>: no visible global function definition for ‘Rle’ PMDviterbiSegmentation : <anonymous>: no visible global function definition for ‘runValue’ calculateAlphaDistr : <anonymous>: no visible global function definition for ‘Rle’ calculateFDRs: no visible global function definition for ‘values’ calculateFDRs: no visible global function definition for ‘queryHits’ calculateFDRs: no visible global function definition for ‘values<-’ calculateFDRs : <anonymous>: no visible global function definition for ‘Rle’ calculateFDRs : <anonymous>: no visible global function definition for ‘values’ calculateFDRs : <anonymous>: no visible global function definition for ‘runValue’ createGRangesObjectPMDSegmentation : <anonymous>: no visible global function definition for ‘Rle’ createGRangesObjectPMDSegmentation : <anonymous>: no visible global function definition for ‘nrun’ createGRangesObjectPMDSegmentation : <anonymous>: no visible global function definition for ‘runValue’ plotAlphaDistributionOneChr: no visible global function definition for ‘values’ plotFinalSegmentation: no visible global function definition for ‘values’ plotFinalSegmentation: no visible global function definition for ‘Rle’ plotPMDSegmentation: no visible global function definition for ‘values’ readMethylome: no visible global function definition for ‘values’ removeSNPs: no visible global function definition for ‘queryHits’ savePMDSegments: no visible global function definition for ‘values’ saveUMRLMRSegments: no visible global function definition for ‘values’ segmentUMRsLMRs: no visible global function definition for ‘values’ segmentUMRsLMRs : <anonymous>: no visible global function definition for ‘Rle’ segmentUMRsLMRs : <anonymous>: no visible global function definition for ‘values’ segmentUMRsLMRs : <anonymous>: no visible global function definition for ‘runValue’ segmentUMRsLMRs: no visible global function definition for ‘queryHits’ segmentUMRsLMRs: no visible global function definition for ‘subjectHits’ segmentUMRsLMRs: no visible global function definition for ‘Rle’ segmentUMRsLMRs: no visible global function definition for ‘values<-’ segmentUMRsLMRs: no visible global function definition for ‘DataFrame’ segmentUMRsLMRs: no visible global function definition for ‘colorRampPalette’ trainPMDHMM: no visible global function definition for ‘values’ Undefined global functions or variables: DataFrame Rle colorRampPalette nrun predict queryHits runValue subjectHits values values<- Consider adding importFrom("grDevices", "colorRampPalette") importFrom("stats", "predict") to your NAMESPACE file. * 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘MethylSeekR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: MethylSeekR-package > ### Title: Segmentation of Bis-seq methylation data > ### Aliases: MethylSeekR-package MethylSeekR > ### Keywords: package > > ### ** Examples > > > library(MethylSeekR) > > # get chromosome lengths > library("BSgenome.Hsapiens.UCSC.hg18") 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 > sLengths=seqlengths(Hsapiens) > > # read methylation data > methFname <- system.file("extdata", "Lister2009_imr90_hg18_chr22.tab", + package="MethylSeekR") > meth.gr <- readMethylome(FileName=methFname, seqLengths=sLengths) reading methylome data Read 200000 records > > #read SNP data > snpFname <- system.file("extdata", "SNVs_hg18_chr22.tab", + package="MethylSeekR") > snps.gr <- readSNPTable(FileName=snpFname, seqLengths=sLengths) reading SNP table Read 11750 records > > # remove SNPs > meth.gr <- removeSNPs(meth.gr, snps.gr) removing SNPs 11604 (6.2%) CpGs removed > > #calculate alpha distribution for one chromosome > plotAlphaDistributionOneChr(m=meth.gr, chr.sel="chr22", num.cores=1) determining alpha distribution for chromosome: chr22 > > #segment PMDs > PMDsegments.gr <- segmentPMDs(m=meth.gr, chr.sel="chr22", num.cores=1, + seqLengths=sLengths) training PMD-HMM on chromosome chr22 performing viterbi segmentation creating GRanges object > > #plot PMD segmentation examples > plotPMDSegmentation(m=meth.gr, segs=PMDsegments.gr, numRegions=1) > > #save PMD segments > savePMDSegments(PMDs=PMDsegments.gr, GRangesFilename="PMDs.gr.rds", + TableFilename="PMDs.tab") > > #load CpG islands > library(rtracklayer) > session <- browserSession() > genome(session) <- "hg18" > query <- ucscTableQuery(session, table = "cpgIslandExt") Error in load_package_gracefully("GenomeInfoDb", "Seqinfo(genome=\"", : Could not load package GenomeInfoDb. Is it installed? Note that Seqinfo(genome="hg18") requires the GenomeInfoDb package. Please install it with: BiocManager::install("GenomeInfoDb") Calls: ucscTableQuery ... .make_Seqinfo_from_genome -> load_package_gracefully 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 ‘MethylSeekR.Rnw’ using Sweave Loading required package: rtracklayer Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics 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 Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: IRanges Loading required package: Seqinfo Loading required package: parallel Loading required package: mhsmm Loading required package: mvtnorm 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 reading methylome data Read 200000 records reading SNP table Read 11750 records removing SNPs 11604 (6.2%) CpGs removed determining alpha distribution for chromosome: chr22 training PMD-HMM on chromosome chr22 performing viterbi segmentation creating GRanges object determining alpha distribution for chromosome: chr22 Error: processing vignette 'MethylSeekR.Rnw' failed with diagnostics: chunk 18 Error in load_package_gracefully("GenomeInfoDb", "Seqinfo(genome=\"", : Could not load package GenomeInfoDb. Is it installed? Note that Seqinfo(genome="hg18") requires the GenomeInfoDb package. Please install it with: BiocManager::install("GenomeInfoDb") --- failed re-building ‘MethylSeekR.Rnw’ SUMMARY: processing the following file failed: ‘MethylSeekR.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 3 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/MethylSeekR.Rcheck/00check.log’ for details.
MethylSeekR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL MethylSeekR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘MethylSeekR’ ... ** this is package ‘MethylSeekR’ version ‘1.49.0’ ** using staged installation ** R ** 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 (MethylSeekR)
MethylSeekR.Rcheck/MethylSeekR-Ex.timings
name | user | system | elapsed |