Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:14 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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To the developers/maintainers of the MethylSeekR package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1165/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MethylSeekR 1.39.0 (landing page) Lukas Burger
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: MethylSeekR |
Version: 1.39.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MethylSeekR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MethylSeekR_1.39.0.tar.gz |
StartedAt: 2023-02-07 07:58:12 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 08:06:13 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 480.7 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: MethylSeekR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MethylSeekR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MethylSeekR_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MethylSeekR.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘MethylSeekR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MethylSeekR’ version ‘1.39.0’ * 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 R 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 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 > 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") Killed * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘MethylSeekR.Rnw’... failed to complete the test ERROR Errors in running code in vignettes: when running code in ‘MethylSeekR.Rnw’ ... > plotAlphaDistributionOneChr(m = meth.gr, chr.sel = "chr22", + num.cores = 1) determining alpha distribution for chromosome: chr22 > PMDsegments.gr <- segmentPMDs(m = meth.gr, chr.sel = "chr22", + seqLengths = sLengths, num.cores = 1) training PMD-HMM on chromosome chr22 Killed ... incomplete output. Crash? * checking re-building of vignette outputs ... NOTE 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 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, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb 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 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 Killed * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 4 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/MethylSeekR.Rcheck/00check.log’ for details.
MethylSeekR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MethylSeekR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘MethylSeekR’ ... ** 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
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