Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:27 -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 scmeth package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scmeth.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 1792/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scmeth 1.19.0 (landing page) Divy Kangeyan
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: scmeth |
Version: 1.19.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:scmeth.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings scmeth_1.19.0.tar.gz |
StartedAt: 2023-02-07 14:55:45 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 15:04:26 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 521.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: scmeth.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:scmeth.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings scmeth_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/scmeth.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 ‘scmeth/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scmeth’ version ‘1.19.0’ * 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 ‘scmeth’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * 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: ‘reshape2’ 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 ... OK * 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 ‘scmeth-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: report > ### Title: Generates an inclusive report on methylation analysis > ### Aliases: report > > ### ** Examples > > library(BSgenome.Hsapiens.NCBI.GRCh38) Loading required package: BSgenome 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 Loading required package: stats4 Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: IRanges Attaching package: ‘IRanges’ The following object is masked from ‘package:scmeth’: coverage Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: Biostrings Loading required package: XVector Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit Loading required package: rtracklayer > directory <- system.file("extdata/bismark_data", package='scmeth') > bs <- HDF5Array::loadHDF5SummarizedExperiment(directory) > mbiasDirectory=system.file("extdata", package='scmeth') > outDir <- system.file(package='scmeth') > report(bs, outDir, Hsapiens, 'hg38', mbiasDir=mbiasDirectory, small=TRUE) processing file: qcReport.Rmd Killed * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘my-vignette.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘my-vignette.Rmd’ using rmarkdown Killed * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/scmeth.Rcheck/00check.log’ for details.
scmeth.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL scmeth ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘scmeth’ ... ** 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 (scmeth)
scmeth.Rcheck/scmeth-Ex.timings
name | user | system | elapsed | |
bsConversionPlot | 0.196 | 0.000 | 0.200 | |
chromosomeCoverage | 0.541 | 0.027 | 0.595 | |
coverage | 0.148 | 0.003 | 0.152 | |
cpgDensity | 3.398 | 0.228 | 3.645 | |
cpgDiscretization | 0.252 | 0.005 | 0.257 | |
downsample | 1.354 | 0.028 | 1.385 | |
featureCoverage | 2.303 | 0.106 | 26.422 | |
mbiasplot | 0.010 | 0.000 | 0.011 | |
methylationDist | 0.225 | 0.020 | 0.245 | |
readmetrics | 0.092 | 0.000 | 0.092 | |
repMask | 10.307 | 0.708 | 21.504 | |