Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-04-17 11:36:28 -0400 (Wed, 17 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
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 2157/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
trackViewer 1.38.2 (landing page) Jianhong Ou
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the trackViewer package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/trackViewer.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: trackViewer |
Version: 1.38.2 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:trackViewer.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings trackViewer_1.38.2.tar.gz |
StartedAt: 2024-04-16 04:50:58 -0400 (Tue, 16 Apr 2024) |
EndedAt: 2024-04-16 05:21:53 -0400 (Tue, 16 Apr 2024) |
EllapsedTime: 1855.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: trackViewer.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:trackViewer.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings trackViewer_1.38.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/trackViewer.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘trackViewer/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘trackViewer’ version ‘1.38.2’ * 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 ‘trackViewer’ 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 loading without being on the library search path ... OK * checking dependencies in R code ... OK * 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed trackViewer-package 21.054 0.316 21.370 viewTracks 15.235 0.164 15.399 browseTracks 14.387 0.426 14.816 parseWIG 14.556 0.204 14.760 geneModelFromTxdb 5.680 0.300 5.980 viewGene 5.318 0.064 5.383 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘changeTracksStyles.Rmd’ using ‘UTF-8’... OK ‘dandelionPlot.Rmd’ using ‘UTF-8’... OK ‘lollipopPlot.Rmd’ using ‘UTF-8’... OK ‘plotInteractionData.Rmd’ using ‘UTF-8’... OK ‘trackViewer.Rmd’ using ‘UTF-8’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
trackViewer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL trackViewer ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’ * installing *source* package ‘trackViewer’ ... ** 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 (trackViewer)
trackViewer.Rcheck/tests/runTests.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) 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. > require("trackViewer") || stop("unable to load Package:trackViewer") Loading required package: trackViewer 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 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: GenomeInfoDb Loading required package: grid [1] TRUE > require("RUnit") || stop("unable to load Package:RUnit") Loading required package: RUnit [1] TRUE > BiocGenerics:::testPackage("trackViewer") RUNIT TEST PROTOCOL -- Tue Apr 16 04:59:04 2024 *********************************************** Number of test functions: 2 Number of errors: 0 Number of failures: 0 1 Test Suite : trackViewer RUnit Tests - 2 test functions, 0 errors, 0 failures Number of test functions: 2 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 17.539 0.996 18.527
trackViewer.Rcheck/trackViewer-Ex.timings
name | user | system | elapsed | |
ARA | 2.691 | 0.156 | 2.849 | |
GIoperator | 0.358 | 0.016 | 0.374 | |
GRoperator | 1.962 | 0.116 | 2.078 | |
addArrowMark | 0.013 | 0.000 | 0.013 | |
addGuideLine | 0.004 | 0.000 | 0.004 | |
addInteractionAnnotation | 0.680 | 0.020 | 0.699 | |
browseTracks | 14.387 | 0.426 | 14.816 | |
coverageGR | 0.196 | 0.000 | 0.197 | |
dandelion.plot | 2.142 | 0.016 | 2.158 | |
geneModelFromTxdb | 5.68 | 0.30 | 5.98 | |
geneTrack | 1.926 | 0.048 | 1.974 | |
getCurTrackViewport | 0.003 | 0.000 | 0.003 | |
getGeneIDsFromTxDb | 0.918 | 0.020 | 0.938 | |
getLocation | 1.421 | 0.024 | 1.445 | |
gi2track | 0.043 | 0.000 | 0.043 | |
gieStain | 0.004 | 0.000 | 0.005 | |
ideogramPlot | 0 | 0 | 0 | |
importBam | 0.288 | 0.000 | 0.288 | |
importData | 2.763 | 0.048 | 2.811 | |
importGInteractions | 0.525 | 0.004 | 0.531 | |
importScSeqScore | 0 | 0 | 0 | |
importScore | 0.609 | 0.004 | 0.614 | |
listChromosomes | 0.435 | 0.000 | 0.434 | |
listResolutions | 0.003 | 0.000 | 0.003 | |
loadIdeogram | 0 | 0 | 0 | |
lolliplot | 0.931 | 0.000 | 0.931 | |
optimizeStyle | 0.527 | 0.008 | 0.535 | |
parse2GRanges | 0.011 | 0.000 | 0.011 | |
parseWIG | 14.556 | 0.204 | 14.760 | |
plotGInteractions | 1.163 | 0.028 | 1.191 | |
plotGRanges | 1.469 | 0.000 | 1.469 | |
plotIdeo | 0 | 0 | 0 | |
plotOneIdeo | 0 | 0 | 0 | |
trackStyle-class | 0.044 | 0.000 | 0.044 | |
trackViewer-package | 21.054 | 0.316 | 21.370 | |
trackViewerStyle-class | 0 | 0 | 0 | |
viewGene | 5.318 | 0.064 | 5.383 | |
viewTracks | 15.235 | 0.164 | 15.399 | |