Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-11 14:40 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
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 2268/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
VplotR 1.14.0 (landing page) Jacques Serizay
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the VplotR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VplotR.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: VplotR |
Version: 1.14.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:VplotR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings VplotR_1.14.0.tar.gz |
StartedAt: 2024-06-10 04:33:58 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 04:40:36 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 397.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: VplotR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:VplotR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings VplotR_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/VplotR.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * 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 ‘VplotR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘VplotR’ version ‘1.14.0’ * 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 ‘VplotR’ can be installed ... OK * checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: data 2.9Mb figures 2.1Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 ... 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 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed nucleosomeEnrichment.GRanges 9.354 1.355 10.711 nucleosomeEnrichment.Vmat 6.765 1.104 7.869 nucleosomeEnrichment 5.644 0.860 6.506 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/VplotR.Rcheck/00check.log’ for details.
VplotR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL VplotR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘VplotR’ ... ** 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 (VplotR)
VplotR.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 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. > library(testthat) > library(VplotR) 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, 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: ggplot2 > > test_check("VplotR") [ FAIL 0 | WARN 18 | SKIP 0 | PASS 4 ] [ FAIL 0 | WARN 18 | SKIP 0 | PASS 4 ] > > proc.time() user system elapsed 64.800 4.461 69.253
VplotR.Rcheck/VplotR-Ex.timings
name | user | system | elapsed | |
ABF1_sacCer3 | 0.052 | 0.008 | 0.060 | |
ATAC_ce11_Serizay2020 | 0.223 | 0.007 | 0.231 | |
CTCF_hg38 | 0.029 | 0.000 | 0.029 | |
MNase_sacCer3_Henikoff2011 | 0.091 | 0.000 | 0.091 | |
MNase_sacCer3_Henikoff2011_subset | 0.055 | 0.000 | 0.054 | |
REB1_sacCer3 | 0.007 | 0.007 | 0.015 | |
alignToTSS | 0.089 | 0.008 | 0.097 | |
bam_test | 0.038 | 0.000 | 0.038 | |
ce11_all_REs | 0.027 | 0.000 | 0.027 | |
ce11_proms | 0.018 | 0.000 | 0.018 | |
computeVmat | 2.495 | 0.167 | 2.663 | |
deconvolveBidirectionalPromoters | 0.100 | 0.012 | 0.112 | |
getFragmentsDistribution | 0.129 | 0.004 | 0.133 | |
importPEBamFiles | 0.197 | 0.003 | 0.200 | |
normalizeVmat | 0.961 | 0.025 | 0.985 | |
nucleosomeEnrichment.GRanges | 9.354 | 1.355 | 10.711 | |
nucleosomeEnrichment | 5.644 | 0.860 | 6.506 | |
nucleosomeEnrichment.Vmat | 6.765 | 1.104 | 7.869 | |
plotFootprint | 0.406 | 0.012 | 0.418 | |
plotProfile | 0.715 | 0.003 | 0.719 | |
plotVmat.GRanges | 1.192 | 0.012 | 1.205 | |
plotVmat | 1.189 | 0.019 | 1.209 | |
plotVmat.Vmat | 1.528 | 0.036 | 1.565 | |
plotVmat.VmatList | 2.174 | 0.007 | 2.182 | |
plotVmat.default | 1.515 | 0.032 | 1.547 | |
plotVmat.list | 2.232 | 0.004 | 2.236 | |
sampleGRanges.GRanges | 2.066 | 0.640 | 2.706 | |
sampleGRanges | 2.198 | 0.753 | 2.950 | |
shiftATACGranges | 0.074 | 0.003 | 0.078 | |
shuffleVmat | 0.927 | 0.044 | 0.972 | |
theme_ggplot2 | 0.117 | 0.001 | 0.116 | |