Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:57 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the VplotR package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 2010/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
VplotR 1.2.0 (landing page) Jacques Serizay
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: VplotR |
Version: 1.2.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:VplotR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings VplotR_1.2.0.tar.gz |
StartedAt: 2021-10-15 01:10:44 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 01:18:04 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 439.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: VplotR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:VplotR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings VplotR_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/VplotR.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘VplotR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘VplotR’ version ‘1.2.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 ... 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 ... 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 12.150 1.160 13.323 nucleosomeEnrichment.Vmat 10.069 0.702 10.784 nucleosomeEnrichment 8.208 1.246 9.464 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.13-bioc/meat/VplotR.Rcheck/00check.log’ for details.
VplotR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL VplotR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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. > library(testthat) > library(VplotR) Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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, 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: ggplot2 > > test_check("VplotR") [ FAIL 0 | WARN 15 | SKIP 0 | PASS 4 ] > > proc.time() user system elapsed 112.240 6.986 119.320
VplotR.Rcheck/VplotR-Ex.timings
name | user | system | elapsed | |
ABF1_sacCer3 | 0.135 | 0.017 | 0.152 | |
ATAC_ce11_Serizay2020 | 0.372 | 0.023 | 0.395 | |
CTCF_hg38 | 0.059 | 0.010 | 0.070 | |
MNase_sacCer3_Henikoff2011 | 0.158 | 0.012 | 0.171 | |
MNase_sacCer3_Henikoff2011_subset | 0.143 | 0.006 | 0.149 | |
REB1_sacCer3 | 0.043 | 0.004 | 0.048 | |
alignToTSS | 0.189 | 0.006 | 0.194 | |
bam_test | 0.076 | 0.003 | 0.080 | |
ce11_all_REs | 0.040 | 0.004 | 0.045 | |
ce11_proms | 0.029 | 0.003 | 0.033 | |
computeVmat | 3.006 | 0.076 | 3.094 | |
deconvolveBidirectionalPromoters | 0.255 | 0.010 | 0.269 | |
getFragmentsDistribution | 0.249 | 0.013 | 0.265 | |
importPEBamFiles | 0.452 | 0.014 | 0.467 | |
normalizeVmat | 2.518 | 0.056 | 2.580 | |
nucleosomeEnrichment.GRanges | 12.150 | 1.160 | 13.323 | |
nucleosomeEnrichment | 8.208 | 1.246 | 9.464 | |
nucleosomeEnrichment.Vmat | 10.069 | 0.702 | 10.784 | |
plotFootprint | 0.670 | 0.173 | 0.844 | |
plotProfile | 0.866 | 0.007 | 0.873 | |
plotVmat.GRanges | 2.270 | 0.035 | 2.307 | |
plotVmat | 2.202 | 0.051 | 2.255 | |
plotVmat.Vmat | 2.672 | 0.093 | 2.770 | |
plotVmat.VmatList | 4.165 | 0.075 | 4.241 | |
plotVmat.default | 2.654 | 0.106 | 2.761 | |
plotVmat.list | 3.675 | 0.052 | 3.729 | |
sampleGRanges.GRanges | 3.887 | 0.403 | 4.299 | |
sampleGRanges | 4.026 | 0.408 | 4.442 | |
shiftATACGranges | 0.124 | 0.002 | 0.127 | |
shuffleVmat | 1.556 | 0.092 | 1.648 | |
theme_ggplot2 | 0.114 | 0.002 | 0.115 | |