Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-01 11:42 -0400 (Mon, 01 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4693 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4409 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4407 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4356 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4407 |
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 165/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BindingSiteFinder 2.3.1 (landing page) Mirko Brüggemann
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the BindingSiteFinder package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BindingSiteFinder.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: BindingSiteFinder |
Version: 2.3.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BindingSiteFinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BindingSiteFinder_2.3.1.tar.gz |
StartedAt: 2024-06-30 19:51:21 -0400 (Sun, 30 Jun 2024) |
EndedAt: 2024-06-30 19:56:06 -0400 (Sun, 30 Jun 2024) |
EllapsedTime: 285.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BindingSiteFinder.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BindingSiteFinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BindingSiteFinder_2.3.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BindingSiteFinder.Rcheck’ * using R version 4.4.1 RC (2024-06-06 r86719) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BindingSiteFinder/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BindingSiteFinder’ version ‘2.3.1’ * 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 ‘BindingSiteFinder’ 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 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 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 quickFigure 9.704 0.276 10.119 bindingSiteDefinednessPlot 8.848 0.209 9.092 BSFind 8.825 0.138 8.977 processingStepsFlowChart 8.592 0.129 8.745 calculateBsFoldChange 6.104 0.136 6.244 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
BindingSiteFinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BindingSiteFinder ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘BindingSiteFinder’ ... ** 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 (BindingSiteFinder)
BindingSiteFinder.Rcheck/tests/testthat.Rout
R version 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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("BindingSiteFinder") 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 > test_check("BindingSiteFinder") [1] "make bs" [1] "calc ratio" [1] "make bs" [1] "calc ratio" [ FAIL 0 | WARN 1 | SKIP 0 | PASS 239 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 239 ] > > proc.time() user system elapsed 85.520 1.915 87.713
BindingSiteFinder.Rcheck/BindingSiteFinder-Ex.timings
name | user | system | elapsed | |
BSFDataSet | 0.058 | 0.001 | 0.061 | |
BSFind | 8.825 | 0.138 | 8.977 | |
add-BSFDataSet | 0.664 | 0.020 | 0.685 | |
annotateWithScore | 0.438 | 0.008 | 0.449 | |
assignToGenes | 0.649 | 0.012 | 0.662 | |
assignToTranscriptRegions | 0.766 | 0.012 | 0.780 | |
bindingSiteCoveragePlot | 4.231 | 0.103 | 4.345 | |
bindingSiteDefinednessPlot | 8.848 | 0.209 | 9.092 | |
calculateBsBackground | 1.483 | 0.031 | 1.517 | |
calculateBsFoldChange | 6.104 | 0.136 | 6.244 | |
calculateSignalToFlankScore | 0.478 | 0.016 | 0.494 | |
clipCoverage | 0.579 | 0.028 | 0.607 | |
collapseReplicates | 0.062 | 0.004 | 0.066 | |
combineBSF | 0.981 | 0.023 | 1.004 | |
coverageOverRanges | 0.337 | 0.018 | 0.355 | |
duplicatedSitesPlot | 0.193 | 0.004 | 0.198 | |
estimateBsWidth | 3.277 | 0.074 | 3.353 | |
estimateBsWidthPlot | 2.776 | 0.090 | 2.865 | |
exportTargetGenes | 0.010 | 0.000 | 0.011 | |
exportToBED | 0.020 | 0.001 | 0.022 | |
filterBsBackground | 1.129 | 0.011 | 1.141 | |
geneOverlapsPlot | 0.844 | 0.010 | 0.855 | |
getMeta | 0.012 | 0.001 | 0.012 | |
getName | 0.010 | 0.001 | 0.012 | |
getRanges | 0.016 | 0.001 | 0.017 | |
getSignal | 0.023 | 0.001 | 0.024 | |
getSummary | 0.348 | 0.008 | 0.356 | |
globalScorePlot | 0.404 | 0.009 | 0.414 | |
imputeBsDifferencesForTestdata | 0.612 | 0.012 | 0.624 | |
makeBindingSites | 0.666 | 0.014 | 0.681 | |
makeBsSummaryPlot | 0.356 | 0.006 | 0.362 | |
mergeCrosslinkDiagnosticsPlot | 0.418 | 0.006 | 0.425 | |
mergeSummaryPlot | 1.196 | 0.066 | 1.262 | |
plotBsBackgroundFilter | 1.500 | 0.037 | 1.545 | |
plotBsMA | 4.237 | 0.044 | 4.288 | |
plotBsVolcano | 3.868 | 0.096 | 3.972 | |
processingStepsFlowChart | 8.592 | 0.129 | 8.745 | |
processingStepsTable | 0.022 | 0.002 | 0.024 | |
pureClipGeneWiseFilter | 0.133 | 0.005 | 0.139 | |
pureClipGlobalFilter | 0.020 | 0.001 | 0.022 | |
pureClipGlobalFilterPlot | 0.091 | 0.003 | 0.095 | |
quickFigure | 9.704 | 0.276 | 10.119 | |
rangeCoveragePlot | 1.805 | 0.129 | 1.943 | |
reproducibilityCutoffPlot | 0.854 | 0.038 | 0.898 | |
reproducibilityFilter | 0.507 | 0.023 | 0.532 | |
reproducibilityFilterPlot | 0.615 | 0.018 | 0.653 | |
reproducibilitySamplesPlot | 0.541 | 0.009 | 0.567 | |
reproducibilityScatterPlot | 1.141 | 0.024 | 1.186 | |
setMeta | 0.011 | 0.001 | 0.013 | |
setName | 0.011 | 0.001 | 0.011 | |
setRanges | 0.019 | 0.001 | 0.019 | |
setSignal | 0.018 | 0.001 | 0.020 | |
setSummary | 0.010 | 0.001 | 0.012 | |
show | 0.010 | 0.001 | 0.011 | |
subset-BSFDataSet | 0.015 | 0.001 | 0.015 | |
summary | 0.017 | 0.002 | 0.019 | |
supportRatio | 1.065 | 0.020 | 1.097 | |
supportRatioPlot | 1.129 | 0.029 | 1.162 | |
targetGeneSpectrumPlot | 0.696 | 0.010 | 0.708 | |
transcriptRegionOverlapsPlot | 0.803 | 0.008 | 0.818 | |
transcriptRegionSpectrumPlot | 0.837 | 0.018 | 0.859 | |