Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-18 12:05 -0400 (Mon, 18 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4596 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4538 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
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 173/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BindingSiteFinder 2.7.1 (landing page) Mirko Brüggemann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / 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: 2.7.1 |
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_2.7.1.tar.gz |
StartedAt: 2025-08-17 18:17:20 -0400 (Sun, 17 Aug 2025) |
EndedAt: 2025-08-17 18:22:25 -0400 (Sun, 17 Aug 2025) |
EllapsedTime: 304.8 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_2.7.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BindingSiteFinder.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BindingSiteFinder/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BindingSiteFinder’ version ‘2.7.1’ * 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: BSFind.Rd: GenomicRanges, CompressedGRangesList annotateWithScore.Rd: GenomicRanges assignToGenes.Rd: GenomicRanges, overlaps assignToTranscriptRegions.Rd: CompressedGRangesList, overlaps bindingSiteDefinednessPlot.Rd: ggplot calculateBsBackground.Rd: GenomicRanges duplicatedSitesPlot.Rd: ggplot estimateBsWidth.Rd: GenomicRanges estimateBsWidthPlot.Rd: ggplot geneOverlapsPlot.Rd: ggplot geneRegulationPlot.Rd: GenomicRanges globalScorePlot.Rd: ggplot makeBsSummaryPlot.Rd: ggplot mergeCrosslinkDiagnosticsPlot.Rd: ggplot plotBsBackgroundFilter.Rd: ggplot plotBsMA.Rd: ggplot plotBsVolcano.Rd: ggplot processingStepsFlowChart.Rd: ggplot pureClipGeneWiseFilter.Rd: GenomicRanges, overlaps pureClipGlobalFilter.Rd: GenomicRanges pureClipGlobalFilterPlot.Rd: ggplot reproducibilityFilterPlot.Rd: ggplot reproducibilitySamplesPlot.Rd: ggplot targetGeneSpectrumPlot.Rd: ggplot transcriptRegionOverlapsPlot.Rd: ggplot transcriptRegionSpectrumPlot.Rd: ggplot Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 9.573 0.163 9.765 BSFind 8.839 0.228 9.111 bindingSiteDefinednessPlot 8.740 0.190 8.996 processingStepsFlowChart 8.119 0.162 8.317 calculateBsFoldChange 6.024 0.163 6.307 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.22-bioc/meat/BindingSiteFinder.Rcheck/00check.log’ for details.
BindingSiteFinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BindingSiteFinder ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘BindingSiteFinder’ ... ** this is package ‘BindingSiteFinder’ version ‘2.7.1’ ** 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 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" Copyright (C) 2025 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 Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: Seqinfo > test_check("BindingSiteFinder") [1] "make bs" [1] "calc ratio" [1] "make bs" [1] "calc ratio" [ FAIL 0 | WARN 0 | SKIP 0 | PASS 240 ] > > proc.time() user system elapsed 86.074 1.878 88.092
BindingSiteFinder.Rcheck/BindingSiteFinder-Ex.timings
name | user | system | elapsed | |
BSFDataSet | 0.087 | 0.007 | 0.101 | |
BSFind | 8.839 | 0.228 | 9.111 | |
add-BSFDataSet | 0.672 | 0.018 | 0.689 | |
annotateWithScore | 0.422 | 0.003 | 0.440 | |
assignToGenes | 0.639 | 0.008 | 0.650 | |
assignToTranscriptRegions | 0.780 | 0.038 | 0.818 | |
bindingSiteCoveragePlot | 4.090 | 0.100 | 4.316 | |
bindingSiteDefinednessPlot | 8.740 | 0.190 | 8.996 | |
calculateBsBackground | 1.499 | 0.050 | 1.551 | |
calculateBsFoldChange | 6.024 | 0.163 | 6.307 | |
calculateSignalToFlankScore | 0.486 | 0.012 | 0.499 | |
clipCoverage | 0.615 | 0.029 | 0.648 | |
collapseReplicates | 0.078 | 0.007 | 0.092 | |
combineBSF | 1.017 | 0.042 | 1.074 | |
coverageOverRanges | 0.906 | 0.026 | 0.938 | |
duplicatedSitesPlot | 0.199 | 0.005 | 0.207 | |
estimateBsWidth | 2.952 | 0.090 | 3.067 | |
estimateBsWidthPlot | 3.074 | 0.086 | 3.161 | |
exportTargetGenes | 0.023 | 0.000 | 0.023 | |
exportToBED | 0.567 | 0.012 | 0.583 | |
filterBsBackground | 1.174 | 0.034 | 1.215 | |
geneOverlapsPlot | 0.872 | 0.014 | 0.886 | |
geneRegulationPlot | 3.645 | 0.073 | 3.724 | |
getMeta | 0.024 | 0.001 | 0.026 | |
getName | 0.024 | 0.001 | 0.025 | |
getRanges | 0.030 | 0.002 | 0.031 | |
getSignal | 0.035 | 0.001 | 0.036 | |
getSummary | 0.374 | 0.006 | 0.381 | |
globalScorePlot | 0.461 | 0.007 | 0.469 | |
imputeBsDifferencesForTestdata | 0.707 | 0.011 | 0.718 | |
makeBindingSites | 0.786 | 0.017 | 0.802 | |
makeBsSummaryPlot | 0.430 | 0.012 | 0.445 | |
mergeCrosslinkDiagnosticsPlot | 0.428 | 0.014 | 0.443 | |
mergeSummaryPlot | 1.220 | 0.023 | 1.247 | |
plotBsBackgroundFilter | 1.593 | 0.046 | 1.654 | |
plotBsMA | 4.768 | 0.079 | 4.885 | |
plotBsVolcano | 3.770 | 0.067 | 3.868 | |
processingStepsFlowChart | 8.119 | 0.162 | 8.317 | |
processingStepsTable | 0.035 | 0.001 | 0.036 | |
pureClipGeneWiseFilter | 0.128 | 0.004 | 0.131 | |
pureClipGlobalFilter | 0.034 | 0.002 | 0.035 | |
pureClipGlobalFilterPlot | 0.102 | 0.002 | 0.104 | |
quickFigure | 9.573 | 0.163 | 9.765 | |
rangeCoveragePlot | 1.799 | 0.056 | 1.859 | |
reproducibilityCutoffPlot | 1.354 | 0.029 | 1.396 | |
reproducibilityFilter | 0.501 | 0.012 | 0.525 | |
reproducibilityFilterPlot | 0.605 | 0.014 | 0.622 | |
reproducibilitySamplesPlot | 0.544 | 0.012 | 0.568 | |
reproducibilityScatterPlot | 1.133 | 0.023 | 1.160 | |
setMeta | 0.025 | 0.002 | 0.026 | |
setName | 0.023 | 0.001 | 0.024 | |
setRanges | 0.031 | 0.002 | 0.033 | |
setSignal | 0.032 | 0.001 | 0.033 | |
setSummary | 0.023 | 0.001 | 0.024 | |
show | 0.023 | 0.002 | 0.024 | |
subset-BSFDataSet | 0.027 | 0.001 | 0.028 | |
summary | 0.029 | 0.001 | 0.031 | |
supportRatio | 1.051 | 0.020 | 1.072 | |
supportRatioPlot | 1.095 | 0.016 | 1.112 | |
targetGeneSpectrumPlot | 0.696 | 0.007 | 0.705 | |
transcriptRegionOverlapsPlot | 0.862 | 0.046 | 0.920 | |
transcriptRegionSpectrumPlot | 0.805 | 0.011 | 0.824 | |