Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 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" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 165/2239 | 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 | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
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: 2024-06-10 00:18:19 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 00:53:44 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 2125.2 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 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-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 Monterey 12.7.4 * 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 76.245 0.601 82.914 bindingSiteDefinednessPlot 65.782 2.435 131.176 processingStepsFlowChart 65.671 0.925 71.511 BSFind 65.022 0.858 71.395 calculateBsFoldChange 40.405 2.349 73.634 plotBsVolcano 27.454 5.790 46.938 plotBsMA 28.564 0.895 32.195 estimateBsWidth 21.303 2.641 27.098 estimateBsWidthPlot 22.000 0.529 24.184 bindingSiteCoveragePlot 17.289 0.589 20.210 calculateBsBackground 12.558 2.589 34.270 rangeCoveragePlot 14.590 0.175 15.348 plotBsBackgroundFilter 11.759 0.303 13.556 mergeSummaryPlot 9.435 0.137 10.415 filterBsBackground 9.105 0.186 10.085 reproducibilityScatterPlot 8.965 0.076 9.568 supportRatioPlot 8.583 0.063 9.156 supportRatio 8.346 0.071 9.085 combineBSF 7.056 0.158 7.590 geneOverlapsPlot 6.994 0.158 8.577 transcriptRegionSpectrumPlot 6.749 0.165 9.036 transcriptRegionOverlapsPlot 6.551 0.080 7.392 reproducibilityCutoffPlot 6.232 0.045 6.993 assignToTranscriptRegions 5.999 0.051 6.299 makeBindingSites 5.930 0.092 6.564 imputeBsDifferencesForTestdata 5.610 0.081 6.168 targetGeneSpectrumPlot 5.644 0.036 5.957 assignToGenes 5.252 0.040 5.660 add-BSFDataSet 5.029 0.065 5.277 reproducibilityFilterPlot 4.890 0.150 5.345 calculateSignalToFlankScore 3.668 0.664 5.456 * 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-x86_64/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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 655.801 8.635 747.002
BindingSiteFinder.Rcheck/BindingSiteFinder-Ex.timings
name | user | system | elapsed | |
BSFDataSet | 0.366 | 0.009 | 0.394 | |
BSFind | 65.022 | 0.858 | 71.395 | |
add-BSFDataSet | 5.029 | 0.065 | 5.277 | |
annotateWithScore | 3.583 | 0.042 | 4.163 | |
assignToGenes | 5.252 | 0.040 | 5.660 | |
assignToTranscriptRegions | 5.999 | 0.051 | 6.299 | |
bindingSiteCoveragePlot | 17.289 | 0.589 | 20.210 | |
bindingSiteDefinednessPlot | 65.782 | 2.435 | 131.176 | |
calculateBsBackground | 12.558 | 2.589 | 34.270 | |
calculateBsFoldChange | 40.405 | 2.349 | 73.634 | |
calculateSignalToFlankScore | 3.668 | 0.664 | 5.456 | |
clipCoverage | 4.243 | 0.082 | 4.523 | |
collapseReplicates | 0.278 | 0.013 | 0.393 | |
combineBSF | 7.056 | 0.158 | 7.590 | |
coverageOverRanges | 2.354 | 0.074 | 2.726 | |
duplicatedSitesPlot | 1.408 | 0.099 | 1.679 | |
estimateBsWidth | 21.303 | 2.641 | 27.098 | |
estimateBsWidthPlot | 22.000 | 0.529 | 24.184 | |
exportTargetGenes | 0.036 | 0.004 | 0.049 | |
exportToBED | 0.036 | 0.004 | 0.055 | |
filterBsBackground | 9.105 | 0.186 | 10.085 | |
geneOverlapsPlot | 6.994 | 0.158 | 8.577 | |
getMeta | 0.044 | 0.003 | 0.055 | |
getName | 0.040 | 0.002 | 0.057 | |
getRanges | 0.082 | 0.006 | 0.103 | |
getSignal | 0.144 | 0.008 | 0.175 | |
getSummary | 2.771 | 0.053 | 2.985 | |
globalScorePlot | 3.325 | 0.059 | 3.659 | |
imputeBsDifferencesForTestdata | 5.610 | 0.081 | 6.168 | |
makeBindingSites | 5.930 | 0.092 | 6.564 | |
makeBsSummaryPlot | 3.079 | 0.045 | 3.292 | |
mergeCrosslinkDiagnosticsPlot | 3.595 | 0.046 | 3.872 | |
mergeSummaryPlot | 9.435 | 0.137 | 10.415 | |
plotBsBackgroundFilter | 11.759 | 0.303 | 13.556 | |
plotBsMA | 28.564 | 0.895 | 32.195 | |
plotBsVolcano | 27.454 | 5.790 | 46.938 | |
processingStepsFlowChart | 65.671 | 0.925 | 71.511 | |
processingStepsTable | 0.154 | 0.010 | 0.206 | |
pureClipGeneWiseFilter | 0.810 | 0.008 | 0.973 | |
pureClipGlobalFilter | 0.112 | 0.002 | 0.116 | |
pureClipGlobalFilterPlot | 0.667 | 0.007 | 0.747 | |
quickFigure | 76.245 | 0.601 | 82.914 | |
rangeCoveragePlot | 14.590 | 0.175 | 15.348 | |
reproducibilityCutoffPlot | 6.232 | 0.045 | 6.993 | |
reproducibilityFilter | 3.793 | 0.025 | 4.098 | |
reproducibilityFilterPlot | 4.890 | 0.150 | 5.345 | |
reproducibilitySamplesPlot | 4.209 | 0.073 | 4.615 | |
reproducibilityScatterPlot | 8.965 | 0.076 | 9.568 | |
setMeta | 0.048 | 0.003 | 0.059 | |
setName | 0.041 | 0.002 | 0.044 | |
setRanges | 0.100 | 0.003 | 0.107 | |
setSignal | 0.106 | 0.002 | 0.113 | |
setSummary | 0.041 | 0.002 | 0.045 | |
show | 0.042 | 0.003 | 0.047 | |
subset-BSFDataSet | 0.069 | 0.002 | 0.075 | |
summary | 0.088 | 0.003 | 0.120 | |
supportRatio | 8.346 | 0.071 | 9.085 | |
supportRatioPlot | 8.583 | 0.063 | 9.156 | |
targetGeneSpectrumPlot | 5.644 | 0.036 | 5.957 | |
transcriptRegionOverlapsPlot | 6.551 | 0.080 | 7.392 | |
transcriptRegionSpectrumPlot | 6.749 | 0.165 | 9.036 | |