Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:38:53 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 166/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BindingSiteFinder 2.1.0 (landing page) Mirko Brüggemann
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | 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: 2.1.0 |
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_2.1.0.tar.gz |
StartedAt: 2024-03-02 00:37:05 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 01:14:26 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 2241.6 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_2.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BindingSiteFinder.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BindingSiteFinder/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BindingSiteFinder’ version ‘2.1.0’ * 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 ‘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 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed quickFigure 72.957 1.082 93.158 processingStepsFlowChart 64.777 5.361 103.152 BSFind 63.191 1.159 75.506 bindingSiteDefinednessPlot 59.642 1.124 100.476 calculateBsFoldChange 38.475 2.785 90.838 plotBsMA 26.557 0.498 30.140 plotBsVolcano 25.868 0.525 31.632 estimateBsWidthPlot 21.404 0.623 24.435 estimateBsWidth 16.253 3.156 33.120 bindingSiteCoveragePlot 15.737 0.583 25.821 rangeCoveragePlot 13.111 0.447 16.977 plotBsBackgroundFilter 11.325 0.325 13.364 calculateBsBackground 10.651 0.322 21.129 mergeSummaryPlot 9.013 0.149 10.382 filterBsBackground 8.828 0.125 9.585 reproducibilityScatterPlot 8.738 0.179 11.597 supportRatioPlot 8.142 0.177 10.124 supportRatio 8.096 0.146 10.529 combineBSF 6.824 0.183 7.884 geneOverlapsPlot 6.734 0.148 8.112 transcriptRegionSpectrumPlot 6.472 0.162 7.964 transcriptRegionOverlapsPlot 6.464 0.145 8.635 reproducibilityCutoffPlot 6.082 0.148 7.796 targetGeneSpectrumPlot 5.806 0.153 7.861 makeBindingSites 5.759 0.119 6.752 imputeBsDifferencesForTestdata 5.434 0.089 6.159 reproducibilityFilterPlot 4.799 0.097 6.446 clipCoverage 4.280 0.315 10.200 reproducibilitySamplesPlot 4.158 0.073 5.351 add-BSFDataSet 4.093 0.080 5.566 calculateSignalToFlankScore 3.478 0.181 8.514 annotateWithScore 2.987 0.056 7.236 * 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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 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 236 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 236 ] > > proc.time() user system elapsed 625.582 11.223 738.395
BindingSiteFinder.Rcheck/BindingSiteFinder-Ex.timings
name | user | system | elapsed | |
BSFDataSet | 0.385 | 0.013 | 0.536 | |
BSFind | 63.191 | 1.159 | 75.506 | |
add-BSFDataSet | 4.093 | 0.080 | 5.566 | |
annotateWithScore | 2.987 | 0.056 | 7.236 | |
assignToGenes | 4.289 | 0.089 | 4.473 | |
assignToTranscriptRegions | 4.443 | 0.116 | 4.662 | |
bindingSiteCoveragePlot | 15.737 | 0.583 | 25.821 | |
bindingSiteDefinednessPlot | 59.642 | 1.124 | 100.476 | |
calculateBsBackground | 10.651 | 0.322 | 21.129 | |
calculateBsFoldChange | 38.475 | 2.785 | 90.838 | |
calculateSignalToFlankScore | 3.478 | 0.181 | 8.514 | |
clipCoverage | 4.280 | 0.315 | 10.200 | |
collapseReplicates | 0.276 | 0.017 | 0.323 | |
combineBSF | 6.824 | 0.183 | 7.884 | |
coverageOverRanges | 2.202 | 0.061 | 2.601 | |
duplicatedSitesPlot | 1.363 | 0.109 | 1.672 | |
estimateBsWidth | 16.253 | 3.156 | 33.120 | |
estimateBsWidthPlot | 21.404 | 0.623 | 24.435 | |
exportTargetGenes | 0.036 | 0.005 | 0.048 | |
exportToBED | 0.037 | 0.003 | 0.045 | |
filterBsBackground | 8.828 | 0.125 | 9.585 | |
geneOverlapsPlot | 6.734 | 0.148 | 8.112 | |
getMeta | 0.043 | 0.003 | 0.096 | |
getName | 0.040 | 0.002 | 0.044 | |
getRanges | 0.077 | 0.006 | 0.087 | |
getSignal | 0.139 | 0.006 | 0.171 | |
getSummary | 2.685 | 0.058 | 3.077 | |
globalScorePlot | 3.311 | 0.059 | 3.692 | |
imputeBsDifferencesForTestdata | 5.434 | 0.089 | 6.159 | |
makeBindingSites | 5.759 | 0.119 | 6.752 | |
makeBsSummaryPlot | 3.042 | 0.065 | 3.563 | |
mergeCrosslinkDiagnosticsPlot | 3.456 | 0.089 | 4.103 | |
mergeSummaryPlot | 9.013 | 0.149 | 10.382 | |
plotBsBackgroundFilter | 11.325 | 0.325 | 13.364 | |
plotBsMA | 26.557 | 0.498 | 30.140 | |
plotBsVolcano | 25.868 | 0.525 | 31.632 | |
processingStepsFlowChart | 64.777 | 5.361 | 103.152 | |
processingStepsTable | 0.118 | 0.006 | 0.147 | |
pureClipGeneWiseFilter | 0.804 | 0.011 | 0.953 | |
pureClipGlobalFilter | 0.110 | 0.004 | 0.134 | |
pureClipGlobalFilterPlot | 0.632 | 0.009 | 0.731 | |
quickFigure | 72.957 | 1.082 | 93.158 | |
rangeCoveragePlot | 13.111 | 0.447 | 16.977 | |
reproducibilityCutoffPlot | 6.082 | 0.148 | 7.796 | |
reproducibilityFilter | 3.761 | 0.083 | 4.909 | |
reproducibilityFilterPlot | 4.799 | 0.097 | 6.446 | |
reproducibilitySamplesPlot | 4.158 | 0.073 | 5.351 | |
reproducibilityScatterPlot | 8.738 | 0.179 | 11.597 | |
setMeta | 0.047 | 0.005 | 0.063 | |
setName | 0.039 | 0.003 | 0.050 | |
setRanges | 0.099 | 0.003 | 0.131 | |
setSignal | 0.107 | 0.005 | 0.151 | |
setSummary | 0.041 | 0.003 | 0.069 | |
show | 0.042 | 0.004 | 0.051 | |
subset-BSFDataSet | 0.069 | 0.005 | 0.080 | |
summary | 0.086 | 0.007 | 0.121 | |
supportRatio | 8.096 | 0.146 | 10.529 | |
supportRatioPlot | 8.142 | 0.177 | 10.124 | |
targetGeneSpectrumPlot | 5.806 | 0.153 | 7.861 | |
transcriptRegionOverlapsPlot | 6.464 | 0.145 | 8.635 | |
transcriptRegionSpectrumPlot | 6.472 | 0.162 | 7.964 | |