Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:36:13 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
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 167/2270 | 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 | |||||||||
lconway | 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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BindingSiteFinder.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BindingSiteFinder_2.1.0.tar.gz |
StartedAt: 2024-03-27 20:33:18 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 20:48:37 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 918.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BindingSiteFinder.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BindingSiteFinder.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BindingSiteFinder_2.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BindingSiteFinder.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 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 loading without being on the library search path ... 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 processingStepsFlowChart 35.987 0.256 36.332 quickFigure 28.828 0.176 29.004 BSFind 25.756 0.431 26.190 bindingSiteDefinednessPlot 25.016 0.420 25.437 calculateBsFoldChange 17.593 0.192 17.814 plotBsVolcano 12.469 0.071 12.542 plotBsMA 10.328 0.104 10.432 estimateBsWidth 10.200 0.048 10.249 estimateBsWidthPlot 9.743 0.068 9.812 bindingSiteCoveragePlot 9.174 0.212 9.414 rangeCoveragePlot 5.413 0.012 5.424 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
BindingSiteFinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL BindingSiteFinder ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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) (2024-03-18 r86148) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 253.809 2.740 256.546
BindingSiteFinder.Rcheck/BindingSiteFinder-Ex.timings
name | user | system | elapsed | |
BSFDataSet | 0.208 | 0.004 | 0.213 | |
BSFind | 25.756 | 0.431 | 26.190 | |
add-BSFDataSet | 2.029 | 0.021 | 2.049 | |
annotateWithScore | 1.313 | 0.007 | 1.323 | |
assignToGenes | 1.851 | 0.000 | 1.851 | |
assignToTranscriptRegions | 2.204 | 0.004 | 2.208 | |
bindingSiteCoveragePlot | 9.174 | 0.212 | 9.414 | |
bindingSiteDefinednessPlot | 25.016 | 0.420 | 25.437 | |
calculateBsBackground | 4.723 | 0.036 | 4.759 | |
calculateBsFoldChange | 17.593 | 0.192 | 17.814 | |
calculateSignalToFlankScore | 1.498 | 0.000 | 1.498 | |
clipCoverage | 1.797 | 0.000 | 1.798 | |
collapseReplicates | 0.188 | 0.000 | 0.188 | |
combineBSF | 3.057 | 0.008 | 3.066 | |
coverageOverRanges | 0.974 | 0.000 | 0.974 | |
duplicatedSitesPlot | 0.584 | 0.008 | 0.592 | |
estimateBsWidth | 10.200 | 0.048 | 10.249 | |
estimateBsWidthPlot | 9.743 | 0.068 | 9.812 | |
exportTargetGenes | 0.027 | 0.000 | 0.027 | |
exportToBED | 0.026 | 0.000 | 0.026 | |
filterBsBackground | 3.476 | 0.008 | 3.484 | |
geneOverlapsPlot | 2.514 | 0.036 | 2.549 | |
getMeta | 0.03 | 0.00 | 0.03 | |
getName | 0.028 | 0.000 | 0.028 | |
getRanges | 0.045 | 0.000 | 0.045 | |
getSignal | 0.067 | 0.000 | 0.067 | |
getSummary | 1.133 | 0.012 | 1.144 | |
globalScorePlot | 1.352 | 0.000 | 1.352 | |
imputeBsDifferencesForTestdata | 2.028 | 0.004 | 2.033 | |
makeBindingSites | 2.315 | 0.000 | 2.316 | |
makeBsSummaryPlot | 1.210 | 0.024 | 1.234 | |
mergeCrosslinkDiagnosticsPlot | 1.469 | 0.016 | 1.485 | |
mergeSummaryPlot | 3.782 | 0.040 | 3.822 | |
plotBsBackgroundFilter | 4.352 | 0.076 | 4.432 | |
plotBsMA | 10.328 | 0.104 | 10.432 | |
plotBsVolcano | 12.469 | 0.071 | 12.542 | |
processingStepsFlowChart | 35.987 | 0.256 | 36.332 | |
processingStepsTable | 0.061 | 0.000 | 0.061 | |
pureClipGeneWiseFilter | 0.351 | 0.000 | 0.351 | |
pureClipGlobalFilter | 0.057 | 0.000 | 0.057 | |
pureClipGlobalFilterPlot | 0.270 | 0.004 | 0.274 | |
quickFigure | 28.828 | 0.176 | 29.004 | |
rangeCoveragePlot | 5.413 | 0.012 | 5.424 | |
reproducibilityCutoffPlot | 2.425 | 0.000 | 2.425 | |
reproducibilityFilter | 1.513 | 0.000 | 1.514 | |
reproducibilityFilterPlot | 1.897 | 0.016 | 1.913 | |
reproducibilitySamplesPlot | 1.613 | 0.016 | 1.630 | |
reproducibilityScatterPlot | 3.358 | 0.008 | 3.366 | |
setMeta | 0.031 | 0.000 | 0.031 | |
setName | 0.028 | 0.000 | 0.027 | |
setRanges | 0.051 | 0.000 | 0.051 | |
setSignal | 0.054 | 0.000 | 0.053 | |
setSummary | 0.029 | 0.000 | 0.028 | |
show | 0.028 | 0.000 | 0.028 | |
subset-BSFDataSet | 0.06 | 0.00 | 0.06 | |
summary | 0.047 | 0.000 | 0.047 | |
supportRatio | 3.198 | 0.016 | 3.214 | |
supportRatioPlot | 3.333 | 0.000 | 3.333 | |
targetGeneSpectrumPlot | 2.072 | 0.000 | 2.072 | |
transcriptRegionOverlapsPlot | 2.393 | 0.044 | 2.437 | |
transcriptRegionSpectrumPlot | 2.402 | 0.008 | 2.411 | |