Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:30 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
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 168/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BindingSiteFinder 2.2.0 (landing page) Mirko Brüggemann
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the BindingSiteFinder package: - 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: 2.2.0 |
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_2.2.0.tar.gz |
StartedAt: 2024-05-06 19:54:53 -0400 (Mon, 06 May 2024) |
EndedAt: 2024-05-06 19:59:12 -0400 (Mon, 06 May 2024) |
EllapsedTime: 258.3 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_2.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/BindingSiteFinder.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 ‘2.2.0’ * 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 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 9.144 0.157 9.313 BSFind 8.287 0.098 8.399 processingStepsFlowChart 8.009 0.148 8.163 bindingSiteDefinednessPlot 7.153 0.110 7.263 calculateBsFoldChange 6.152 0.129 6.332 * 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 4.4.0 (2024-04-24) -- "Puppy Cup" 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': anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, 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': expand.grid, I, 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 76.979 1.306 78.342
BindingSiteFinder.Rcheck/BindingSiteFinder-Ex.timings
name | user | system | elapsed | |
BSFDataSet | 0.067 | 0.001 | 0.069 | |
BSFind | 8.287 | 0.098 | 8.399 | |
add-BSFDataSet | 0.606 | 0.017 | 0.622 | |
annotateWithScore | 0.380 | 0.008 | 0.389 | |
assignToGenes | 0.557 | 0.007 | 0.564 | |
assignToTranscriptRegions | 0.648 | 0.005 | 0.654 | |
bindingSiteCoveragePlot | 3.645 | 0.081 | 3.727 | |
bindingSiteDefinednessPlot | 7.153 | 0.110 | 7.263 | |
calculateBsBackground | 1.265 | 0.008 | 1.274 | |
calculateBsFoldChange | 6.152 | 0.129 | 6.332 | |
calculateSignalToFlankScore | 0.865 | 0.033 | 0.898 | |
clipCoverage | 0.497 | 0.024 | 0.521 | |
collapseReplicates | 0.047 | 0.003 | 0.050 | |
combineBSF | 0.824 | 0.010 | 0.834 | |
coverageOverRanges | 0.727 | 0.013 | 0.740 | |
duplicatedSitesPlot | 0.159 | 0.003 | 0.162 | |
estimateBsWidth | 2.578 | 0.051 | 2.632 | |
estimateBsWidthPlot | 3.094 | 0.068 | 3.162 | |
exportTargetGenes | 0.009 | 0.000 | 0.010 | |
exportToBED | 0.009 | 0.001 | 0.009 | |
filterBsBackground | 1.056 | 0.012 | 1.067 | |
geneOverlapsPlot | 0.808 | 0.046 | 0.854 | |
getMeta | 0.010 | 0.000 | 0.011 | |
getName | 0.009 | 0.001 | 0.010 | |
getRanges | 0.015 | 0.001 | 0.016 | |
getSignal | 0.020 | 0.001 | 0.021 | |
getSummary | 0.325 | 0.009 | 0.332 | |
globalScorePlot | 0.397 | 0.005 | 0.403 | |
imputeBsDifferencesForTestdata | 0.614 | 0.004 | 0.617 | |
makeBindingSites | 0.680 | 0.007 | 0.688 | |
makeBsSummaryPlot | 0.366 | 0.005 | 0.371 | |
mergeCrosslinkDiagnosticsPlot | 0.402 | 0.004 | 0.405 | |
mergeSummaryPlot | 1.504 | 0.041 | 1.546 | |
plotBsBackgroundFilter | 1.479 | 0.043 | 1.528 | |
plotBsMA | 3.921 | 0.073 | 3.994 | |
plotBsVolcano | 3.706 | 0.041 | 3.747 | |
processingStepsFlowChart | 8.009 | 0.148 | 8.163 | |
processingStepsTable | 0.019 | 0.001 | 0.020 | |
pureClipGeneWiseFilter | 0.096 | 0.002 | 0.099 | |
pureClipGlobalFilter | 0.018 | 0.001 | 0.018 | |
pureClipGlobalFilterPlot | 0.073 | 0.001 | 0.074 | |
quickFigure | 9.144 | 0.157 | 9.313 | |
rangeCoveragePlot | 1.461 | 0.038 | 1.500 | |
reproducibilityCutoffPlot | 0.680 | 0.007 | 0.688 | |
reproducibilityFilter | 0.467 | 0.016 | 0.482 | |
reproducibilityFilterPlot | 0.590 | 0.013 | 0.603 | |
reproducibilitySamplesPlot | 0.507 | 0.010 | 0.518 | |
reproducibilityScatterPlot | 1.030 | 0.015 | 1.045 | |
setMeta | 0.011 | 0.001 | 0.011 | |
setName | 0.010 | 0.001 | 0.011 | |
setRanges | 0.017 | 0.001 | 0.017 | |
setSignal | 0.017 | 0.001 | 0.018 | |
setSummary | 0.011 | 0.001 | 0.011 | |
show | 0.010 | 0.001 | 0.010 | |
subset-BSFDataSet | 0.014 | 0.001 | 0.014 | |
summary | 0.016 | 0.001 | 0.017 | |
supportRatio | 0.995 | 0.015 | 1.010 | |
supportRatioPlot | 1.107 | 0.061 | 1.168 | |
targetGeneSpectrumPlot | 0.664 | 0.007 | 0.672 | |
transcriptRegionOverlapsPlot | 0.702 | 0.009 | 0.733 | |
transcriptRegionSpectrumPlot | 0.692 | 0.010 | 0.703 | |