Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 821/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomicDistributions 1.14.0 (landing page) Kristyna Kupkova
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the GenomicDistributions package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicDistributions.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: GenomicDistributions |
Version: 1.14.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicDistributions.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicDistributions_1.14.0.tar.gz |
StartedAt: 2024-12-20 20:30:50 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 20:33:47 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 177.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GenomicDistributions.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicDistributions.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicDistributions_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GenomicDistributions.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GenomicDistributions/DESCRIPTION’ ... OK * this is package ‘GenomicDistributions’ version ‘1.14.0’ * 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 ‘GenomicDistributions’ 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed getGeneModelsFromGTF 7.917 0.449 8.382 * 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
GenomicDistributions.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GenomicDistributions ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘GenomicDistributions’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (GenomicDistributions)
GenomicDistributions.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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("GenomicDistributions") Loading required package: IRanges 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, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 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: GenomicRanges Loading required package: GenomeInfoDb > > test_check("GenomicDistributions") [ FAIL 0 | WARN 0 | SKIP 1 | PASS 48 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test_all.R:139:1' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 48 ] > > proc.time() user system elapsed 29.396 1.552 29.637
GenomicDistributions.Rcheck/GenomicDistributions-Ex.timings
name | user | system | elapsed | |
binBSGenome | 0 | 0 | 0 | |
binChroms | 0.017 | 0.001 | 0.018 | |
binRegion | 0.001 | 0.001 | 0.001 | |
calcChromBins | 2.154 | 0.071 | 1.703 | |
calcChromBinsRef | 0.039 | 0.002 | 0.021 | |
calcChromBinsRefSlow | 0.051 | 0.002 | 0.027 | |
calcCumulativePartitions | 2.680 | 0.097 | 2.584 | |
calcCumulativePartitionsRef | 1.324 | 0.087 | 1.419 | |
calcDinuclFreq | 0 | 0 | 0 | |
calcDinuclFreqRef | 0 | 0 | 0 | |
calcExpectedPartitions | 2.027 | 0.120 | 2.148 | |
calcExpectedPartitionsRef | 1.254 | 0.100 | 1.360 | |
calcFeatureDist | 0.035 | 0.003 | 0.037 | |
calcFeatureDistRefTSS | 0.187 | 0.024 | 0.127 | |
calcGCContent | 0.001 | 0.000 | 0.000 | |
calcGCContentRef | 0 | 0 | 0 | |
calcNearestNeighbors | 0.040 | 0.003 | 0.023 | |
calcNeighborDist | 0.027 | 0.003 | 0.016 | |
calcPartitions | 2.025 | 0.113 | 2.015 | |
calcPartitionsRef | 1.558 | 0.118 | 1.677 | |
calcSummarySignal | 0.049 | 0.003 | 0.033 | |
calcWidth | 0.001 | 0.000 | 0.001 | |
dot-validateInputs | 0 | 0 | 0 | |
dtToGr | 0.018 | 0.001 | 0.010 | |
genomePartitionList | 1.330 | 0.091 | 1.246 | |
getChromSizes | 0.003 | 0.002 | 0.005 | |
getChromSizesFromFasta | 0.011 | 0.001 | 0.013 | |
getGeneModels | 0.033 | 0.004 | 0.038 | |
getGeneModelsFromGTF | 7.917 | 0.449 | 8.382 | |
getGenomeBins | 1.263 | 0.071 | 1.135 | |
getTssFromGTF | 0.141 | 0.008 | 0.149 | |
loadBSgenome | 0.000 | 0.001 | 0.000 | |
loadEnsDb | 0 | 0 | 0 | |
nlist | 0.001 | 0.001 | 0.001 | |
plotChromBins | 0.059 | 0.001 | 0.060 | |
plotCumulativePartitions | 2.916 | 0.205 | 3.095 | |
plotDinuclFreq | 0.033 | 0.002 | 0.018 | |
plotExpectedPartitions | 1.764 | 0.136 | 1.755 | |
plotFeatureDist | 0.440 | 0.030 | 0.281 | |
plotGCContent | 0.068 | 0.002 | 0.036 | |
plotNeighborDist | 0.023 | 0.000 | 0.012 | |
plotPartitions | 2.489 | 0.123 | 2.568 | |
plotQTHist | 0.019 | 0.001 | 0.020 | |
plotSummarySignal | 0.086 | 0.008 | 0.052 | |
retrieveFile | 0.002 | 0.001 | 0.001 | |