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 12:06 -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 1716/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
regioneReloaded 1.8.0 (landing page) Roberto Malinverni
| 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 regioneReloaded package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/regioneReloaded.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: regioneReloaded |
Version: 1.8.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:regioneReloaded.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings regioneReloaded_1.8.0.tar.gz |
StartedAt: 2024-12-20 08:21:26 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 08:36:04 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 878.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: regioneReloaded.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:regioneReloaded.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings regioneReloaded_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/regioneReloaded.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘regioneReloaded/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘regioneReloaded’ version ‘1.8.0’ * 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 ‘regioneReloaded’ 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 data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed crosswisePermTest 40.214 0.390 42.156 multiLocalZscore 16.085 0.053 16.215 multiLocalZScore-class 8.237 0.044 8.312 genoMatriXeR-class 7.945 0.039 8.092 * 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
regioneReloaded.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL regioneReloaded ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘regioneReloaded’ ... ** using staged installation ** R ** data ** 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 (regioneReloaded)
regioneReloaded.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: 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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(regioneReloaded) Loading required package: regioneR 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, saveRDS, 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("regioneReloaded") [1] "method selected for hclustering: average" complete average single ward.D2 median centroid mcquitty 0.7497654 0.7857181 0.6514804 0.7363304 0.3459672 0.4561003 0.7516609 [1] "method selected for hclustering: complete" complete average single ward.D2 median centroid mcquitty 0.9098230 0.8541174 0.7986368 0.8320493 0.8348816 0.8510903 0.8475492 [1] "method selected for hclustering: average" complete average single ward.D2 median centroid mcquitty 0.8909663 0.8944326 0.7892161 0.8311822 0.8813696 0.8857083 0.8784679 [1] "resampleRegions function need that universe parameters in not NULL universe will created using all the regions present in Blist" [1] "resampleRegions function need that universe parameters in not NULL universe will created using all the regions present in Blist" [1] "resampleRegions function need that universe parameters in not NULL universe will created using all the regions present in Blist" [1] "resampleRegions function need that universe parameters in not NULL universe will created using all the regions present in Blist" [1] "resampleRegions function need that universe parameters in not NULL universe will created using all the regions present in Blist" [1] "resampleRegions function need that universe parameters in not NULL universe will created using all the regions present in Blist" [1] "method selected for hclustering: average" complete average single ward.D2 median centroid mcquitty 0.7515325 0.7716179 0.6542890 0.7136237 0.2223408 0.5618311 0.7245865 [1] "method selected for hclustering: average" complete average single ward.D2 median centroid mcquitty 0.7497654 0.7857181 0.6514804 0.7363304 0.3459672 0.4561003 0.7516609 [1] "method selected for hclustering: complete" complete average single ward.D2 median centroid mcquitty 0.9098230 0.8541174 0.7986368 0.8320493 0.8348816 0.8510903 0.8475492 [1] "method selected for hclustering: average" complete average single ward.D2 median centroid mcquitty 0.8909663 0.8944326 0.7892161 0.8311822 0.8813696 0.8857083 0.8784679 [ FAIL 0 | WARN 132 | SKIP 6 | PASS 60 ] ══ Skipped tests (6) ═══════════════════════════════════════════════════════════ • On CRAN (6): 'test-crosswisePermTest.R:9:3', 'test-crosswisePermTest.R:67:3', 'test-crosswisePermTest.R:99:3', 'test-getMatrix.R:6:3', 'test-getMultiEvaluation.R:2:3', 'test-getParameters.R:7:3' [ FAIL 0 | WARN 132 | SKIP 6 | PASS 60 ] > > proc.time() user system elapsed 437.322 42.264 311.616
regioneReloaded.Rcheck/regioneReloaded-Ex.timings
name | user | system | elapsed | |
chooseHclustMet | 0.015 | 0.002 | 0.017 | |
createUniverse | 0.649 | 0.010 | 0.662 | |
crosswisePermTest | 40.214 | 0.390 | 42.156 | |
genoMatriXeR-class | 7.945 | 0.039 | 8.092 | |
getHClust | 0.051 | 0.006 | 0.058 | |
getMatrix | 0.119 | 0.075 | 0.193 | |
getMultiEvaluation | 0.036 | 0.014 | 0.050 | |
getParameters | 0.028 | 0.003 | 0.032 | |
makeCrosswiseMatrix | 0.039 | 0.003 | 0.042 | |
makeLZMatrix | 0.026 | 0.004 | 0.030 | |
multiLocalZScore-class | 8.237 | 0.044 | 8.312 | |
multiLocalZscore | 16.085 | 0.053 | 16.215 | |
plotCrosswiseDimRed | 4.551 | 0.057 | 4.632 | |
plotCrosswiseMatrix | 0.871 | 0.021 | 0.930 | |
plotLocalZScoreMatrix | 0.026 | 0.004 | 0.031 | |
plotSingleLZ | 0.915 | 0.012 | 0.972 | |
plotSinglePT | 1.717 | 0.018 | 1.988 | |
randomizeRegionsPerc | 0.699 | 0.007 | 0.722 | |
similarRegionSet | 2.813 | 0.024 | 2.911 | |