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 12:08 -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 1980/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
singscore 1.26.0 (landing page) Malvika Kharbanda
| 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 singscore package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/singscore.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: singscore |
Version: 1.26.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:singscore.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings singscore_1.26.0.tar.gz |
StartedAt: 2024-12-21 09:45:10 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 09:49:51 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 280.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: singscore.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:singscore.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings singscore_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/singscore.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 ‘singscore/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘singscore’ version ‘1.26.0’ * 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 ‘singscore’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ...Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]], : It is recommended to use ‘given’ instead of ‘middle’. 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 ... NOTE plotDispersion: no visible binding for global variable ‘Score’ plotDispersion: no visible binding for global variable ‘Dispersion’ plotDispersion: no visible binding for global variable ‘Class’ plotDispersion: no visible binding for global variable ‘SampleText’ plotDispersion: no visible binding for global variable ‘SampleLabel’ plotRankDensity_intl: no visible binding for global variable ‘Ranks’ plotRankDensity_intl: no visible binding for global variable ‘upDown’ plotRankDensity_intl: no visible binding for global variable ‘..density..’ plotRankDensity_intl: no visible binding for global variable ‘EntrezID’ plotScoreLandscape: no visible binding for global variable ‘sc1’ plotScoreLandscape: no visible binding for global variable ‘sc2’ projectScoreLandscape: no visible binding for global variable ‘SampleText’ projectScoreLandscape: no visible binding for global variable ‘Class’ projectScoreLandscape: no visible binding for global variable ‘SampleLabel’ Undefined global functions or variables: ..density.. Class Dispersion EntrezID Ranks SampleLabel SampleText Score sc1 sc2 upDown * 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/singscore.Rcheck/00check.log’ for details.
singscore.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL singscore ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘singscore’ ... ** using staged installation Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]], : It is recommended to use ‘given’ instead of ‘middle’. Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]], : It is recommended to use ‘given’ instead of ‘middle’. ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (singscore)
singscore.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(singscore) > > test_check("singscore") [ FAIL 0 | WARN 41 | SKIP 0 | PASS 143 ] [ FAIL 0 | WARN 41 | SKIP 0 | PASS 143 ] > > proc.time() user system elapsed 22.911 0.743 23.774
singscore.Rcheck/singscore-Ex.timings
name | user | system | elapsed | |
generateNull | 3.925 | 0.032 | 3.982 | |
getPvals | 0.071 | 0.002 | 0.074 | |
getStableGenes | 0.780 | 0.056 | 0.841 | |
multiScore | 0.019 | 0.001 | 0.020 | |
plotDispersion | 0.895 | 0.058 | 0.990 | |
plotNull | 0.683 | 0.018 | 0.703 | |
plotRankDensity | 0.330 | 0.005 | 0.336 | |
plotScoreLandscape | 0.109 | 0.002 | 0.111 | |
rankGenes | 0.073 | 0.002 | 0.077 | |
simpleScore | 0.007 | 0.000 | 0.007 | |