Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-16 11:44 -0400 (Fri, 16 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4420 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
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 1526/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PhosR 1.15.0 (landing page) Taiyun Kim
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the PhosR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PhosR.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: PhosR |
Version: 1.15.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PhosR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PhosR_1.15.0.tar.gz |
StartedAt: 2024-08-15 23:15:37 -0400 (Thu, 15 Aug 2024) |
EndedAt: 2024-08-15 23:17:37 -0400 (Thu, 15 Aug 2024) |
EllapsedTime: 120.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PhosR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PhosR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PhosR_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PhosR.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PhosR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PhosR’ version ‘1.15.0’ * 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 ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘PhosR’ 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘stringi’ All declared Imports should be used. Unexported objects imported by ':::' calls: ‘BiocGenerics:::replaceSlots’ ‘S4Vectors:::disableValidity’ ‘SummarizedExperiment:::.SummarizedExperiment.charbound’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE abundPlot: no visible binding for global variable ‘.’ Undefined global functions or variables: . * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed siteAnnotate 8.382 0.288 8.672 kinaseSubstratePred 8.330 0.257 8.594 kinaseSubstrateScore 5.442 0.131 5.579 minmax 5.316 0.136 5.457 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/PhosR.Rcheck/00check.log’ for details.
PhosR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PhosR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘PhosR’ ... ** using staged installation ** R ** data ** 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 (PhosR)
PhosR.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" 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(PhosR) > > test_check("PhosR") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 58 ] > > proc.time() user system elapsed 3.296 0.136 3.436
PhosR.Rcheck/PhosR-Ex.timings
name | user | system | elapsed | |
PhosphoExperiment-methods | 0.126 | 0.003 | 0.130 | |
PhosphoExperiment-operate | 0.172 | 0.003 | 0.176 | |
PhosphoExperiment | 0.105 | 0.002 | 0.106 | |
RUVphospho | 0.091 | 0.003 | 0.093 | |
Signalomes | 0 | 0 | 0 | |
createFrequencyMat | 0.048 | 0.001 | 0.049 | |
frequencyScoring | 0.115 | 0.004 | 0.118 | |
getSPS | 0.806 | 0.019 | 0.826 | |
kinaseSubstrateHeatmap | 0 | 0 | 0 | |
kinaseSubstratePred | 8.330 | 0.257 | 8.594 | |
kinaseSubstrateProfile | 2.614 | 0.015 | 2.631 | |
kinaseSubstrateScore | 5.442 | 0.131 | 5.579 | |
mIntersect | 0.327 | 0.003 | 0.330 | |
matANOVA | 2.398 | 0.003 | 2.402 | |
meanAbundance | 0.098 | 0.002 | 0.100 | |
medianScaling | 0.081 | 0.001 | 0.082 | |
minmax | 5.316 | 0.136 | 5.457 | |
pathwayOverrepresent | 0 | 0 | 0 | |
pathwayRankBasedEnrichment | 0.000 | 0.000 | 0.001 | |
phosCollapse | 0.299 | 0.008 | 0.307 | |
plotQC | 1.321 | 0.025 | 1.349 | |
ptImpute | 0.078 | 0.001 | 0.079 | |
scImpute | 0.192 | 0.003 | 0.196 | |
selectGrps | 0.053 | 0.002 | 0.055 | |
selectLocalisedSites | 0.034 | 0.002 | 0.036 | |
selectOverallPercent | 0.020 | 0.001 | 0.022 | |
selectTimes | 0.005 | 0.001 | 0.006 | |
siteAnnotate | 8.382 | 0.288 | 8.672 | |
standardise | 2.693 | 0.048 | 2.741 | |
tImpute | 0.057 | 0.003 | 0.061 | |