Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-16 12:06 -0400 (Sat, 16 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4596 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4538 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
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 1562/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PhosR 1.19.0 (landing page) Taiyun Kim
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / 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: 1.19.0 |
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_1.19.0.tar.gz |
StartedAt: 2025-08-15 21:31:06 -0400 (Fri, 15 Aug 2025) |
EndedAt: 2025-08-15 21:33:09 -0400 (Fri, 15 Aug 2025) |
EllapsedTime: 123.5 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_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/PhosR.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PhosR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PhosR’ version ‘1.19.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 24 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: PhosphoExperiment-operate.Rd: SummarizedExperiment-class PhosphoExperiment.Rd: SummarizedExperiment-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 kinaseSubstratePred 8.608 0.295 8.907 siteAnnotate 8.380 0.356 8.753 minmax 5.382 0.130 5.528 kinaseSubstrateScore 5.200 0.139 5.349 * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.22-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/4.5-arm64/Resources/library’ * installing *source* package ‘PhosR’ ... ** this is package ‘PhosR’ version ‘1.19.0’ ** 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 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" Copyright (C) 2025 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 3.599 0.142 3.739
PhosR.Rcheck/PhosR-Ex.timings
name | user | system | elapsed | |
PhosphoExperiment-methods | 0.117 | 0.003 | 0.120 | |
PhosphoExperiment-operate | 0.161 | 0.003 | 0.164 | |
PhosphoExperiment | 0.099 | 0.001 | 0.100 | |
RUVphospho | 0.117 | 0.002 | 0.119 | |
Signalomes | 0 | 0 | 0 | |
createFrequencyMat | 0.046 | 0.001 | 0.047 | |
frequencyScoring | 0.116 | 0.004 | 0.120 | |
getSPS | 0.797 | 0.018 | 0.816 | |
kinaseSubstrateHeatmap | 0 | 0 | 0 | |
kinaseSubstratePred | 8.608 | 0.295 | 8.907 | |
kinaseSubstrateProfile | 2.517 | 0.012 | 2.530 | |
kinaseSubstrateScore | 5.200 | 0.139 | 5.349 | |
mIntersect | 0.387 | 0.016 | 0.406 | |
matANOVA | 2.575 | 0.005 | 2.579 | |
meanAbundance | 0.110 | 0.004 | 0.113 | |
medianScaling | 0.079 | 0.002 | 0.081 | |
minmax | 5.382 | 0.130 | 5.528 | |
pathwayOverrepresent | 0 | 0 | 0 | |
pathwayRankBasedEnrichment | 0 | 0 | 0 | |
phosCollapse | 0.301 | 0.009 | 0.310 | |
plotQC | 1.349 | 0.036 | 1.385 | |
ptImpute | 0.075 | 0.000 | 0.076 | |
scImpute | 0.182 | 0.001 | 0.184 | |
selectGrps | 0.050 | 0.002 | 0.051 | |
selectLocalisedSites | 0.039 | 0.001 | 0.040 | |
selectOverallPercent | 0.019 | 0.001 | 0.020 | |
selectTimes | 0.005 | 0.001 | 0.005 | |
siteAnnotate | 8.380 | 0.356 | 8.753 | |
standardise | 2.544 | 0.012 | 2.558 | |
tImpute | 0.063 | 0.003 | 0.067 | |