Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-18 12:05 -0400 (Sat, 18 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4632 |
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 2041/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SmartPhos 0.99.30 (landing page) Shubham Agrawal
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the SmartPhos package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SmartPhos.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: SmartPhos |
Version: 0.99.30 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SmartPhos.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SmartPhos_0.99.30.tar.gz |
StartedAt: 2025-10-18 01:37:30 -0400 (Sat, 18 Oct 2025) |
EndedAt: 2025-10-18 01:43:33 -0400 (Sat, 18 Oct 2025) |
EllapsedTime: 363.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SmartPhos.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SmartPhos.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SmartPhos_0.99.30.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SmartPhos.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SmartPhos/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SmartPhos’ version ‘0.99.30’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 36 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘SmartPhos’ can be installed ... OK * checking installed package size ... INFO installed size is 7.1Mb sub-directories of 1Mb or more: data 1.3Mb shiny-app 5.4Mb * 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 ... NOTE Namespaces in Imports field not imported from: ‘DT’ ‘XML’ ‘cowplot’ ‘factoextra’ ‘ggbeeswarm’ ‘grid’ ‘plotly’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’ ‘shinythemes’ ‘tools’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE runFisher: no visible binding for global variable ‘signature’ runGSEAforPhospho: no visible binding for global variable ‘signature’ Undefined global functions or variables: signature Consider adding importFrom("methods", "signature") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/SmartPhos.Rcheck/00check.log’ for details.
SmartPhos.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SmartPhos ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘SmartPhos’ ... ** this is package ‘SmartPhos’ version ‘0.99.30’ ** using staged installation ** R ** data ** 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 (SmartPhos)
SmartPhos.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 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/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(SmartPhos) > > test_check("SmartPhos") harmonizing input: removing 5 sampleMap rows not in names(experiments) harmonizing input: removing 5 sampleMap rows not in names(experiments) Running gene set analysis: Checking arguments...done! Final gene/gene-set association: 20 genes and 22 gene sets Details: Calculating gene set statistics from 20 out of 65 gene-level statistics Removed 4366 genes from GSC due to lack of matching gene statistics Removed 28 gene sets containing no genes after gene removal Removed additionally 0 gene sets not matching the size limits Loaded additional information for 22 gene sets Calculating gene set statistics...done! Calculating gene set significance...done! Adjusting for multiple testing...done! Running gene set analysis: Checking arguments...done! Final gene/gene-set association: 20 genes and 22 gene sets Details: Calculating gene set statistics from 20 out of 65 gene-level statistics Removed 4366 genes from GSC due to lack of matching gene statistics Removed 28 gene sets containing no genes after gene removal Removed additionally 0 gene sets not matching the size limits Loaded additional information for 22 gene sets Calculating gene set statistics...done! Calculating gene set significance...done! Adjusting for multiple testing...done! Imputing along margin 2 (samples/columns). Imputing along margin 2 (samples/columns). New names: * `` -> `...1` * `` -> `...2` * `` -> `...3` [ FAIL 0 | WARN 0 | SKIP 0 | PASS 309 ] > > proc.time() user system elapsed 72.946 5.047 79.354
SmartPhos.Rcheck/SmartPhos-Ex.timings
name | user | system | elapsed | |
Homo_sapien_kinase_substrate_network | 0.087 | 0.004 | 0.093 | |
Mus_musculus_kinase_substrate_network | 0.063 | 0.002 | 0.065 | |
addZeroTime | 0.423 | 0.024 | 0.454 | |
calcKinaseScore | 0.923 | 0.050 | 0.978 | |
clusterEnrich | 1.373 | 0.054 | 1.438 | |
clusterTS | 1.280 | 0.045 | 1.331 | |
dda_example | 0.004 | 0.002 | 0.005 | |
dia_example | 0.008 | 0.002 | 0.010 | |
enrichDifferential | 0.593 | 0.027 | 0.629 | |
getDecouplerNetwork | 0.764 | 1.151 | 1.941 | |
getRatioMatrix | 0.777 | 0.024 | 0.804 | |
intensityBoxPlot | 1.677 | 0.043 | 1.730 | |
makeSmartPhosDirectory | 0.003 | 0.040 | 0.051 | |
medianNorm | 0.000 | 0.001 | 0.001 | |
mscale | 0.001 | 0.001 | 0.001 | |
normByFullProteome | 0.360 | 0.005 | 0.369 | |
performCombinedNormalization | 0.165 | 0.226 | 0.397 | |
performDifferentialExp | 0.445 | 0.021 | 0.473 | |
plotHeatmap | 0.553 | 0.023 | 0.582 | |
plotIntensity | 1.276 | 0.026 | 1.308 | |
plotKinaseDE | 0.442 | 0.003 | 0.446 | |
plotKinaseTimeSeries | 0.380 | 0.003 | 0.385 | |
plotLogRatio | 1.209 | 0.010 | 1.225 | |
plotMissing | 0.469 | 0.021 | 0.492 | |
plotPCA | 0.305 | 0.004 | 0.309 | |
plotTimeSeries | 0.676 | 0.022 | 0.711 | |
plotVolcano | 0.758 | 0.021 | 0.785 | |
preprocessPhos | 0.464 | 0.019 | 0.486 | |
preprocessProteome | 0.437 | 0.019 | 0.457 | |
readExperiment | 0.173 | 0.004 | 0.178 | |
readExperimentDIA | 3.293 | 0.588 | 3.986 | |
readPhosphoExperiment | 0.027 | 0.005 | 0.033 | |
readPhosphoExperimentDIA | 1.832 | 0.316 | 2.147 | |
readProteomeExperiment | 0.027 | 0.007 | 0.034 | |
readProteomeExperimentDIA | 1.769 | 0.410 | 2.174 | |
runFisher | 0.570 | 0.070 | 0.648 | |
runSmartPhos | 0 | 0 | 0 | |
swissProt | 0.226 | 0.023 | 0.252 | |