Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:45 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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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" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 2123/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TIN 1.37.0 (landing page) Bjarne Johannessen
| 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 | OK | ||||||||||
To the developers/maintainers of the TIN package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TIN.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: TIN |
Version: 1.37.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TIN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TIN_1.37.0.tar.gz |
StartedAt: 2024-08-21 00:57:10 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 00:58:23 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 72.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TIN.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TIN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TIN_1.37.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/TIN.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 ‘TIN/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TIN’ version ‘1.37.0’ * 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 ‘TIN’ 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 ... NOTE aberrantExonUsage: no visible global function definition for ‘quantile’ aberrantExonUsage: no visible global function definition for ‘ave’ clusterPlot: no visible global function definition for ‘dist’ clusterPlot: no visible global function definition for ‘hclust’ clusterPlot: no visible global function definition for ‘colorRampPalette’ clusterPlot: no visible global function definition for ‘par’ clusterPlot: no visible global function definition for ‘png’ clusterPlot: no visible global function definition for ‘jpeg’ clusterPlot: no visible global function definition for ‘postscript’ clusterPlot: no visible global function definition for ‘pdf’ clusterPlot: no visible global function definition for ‘bmp’ clusterPlot: no visible global function definition for ‘dev.off’ correlationPlot: no visible global function definition for ‘png’ correlationPlot: no visible global function definition for ‘jpeg’ correlationPlot: no visible global function definition for ‘postscript’ correlationPlot: no visible global function definition for ‘pdf’ correlationPlot: no visible global function definition for ‘bmp’ correlationPlot: no visible global function definition for ‘hist’ correlationPlot: no visible global function definition for ‘axis’ correlationPlot: no visible global function definition for ‘points’ correlationPlot: no visible global function definition for ‘dev.off’ firmaAnalysis: no visible global function definition for ‘data’ geneSetCorrelation: no visible global function definition for ‘median’ posNegCorrPlot: no visible global function definition for ‘png’ posNegCorrPlot: no visible global function definition for ‘jpeg’ posNegCorrPlot: no visible global function definition for ‘postscript’ posNegCorrPlot: no visible global function definition for ‘pdf’ posNegCorrPlot: no visible global function definition for ‘bmp’ posNegCorrPlot: no visible global function definition for ‘axis’ posNegCorrPlot: no visible global function definition for ‘points’ posNegCorrPlot: no visible global function definition for ‘dev.off’ readGeneSummaries: no visible global function definition for ‘data’ readGeneSummaries: no visible global function definition for ‘read.table’ scatterPlot: no visible global function definition for ‘png’ scatterPlot: no visible global function definition for ‘jpeg’ scatterPlot: no visible global function definition for ‘postscript’ scatterPlot: no visible global function definition for ‘pdf’ scatterPlot: no visible global function definition for ‘bmp’ scatterPlot: no visible global function definition for ‘ave’ scatterPlot: no visible global function definition for ‘axis’ scatterPlot: no visible global function definition for ‘text’ scatterPlot: no visible global function definition for ‘mtext’ scatterPlot: no visible global function definition for ‘points’ scatterPlot: no visible global function definition for ‘dev.off’ Undefined global functions or variables: ave axis bmp colorRampPalette data dev.off dist hclust hist jpeg median mtext par pdf png points postscript quantile read.table text Consider adding importFrom("grDevices", "bmp", "colorRampPalette", "dev.off", "jpeg", "pdf", "png", "postscript") importFrom("graphics", "axis", "hist", "mtext", "par", "points", "text") importFrom("stats", "ave", "dist", "hclust", "median", "quantile") importFrom("utils", "data", "read.table") to your NAMESPACE file. * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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/TIN.Rcheck/00check.log’ for details.
TIN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TIN ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘TIN’ ... ** 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 (TIN)
TIN.Rcheck/tests/runTests.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. > BiocGenerics:::testPackage("TIN") Attaching package: 'R.oo' The following object is masked from 'package:R.methodsS3': throw The following objects are masked from 'package:methods': getClasses, getMethods The following objects are masked from 'package:base': attach, detach, load, save Attaching package: 'R.utils' The following object is masked from 'package:utils': timestamp The following objects are masked from 'package:base': cat, commandArgs, getOption, isOpen, nullfile, parse, use, warnings Attaching package: 'R.filesets' The following object is masked from 'package:R.utils': validate The following objects are masked from 'package:base': append, readLines Attaching package: 'aroma.core' The following objects are masked from 'package:base': .Machine, colMeans, colSums, library, require, write Loading required package: aroma.light aroma.light v3.35.0 (2024-08-20) successfully loaded. See ?aroma.light for help. Attaching package: 'aroma.light' The following objects are masked from 'package:aroma.affymetrix': averageQuantile, normalizeQuantile, plotDensity, plotMvsA, plotXYCurve The following objects are masked from 'package:aroma.core': callNaiveGenotypes, normalizeTumorBoost Loading required package: affxparser Attaching package: 'affxparser' The following object is masked from 'package:aroma.affymetrix': writeCdf The following object is masked from 'package:R.utils': findFiles The following object is masked _by_ package:aroma.affymetrix: writeCdf The following object is masked from package:R.utils: findFiles Attaching package: 'aroma.affymetrix' The following objects are masked _by_ 'package:aroma.light': averageQuantile, normalizeQuantile, plotDensity, plotMvsA, plotXYCurve The following object is masked from 'package:affxparser': writeCdf RUNIT TEST PROTOCOL -- Wed Aug 21 00:58:19 2024 *********************************************** Number of test functions: 5 Number of errors: 0 Number of failures: 0 1 Test Suite : TIN RUnit Tests - 5 test functions, 0 errors, 0 failures Number of test functions: 5 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 10.485 0.248 10.739
TIN.Rcheck/TIN-Ex.timings
name | user | system | elapsed | |
aberrantExonUsage | 0.254 | 0.005 | 0.259 | |
clusterPlot | 0.055 | 0.010 | 0.067 | |
correlation | 0.039 | 0.007 | 0.046 | |
correlationPlot | 0.846 | 0.085 | 0.935 | |
firmaAnalysis | 0.005 | 0.001 | 0.007 | |
geneSetCorrelation | 3.148 | 0.027 | 3.186 | |
posNegCorrPlot | 1.110 | 0.067 | 1.186 | |
probesetPermutations | 0.303 | 0.012 | 0.315 | |
readGeneSummaries | 0.013 | 0.002 | 0.015 | |
scatterPlot | 0.108 | 0.010 | 0.118 | |