Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-09 21:31 -0500 (Sat, 09 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1301/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MOGAMUN 1.16.0 (landing page) Elva-María Novoa-del-Toro
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
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 MOGAMUN package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MOGAMUN.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: MOGAMUN |
Version: 1.16.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MOGAMUN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MOGAMUN_1.16.0.tar.gz |
StartedAt: 2024-11-09 07:34:15 -0500 (Sat, 09 Nov 2024) |
EndedAt: 2024-11-09 07:38:17 -0500 (Sat, 09 Nov 2024) |
EllapsedTime: 242.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MOGAMUN.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MOGAMUN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MOGAMUN_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MOGAMUN.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 ‘MOGAMUN/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MOGAMUN’ version ‘1.16.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘MOGAMUN’ 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 ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘unitTests.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: OK
MOGAMUN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MOGAMUN ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘MOGAMUN’ ... ** using staged installation ** R ** 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 (MOGAMUN)
MOGAMUN.Rcheck/tests/unitTests.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. > # Our package. Used for the test suite name > pkgname <- c("MOGAMUN", "RUnit") > > for (p in pkgname) { + require(p, quietly=TRUE, character.only=TRUE) || + stop("package '", p, "' not found") + } > > pkgname <- "MOGAMUN" > > # Determine which files to load (have to start with test_ and end with .R) > pattern <- "^test.*\\.R$" > > # Which functions to run. Have to start with 'test.' > testFunctionRegexp = "^test.+" > > # Path to the unit tests folder in the package > directory <- paste0(system.file("tests", package=pkgname), "/") > if (.Platform$OS.type == "windows") { # windows needs the absolute file names + directory <- list.files(directory, pattern = pattern, full.names = TRUE) + } > > for (dir in directory) { + # Define RUnit test suite + suite <- defineTestSuite(name=paste(pkgname, "RUnit Tests"), + dirs=dir, + testFileRegexp=pattern, + testFuncRegexp = testFunctionRegexp, + rngKind="default", + rngNormalKind="default") + + # Run tests + result <- runTestSuite(suite) + + # Display result tests on the console + printTextProtocol(result) + + # Write results in JUnit-like xml format + printJUnitProtocol(result, fileName="junit.xml") + } Executing test function test.mogamun_init ... done successfully. Executing test function test.mogamun_load_data ... Timing stopped at: 0.012 0.001 0.013 Error in LoadedData$GenesWithNodesScores$nodescore >= 0 && LoadedData$GenesWithNodesScores$nodescore <= : 'length = 1000' in coercion to 'logical(1)' done successfully. Executing test function test.mogamun_postprocess ... [1] "Run 1. Gen. 1 completed" [1] "FINISH TIME, RUN 1: 2024-11-09 07:38:14.738004" Timing stopped at: 0.324 0.013 0.332 Error in checkIdentical(RealOutput, ExpectedOutput) : FALSE In addition: Warning message: In dir.create(ResultsPath, recursive = TRUE) : '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/MOGAMUN/SampleResults//Experiment_2024-11-09' already exists done successfully. Executing test function test.mogamun_run ... [1] "Run 1. Gen. 1 completed" [1] "FINISH TIME, RUN 1: 2024-11-09 07:38:15.046856" Timing stopped at: 0.261 0.01 0.272 Error in checkEquals(length(list.files(ResDirAll)), 2) : Mean relative difference: 0.75 In addition: Warning message: In dir.create(ResultsPath, recursive = TRUE) : '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/MOGAMUN/SampleResults//Experiment_2024-11-09' already exists done successfully. RUNIT TEST PROTOCOL -- Sat Nov 9 07:38:15 2024 *********************************************** Number of test functions: 4 Number of errors: 1 Number of failures: 2 1 Test Suite : MOGAMUN RUnit Tests - 4 test functions, 1 error, 2 failures ERROR in test.mogamun_load_data: Error in LoadedData$GenesWithNodesScores$nodescore >= 0 && LoadedData$GenesWithNodesScores$nodescore <= : 'length = 1000' in coercion to 'logical(1)' FAILURE in test.mogamun_postprocess: Error in checkIdentical(RealOutput, ExpectedOutput) : FALSE FAILURE in test.mogamun_run: Error in checkEquals(length(list.files(ResDirAll)), 2) : Mean relative difference: 0.75 Details *************************** Test Suite: MOGAMUN RUnit Tests Test function regexp: ^test.+ Test file regexp: ^test.*\.R$ Involved directory: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/MOGAMUN/tests/ --------------------------- Test file: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/MOGAMUN/tests//test.mogamun.R test.mogamun_init: (13 checks) ... OK (0 seconds) test.mogamun_load_data: ERROR !! Error in LoadedData$GenesWithNodesScores$nodescore >= 0 && LoadedData$GenesWithNodesScores$nodescore <= : 'length = 1000' in coercion to 'logical(1)' test.mogamun_postprocess: FAILURE !! (check number 2) Error in checkIdentical(RealOutput, ExpectedOutput) : FALSE test.mogamun_run: FAILURE !! (check number 2) Error in checkEquals(length(list.files(ResDirAll)), 2) : Mean relative difference: 0.75 > > > proc.time() user system elapsed 1.135 0.068 1.196
MOGAMUN.Rcheck/MOGAMUN-Ex.timings
name | user | system | elapsed | |
mogamun_init | 0.000 | 0.000 | 0.001 | |
mogamun_load_data | 0.012 | 0.001 | 0.014 | |
mogamun_postprocess | 0.337 | 0.018 | 0.646 | |
mogamun_run | 0.277 | 0.008 | 0.285 | |