Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:11 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 |
To the developers/maintainers of the MOGAMUN package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1244/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MOGAMUN 1.8.0 (landing page) Elva-María Novoa-del-Toro
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: MOGAMUN |
Version: 1.8.0 |
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:MOGAMUN.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings MOGAMUN_1.8.0.tar.gz |
StartedAt: 2023-04-10 22:05:38 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 22:06:31 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 53.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MOGAMUN.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:MOGAMUN.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings MOGAMUN_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/MOGAMUN.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘MOGAMUN/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MOGAMUN’ version ‘1.8.0’ * 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 ... 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 R 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 loading without being on the library search path ... 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 in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘MOGAMUN_Vignette.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
MOGAMUN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL MOGAMUN ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) 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: 0.027 0 0.027 Error in is.igraph(LoadedData$Multiplex[[i]]) : could not find function "is.igraph" In addition: Warning messages: 1: In LoadedData$GenesWithNodesScores$nodescore >= 0 && LoadedData$GenesWithNodesScores$nodescore <= : 'length(x) = 1000 > 1' in coercion to 'logical(1)' 2: In LoadedData$GenesWithNodesScores$nodescore >= 0 && LoadedData$GenesWithNodesScores$nodescore <= : 'length(x) = 1000 > 1' in coercion to 'logical(1)' done successfully. Executing test function test.mogamun_postprocess ... [1] "Run 1. Gen. 1 completed" [1] "FINISH TIME, RUN 1: 2023-04-10 22:06:24" Timing stopped at: 0.809 0.051 0.86 Error in checkIdentical(RealOutput, ExpectedOutput) : FALSE In addition: Warning message: In dir.create(ResultsPath, recursive = TRUE) : '/home/biocbuild/bbs-3.16-bioc/R/site-library/MOGAMUN/SampleResults//Experiment_2023-04-10' already exists done successfully. Executing test function test.mogamun_run ... [1] "Run 1. Gen. 1 completed" [1] "FINISH TIME, RUN 1: 2023-04-10 22:06:25" Timing stopped at: 0.727 0 0.727 Error in checkEquals(length(list.files(ResDirAll)), 2) : Mean relative difference: 0.75 In addition: Warning message: In dir.create(ResultsPath, recursive = TRUE) : '/home/biocbuild/bbs-3.16-bioc/R/site-library/MOGAMUN/SampleResults//Experiment_2023-04-10' already exists done successfully. RUNIT TEST PROTOCOL -- Mon Apr 10 22:06:25 2023 *********************************************** Number of test functions: 4 Number of errors: 1 Number of failures: 2 1 Test Suite : MOGAMUN RUnit Tests - 4 test functions, 1 error, 2 failures ERROR in test.mogamun_load_data: Error in is.igraph(LoadedData$Multiplex[[i]]) : could not find function "is.igraph" 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: /home/biocbuild/bbs-3.16-bioc/R/site-library/MOGAMUN/tests/ --------------------------- Test file: /home/biocbuild/bbs-3.16-bioc/R/site-library/MOGAMUN/tests//test.mogamun.R test.mogamun_init: (13 checks) ... OK (0 seconds) test.mogamun_load_data: ERROR !! Error in is.igraph(LoadedData$Multiplex[[i]]) : could not find function "is.igraph" 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 3.247 0.202 3.434
MOGAMUN.Rcheck/MOGAMUN-Ex.timings
name | user | system | elapsed | |
mogamun_init | 0 | 0 | 0 | |
mogamun_load_data | 0.027 | 0.000 | 0.028 | |
mogamun_postprocess | 0.987 | 0.080 | 1.066 | |
mogamun_run | 0.818 | 0.000 | 0.817 | |