Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1218/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
methInheritSim 1.28.0 (landing page) Pascal Belleau
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the methInheritSim package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methInheritSim.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: methInheritSim |
Version: 1.28.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:methInheritSim.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings methInheritSim_1.28.0.tar.gz |
StartedAt: 2024-12-20 03:17:55 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 03:23:55 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 360.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: methInheritSim.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:methInheritSim.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings methInheritSim_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/methInheritSim.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'methInheritSim/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'methInheritSim' version '1.28.0' * 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 ... 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 whether package 'methInheritSim' 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 ... NOTE checkRd: (-1) dataSimExample.Rd:85-86: Lost braces 85 | \item \code{\link{runSim}} {for running a | ^ checkRd: (-1) methInheritSim-package.Rd:14-15: Lost braces 14 | \item \code{\link{runSim}} { for simulating a multigeneration methylation | ^ checkRd: (-1) samplesForChrSynthetic.Rd:59-60: Lost braces 59 | \item \code{\link{runSim}} {for running a | ^ * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed samplesForChrSynthetic 14.05 0.11 14.17 runSim 8.06 0.09 8.16 * 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: 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/methInheritSim.Rcheck/00check.log' for details.
methInheritSim.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL methInheritSim ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'methInheritSim' ... ** 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 (methInheritSim)
methInheritSim.Rcheck/tests/runTests.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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. > ## Run all tests presnt in the package > BiocGenerics:::testPackage("methInheritSim") Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb uniting... two groups detected: will calculate methylation difference as the difference of treatment (group: 1) - control (group: 0) uniting... two groups detected: will calculate methylation difference as the difference of treatment (group: 1) - control (group: 0) uniting... two groups detected: will calculate methylation difference as the difference of treatment (group: 1) - control (group: 0) uniting... two groups detected: will calculate methylation difference as the difference of treatment (group: 1) - control (group: 0) uniting... two groups detected: will calculate methylation difference as the difference of treatment (group: 1) - control (group: 0) uniting... two groups detected: will calculate methylation difference as the difference of treatment (group: 1) - control (group: 0) uniting... two groups detected: will calculate methylation difference as the difference of treatment (group: 1) - control (group: 0) uniting... two groups detected: will calculate methylation difference as the difference of treatment (group: 1) - control (group: 0) uniting... two groups detected: will calculate methylation difference as the difference of treatment (group: 1) - control (group: 0) uniting... two groups detected: will calculate methylation difference as the difference of treatment (group: 1) - control (group: 0) uniting... two groups detected: will calculate methylation difference as the difference of treatment (group: 1) - control (group: 0) RUNIT TEST PROTOCOL -- Fri Dec 20 03:23:43 2024 *********************************************** Number of test functions: 104 Number of errors: 0 Number of failures: 0 1 Test Suite : methInheritSim RUnit Tests - 104 test functions, 0 errors, 0 failures Number of test functions: 104 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 34.26 1.35 35.64
methInheritSim.Rcheck/methInheritSim-Ex.timings
name | user | system | elapsed | |
calculateNbDiffCase | 0 | 0 | 0 | |
createSampleID | 0 | 0 | 0 | |
dataSimExample | 0.10 | 0.04 | 0.14 | |
estBetaAlpha | 0 | 0 | 0 | |
estBetaBeta | 0 | 0 | 0 | |
fixSeed | 0 | 0 | 0 | |
getDiffCase | 0 | 0 | 0 | |
getDiffMeth | 0.15 | 0.03 | 0.17 | |
getSim | 0.70 | 0.03 | 0.74 | |
getSyntheticChr | 0.25 | 0.03 | 0.28 | |
runOnEachSynCHR | 2.31 | 0.11 | 2.43 | |
runSim | 8.06 | 0.09 | 8.16 | |
samplesForChrSynthetic | 14.05 | 0.11 | 14.17 | |
saveData | 0 | 0 | 0 | |
simEachGeneration | 0.63 | 0.02 | 0.64 | |
simInheritance | 1.21 | 0.01 | 1.24 | |
testIfAlreadyDone | 0 | 0 | 0 | |
validateRunSimDoubleParameters | 0 | 0 | 0 | |
validateRunSimIntegerParameters | 0 | 0 | 0 | |
validateRunSimLogicalParameters | 0.04 | 0.02 | 0.04 | |
validateRunSimOtherParameters | 0.03 | 0.00 | 0.04 | |
validateRunSimParameters | 0.03 | 0.00 | 0.04 | |