Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-08-16 11:44 -0400 (Fri, 16 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
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" | 4420 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
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 1215/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
methylInheritance 1.29.0 (landing page) Astrid Deschênes
| 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 methylInheritance package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methylInheritance.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: methylInheritance |
Version: 1.29.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:methylInheritance.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings methylInheritance_1.29.0.tar.gz |
StartedAt: 2024-08-15 22:24:31 -0400 (Thu, 15 Aug 2024) |
EndedAt: 2024-08-15 22:27:22 -0400 (Thu, 15 Aug 2024) |
EllapsedTime: 170.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: methylInheritance.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:methylInheritance.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings methylInheritance_1.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/methylInheritance.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 ‘methylInheritance/DESCRIPTION’ ... OK * this is package ‘methylInheritance’ version ‘1.29.0’ * 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 ‘methylInheritance’ 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) demoForTransgenerationalAnalysis.Rd:59-61: Lost braces 59 | \item \code{\link{runPermutation}} {for running a | ^ checkRd: (-1) demoForTransgenerationalAnalysis.Rd:62-63: Lost braces 62 | \item \code{\link{runObservation}} {for running an | ^ checkRd: (-1) isInterGenerationResults.Rd:21: Lost braces; missing escapes or markup? 21 | "_permutation_{permutationID}.RDS" extension.} | ^ checkRd: (-1) methylInheritance-package.Rd:19-21: Lost braces 19 | \item \code{\link{runPermutation}} {for running a | ^ checkRd: (-1) methylInheritance-package.Rd:22-23: Lost braces 22 | \item \code{\link{runObservation}} {for running an | ^ checkRd: (-1) methylInheritanceResults.Rd:293-294: Lost braces 293 | \item \code{\link{extractInfo}} {for extracting the | ^ checkRd: (-1) readInterGenerationResults.Rd:25: Lost braces; missing escapes or markup? 25 | "_permutation_{permutationID}.RDS" extension.} | ^ checkRd: (-1) runOnePermutationOnAllGenerations.Rd:144-173: Lost braces 144 | itemize{ | ^ checkRd: (-1) samplesForTransgenerationalAnalysis.Rd:48-50: Lost braces 48 | \item \code{\link{runPermutation}} {for running a | ^ checkRd: (-1) saveInterGenerationResults.Rd:27: Lost braces; missing escapes or markup? 27 | "_permutation_{permutationID}.RDS" extension.} | ^ * 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 runPermutation 28.014 0.419 28.436 runObservation 13.000 0.226 13.226 samplesForTransgenerationalAnalysis 9.098 0.249 9.368 * 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/methylInheritance.Rcheck/00check.log’ for details.
methylInheritance.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL methylInheritance ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘methylInheritance’ ... ** 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 (methylInheritance)
methylInheritance.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. > ## Run all tests presnt in the package > BiocGenerics:::testPackage("methylInheritance") 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, 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 Loading required package: GenomeInfoDb uniting... uniting... uniting... uniting... uniting... uniting... uniting... uniting... uniting... uniting... uniting... uniting... uniting... uniting... uniting... uniting... uniting... uniting... Permutation Analysis Number of Generations: 3 Number of Permutations: 20 Observation Results: SOURCE ELEMENT ANALYSIS TYPE RESULT 1 OBSERVATION SITES i2 HYPER1 4 2 OBSERVATION SITES i2 HYPER2 1 3 OBSERVATION SITES i2 HYPO1 2 4 OBSERVATION SITES i2 HYPO2 2 5 OBSERVATION SITES iAll HYPER 0 6 OBSERVATION SITES iAll HYPO 0 7 OBSERVATION TILES i2 HYPER1 1000 8 OBSERVATION TILES i2 HYPER2 0 9 OBSERVATION TILES i2 HYPO1 0 10 OBSERVATION TILES i2 HYPO2 0 11 OBSERVATION TILES iAll HYPER 0 12 OBSERVATION TILES iAll HYPO 0 RUNIT TEST PROTOCOL -- Thu Aug 15 22:27:18 2024 *********************************************** Number of test functions: 75 Number of errors: 0 Number of failures: 0 1 Test Suite : methylInheritance RUnit Tests - 75 test functions, 0 errors, 0 failures Number of test functions: 75 Number of errors: 0 Number of failures: 0 Warning messages: 1: Use of `formatForGraphDataFrame$RESULT` is discouraged. ℹ Use `RESULT` instead. 2: In max(i) : no non-missing arguments to max; returning -Inf 3: In max(i) : no non-missing arguments to max; returning -Inf > > proc.time() user system elapsed 11.493 0.223 11.736
methylInheritance.Rcheck/methylInheritance-Ex.timings
name | user | system | elapsed | |
calculateSignificantLevel | 0.005 | 0.001 | 0.006 | |
createDataStructure | 0.017 | 0.001 | 0.020 | |
createOutputDir | 0.000 | 0.000 | 0.001 | |
demoForTransgenerationalAnalysis | 1.430 | 0.025 | 1.457 | |
extractInfo | 0.046 | 0.001 | 0.047 | |
formatInputMethylData | 0.087 | 0.009 | 0.096 | |
getGRangesFromMethylDiff | 0.041 | 0.002 | 0.044 | |
interGeneration | 0.270 | 0.001 | 0.271 | |
isInterGenerationResults | 0 | 0 | 0 | |
loadAllRDSResults | 0.046 | 0.001 | 0.047 | |
loadConvergenceData | 0.053 | 0.000 | 0.054 | |
mergePermutationAndObservation | 0.000 | 0.000 | 0.001 | |
methylInheritanceAllResults | 0.001 | 0.001 | 0.002 | |
methylInheritanceResults | 0.003 | 0.000 | 0.004 | |
plotConvergenceGraph | 0.155 | 0.004 | 0.158 | |
plotGraph | 0.114 | 0.001 | 0.115 | |
readInterGenerationResults | 0.010 | 0.001 | 0.011 | |
runObservation | 13.000 | 0.226 | 13.226 | |
runOnePermutationOnAllGenerations | 3.231 | 0.087 | 3.320 | |
runPermutation | 28.014 | 0.419 | 28.436 | |
samplesForTransgenerationalAnalysis | 9.098 | 0.249 | 9.368 | |
saveInterGenerationResults | 0.239 | 0.002 | 0.241 | |
validateExtractInfo | 0.001 | 0.001 | 0.001 | |
validateLoadConvergenceData | 0 | 0 | 0 | |
validateMergePermutationAndObservation | 0.001 | 0.000 | 0.001 | |
validateRunObservation | 0.052 | 0.003 | 0.055 | |
validateRunPermutation | 0.053 | 0.004 | 0.058 | |