Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-09-25 11:39 -0400 (Thu, 25 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4827 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4581 |
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 1255/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
methylInheritance 1.32.0 (landing page) Astrid Deschênes
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / 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: 1.32.0 |
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_1.32.0.tar.gz |
StartedAt: 2025-09-23 06:00:19 -0400 (Tue, 23 Sep 2025) |
EndedAt: 2025-09-23 06:20:29 -0400 (Tue, 23 Sep 2025) |
EllapsedTime: 1209.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: methylInheritance.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/methylInheritance.Rcheck’ * using R version 4.5.1 RC (2025-06-05 r88288) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘methylInheritance/DESCRIPTION’ ... OK * this is package ‘methylInheritance’ version ‘1.32.0’ * 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 275.094 1.590 299.583 runObservation 127.569 0.934 130.246 samplesForTransgenerationalAnalysis 86.752 0.908 93.212 runOnePermutationOnAllGenerations 31.179 0.283 32.541 demoForTransgenerationalAnalysis 13.604 0.319 14.040 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ ERROR Running the tests in ‘tests/runTests.R’ failed. Last 13 lines of output: Test files with failing tests test_methylInheritanceMethods.R test.plotConvergenceGraph_good_01 Error in BiocGenerics:::testPackage("methylInheritance") : unit tests failed for package methylInheritance In addition: 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 Execution halted * 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 ERROR, 1 NOTE See ‘/Users/biocbuild/bbs-3.21-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/4.5-x86_64/Resources/library’ * installing *source* package ‘methylInheritance’ ... ** this is package ‘methylInheritance’ version ‘1.32.0’ ** 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.fail
R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-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 Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, 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... Timing stopped at: 0.87 0.021 0.939 Error in S7::prop(x, "meta")[[i]] : subscript out of bounds In addition: Warning message: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. ℹ The deprecated feature was likely used in the methylInheritance package. Please report the issue at <https://github.com/adeschen/methylInheritance/issues>. 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 -- Tue Sep 23 06:20:12 2025 *********************************************** Number of test functions: 75 Number of errors: 1 Number of failures: 0 1 Test Suite : methylInheritance RUnit Tests - 75 test functions, 1 error, 0 failures ERROR in test.plotConvergenceGraph_good_01: Error in S7::prop(x, "meta")[[i]] : subscript out of bounds Test files with failing tests test_methylInheritanceMethods.R test.plotConvergenceGraph_good_01 Error in BiocGenerics:::testPackage("methylInheritance") : unit tests failed for package methylInheritance In addition: 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 Execution halted
methylInheritance.Rcheck/methylInheritance-Ex.timings
name | user | system | elapsed | |
calculateSignificantLevel | 0.035 | 0.004 | 0.041 | |
createDataStructure | 0.133 | 0.003 | 0.138 | |
createOutputDir | 0.001 | 0.002 | 0.003 | |
demoForTransgenerationalAnalysis | 13.604 | 0.319 | 14.040 | |
extractInfo | 0.432 | 0.005 | 0.443 | |
formatInputMethylData | 0.421 | 0.074 | 0.499 | |
getGRangesFromMethylDiff | 0.136 | 0.005 | 0.143 | |
interGeneration | 3.493 | 0.046 | 3.569 | |
isInterGenerationResults | 0.002 | 0.001 | 0.003 | |
loadAllRDSResults | 0.434 | 0.006 | 0.440 | |
loadConvergenceData | 0.501 | 0.004 | 0.508 | |
mergePermutationAndObservation | 0.005 | 0.002 | 0.007 | |
methylInheritanceAllResults | 0.01 | 0.01 | 0.02 | |
methylInheritanceResults | 0.031 | 0.011 | 0.042 | |
plotConvergenceGraph | 1.642 | 0.016 | 1.668 | |
plotGraph | 1.182 | 0.016 | 1.210 | |
readInterGenerationResults | 0.087 | 0.005 | 0.093 | |
runObservation | 127.569 | 0.934 | 130.246 | |
runOnePermutationOnAllGenerations | 31.179 | 0.283 | 32.541 | |
runPermutation | 275.094 | 1.590 | 299.583 | |
samplesForTransgenerationalAnalysis | 86.752 | 0.908 | 93.212 | |
saveInterGenerationResults | 2.325 | 0.020 | 2.662 | |
validateExtractInfo | 0.003 | 0.010 | 0.024 | |
validateLoadConvergenceData | 0.002 | 0.001 | 0.010 | |
validateMergePermutationAndObservation | 0.002 | 0.002 | 0.003 | |
validateRunObservation | 0.155 | 0.012 | 0.187 | |
validateRunPermutation | 0.156 | 0.013 | 0.188 | |