Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-10-19 13:21:48 -0400 (Wed, 19 Oct 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
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 methylInheritance package: - Please 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 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 1151/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
methylInheritance 1.20.0 (landing page) Astrid DeschĂȘnes
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: methylInheritance |
Version: 1.20.0 |
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:methylInheritance.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings methylInheritance_1.20.0.tar.gz |
StartedAt: 2022-10-19 01:46:53 -0400 (Wed, 19 Oct 2022) |
EndedAt: 2022-10-19 01:56:08 -0400 (Wed, 19 Oct 2022) |
EllapsedTime: 555.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: methylInheritance.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:methylInheritance.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings methylInheritance_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/methylInheritance.Rcheck' * using R version 4.2.1 (2022-06-23 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'methylInheritance/DESCRIPTION' ... OK * this is package 'methylInheritance' version '1.20.0' * 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 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 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 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 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 122.49 1.47 124.02 runObservation 57.40 1.02 58.41 samplesForTransgenerationalAnalysis 39.26 0.48 39.92 runOnePermutationOnAllGenerations 13.22 0.42 13.65 demoForTransgenerationalAnalysis 5.63 0.18 5.81 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'runTests.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
methylInheritance.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL methylInheritance ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.15-bioc/R/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 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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. > ## 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, 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, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' 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... 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 -- Wed Oct 19 01:55:55 2022 *********************************************** 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. 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 41.51 1.26 43.51
methylInheritance.Rcheck/methylInheritance-Ex.timings
name | user | system | elapsed | |
calculateSignificantLevel | 0.02 | 0.00 | 0.01 | |
createDataStructure | 0.07 | 0.02 | 0.10 | |
createOutputDir | 0 | 0 | 0 | |
demoForTransgenerationalAnalysis | 5.63 | 0.18 | 5.81 | |
extractInfo | 0.15 | 0.00 | 0.16 | |
formatInputMethylData | 0.22 | 0.05 | 0.26 | |
getGRangesFromMethylDiff | 0.09 | 0.00 | 0.09 | |
interGeneration | 1.02 | 0.00 | 1.02 | |
isInterGenerationResults | 0 | 0 | 0 | |
loadAllRDSResults | 0.27 | 0.00 | 0.27 | |
loadConvergenceData | 0.29 | 0.00 | 0.31 | |
mergePermutationAndObservation | 0 | 0 | 0 | |
methylInheritanceAllResults | 0 | 0 | 0 | |
methylInheritanceResults | 0.03 | 0.00 | 0.04 | |
plotConvergenceGraph | 0.69 | 0.03 | 0.71 | |
plotGraph | 0.38 | 0.00 | 0.38 | |
readInterGenerationResults | 0.03 | 0.00 | 0.03 | |
runObservation | 57.40 | 1.02 | 58.41 | |
runOnePermutationOnAllGenerations | 13.22 | 0.42 | 13.65 | |
runPermutation | 122.49 | 1.47 | 124.02 | |
samplesForTransgenerationalAnalysis | 39.26 | 0.48 | 39.92 | |
saveInterGenerationResults | 0.92 | 0.02 | 0.97 | |
validateExtractInfo | 0.02 | 0.00 | 0.02 | |
validateLoadConvergenceData | 0 | 0 | 0 | |
validateMergePermutationAndObservation | 0 | 0 | 0 | |
validateRunObservation | 0.12 | 0.00 | 0.14 | |
validateRunPermutation | 0.09 | 0.00 | 0.09 | |