Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-08-21 11:41 -0400 (Wed, 21 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" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 1167/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MEAL 1.35.0 (landing page) Xavier EscribĂ Montagut
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the MEAL package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MEAL.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: MEAL |
Version: 1.35.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MEAL.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MEAL_1.35.0.tar.gz |
StartedAt: 2024-08-21 02:22:41 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 02:29:17 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 395.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MEAL.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MEAL.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MEAL_1.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/MEAL.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'MEAL/DESCRIPTION' ... OK * this is package 'MEAL' version '1.35.0' * 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 'MEAL' 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 ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... NOTE Problems with news in 'NEWS': Cannot process chunk/lines: MAJOR CHANGES Cannot process chunk/lines: o Substitute AnalysisResults and AnalysisRegionResults by ResultSet. Cannot process chunk/lines: o Substitute MethylationSet by GenomicRatioSet. Cannot process chunk/lines: USER-VISIBLE CHANGES Cannot process chunk/lines: o Rename analysis functions. Cannot process chunk/lines: o Create wrappers for each DMR methd Cannot process chunk/lines: NEW FEATURES Cannot process chunk/lines: o Add differences of variances analysis. Cannot process chunk/lines: o Add new plot to simultaneously show all results of the same region. Cannot process chunk/lines: NEW FEATURES Cannot process chunk/lines: o Add function to add matrices to MDS. Cannot process chunk/lines: o Add Methylation-SNPs correlation. Cannot process chunk/lines: USER-VISIBLE CHANGES Cannot process chunk/lines: o Move prepareMethylationSet from MultiDataSet to MEAL. Cannot process chunk/lines: o Defunct multiCorrMethExprs. Cannot process chunk/lines: BUGS FIXES Cannot process chunk/lines: o Solve a bug in DARegion when running DMRcate. * 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 ... WARNING '::' or ':::' import not declared from: 'sva' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE plotRegion: no visible global function definition for 'subsetByOverlaps' plotRegion: no visible global function definition for 'mcols<-' runRDA: no visible global function definition for 'rowData' runSVA: no visible global function definition for 'resid' runSVA: no visible global function definition for 'quantile' Undefined global functions or variables: mcols<- quantile resid rowData subsetByOverlaps Consider adding importFrom("stats", "quantile", "resid") to your NAMESPACE file. * 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 ... WARNING Undocumented arguments in Rd file 'getProbeResults.Rd' 'robust' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed exportResults 5.76 0.3 6.71 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.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 WARNINGs, 3 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/MEAL.Rcheck/00check.log' for details.
MEAL.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL MEAL ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'MEAL' ... ** using staged installation ** R ** 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 (MEAL)
MEAL.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 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. > library(testthat) > library(MEAL) Loading required package: Biobase 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: MultiDataSet Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) > > test_check("MEAL") [ FAIL 0 | WARN 6 | SKIP 0 | PASS 31 ] [ FAIL 0 | WARN 6 | SKIP 0 | PASS 31 ] > > proc.time() user system elapsed 30.82 2.01 33.17
MEAL.Rcheck/MEAL-Ex.timings
name | user | system | elapsed | |
exportResults | 5.76 | 0.30 | 6.71 | |
getGeneVals | 0 | 0 | 0 | |
plotFeature | 1.08 | 0.17 | 1.27 | |
plotRDA | 1.97 | 0.08 | 2.08 | |
runDiffMeanAnalysis | 0.58 | 0.09 | 0.67 | |
runDiffVarAnalysis | 1.03 | 0.14 | 1.17 | |
runPipeline | 0.86 | 0.11 | 0.97 | |
runRDA | 0.61 | 0.11 | 0.73 | |
runRegionAnalysis | 0.67 | 0.05 | 0.73 | |
topRDAhits | 0.79 | 0.06 | 0.87 | |