Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-21 11:41 -0400 (Thu, 21 Aug 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" | 4824 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 1233/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
metagenomeSeq 1.50.0 (landing page) Joseph N. Paulson
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | 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 | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the metagenomeSeq package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metagenomeSeq.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: metagenomeSeq |
Version: 1.50.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metagenomeSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metagenomeSeq_1.50.0.tar.gz |
StartedAt: 2025-08-20 02:34:59 -0400 (Wed, 20 Aug 2025) |
EndedAt: 2025-08-20 02:39:05 -0400 (Wed, 20 Aug 2025) |
EllapsedTime: 245.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: metagenomeSeq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metagenomeSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metagenomeSeq_1.50.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/metagenomeSeq.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘metagenomeSeq/DESCRIPTION’ ... OK * this is package ‘metagenomeSeq’ version ‘1.50.0’ * 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 ‘metagenomeSeq’ 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed wrenchNorm 14.605 1.211 15.837 MRfulltable 1.076 0.043 5.896 * 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: OK
metagenomeSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL metagenomeSeq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘metagenomeSeq’ ... ** this is package ‘metagenomeSeq’ version ‘1.50.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for ‘MRihw’ with signature ‘"fitFeatureModelResults"’: no definition for class “fitFeatureModelResults” in method for ‘MRihw’ with signature ‘"fitZigResults"’: no definition for class “fitZigResults” ** 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 (metagenomeSeq)
metagenomeSeq.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" Copyright (C) 2025 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. > library("testthat") > packageVersion("metagenomeSeq") [1] '1.50.0' > # As suggested for opt-out option on testing by users, > # recommended by CRAN: http://adv-r.had.co.nz/Testing.html > # Previously, best practice was to put all test files in inst/tests > # and ensure that R CMD check ran them by putting the following code in tests/test-all.R: > # >library(testthat) > # >library(yourpackage) > # >test_package("yourpackage") > # Now, recommended practice is to put your tests in tests/testthat, > # and ensure R CMD check runs them by putting the following code in tests/test-all.R: > # >library(testthat) > # >test_check("yourpackage") > # The advantage of this new structure is that the user has control over whether or not tests are installed using the –install-tests parameter to > # R CMD install, or INSTALL_opts = c(“–install-tests”) argument to install.packages(). I’m not sure why you wouldn’t want to install the tests, > # but now you have the flexibility as requested by CRAN maintainers. > test_check("metagenomeSeq") Loading required package: metagenomeSeq Loading required package: Biobase 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: limma Attaching package: 'limma' The following object is masked from 'package:BiocGenerics': plotMA Loading required package: glmnet Loading required package: Matrix Loaded glmnet 4.1-10 Loading required package: RColorBrewer [ FAIL 0 | WARN 6 | SKIP 0 | PASS 15 ] [ FAIL 0 | WARN 6 | SKIP 0 | PASS 15 ] > > proc.time() user system elapsed 89.361 6.898 96.984
metagenomeSeq.Rcheck/metagenomeSeq-Ex.timings
name | user | system | elapsed | |
MRcoefs | 1.207 | 0.060 | 1.268 | |
MRcounts | 0.583 | 0.024 | 0.638 | |
MRexperiment-class | 0.000 | 0.000 | 0.001 | |
MRfulltable | 1.076 | 0.043 | 5.896 | |
MRtable | 1.005 | 0.037 | 1.042 | |
aggregateBySample | 0.166 | 0.010 | 0.177 | |
aggregateByTaxonomy | 0.180 | 0.016 | 0.195 | |
biom2MRexperiment | 0.229 | 0.015 | 0.246 | |
calcNormFactors | 0.686 | 0.092 | 0.777 | |
correctIndices | 0.127 | 0.040 | 0.166 | |
correlationTest | 0.250 | 0.022 | 0.273 | |
cumNorm | 0.449 | 0.118 | 0.568 | |
cumNormMat | 0.504 | 0.089 | 0.594 | |
cumNormStat | 0.730 | 0.073 | 0.804 | |
cumNormStatFast | 0.311 | 0.046 | 0.357 | |
expSummary | 0.122 | 0.017 | 0.139 | |
exportMat | 1.286 | 2.474 | 3.805 | |
exportStats | 0.449 | 0.034 | 0.484 | |
extractMR | 1.118 | 1.032 | 2.170 | |
filterData | 0.179 | 0.023 | 0.203 | |
fitDO | 0.747 | 0.031 | 3.442 | |
fitFeatureModel | 0.802 | 0.060 | 0.864 | |
fitLogNormal | 1.823 | 0.227 | 2.050 | |
fitMultipleTimeSeries | 1.951 | 0.282 | 2.238 | |
fitPA | 0.446 | 0.029 | 3.027 | |
fitSSTimeSeries | 0.724 | 0.049 | 0.772 | |
fitTimeSeries | 0.495 | 0.099 | 0.593 | |
fitZig | 1.617 | 0.249 | 1.868 | |
libSize-set | 0.359 | 0.018 | 0.378 | |
libSize | 0.325 | 0.021 | 0.346 | |
loadBiom | 0.036 | 0.001 | 0.037 | |
loadMeta | 0.020 | 0.001 | 0.022 | |
loadMetaQ | 0.000 | 0.000 | 0.001 | |
loadPhenoData | 0.008 | 0.001 | 0.009 | |
makeLabels | 0.000 | 0.000 | 0.001 | |
mergeMRexperiments | 1.731 | 0.204 | 1.938 | |
newMRexperiment | 0.028 | 0.000 | 0.028 | |
normFactors-set | 0.388 | 0.029 | 0.416 | |
normFactors | 0.352 | 0.019 | 0.372 | |
plotBubble | 0.306 | 0.039 | 2.915 | |
plotClassTimeSeries | 1.295 | 0.215 | 1.512 | |
plotCorr | 0.480 | 0.038 | 0.518 | |
plotFeature | 0.200 | 0.027 | 0.227 | |
plotGenus | 0.166 | 0.036 | 0.202 | |
plotMRheatmap | 1.824 | 0.124 | 1.950 | |
plotOTU | 0.167 | 0.032 | 0.200 | |
plotOrd | 0.256 | 0.028 | 0.285 | |
plotRare | 0.160 | 0.023 | 0.183 | |
plotTimeSeries | 1.226 | 0.136 | 1.361 | |
posteriorProbs | 1.885 | 0.228 | 2.115 | |
returnAppropriateObj | 0.328 | 0.017 | 0.345 | |
ssFit | 0 | 0 | 0 | |
ssIntervalCandidate | 0.000 | 0.001 | 0.000 | |
ssPerm | 0 | 0 | 0 | |
ssPermAnalysis | 0.000 | 0.001 | 0.000 | |
trapz | 0 | 0 | 0 | |
ts2MRexperiment | 1.905 | 0.246 | 2.154 | |
uniqueFeatures | 0.126 | 0.018 | 0.145 | |
wrenchNorm | 14.605 | 1.211 | 15.837 | |
zigControl | 0.000 | 0.000 | 0.001 | |