Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1207/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
metagenomeSeq 1.48.0 (landing page) Joseph N. Paulson
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | 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: 1.48.0 |
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_1.48.0.tar.gz |
StartedAt: 2024-12-21 00:33:43 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 00:37:43 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 239.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: metagenomeSeq.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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_1.48.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/metagenomeSeq.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘metagenomeSeq/DESCRIPTION’ ... OK * this is package ‘metagenomeSeq’ version ‘1.48.0’ * 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 13.43 1.128 14.571 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ── Failure ('test-fitZig.R:67:3'): `fitZig` function treats a matrix the same ── `fit` not equal to `fit2`. Component "eb": Component "df.prior": Mean relative difference: 0.01522971 Component "eb": Component "s2.prior": Mean relative difference: 0.0208853 Component "eb": Component "var.prior": Mean relative difference: 0.01489299 Component "eb": Component "s2.post": Mean relative difference: 0.002818974 Component "eb": Component "t": Mean relative difference: 0.001476944 Component "eb": Component "df.total": Mean relative difference: 0.002226407 Component "eb": Component "p.value": Mean relative difference: 0.001045802 Component "eb": Component "lods": Mean relative difference: 0.002124969 Component "eb": Component "F": Mean relative difference: 0.002818882 [ FAIL 2 | WARN 6 | SKIP 0 | PASS 13 ] Error: Test failures 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 See ‘/Users/biocbuild/bbs-3.20-bioc/meat/metagenomeSeq.Rcheck/00check.log’ for details.
metagenomeSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL metagenomeSeq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘metagenomeSeq’ ... ** 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.fail
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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. > library("testthat") > packageVersion("metagenomeSeq") [1] '1.48.0' > # 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 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, saveRDS, 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: limma Attaching package: 'limma' The following object is masked from 'package:BiocGenerics': plotMA Loading required package: glmnet Loading required package: Matrix Loaded glmnet 4.1-8 Loading required package: RColorBrewer [ FAIL 2 | WARN 6 | SKIP 0 | PASS 13 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-fitZig.R:35:3'): `fitZig` function provides expected values prior to split ── `fit` not equal to `fit2`. Component "eb": Component "df.prior": Mean relative difference: 0.01522971 Component "eb": Component "s2.prior": Mean relative difference: 0.0208853 Component "eb": Component "var.prior": Mean relative difference: 0.01489299 Component "eb": Component "s2.post": Mean relative difference: 0.002818974 Component "eb": Component "t": Mean relative difference: 0.001476944 Component "eb": Component "df.total": Mean relative difference: 0.002226407 Component "eb": Component "p.value": Mean relative difference: 0.001045802 Component "eb": Component "lods": Mean relative difference: 0.002124969 Component "eb": Component "F": Mean relative difference: 0.002818882 ── Failure ('test-fitZig.R:67:3'): `fitZig` function treats a matrix the same ── `fit` not equal to `fit2`. Component "eb": Component "df.prior": Mean relative difference: 0.01522971 Component "eb": Component "s2.prior": Mean relative difference: 0.0208853 Component "eb": Component "var.prior": Mean relative difference: 0.01489299 Component "eb": Component "s2.post": Mean relative difference: 0.002818974 Component "eb": Component "t": Mean relative difference: 0.001476944 Component "eb": Component "df.total": Mean relative difference: 0.002226407 Component "eb": Component "p.value": Mean relative difference: 0.001045802 Component "eb": Component "lods": Mean relative difference: 0.002124969 Component "eb": Component "F": Mean relative difference: 0.002818882 [ FAIL 2 | WARN 6 | SKIP 0 | PASS 13 ] Error: Test failures Execution halted
metagenomeSeq.Rcheck/metagenomeSeq-Ex.timings
name | user | system | elapsed | |
MRcoefs | 1.255 | 0.045 | 1.299 | |
MRcounts | 0.586 | 0.019 | 0.605 | |
MRexperiment-class | 0 | 0 | 0 | |
MRfulltable | 0.988 | 0.033 | 3.756 | |
MRtable | 0.586 | 0.015 | 0.610 | |
aggregateBySample | 0.175 | 0.008 | 0.182 | |
aggregateByTaxonomy | 0.199 | 0.012 | 0.210 | |
biom2MRexperiment | 0.238 | 0.015 | 0.256 | |
calcNormFactors | 0.702 | 0.089 | 0.792 | |
correctIndices | 0.141 | 0.012 | 0.153 | |
correlationTest | 0.290 | 0.021 | 0.311 | |
cumNorm | 0.473 | 0.092 | 0.565 | |
cumNormMat | 0.530 | 0.088 | 0.618 | |
cumNormStat | 0.758 | 0.064 | 0.822 | |
cumNormStatFast | 0.344 | 0.013 | 0.357 | |
expSummary | 0.135 | 0.013 | 0.147 | |
exportMat | 1.340 | 2.371 | 3.715 | |
exportStats | 0.434 | 0.023 | 0.458 | |
extractMR | 1.187 | 1.000 | 2.199 | |
filterData | 0.205 | 0.025 | 0.231 | |
fitDO | 0.472 | 0.028 | 3.050 | |
fitFeatureModel | 1.150 | 0.076 | 1.227 | |
fitLogNormal | 1.928 | 0.178 | 2.106 | |
fitMultipleTimeSeries | 2.199 | 0.241 | 2.441 | |
fitPA | 0.377 | 0.029 | 2.893 | |
fitSSTimeSeries | 0.524 | 0.029 | 0.557 | |
fitTimeSeries | 0.531 | 0.044 | 0.574 | |
fitZig | 1.651 | 0.112 | 1.763 | |
libSize-set | 0.343 | 0.011 | 0.355 | |
libSize | 0.404 | 0.022 | 0.426 | |
loadBiom | 0.037 | 0.001 | 0.039 | |
loadMeta | 0.019 | 0.001 | 0.021 | |
loadMetaQ | 0 | 0 | 0 | |
loadPhenoData | 0.008 | 0.001 | 0.009 | |
makeLabels | 0 | 0 | 0 | |
mergeMRexperiments | 1.798 | 0.173 | 1.981 | |
newMRexperiment | 0.028 | 0.000 | 0.028 | |
normFactors-set | 0.374 | 0.032 | 0.406 | |
normFactors | 0.314 | 0.028 | 0.343 | |
plotBubble | 0.339 | 0.030 | 2.885 | |
plotClassTimeSeries | 1.337 | 0.183 | 1.522 | |
plotCorr | 0.503 | 0.037 | 0.540 | |
plotFeature | 0.220 | 0.018 | 0.238 | |
plotGenus | 0.175 | 0.024 | 0.199 | |
plotMRheatmap | 1.899 | 0.107 | 2.011 | |
plotOTU | 0.189 | 0.020 | 0.211 | |
plotOrd | 0.268 | 0.021 | 0.288 | |
plotRare | 0.169 | 0.020 | 0.190 | |
plotTimeSeries | 1.305 | 0.195 | 1.501 | |
posteriorProbs | 1.635 | 0.209 | 1.875 | |
returnAppropriateObj | 0.387 | 0.016 | 0.403 | |
ssFit | 0 | 0 | 0 | |
ssIntervalCandidate | 0 | 0 | 0 | |
ssPerm | 0 | 0 | 0 | |
ssPermAnalysis | 0 | 0 | 0 | |
trapz | 0.001 | 0.001 | 0.001 | |
ts2MRexperiment | 1.977 | 0.283 | 2.263 | |
uniqueFeatures | 0.147 | 0.014 | 0.162 | |
wrenchNorm | 13.430 | 1.128 | 14.571 | |
zigControl | 0 | 0 | 0 | |