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 12:04 -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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:metagenomeSeq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings metagenomeSeq_1.48.0.tar.gz |
StartedAt: 2024-12-20 02:22:47 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 02:30:17 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 449.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: metagenomeSeq.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:metagenomeSeq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings metagenomeSeq_1.48.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/metagenomeSeq.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘metagenomeSeq/DESCRIPTION’ ... OK * this is package ‘metagenomeSeq’ version ‘1.48.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 loading without being on the library search path ... 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 wrenchNorm 12.813 0.19 13.004 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR See ‘/home/biocbuild/bbs-3.20-bioc/meat/metagenomeSeq.Rcheck/00check.log’ for details.
metagenomeSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL metagenomeSeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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: x86_64-pc-linux-gnu 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 | 0.918 | 0.069 | 0.987 | |
MRcounts | 0.390 | 0.024 | 0.415 | |
MRexperiment-class | 0 | 0 | 0 | |
MRfulltable | 0.839 | 0.032 | 4.263 | |
MRtable | 0.822 | 0.006 | 0.829 | |
aggregateBySample | 0.134 | 0.007 | 0.142 | |
aggregateByTaxonomy | 0.145 | 0.009 | 0.155 | |
biom2MRexperiment | 0.179 | 0.003 | 0.184 | |
calcNormFactors | 0.540 | 0.016 | 0.556 | |
correctIndices | 0.091 | 0.012 | 0.105 | |
correlationTest | 0.203 | 0.013 | 0.216 | |
cumNorm | 0.381 | 0.011 | 0.393 | |
cumNormMat | 0.416 | 0.017 | 0.433 | |
cumNormStat | 0.566 | 0.004 | 0.570 | |
cumNormStatFast | 0.285 | 0.007 | 0.292 | |
expSummary | 0.089 | 0.010 | 0.099 | |
exportMat | 0.784 | 0.329 | 1.113 | |
exportStats | 0.334 | 0.001 | 0.335 | |
extractMR | 0.518 | 0.164 | 0.682 | |
filterData | 0.142 | 0.006 | 0.148 | |
fitDO | 0.305 | 0.001 | 2.276 | |
fitFeatureModel | 0.854 | 0.001 | 0.855 | |
fitLogNormal | 1.458 | 0.027 | 1.485 | |
fitMultipleTimeSeries | 1.544 | 0.005 | 1.548 | |
fitPA | 0.305 | 0.011 | 2.211 | |
fitSSTimeSeries | 0.373 | 0.010 | 0.383 | |
fitTimeSeries | 0.378 | 0.006 | 0.384 | |
fitZig | 1.328 | 0.012 | 1.340 | |
libSize-set | 0.262 | 0.001 | 0.263 | |
libSize | 0.245 | 0.000 | 0.245 | |
loadBiom | 0.032 | 0.000 | 0.032 | |
loadMeta | 0.015 | 0.000 | 0.015 | |
loadMetaQ | 0 | 0 | 0 | |
loadPhenoData | 0.006 | 0.000 | 0.007 | |
makeLabels | 0.000 | 0.000 | 0.001 | |
mergeMRexperiments | 1.263 | 0.213 | 1.476 | |
newMRexperiment | 0.024 | 0.000 | 0.024 | |
normFactors-set | 0.265 | 0.011 | 0.275 | |
normFactors | 0.241 | 0.010 | 0.250 | |
plotBubble | 0.246 | 0.014 | 2.165 | |
plotClassTimeSeries | 0.953 | 0.018 | 0.972 | |
plotCorr | 0.392 | 0.008 | 0.401 | |
plotFeature | 0.143 | 0.009 | 0.152 | |
plotGenus | 0.127 | 0.015 | 0.142 | |
plotMRheatmap | 1.573 | 0.036 | 1.609 | |
plotOTU | 0.133 | 0.009 | 0.143 | |
plotOrd | 0.201 | 0.007 | 0.208 | |
plotRare | 0.110 | 0.014 | 0.124 | |
plotTimeSeries | 0.927 | 0.004 | 0.930 | |
posteriorProbs | 1.486 | 0.042 | 1.527 | |
returnAppropriateObj | 0.228 | 0.016 | 0.244 | |
ssFit | 0 | 0 | 0 | |
ssIntervalCandidate | 0 | 0 | 0 | |
ssPerm | 0 | 0 | 0 | |
ssPermAnalysis | 0.001 | 0.000 | 0.000 | |
trapz | 0 | 0 | 0 | |
ts2MRexperiment | 1.420 | 0.008 | 1.428 | |
uniqueFeatures | 0.108 | 0.002 | 0.110 | |
wrenchNorm | 12.813 | 0.190 | 13.004 | |
zigControl | 0.001 | 0.000 | 0.000 | |