Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-20 12:03 -0400 (Sat, 20 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4814 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4603 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4547 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4553 |
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 1278/2333 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
miaViz 1.17.9 (landing page) Tuomas Borman
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the miaViz package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/miaViz.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: miaViz |
Version: 1.17.9 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:miaViz.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings miaViz_1.17.9.tar.gz |
StartedAt: 2025-09-20 01:39:05 -0400 (Sat, 20 Sep 2025) |
EndedAt: 2025-09-20 01:48:07 -0400 (Sat, 20 Sep 2025) |
EllapsedTime: 542.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: miaViz.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:miaViz.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings miaViz_1.17.9.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/miaViz.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘miaViz/DESCRIPTION’ ... OK * this is package ‘miaViz’ version ‘1.17.9’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘miaViz’ 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 ... NOTE .apply_beeswarm: no visible binding for global variable ‘.row_id’ .apply_vipor_spread: no visible binding for global variable ‘.row_id’ Undefined global functions or variables: .row_id * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: plotColTile.Rd: retrieveFeatureInfo, retrieveCellInfo plotGraph.Rd: ggtree plotPrevalence.Rd: agglomerate-methods plotTree.Rd: ggtree Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 ... ERROR Running examples in ‘miaViz-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: plotLoadings > ### Title: Plot feature loadings for TreeSummarizedExperiment objects or > ### feature loadings numeric matrix. > ### Aliases: plotLoadings plotLoadings,TreeSummarizedExperiment-method > ### plotLoadings,SingleCellExperiment-method plotLoadings,matrix-method > > ### ** Examples > > > library(mia) > library(scater) Loading required package: scuttle > data("GlobalPatterns", package = "mia") > tse <- GlobalPatterns > > # Calculate PCA > tse <- agglomerateByPrevalence(tse, rank="Phylum", update.tree = TRUE) > tse <- transformAssay(tse, method = "clr", pseudocount = 1) > tse <- runPCA(tse, ncomponents = 5, assay.type = "clr") > > # Plotting feature loadings with tree > plotLoadings(tse, dimred = "PCA", layout = "heatmap", add.tree = TRUE) |> + # Remove this line to see messages + suppressMessages() Error: <ggtree> object properties are invalid: - @mapping must be <ggplot2::mapping>, not S3<data.frame> Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotAbundance 19.617 0.533 20.152 plotDMN 18.554 0.062 18.618 plotBoxplot 5.633 0.033 5.666 * 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: 9. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 10. └─base_ops[[.Generic]](e1, e2) 11. ├─S7::S7_dispatch() 12. └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...) 13. └─ggplot2:::add_ggplot(e1, e2, e2name) 14. ├─ggplot2::ggplot_add(object, p, objectname) 15. └─ggnewscale:::ggplot_add.new_aes(object, p, objectname) 16. ├─base::`$<-`(`*tmp*`, "mapping", value = `<df[,4]>`) 17. └─ggplot2:::`$<-.ggplot2::gg`(`*tmp*`, "mapping", value = `<df[,4]>`) 18. └─S7::`props<-`(`*tmp*`, value = `[[<-`(S7::props(x), i, value)) 19. └─S7::validate(object) [ FAIL 1 | WARN 3 | SKIP 2 | PASS 214 ] 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: 2 ERRORs, 2 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/miaViz.Rcheck/00check.log’ for details.
miaViz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL miaViz ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘miaViz’ ... ** this is package ‘miaViz’ version ‘1.17.9’ ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (miaViz)
miaViz.Rcheck/tests/testthat.Rout.fail
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" Copyright (C) 2025 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) > library(miaViz) Loading required package: ggplot2 Loading required package: ggraph Loading required package: mia Loading required package: MultiAssayExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 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 Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: Seqinfo Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Loading required package: SingleCellExperiment Loading required package: TreeSummarizedExperiment Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit This is mia version 1.17.9 - Online documentation and vignettes: https://microbiome.github.io/mia/ - Online book 'Orchestrating Microbiome Analysis (OMA)': https://microbiome.github.io/OMA/docs/devel/ Attaching package: 'miaViz' The following object is masked from 'package:mia': plotNMDS > > test_check("miaViz") initial value 0.000000 final value 0.000000 converged [ FAIL 1 | WARN 3 | SKIP 2 | PASS 214 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • {miaTime} is not installed (2): 'test-2plotSeries.R:5:5', 'test-plotMediation.R:3:5' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-plotLoadings.R:34:3'): plot Loadings ─────────────────────────── Error: <ggtree> object properties are invalid: - @mapping must be <ggplot2::mapping>, not S3<data.frame> Backtrace: ▆ 1. ├─miaViz::plotLoadings(...) at test-plotLoadings.R:34:3 2. └─miaViz::plotLoadings(...) 3. └─miaViz (local) .local(x, ...) 4. └─miaViz:::.loadings_tree_plotter(mat, tree, row.var, ...) 5. └─S7:::Ops.S7_object(plot_out, new_scale_fill()) 6. ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd) 7. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 8. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 9. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 10. └─base_ops[[.Generic]](e1, e2) 11. ├─S7::S7_dispatch() 12. └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...) 13. └─ggplot2:::add_ggplot(e1, e2, e2name) 14. ├─ggplot2::ggplot_add(object, p, objectname) 15. └─ggnewscale:::ggplot_add.new_aes(object, p, objectname) 16. ├─base::`$<-`(`*tmp*`, "mapping", value = `<df[,4]>`) 17. └─ggplot2:::`$<-.ggplot2::gg`(`*tmp*`, "mapping", value = `<df[,4]>`) 18. └─S7::`props<-`(`*tmp*`, value = `[[<-`(S7::props(x), i, value)) 19. └─S7::validate(object) [ FAIL 1 | WARN 3 | SKIP 2 | PASS 214 ] Error: Test failures Execution halted
miaViz.Rcheck/miaViz-Ex.timings
name | user | system | elapsed | |
getNeatOrder | 1.914 | 0.070 | 1.984 | |
plotAbundance | 19.617 | 0.533 | 20.152 | |
plotAbundanceDensity | 3.895 | 0.074 | 3.970 | |
plotBoxplot | 5.633 | 0.033 | 5.666 | |
plotCCA | 3.260 | 0.013 | 3.274 | |
plotColTile | 0.753 | 0.003 | 0.756 | |
plotDMN | 18.554 | 0.062 | 18.618 | |
plotGraph | 0.001 | 0.000 | 0.001 | |
plotHistogram | 2.962 | 0.232 | 3.195 | |