Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-14 12:03 -0400 (Tue, 14 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4864 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4610 |
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 1280/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mia 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 | TIMEOUT | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | TIMEOUT | ||||||||||
To the developers/maintainers of the mia package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mia.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: mia |
Version: 1.17.9 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:mia.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings mia_1.17.9.tar.gz |
StartedAt: 2025-10-14 01:56:03 -0400 (Tue, 14 Oct 2025) |
EndedAt: 2025-10-14 02:25:48 -0400 (Tue, 14 Oct 2025) |
EllapsedTime: 1784.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: mia.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:mia.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings mia_1.17.9.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/mia.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 ‘mia/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘mia’ version ‘1.17.9’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 24 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘mia’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking installed package size ... INFO installed size is 7.8Mb sub-directories of 1Mb or more: data 1.6Mb extdata 1.2Mb libs 3.6Mb * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE 'library' or 'require' call to ‘topicdoc’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * 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 ... NOTE Package unavailable to check Rd xrefs: ‘picante’ Unknown package ‘https’ in Rd xrefs Non-topic package-anchored link(s) in Rd file 'calculateDMN.Rd': ‘[DirichletMultinomial:fitted]{accessors for DMN objects}’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: addCluster.Rd: BlusterParam-class 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘mia-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: getLDA > ### Title: Latent Dirichlet Allocation > ### Aliases: getLDA addLDA getLDA,SummarizedExperiment-method > ### addLDA,SummarizedExperiment-method > > ### ** Examples > > data(GlobalPatterns) > tse <- GlobalPatterns > > # Reduce the number of features > tse <- agglomerateByPrevalence(tse, rank="Phylum") Loading required namespace: GenomeInfoDb Failed with error: ‘there is no package called ‘GenomeInfoDb’’ Error in .requirePackage(package) : unable to load required package ‘GenomeInfoDb’ Calls: agglomerateByPrevalence ... .extendsForS3 -> extends -> getClassDef -> .requirePackage Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed addAlpha 9.278 0.17 9.449 * 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: ▆ 1. └─mia (local) test_internal_.estimate_richness(tse) at test-5richness.R:77:5 2. ├─mia::addAlpha(tse, index = indices) at test-5richness.R:21:9 3. └─mia::addAlpha(tse, index = indices) 4. ├─base::do.call(getAlpha, args) 5. ├─mia (local) `<stndrdGn>`(x = `<TrSmmrzE[,3]>`, index = `<chr>`) 6. └─mia (local) `<stndrdGn>`(x = `<TrSmmrzE[,3]>`, index = `<chr>`) 7. └─mia (local) .local(x, ...) 8. ├─BiocParallel::bplapply(...) 9. └─BiocParallel::bplapply(...) 10. └─BiocParallel:::.bpinit(...) [ FAIL 1 | WARN 3 | SKIP 4 | PASS 1330 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘mia.Rmd’ using rmarkdown Failed with error: 'there is no package called 'GenomeInfoDb'' Quitting from mia.Rmd:55-59 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `.requirePackage()`: ! unable to load required package 'GenomeInfoDb' --- Backtrace: ▆ 1. ├─tools::buildVignettes(...) 2. │ ├─base::tryCatch(...) 3. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 6. │ └─engine$weave(file, quiet = quiet, encoding = enc) 7. │ └─knitr:::vweave_rmarkdown(...) 8. │ └─rmarkdown::render(...) 9. │ └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 10. │ └─knitr:::process_file(text, output) 11. │ ├─xfun:::handle_error(...) 12. │ ├─base::withCallingHandlers(...) 13. │ └─knitr:::process_group(group) 14. │ └─knitr:::call_block(x) 15. │ └─knitr:::block_exec(params) 16. │ └─knitr:::eng_r(options) 17. │ ├─knitr:::in_input_dir(...) 18. │ │ └─knitr:::in_dir(input_dir(), expr) 19. │ └─knitr (local) evaluate(...) 20. │ └─evaluate::evaluate(...) 21. │ ├─base::withRestarts(...) 22. │ │ └─base (local) withRestartList(expr, restarts) 23. │ │ ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 24. │ │ │ └─base (local) doWithOneRestart(return(expr), restart) 25. │ │ └─base (local) withRestartList(expr, restarts[-nr]) 26. │ │ └─base (local) withOneRestart(expr, restarts[[1L]]) 27. │ │ └─base (local) doWithOneRestart(return(expr), restart) 28. │ ├─evaluate:::with_handlers(...) 29. │ │ ├─base::eval(call) 30. │ │ │ └─base::eval(call) 31. │ │ └─base::withCallingHandlers(...) 32. │ └─watcher$print_value(ev$value, ev$visible, envir) 33. │ ├─base::withVisible(handle_value(handler, value, visible, envir)) 34. │ └─evaluate:::handle_value(handler, value, visible, envir) 35. │ └─handler$value(value, visible) 36. │ └─knitr (local) fun(x, options = options) 37. │ ├─base::withVisible(knit_print(x, ...)) 38. │ ├─knitr::knit_print(x, ...) 39. │ └─knitr:::knit_print.default(x, ...) 40. │ └─knitr::normal_print(x) 41. │ ├─methods::show(x) 42. │ └─methods::show(x) 43. │ ├─BiocGenerics::updateObject(object) 44. │ └─TreeSummarizedExperiment::updateObject(object) 45. │ ├─methods::callNextMethod() 46. │ └─SingleCellExperiment (local) .nextMethod(object = object) 47. │ ├─methods::callNextMethod() 48. │ └─SummarizedExperiment (local) .nextMethod(object = object) 49. │ ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose) 50. │ └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose) 51. │ ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose) 52. │ └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose) 53. │ └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose) 54. └─methods:::.extendsForS3(`<chr>`) 55. └─methods::extends(Class, maybe = FALSE) 56. └─methods::getClassDef(class1) 57. └─methods:::.requirePackage(package) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'mia.Rmd' failed with diagnostics: unable to load required package 'GenomeInfoDb' --- failed re-building ‘mia.Rmd’ SUMMARY: processing the following file failed: ‘mia.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 3 ERRORs, 3 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/mia.Rcheck/00check.log’ for details.
mia.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL mia ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘mia’ ... ** this is package ‘mia’ version ‘1.17.9’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c assay.cpp -o assay.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c faith_R.cpp -o faith_R.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c propmap.cpp -o propmap.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c transformCounts.cpp -o transformCounts.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c tree.cpp -o tree.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o mia.so RcppExports.o assay.o faith_R.o propmap.o transformCounts.o tree.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-mia/00new/mia/libs ** R ** data ** inst ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (mia)
mia.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(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/ > > test_check("mia") ================================================================================ Time difference of 7.66 secs Initializing error rates to maximum possible estimate. selfConsist step 1 . selfConsist step 2 selfConsist step 3 selfConsist step 4 Convergence after 4 rounds. Initializing error rates to maximum possible estimate. selfConsist step 1 . selfConsist step 2 selfConsist step 3 selfConsist step 4 Convergence after 4 rounds. initial value 0.383462 iter 5 value 0.161655 iter 10 value 0.113278 final value 0.003270 converged initial value 0.000000 final value 0.000000 converged initial value 0.000000 final value 0.000000 converged [ FAIL 1 | WARN 3 | SKIP 4 | PASS 1330 ] ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ • require("miaTime", quietly = TRUE) is not TRUE (4): 'test-2mergeSEs.R:386:5', 'test-3agglomerate.R:197:5', 'test-5prevalence.R:468:5', 'test-mediate.R:3:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-5richness.R:21:9'): .estimate_richness ───────────────────────── <bplist_error/bperror/error/condition> Error: BiocParallel errors 1 remote errors, element index: 3 1 unevaluated and other errors first remote error: Error in .from_Array_to_matrix(x, ...): unused argument (rownames.force = TRUE) Backtrace: ▆ 1. └─mia (local) test_internal_.estimate_richness(tse) at test-5richness.R:77:5 2. ├─mia::addAlpha(tse, index = indices) at test-5richness.R:21:9 3. └─mia::addAlpha(tse, index = indices) 4. ├─base::do.call(getAlpha, args) 5. ├─mia (local) `<stndrdGn>`(x = `<TrSmmrzE[,3]>`, index = `<chr>`) 6. └─mia (local) `<stndrdGn>`(x = `<TrSmmrzE[,3]>`, index = `<chr>`) 7. └─mia (local) .local(x, ...) 8. ├─BiocParallel::bplapply(...) 9. └─BiocParallel::bplapply(...) 10. └─BiocParallel:::.bpinit(...) [ FAIL 1 | WARN 3 | SKIP 4 | PASS 1330 ] Error: Test failures Execution halted
mia.Rcheck/mia-Ex.timings
name | user | system | elapsed | |
addAlpha | 9.278 | 0.170 | 9.449 | |
addCluster | 0.505 | 0.006 | 0.511 | |
addDivergence | 1.405 | 0.153 | 1.559 | |