Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-23 12:06 -0400 (Sat, 23 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4821 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4599 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4553 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4539 |
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 1265/2319 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mia 1.17.5 (landing page) Tuomas Borman
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
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: 1.17.5 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mia.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mia_1.17.5.tar.gz |
StartedAt: 2025-08-22 20:15:34 -0400 (Fri, 22 Aug 2025) |
EndedAt: 2025-08-22 20:29:52 -0400 (Fri, 22 Aug 2025) |
EllapsedTime: 857.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: mia.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mia.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mia_1.17.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/mia.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 13.7.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘mia/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘mia’ version ‘1.17.5’ * 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: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed calculateDMN 28.676 0.022 28.812 addNMF 16.416 3.799 15.692 agglomerate-methods 7.953 0.431 8.628 hierarchy-tree 6.318 0.656 7.295 * 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: x[1]: KCTYMMCHNBNDDDNKSSHBNNRWDMYKKBNNDNYTDRRKDVHNKNDRVGRNDRSBRRAWTBYNHRKKKWRSSR x[1]: KKRAAWKSSKWRRWDWTNDBRVRRAMHHCMRDKKSSRARGSSVSYYHNYBRRVHNDNNHYKRMVVYKVRDNNNS x[1]: RAARSBDKGGKK" y[1]: "SCRAGCGTTRTCCGGAWTTAYTGGGYKTAAAGSGMGCGYAGGYGGHBDNKYAAGTCWGWWGTGAAAKYYYGSG y[1]: GCTCAACCSYRRRMBKSCWKTKGAAACTGBVHKRCTWGAKTKYVKDWGAGGWRRGYGGAATKCSWVGTGTAGCG y[1]: GTGAAATGCKTAGAKATBWSGARGAACWCCRRTKGCGAAGGCRRCTYWCTRGWCKGWVAMTGACGCTGAKGCKC y[1]: GAAAGYGTGGGK" ── Error ('test-mediate.R:69:3'): getMediation ───────────────────────────────── Error in `mediate(fit_m, fit_dv, treat = "Treatment", mediator = "Mediator", treat.value = "Scandinavia", control.value = "CentralEurope", boot = TRUE, sims = 1)`: could not find function "mediate" [ FAIL 2 | WARN 3 | SKIP 0 | PASS 1285 ] 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, 3 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/mia.Rcheck/00check.log’ for details.
mia.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mia ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘mia’ ... ** this is package ‘mia’ version ‘1.17.5’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c assay.cpp -o assay.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c faith_R.cpp -o faith_R.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c propmap.cpp -o propmap.o In file included from propmap.cpp:12: ./propmap.h:31:18: warning: private field 'defaultsize' is not used [-Wunused-private-field] uint32_t defaultsize; ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tree.cpp -o tree.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o mia.so RcppExports.o assay.o faith_R.o propmap.o tree.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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 (2025-06-14 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) > 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 1.17.5 - 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 3.71 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 2 | WARN 3 | SKIP 0 | PASS 1285 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-5prevalence.R:506:5'): agglomerateByPrevalence ─────────────── as.character(referenceSeq(actual)[["Alistipes"]]) not equal to paste0(...). 1/1 mismatches x[1]: "BCNMKCKTTVWYCKKMHTTMYTKKKYKTMMMKNKHDYKYMKDYKKNHNNNYMMKHHNDNNKTKMMMDNBHNBK x[1]: KCTYMMCHNBNDDDNKSSHBNNRWDMYKKBNNDNYTDRRKDVHNKNDRVGRNDRSBRRAWTBYNHRKKKWRSSR x[1]: KKRAAWKSSKWRRWDWTNDBRVRRAMHHCMRDKKSSRARGSSVSYYHNYBRRVHNDNNHYKRMVVYKVRDNNNS x[1]: RAARSBDKGGKK" y[1]: "SCRAGCGTTRTCCGGAWTTAYTGGGYKTAAAGSGMGCGYAGGYGGHBDNKYAAGTCWGWWGTGAAAKYYYGSG y[1]: GCTCAACCSYRRRMBKSCWKTKGAAACTGBVHKRCTWGAKTKYVKDWGAGGWRRGYGGAATKCSWVGTGTAGCG y[1]: GTGAAATGCKTAGAKATBWSGARGAACWCCRRTKGCGAAGGCRRCTYWCTRGWCKGWVAMTGACGCTGAKGCKC y[1]: GAAAGYGTGGGK" ── Error ('test-mediate.R:69:3'): getMediation ───────────────────────────────── Error in `mediate(fit_m, fit_dv, treat = "Treatment", mediator = "Mediator", treat.value = "Scandinavia", control.value = "CentralEurope", boot = TRUE, sims = 1)`: could not find function "mediate" [ FAIL 2 | WARN 3 | SKIP 0 | PASS 1285 ] Error: Test failures Execution halted
mia.Rcheck/mia-Ex.timings
name | user | system | elapsed | |
addAlpha | 4.085 | 0.115 | 4.223 | |
addCluster | 0.211 | 0.014 | 0.227 | |
addDivergence | 0.536 | 0.042 | 0.579 | |
addLDA | 3.594 | 0.037 | 3.634 | |
addMDS | 1.169 | 0.053 | 1.226 | |
addNMF | 16.416 | 3.799 | 15.692 | |
agglomerate-methods | 7.953 | 0.431 | 8.628 | |
agglomerateByPrevalence | 0.930 | 0.036 | 0.996 | |
calculateDMN | 28.676 | 0.022 | 28.812 | |
convertFromDADA2 | 2.195 | 0.118 | 2.330 | |
convertFromPhyloseq | 1.133 | 0.074 | 1.212 | |
getAbundant | 0.758 | 0.017 | 0.786 | |
getCrossAssociation | 2.237 | 0.025 | 2.281 | |
getDissimilarity | 3.526 | 0.621 | 4.134 | |
getDominant | 1.111 | 0.049 | 1.177 | |
getMediation | 0.000 | 0.000 | 0.001 | |
getPERMANOVA | 0.514 | 0.042 | 0.560 | |
getPrevalence | 3.376 | 0.145 | 3.603 | |
hierarchy-tree | 6.318 | 0.656 | 7.295 | |
importBIOM | 0.169 | 0.004 | 0.173 | |
importHUMAnN | 0.057 | 0.001 | 0.059 | |
importMetaPhlAn | 0.714 | 0.009 | 0.729 | |
importMothur | 0.064 | 0.002 | 0.068 | |
importQIIME2 | 0.210 | 0.043 | 0.260 | |
importTaxpasta | 0 | 0 | 0 | |
isContaminant | 0.115 | 0.003 | 0.119 | |
meltSE | 0.385 | 0.037 | 0.424 | |
mergeSEs | 2.008 | 0.062 | 2.088 | |
mia-datasets | 0.174 | 0.003 | 0.177 | |
rarefyAssay | 0.418 | 0.013 | 0.432 | |
runCCA | 1.588 | 0.052 | 1.659 | |
runDPCoA | 0.113 | 0.006 | 0.119 | |
runNMDS | 0.070 | 0.004 | 0.085 | |
splitOn | 4.497 | 0.268 | 4.804 | |
summary | 1.636 | 0.030 | 1.666 | |
taxonomy-methods | 0.482 | 0.010 | 0.497 | |
transformAssay | 3.581 | 0.160 | 3.752 | |
utilization_functions | 2.303 | 0.058 | 2.377 | |