Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-07 12:05 -0400 (Thu, 07 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4815 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4550 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4592 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4534 |
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 1262/2315 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mia 1.17.5 (landing page) Tuomas Borman
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | TIMEOUT | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
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: /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_1.17.5.tar.gz |
StartedAt: 2025-08-07 00:16:20 -0400 (Thu, 07 Aug 2025) |
EndedAt: 2025-08-07 00:50:40 -0400 (Thu, 07 Aug 2025) |
EllapsedTime: 2060.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: mia.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.17.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/mia.Rcheck’ * using R version 4.5.1 (2025-06-13) * 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 24.04.2 LTS * using session charset: UTF-8 * 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking installed package size ... INFO installed size is 7.2Mb sub-directories of 1Mb or more: data 1.6Mb extdata 1.2Mb libs 3.0Mb * 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed calculateDMN 63.281 0.043 63.324 addNMF 39.675 10.644 37.497 agglomerate-methods 24.212 0.867 25.084 hierarchy-tree 20.582 0.249 20.831 splitOn 13.741 0.046 13.789 transformAssay 10.751 0.055 10.808 addAlpha 9.499 0.123 9.624 getPrevalence 8.789 0.017 8.806 getDissimilarity 8.055 0.285 8.266 convertFromDADA2 7.622 0.291 7.915 addLDA 7.479 0.078 7.559 getCrossAssociation 7.399 0.010 7.409 utilization_functions 5.990 0.165 6.153 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 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 ‘1.17.5’ ** 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 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 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
R version 4.5.1 (2025-06-13) -- "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 1.17.5 - 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 7.83 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 0 | WARN 3 | SKIP 4 | PASS 1268 ] ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ • require("miaTime", quietly = TRUE) is not TRUE (4): 'test-2mergeSEs.R:386:5', 'test-3agglomerate.R:157:5', 'test-5prevalence.R:468:5', 'test-mediate.R:3:3' [ FAIL 0 | WARN 3 | SKIP 4 | PASS 1268 ] > > proc.time() user system elapsed 1400.864 33.248 1423.779
mia.Rcheck/mia-Ex.timings
name | user | system | elapsed | |
addAlpha | 9.499 | 0.123 | 9.624 | |
addCluster | 0.496 | 0.023 | 0.519 | |
addDivergence | 1.439 | 0.175 | 1.614 | |
addLDA | 7.479 | 0.078 | 7.559 | |
addMDS | 2.734 | 0.190 | 2.921 | |
addNMF | 39.675 | 10.644 | 37.497 | |
agglomerate-methods | 24.212 | 0.867 | 25.084 | |
agglomerateByPrevalence | 2.820 | 0.051 | 2.871 | |
calculateDMN | 63.281 | 0.043 | 63.324 | |
convertFromDADA2 | 7.622 | 0.291 | 7.915 | |
convertFromPhyloseq | 3.232 | 0.068 | 3.300 | |
getAbundant | 2.135 | 0.008 | 2.143 | |
getCrossAssociation | 7.399 | 0.010 | 7.409 | |
getDissimilarity | 8.055 | 0.285 | 8.266 | |
getDominant | 3.264 | 0.027 | 3.291 | |
getMediation | 0 | 0 | 0 | |
getPERMANOVA | 1.245 | 0.062 | 1.307 | |
getPrevalence | 8.789 | 0.017 | 8.806 | |
hierarchy-tree | 20.582 | 0.249 | 20.831 | |
importBIOM | 0.496 | 0.001 | 0.497 | |
importHUMAnN | 0.185 | 0.000 | 0.185 | |
importMetaPhlAn | 2.352 | 0.004 | 2.357 | |
importMothur | 0.175 | 0.000 | 0.175 | |
importQIIME2 | 0.602 | 0.019 | 0.630 | |
importTaxpasta | 0 | 0 | 0 | |
isContaminant | 0.386 | 0.003 | 0.388 | |
meltSE | 0.772 | 0.017 | 0.789 | |
mergeSEs | 4.842 | 0.013 | 4.857 | |
mia-datasets | 0.420 | 0.001 | 0.422 | |
rarefyAssay | 1.071 | 0.001 | 1.073 | |
runCCA | 4.014 | 0.013 | 4.028 | |
runDPCoA | 0.366 | 0.001 | 0.368 | |
runNMDS | 0.242 | 0.000 | 0.242 | |
splitOn | 13.741 | 0.046 | 13.789 | |
summary | 4.942 | 0.007 | 4.949 | |
taxonomy-methods | 1.396 | 0.003 | 1.399 | |
transformAssay | 10.751 | 0.055 | 10.808 | |
utilization_functions | 5.990 | 0.165 | 6.153 | |