Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-09-27 12:30 -0400 (Fri, 27 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4451 |
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4417 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4456 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4489 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4436 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4435 |
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 1235/2262 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mia 1.13.36 (landing page) Tuomas Borman
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | ERROR | ERROR | skipped | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.13.36 |
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_1.13.36.tar.gz |
StartedAt: 2024-09-26 22:08:40 -0400 (Thu, 26 Sep 2024) |
EndedAt: 2024-09-26 22:38:38 -0400 (Thu, 26 Sep 2024) |
EllapsedTime: 1798.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: mia.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.13.36.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/mia.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘mia/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘mia’ version ‘1.13.36’ * 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 ‘mia’ 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 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 ... NOTE addDissimilarity,SummarizedExperiment: warning in .add_values_to_metadata(x, names = name, value = as.matrix(res)): partial argument match of 'value' to 'values' * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Unknown package ‘https’ in Rd xrefs * 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 ... NOTE Note: found 101 marked UTF-8 strings * 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 addNMF 56.929 13.515 52.897 runCCA 58.574 0.562 59.435 calculateDMN 57.658 0.260 58.209 hierarchy-tree 23.087 2.689 25.968 agglomerate-methods 22.959 0.570 23.704 getDissimilarity 15.801 3.087 9.488 addAlpha 15.061 0.494 15.678 getCrossAssociation 9.516 0.132 9.710 addLDA 8.238 0.182 8.485 convertFromDADA2 7.714 0.389 8.200 mergeSEs 7.898 0.183 8.150 getPrevalence 7.877 0.145 8.074 splitOn 7.069 0.126 7.231 summaries 4.921 0.094 5.045 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-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/4.4-x86_64/Resources/library’ * installing *source* package ‘mia’ ... ** using staged installation ** 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 ** 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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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: 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 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, setdiff, table, tapply, union, 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: GenomeInfoDb 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 Loading required package: MultiAssayExperiment This is mia version 1.13.36 - 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 7.58 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 9 | SKIP 4 | PASS 1062 ] ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ • require("miaTime", quietly = TRUE) is not TRUE (4): 'test-2mergeSEs.R:386:5', 'test-3agglomerate.R:155:5', 'test-5prevalence.R:428:5', 'test-mediate.R:3:3' [ FAIL 0 | WARN 9 | SKIP 4 | PASS 1062 ] > > proc.time() user system elapsed 984.119 155.483 1098.558
mia.Rcheck/mia-Ex.timings
name | user | system | elapsed | |
addAlpha | 15.061 | 0.494 | 15.678 | |
addCluster | 0.838 | 0.026 | 0.872 | |
addDivergence | 1.897 | 0.134 | 2.040 | |
addLDA | 8.238 | 0.182 | 8.485 | |
addNMF | 56.929 | 13.515 | 52.897 | |
agglomerate-methods | 22.959 | 0.570 | 23.704 | |
agglomerateByPrevalence | 4.375 | 0.227 | 4.641 | |
calculateDMN | 57.658 | 0.260 | 58.209 | |
convertFromDADA2 | 7.714 | 0.389 | 8.200 | |
convertFromPhyloseq | 4.091 | 0.184 | 4.307 | |
getCrossAssociation | 9.516 | 0.132 | 9.710 | |
getDissimilarity | 15.801 | 3.087 | 9.488 | |
getDominant | 3.248 | 0.379 | 3.650 | |
getMediation | 0 | 0 | 0 | |
getPrevalence | 7.877 | 0.145 | 8.074 | |
hierarchy-tree | 23.087 | 2.689 | 25.968 | |
importBIOM | 0.893 | 0.015 | 0.914 | |
importHUMAnN | 0.350 | 0.005 | 0.359 | |
importMetaPhlAn | 4.020 | 0.070 | 4.114 | |
importMothur | 0.338 | 0.008 | 0.350 | |
importQIIME2 | 0.974 | 0.163 | 1.202 | |
importTaxpasta | 0.001 | 0.000 | 0.000 | |
isContaminant | 0.457 | 0.013 | 0.475 | |
meltSE | 1.006 | 0.018 | 1.030 | |
mergeSEs | 7.898 | 0.183 | 8.150 | |
mia-datasets | 0.698 | 0.013 | 0.717 | |
rarefyAssay | 1.750 | 0.026 | 1.789 | |
runCCA | 58.574 | 0.562 | 59.435 | |
runDPCoA | 0.460 | 0.012 | 0.475 | |
runNMDS | 0.407 | 0.009 | 0.419 | |
splitOn | 7.069 | 0.126 | 7.231 | |
summaries | 4.921 | 0.094 | 5.045 | |
taxonomy-methods | 1.622 | 0.026 | 1.657 | |
transformAssay | 0.266 | 0.006 | 0.273 | |