Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-22 12:05 -0400 (Fri, 22 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" | 4541 |
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 1147/2319 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Maaslin2 1.23.0 (landing page) Lauren McIver
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the Maaslin2 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Maaslin2.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: Maaslin2 |
Version: 1.23.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.23.0.tar.gz |
StartedAt: 2025-08-21 21:44:11 -0400 (Thu, 21 Aug 2025) |
EndedAt: 2025-08-21 21:47:10 -0400 (Thu, 21 Aug 2025) |
EllapsedTime: 179.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Maaslin2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/Maaslin2.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Maaslin2/DESCRIPTION’ ... OK * this is package ‘Maaslin2’ version ‘1.23.0’ * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 23 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 ‘Maaslin2’ 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 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 maaslin2_association_plots: no visible binding for global variable ‘xnames’ Undefined global functions or variables: xnames * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed Maaslin2 97.26 1.779 99.819 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.22-bioc/meat/Maaslin2.Rcheck/00check.log’ for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘Maaslin2’ ... ** this is package ‘Maaslin2’ version ‘1.23.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (Maaslin2)
Maaslin2.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-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(Maaslin2) > > test_check("Maaslin2") [1] "Creating output folder" [1] "Creating output feature tables folder" [1] "Creating output fits folder" 2025-08-21 21:46:30.0339 INFO::Writing function arguments to log file 2025-08-21 21:46:30.092243 INFO::Verifying options selected are valid 2025-08-21 21:46:30.137498 INFO::Determining format of input files 2025-08-21 21:46:30.139908 INFO::Input format is data samples as rows and metadata samples as rows 2025-08-21 21:46:30.148916 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject) 2025-08-21 21:46:30.150993 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age 2025-08-21 21:46:30.154082 INFO::Filter data based on min abundance and min prevalence 2025-08-21 21:46:30.155291 INFO::Total samples in data: 1595 2025-08-21 21:46:30.156978 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000 2025-08-21 21:46:30.173908 INFO::Total filtered features: 0 2025-08-21 21:46:30.175948 INFO::Filtered feature names from abundance and prevalence filtering: 2025-08-21 21:46:30.190292 INFO::Total filtered features with variance filtering: 0 2025-08-21 21:46:30.191967 INFO::Filtered feature names from variance filtering: 2025-08-21 21:46:30.193182 INFO::Running selected normalization method: TSS 2025-08-21 21:46:31.412708 INFO::Bypass z-score application to metadata 2025-08-21 21:46:31.414666 INFO::Running selected transform method: AST 2025-08-21 21:46:31.43303 INFO::Running selected analysis method: LM 2025-08-21 21:46:32.095537 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis 2025-08-21 21:46:32.655248 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum 2025-08-21 21:46:32.82285 INFO::Fitting model to feature number 3, Bifidobacterium.longum 2025-08-21 21:46:33.01242 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum 2025-08-21 21:46:33.195153 INFO::Fitting model to feature number 5, Collinsella.aerofaciens 2025-08-21 21:46:33.379066 INFO::Fitting model to feature number 6, Bacteroides.caccae 2025-08-21 21:46:33.559856 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus 2025-08-21 21:46:33.75332 INFO::Fitting model to feature number 8, Bacteroides.dorei 2025-08-21 21:46:33.935248 INFO::Fitting model to feature number 9, Bacteroides.eggerthii 2025-08-21 21:46:34.126633 INFO::Fitting model to feature number 10, Bacteroides.faecis 2025-08-21 21:46:34.311553 INFO::Fitting model to feature number 11, Bacteroides.finegoldii 2025-08-21 21:46:34.480302 INFO::Fitting model to feature number 12, Bacteroides.fragilis 2025-08-21 21:46:34.629967 INFO::Fitting model to feature number 13, Bacteroides.intestinalis 2025-08-21 21:46:34.807084 WARNING::Fitting problem for feature 13 a warning was issued 2025-08-21 21:46:34.966691 INFO::Fitting model to feature number 14, Bacteroides.massiliensis 2025-08-21 21:46:35.12295 INFO::Fitting model to feature number 15, Bacteroides.ovatus 2025-08-21 21:46:35.27352 INFO::Fitting model to feature number 16, Bacteroides.salyersiae 2025-08-21 21:46:35.435515 INFO::Fitting model to feature number 17, Bacteroides.stercoris 2025-08-21 21:46:35.591916 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron 2025-08-21 21:46:35.751349 INFO::Fitting model to feature number 19, Bacteroides.uniformis 2025-08-21 21:46:35.913243 INFO::Fitting model to feature number 20, Bacteroides.vulgatus 2025-08-21 21:46:36.065407 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens 2025-08-21 21:46:36.230804 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8 2025-08-21 21:46:36.40085 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis 2025-08-21 21:46:36.559545 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus 2025-08-21 21:46:36.721882 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus 2025-08-21 21:46:36.881611 INFO::Fitting model to feature number 26, Parabacteroides.distasonis 2025-08-21 21:46:37.043717 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii 2025-08-21 21:46:37.211789 INFO::Fitting model to feature number 28, Parabacteroides.merdae 2025-08-21 21:46:37.388163 INFO::Fitting model to feature number 29, Parabacteroides.unclassified 2025-08-21 21:46:37.569534 INFO::Fitting model to feature number 30, Paraprevotella.clara 2025-08-21 21:46:37.738979 INFO::Fitting model to feature number 31, Paraprevotella.unclassified 2025-08-21 21:46:37.924892 INFO::Fitting model to feature number 32, Prevotella.copri 2025-08-21 21:46:38.104252 INFO::Fitting model to feature number 33, Alistipes.finegoldii 2025-08-21 21:46:38.282485 INFO::Fitting model to feature number 34, Alistipes.onderdonkii 2025-08-21 21:46:38.459831 INFO::Fitting model to feature number 35, Alistipes.putredinis 2025-08-21 21:46:38.617849 INFO::Fitting model to feature number 36, Alistipes.shahii 2025-08-21 21:46:38.779371 INFO::Fitting model to feature number 37, Alistipes.unclassified 2025-08-21 21:46:38.945523 INFO::Fitting model to feature number 38, Streptococcus.salivarius 2025-08-21 21:46:39.095994 INFO::Fitting model to feature number 39, Clostridium.bolteae 2025-08-21 21:46:39.262985 INFO::Fitting model to feature number 40, Clostridium.citroniae 2025-08-21 21:46:39.41287 INFO::Fitting model to feature number 41, Clostridium.clostridioforme 2025-08-21 21:46:39.595273 INFO::Fitting model to feature number 42, Clostridium.hathewayi 2025-08-21 21:46:39.744736 INFO::Fitting model to feature number 43, Clostridium.leptum 2025-08-21 21:46:39.88232 INFO::Fitting model to feature number 44, Clostridium.nexile 2025-08-21 21:46:40.036351 INFO::Fitting model to feature number 45, Clostridium.symbiosum 2025-08-21 21:46:40.193512 INFO::Fitting model to feature number 46, Flavonifractor.plautii 2025-08-21 21:46:40.334327 INFO::Fitting model to feature number 47, Eubacterium.eligens 2025-08-21 21:46:40.504212 INFO::Fitting model to feature number 48, Eubacterium.hallii 2025-08-21 21:46:40.66891 INFO::Fitting model to feature number 49, Eubacterium.rectale 2025-08-21 21:46:40.815976 INFO::Fitting model to feature number 50, Eubacterium.siraeum 2025-08-21 21:46:40.971244 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31 2025-08-21 21:46:41.135903 INFO::Fitting model to feature number 52, Eubacterium.ventriosum 2025-08-21 21:46:41.289836 INFO::Fitting model to feature number 53, Ruminococcus.gnavus 2025-08-21 21:46:41.451163 INFO::Fitting model to feature number 54, Ruminococcus.obeum 2025-08-21 21:46:41.613503 INFO::Fitting model to feature number 55, Ruminococcus.torques 2025-08-21 21:46:41.773735 INFO::Fitting model to feature number 56, Coprococcus.comes 2025-08-21 21:46:41.958608 INFO::Fitting model to feature number 57, Dorea.longicatena 2025-08-21 21:46:42.132106 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA 2025-08-21 21:46:42.305495 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA 2025-08-21 21:46:42.473473 INFO::Fitting model to feature number 60, Roseburia.hominis 2025-08-21 21:46:42.642511 INFO::Fitting model to feature number 61, Roseburia.intestinalis 2025-08-21 21:46:42.794454 INFO::Fitting model to feature number 62, Roseburia.inulinivorans 2025-08-21 21:46:42.95681 INFO::Fitting model to feature number 63, Roseburia.unclassified 2025-08-21 21:46:43.133007 INFO::Fitting model to feature number 64, Oscillibacter.unclassified 2025-08-21 21:46:43.296488 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified 2025-08-21 21:46:43.486258 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii 2025-08-21 21:46:43.649505 INFO::Fitting model to feature number 67, Ruminococcus.bromii 2025-08-21 21:46:43.816208 INFO::Fitting model to feature number 68, Ruminococcus.callidus 2025-08-21 21:46:44.00717 INFO::Fitting model to feature number 69, Ruminococcus.lactaris 2025-08-21 21:46:44.201251 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified 2025-08-21 21:46:44.385811 INFO::Fitting model to feature number 71, Coprobacillus.unclassified 2025-08-21 21:46:44.543743 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified 2025-08-21 21:46:44.719097 INFO::Fitting model to feature number 73, Dialister.invisus 2025-08-21 21:46:44.886771 INFO::Fitting model to feature number 74, Veillonella.atypica 2025-08-21 21:46:45.298518 INFO::Fitting model to feature number 75, Veillonella.dispar 2025-08-21 21:46:45.467723 INFO::Fitting model to feature number 76, Veillonella.parvula 2025-08-21 21:46:45.642456 INFO::Fitting model to feature number 77, Veillonella.unclassified 2025-08-21 21:46:45.792482 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47 2025-08-21 21:46:45.963489 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis 2025-08-21 21:46:46.135709 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis 2025-08-21 21:46:46.303733 INFO::Fitting model to feature number 81, Bilophila.unclassified 2025-08-21 21:46:46.473594 INFO::Fitting model to feature number 82, Escherichia.coli 2025-08-21 21:46:46.657774 INFO::Fitting model to feature number 83, Escherichia.unclassified 2025-08-21 21:46:46.810806 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae 2025-08-21 21:46:46.97957 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae 2025-08-21 21:46:47.142224 INFO::Fitting model to feature number 86, Akkermansia.muciniphila 2025-08-21 21:46:47.312614 INFO::Fitting model to feature number 87, C2likevirus.unclassified 2025-08-21 21:46:47.516966 INFO::Counting total values for each feature 2025-08-21 21:46:47.546126 INFO::Writing filtered data to file output/features/filtered_data.tsv 2025-08-21 21:46:47.669212 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv 2025-08-21 21:46:47.825413 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv 2025-08-21 21:46:47.979577 INFO::Writing residuals to file output/fits/residuals.rds 2025-08-21 21:46:48.037159 INFO::Writing fitted values to file output/fits/fitted.rds 2025-08-21 21:46:48.065592 INFO::Writing extracted random effects to file output/fits/ranef.rds 2025-08-21 21:46:48.072726 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv 2025-08-21 21:46:48.082298 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output/significant_results.tsv [1] "Creating output folder" [1] "Creating output feature tables folder" [1] "Creating output fits folder" 2025-08-21 21:46:48.09636 INFO::Writing function arguments to log file 2025-08-21 21:46:48.107287 INFO::Verifying options selected are valid 2025-08-21 21:46:48.108904 INFO::Determining format of input files 2025-08-21 21:46:48.110775 INFO::Input format is data samples as rows and metadata samples as rows 2025-08-21 21:46:48.117915 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject) 2025-08-21 21:46:48.119794 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age 2025-08-21 21:46:48.122318 INFO::Filter data based on min abundance and min prevalence 2025-08-21 21:46:48.123391 INFO::Total samples in data: 1595 2025-08-21 21:46:48.124301 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000 2025-08-21 21:46:48.127511 INFO::Total filtered features: 0 2025-08-21 21:46:48.129131 INFO::Filtered feature names from abundance and prevalence filtering: 2025-08-21 21:46:48.138885 INFO::Total filtered features with variance filtering: 0 2025-08-21 21:46:48.140813 INFO::Filtered feature names from variance filtering: 2025-08-21 21:46:48.142364 INFO::Running selected normalization method: NONE 2025-08-21 21:46:48.143548 INFO::Bypass z-score application to metadata 2025-08-21 21:46:48.144888 INFO::Running selected transform method: AST 2025-08-21 21:46:48.170734 INFO::Running selected analysis method: LM 2025-08-21 21:46:48.172874 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis 2025-08-21 21:46:48.326127 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum 2025-08-21 21:46:48.48656 INFO::Fitting model to feature number 3, Bifidobacterium.longum 2025-08-21 21:46:48.640187 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum 2025-08-21 21:46:48.793059 INFO::Fitting model to feature number 5, Collinsella.aerofaciens 2025-08-21 21:46:48.941417 INFO::Fitting model to feature number 6, Bacteroides.caccae 2025-08-21 21:46:49.087839 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus 2025-08-21 21:46:49.25953 INFO::Fitting model to feature number 8, Bacteroides.dorei 2025-08-21 21:46:49.42917 INFO::Fitting model to feature number 9, Bacteroides.eggerthii 2025-08-21 21:46:49.581818 INFO::Fitting model to feature number 10, Bacteroides.faecis 2025-08-21 21:46:49.741755 INFO::Fitting model to feature number 11, Bacteroides.finegoldii 2025-08-21 21:46:49.895695 INFO::Fitting model to feature number 12, Bacteroides.fragilis 2025-08-21 21:46:50.043364 INFO::Fitting model to feature number 13, Bacteroides.intestinalis 2025-08-21 21:46:50.170022 WARNING::Fitting problem for feature 13 a warning was issued 2025-08-21 21:46:50.336462 INFO::Fitting model to feature number 14, Bacteroides.massiliensis 2025-08-21 21:46:50.477264 INFO::Fitting model to feature number 15, Bacteroides.ovatus 2025-08-21 21:46:50.625766 INFO::Fitting model to feature number 16, Bacteroides.salyersiae 2025-08-21 21:46:50.782668 INFO::Fitting model to feature number 17, Bacteroides.stercoris 2025-08-21 21:46:50.959162 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron 2025-08-21 21:46:51.115516 INFO::Fitting model to feature number 19, Bacteroides.uniformis 2025-08-21 21:46:51.271685 INFO::Fitting model to feature number 20, Bacteroides.vulgatus 2025-08-21 21:46:51.433972 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens 2025-08-21 21:46:51.603581 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8 2025-08-21 21:46:51.764853 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis 2025-08-21 21:46:51.926366 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus 2025-08-21 21:46:52.09457 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus 2025-08-21 21:46:52.247551 INFO::Fitting model to feature number 26, Parabacteroides.distasonis 2025-08-21 21:46:52.404871 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii 2025-08-21 21:46:52.584544 INFO::Fitting model to feature number 28, Parabacteroides.merdae 2025-08-21 21:46:52.735311 INFO::Fitting model to feature number 29, Parabacteroides.unclassified 2025-08-21 21:46:52.895561 INFO::Fitting model to feature number 30, Paraprevotella.clara 2025-08-21 21:46:53.060895 INFO::Fitting model to feature number 31, Paraprevotella.unclassified 2025-08-21 21:46:53.197016 INFO::Fitting model to feature number 32, Prevotella.copri 2025-08-21 21:46:53.354083 INFO::Fitting model to feature number 33, Alistipes.finegoldii 2025-08-21 21:46:53.511536 INFO::Fitting model to feature number 34, Alistipes.onderdonkii 2025-08-21 21:46:53.680769 INFO::Fitting model to feature number 35, Alistipes.putredinis 2025-08-21 21:46:53.835925 INFO::Fitting model to feature number 36, Alistipes.shahii 2025-08-21 21:46:54.006735 INFO::Fitting model to feature number 37, Alistipes.unclassified 2025-08-21 21:46:54.155842 INFO::Fitting model to feature number 38, Streptococcus.salivarius 2025-08-21 21:46:54.315383 INFO::Fitting model to feature number 39, Clostridium.bolteae 2025-08-21 21:46:54.471662 INFO::Fitting model to feature number 40, Clostridium.citroniae 2025-08-21 21:46:54.622131 INFO::Fitting model to feature number 41, Clostridium.clostridioforme 2025-08-21 21:46:54.787194 INFO::Fitting model to feature number 42, Clostridium.hathewayi 2025-08-21 21:46:54.947926 INFO::Fitting model to feature number 43, Clostridium.leptum 2025-08-21 21:46:55.103308 INFO::Fitting model to feature number 44, Clostridium.nexile 2025-08-21 21:46:55.282455 INFO::Fitting model to feature number 45, Clostridium.symbiosum 2025-08-21 21:46:55.435062 INFO::Fitting model to feature number 46, Flavonifractor.plautii 2025-08-21 21:46:55.603188 INFO::Fitting model to feature number 47, Eubacterium.eligens 2025-08-21 21:46:55.757967 INFO::Fitting model to feature number 48, Eubacterium.hallii 2025-08-21 21:46:55.929147 INFO::Fitting model to feature number 49, Eubacterium.rectale 2025-08-21 21:46:56.073669 INFO::Fitting model to feature number 50, Eubacterium.siraeum 2025-08-21 21:46:56.253992 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31 2025-08-21 21:46:56.404589 INFO::Fitting model to feature number 52, Eubacterium.ventriosum 2025-08-21 21:46:56.560982 INFO::Fitting model to feature number 53, Ruminococcus.gnavus 2025-08-21 21:46:56.710798 INFO::Fitting model to feature number 54, Ruminococcus.obeum 2025-08-21 21:46:56.873213 INFO::Fitting model to feature number 55, Ruminococcus.torques 2025-08-21 21:46:57.022562 INFO::Fitting model to feature number 56, Coprococcus.comes 2025-08-21 21:46:57.177504 INFO::Fitting model to feature number 57, Dorea.longicatena 2025-08-21 21:46:57.335135 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA 2025-08-21 21:46:57.490542 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA 2025-08-21 21:46:57.646756 INFO::Fitting model to feature number 60, Roseburia.hominis 2025-08-21 21:46:57.807076 INFO::Fitting model to feature number 61, Roseburia.intestinalis 2025-08-21 21:46:57.957875 INFO::Fitting model to feature number 62, Roseburia.inulinivorans 2025-08-21 21:46:58.104101 INFO::Fitting model to feature number 63, Roseburia.unclassified 2025-08-21 21:46:58.249531 INFO::Fitting model to feature number 64, Oscillibacter.unclassified 2025-08-21 21:46:58.387113 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified 2025-08-21 21:46:58.541455 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii 2025-08-21 21:46:58.67975 INFO::Fitting model to feature number 67, Ruminococcus.bromii 2025-08-21 21:46:58.810709 WARNING::Fitting problem for feature 67 a warning was issued 2025-08-21 21:46:58.962648 INFO::Fitting model to feature number 68, Ruminococcus.callidus 2025-08-21 21:46:59.103229 INFO::Fitting model to feature number 69, Ruminococcus.lactaris 2025-08-21 21:46:59.250827 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified 2025-08-21 21:46:59.410441 INFO::Fitting model to feature number 71, Coprobacillus.unclassified 2025-08-21 21:46:59.565665 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified 2025-08-21 21:46:59.617158 WARNING::Fitting problem for feature 72 a warning was issued 2025-08-21 21:46:59.770584 INFO::Fitting model to feature number 73, Dialister.invisus 2025-08-21 21:46:59.944663 INFO::Fitting model to feature number 74, Veillonella.atypica 2025-08-21 21:47:00.091841 INFO::Fitting model to feature number 75, Veillonella.dispar 2025-08-21 21:47:00.228857 INFO::Fitting model to feature number 76, Veillonella.parvula 2025-08-21 21:47:00.37809 INFO::Fitting model to feature number 77, Veillonella.unclassified 2025-08-21 21:47:00.526412 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47 2025-08-21 21:47:00.667338 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis 2025-08-21 21:47:00.83683 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis 2025-08-21 21:47:00.981154 INFO::Fitting model to feature number 81, Bilophila.unclassified 2025-08-21 21:47:01.133217 INFO::Fitting model to feature number 82, Escherichia.coli 2025-08-21 21:47:01.272469 INFO::Fitting model to feature number 83, Escherichia.unclassified 2025-08-21 21:47:01.41659 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae 2025-08-21 21:47:01.561208 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae 2025-08-21 21:47:01.706604 INFO::Fitting model to feature number 86, Akkermansia.muciniphila 2025-08-21 21:47:01.847131 INFO::Fitting model to feature number 87, C2likevirus.unclassified 2025-08-21 21:47:02.025454 INFO::Counting total values for each feature 2025-08-21 21:47:02.049899 INFO::Writing filtered data to file output2/features/filtered_data.tsv 2025-08-21 21:47:02.173398 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv 2025-08-21 21:47:02.290145 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv 2025-08-21 21:47:02.441275 INFO::Writing residuals to file output2/fits/residuals.rds 2025-08-21 21:47:02.513704 INFO::Writing fitted values to file output2/fits/fitted.rds 2025-08-21 21:47:02.59201 INFO::Writing extracted random effects to file output2/fits/ranef.rds 2025-08-21 21:47:02.600094 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv 2025-08-21 21:47:02.606676 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output2/significant_results.tsv [ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ] > > > proc.time() user system elapsed 33.218 0.711 34.100
Maaslin2.Rcheck/Maaslin2-Ex.timings
name | user | system | elapsed | |
Maaslin2 | 97.260 | 1.779 | 99.819 | |