Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-06 11:41 -0400 (Mon, 06 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4832 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4613 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4554 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4585 |
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 1154/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Maaslin2 1.22.0 (landing page) Lauren McIver
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
kunpeng2 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: Maaslin2 |
Version: 1.22.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Maaslin2_1.22.0.tar.gz |
StartedAt: 2025-10-03 10:51:52 -0000 (Fri, 03 Oct 2025) |
EndedAt: 2025-10-03 10:55:22 -0000 (Fri, 03 Oct 2025) |
EllapsedTime: 209.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Maaslin2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Maaslin2_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Maaslin2/DESCRIPTION’ ... OK * this is package ‘Maaslin2’ version ‘1.22.0’ * 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 loading without being on the library search path ... 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 123.015 1.101 124.46 * 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 ‘/home/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck/00check.log’ for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘Maaslin2’ ... ** this is package ‘Maaslin2’ version ‘1.22.0’ ** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-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(Maaslin2) > > test_check("Maaslin2") [1] "Creating output folder" [1] "Creating output feature tables folder" [1] "Creating output fits folder" 2025-10-03 10:54:33.352079 INFO::Writing function arguments to log file 2025-10-03 10:54:33.409573 INFO::Verifying options selected are valid 2025-10-03 10:54:33.455223 INFO::Determining format of input files 2025-10-03 10:54:33.457365 INFO::Input format is data samples as rows and metadata samples as rows 2025-10-03 10:54:33.465501 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject) 2025-10-03 10:54:33.467524 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age 2025-10-03 10:54:33.471161 INFO::Filter data based on min abundance and min prevalence 2025-10-03 10:54:33.472597 INFO::Total samples in data: 1595 2025-10-03 10:54:33.473881 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000 2025-10-03 10:54:33.483933 INFO::Total filtered features: 0 2025-10-03 10:54:33.495201 INFO::Filtered feature names from abundance and prevalence filtering: 2025-10-03 10:54:33.523101 INFO::Total filtered features with variance filtering: 0 2025-10-03 10:54:33.524843 INFO::Filtered feature names from variance filtering: 2025-10-03 10:54:33.526311 INFO::Running selected normalization method: TSS 2025-10-03 10:54:35.059045 INFO::Bypass z-score application to metadata 2025-10-03 10:54:35.060652 INFO::Running selected transform method: AST 2025-10-03 10:54:35.084868 INFO::Running selected analysis method: LM 2025-10-03 10:54:35.782634 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis 2025-10-03 10:54:36.290042 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum 2025-10-03 10:54:36.529799 INFO::Fitting model to feature number 3, Bifidobacterium.longum 2025-10-03 10:54:36.771544 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum 2025-10-03 10:54:37.028343 INFO::Fitting model to feature number 5, Collinsella.aerofaciens 2025-10-03 10:54:37.262208 INFO::Fitting model to feature number 6, Bacteroides.caccae 2025-10-03 10:54:37.495844 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus 2025-10-03 10:54:37.737993 INFO::Fitting model to feature number 8, Bacteroides.dorei 2025-10-03 10:54:37.974098 INFO::Fitting model to feature number 9, Bacteroides.eggerthii 2025-10-03 10:54:38.211299 INFO::Fitting model to feature number 10, Bacteroides.faecis 2025-10-03 10:54:38.465732 INFO::Fitting model to feature number 11, Bacteroides.finegoldii 2025-10-03 10:54:38.725039 INFO::Fitting model to feature number 12, Bacteroides.fragilis 2025-10-03 10:54:38.954125 INFO::Fitting model to feature number 13, Bacteroides.intestinalis 2025-10-03 10:54:39.146698 WARNING::Fitting problem for feature 13 a warning was issued 2025-10-03 10:54:39.446509 INFO::Fitting model to feature number 14, Bacteroides.massiliensis 2025-10-03 10:54:39.675071 INFO::Fitting model to feature number 15, Bacteroides.ovatus 2025-10-03 10:54:39.905356 INFO::Fitting model to feature number 16, Bacteroides.salyersiae 2025-10-03 10:54:40.138842 INFO::Fitting model to feature number 17, Bacteroides.stercoris 2025-10-03 10:54:40.378986 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron 2025-10-03 10:54:40.611556 INFO::Fitting model to feature number 19, Bacteroides.uniformis 2025-10-03 10:54:41.140607 INFO::Fitting model to feature number 20, Bacteroides.vulgatus 2025-10-03 10:54:41.377849 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens 2025-10-03 10:54:41.613668 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8 2025-10-03 10:54:41.838922 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis 2025-10-03 10:54:42.074826 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus 2025-10-03 10:54:42.316568 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus 2025-10-03 10:54:42.544465 INFO::Fitting model to feature number 26, Parabacteroides.distasonis 2025-10-03 10:54:42.77087 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii 2025-10-03 10:54:43.031312 INFO::Fitting model to feature number 28, Parabacteroides.merdae 2025-10-03 10:54:43.273836 INFO::Fitting model to feature number 29, Parabacteroides.unclassified 2025-10-03 10:54:43.541204 INFO::Fitting model to feature number 30, Paraprevotella.clara 2025-10-03 10:54:43.765055 INFO::Fitting model to feature number 31, Paraprevotella.unclassified 2025-10-03 10:54:44.000097 INFO::Fitting model to feature number 32, Prevotella.copri 2025-10-03 10:54:44.226328 INFO::Fitting model to feature number 33, Alistipes.finegoldii 2025-10-03 10:54:44.474078 INFO::Fitting model to feature number 34, Alistipes.onderdonkii 2025-10-03 10:54:44.694908 INFO::Fitting model to feature number 35, Alistipes.putredinis 2025-10-03 10:54:44.920761 INFO::Fitting model to feature number 36, Alistipes.shahii 2025-10-03 10:54:45.156149 INFO::Fitting model to feature number 37, Alistipes.unclassified 2025-10-03 10:54:45.383121 INFO::Fitting model to feature number 38, Streptococcus.salivarius 2025-10-03 10:54:45.604591 INFO::Fitting model to feature number 39, Clostridium.bolteae 2025-10-03 10:54:45.850891 INFO::Fitting model to feature number 40, Clostridium.citroniae 2025-10-03 10:54:46.098025 INFO::Fitting model to feature number 41, Clostridium.clostridioforme 2025-10-03 10:54:46.351791 INFO::Fitting model to feature number 42, Clostridium.hathewayi 2025-10-03 10:54:46.601455 INFO::Fitting model to feature number 43, Clostridium.leptum 2025-10-03 10:54:46.817928 INFO::Fitting model to feature number 44, Clostridium.nexile 2025-10-03 10:54:47.029703 INFO::Fitting model to feature number 45, Clostridium.symbiosum 2025-10-03 10:54:47.257523 INFO::Fitting model to feature number 46, Flavonifractor.plautii 2025-10-03 10:54:47.480767 INFO::Fitting model to feature number 47, Eubacterium.eligens 2025-10-03 10:54:47.710345 INFO::Fitting model to feature number 48, Eubacterium.hallii 2025-10-03 10:54:47.936206 INFO::Fitting model to feature number 49, Eubacterium.rectale 2025-10-03 10:54:48.157204 INFO::Fitting model to feature number 50, Eubacterium.siraeum 2025-10-03 10:54:48.385388 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31 2025-10-03 10:54:48.602121 INFO::Fitting model to feature number 52, Eubacterium.ventriosum 2025-10-03 10:54:48.825798 INFO::Fitting model to feature number 53, Ruminococcus.gnavus 2025-10-03 10:54:49.07164 INFO::Fitting model to feature number 54, Ruminococcus.obeum 2025-10-03 10:54:49.314866 INFO::Fitting model to feature number 55, Ruminococcus.torques 2025-10-03 10:54:49.56949 INFO::Fitting model to feature number 56, Coprococcus.comes 2025-10-03 10:54:49.811133 INFO::Fitting model to feature number 57, Dorea.longicatena 2025-10-03 10:54:50.026645 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA 2025-10-03 10:54:50.264345 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA 2025-10-03 10:54:50.479993 INFO::Fitting model to feature number 60, Roseburia.hominis 2025-10-03 10:54:50.705064 INFO::Fitting model to feature number 61, Roseburia.intestinalis 2025-10-03 10:54:50.927827 INFO::Fitting model to feature number 62, Roseburia.inulinivorans 2025-10-03 10:54:51.168456 INFO::Fitting model to feature number 63, Roseburia.unclassified 2025-10-03 10:54:51.390849 INFO::Fitting model to feature number 64, Oscillibacter.unclassified 2025-10-03 10:54:51.616466 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified 2025-10-03 10:54:51.833753 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii 2025-10-03 10:54:52.067578 INFO::Fitting model to feature number 67, Ruminococcus.bromii 2025-10-03 10:54:52.281478 INFO::Fitting model to feature number 68, Ruminococcus.callidus 2025-10-03 10:54:52.523352 INFO::Fitting model to feature number 69, Ruminococcus.lactaris 2025-10-03 10:54:52.779474 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified 2025-10-03 10:54:53.033661 INFO::Fitting model to feature number 71, Coprobacillus.unclassified 2025-10-03 10:54:53.267054 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified 2025-10-03 10:54:53.488282 INFO::Fitting model to feature number 73, Dialister.invisus 2025-10-03 10:54:54.025945 INFO::Fitting model to feature number 74, Veillonella.atypica 2025-10-03 10:54:54.253907 INFO::Fitting model to feature number 75, Veillonella.dispar 2025-10-03 10:54:54.488454 INFO::Fitting model to feature number 76, Veillonella.parvula 2025-10-03 10:54:54.718023 INFO::Fitting model to feature number 77, Veillonella.unclassified 2025-10-03 10:54:54.963553 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47 2025-10-03 10:54:55.219508 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis 2025-10-03 10:54:55.456688 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis 2025-10-03 10:54:55.684138 INFO::Fitting model to feature number 81, Bilophila.unclassified 2025-10-03 10:54:55.931563 INFO::Fitting model to feature number 82, Escherichia.coli 2025-10-03 10:54:56.163586 INFO::Fitting model to feature number 83, Escherichia.unclassified 2025-10-03 10:54:56.381445 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae 2025-10-03 10:54:56.610185 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae 2025-10-03 10:54:56.847494 INFO::Fitting model to feature number 86, Akkermansia.muciniphila 2025-10-03 10:54:57.086848 INFO::Fitting model to feature number 87, C2likevirus.unclassified 2025-10-03 10:54:57.402928 INFO::Counting total values for each feature 2025-10-03 10:54:57.45859 INFO::Writing filtered data to file output/features/filtered_data.tsv 2025-10-03 10:54:57.57552 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv 2025-10-03 10:54:57.694423 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv 2025-10-03 10:54:57.817174 INFO::Writing residuals to file output/fits/residuals.rds 2025-10-03 10:54:57.874109 INFO::Writing fitted values to file output/fits/fitted.rds 2025-10-03 10:54:57.905668 INFO::Writing extracted random effects to file output/fits/ranef.rds 2025-10-03 10:54:58.230141 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv 2025-10-03 10:54:58.237783 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" 2025-10-03 10:54:58.254808 INFO::Writing function arguments to log file 2025-10-03 10:54:58.262978 INFO::Verifying options selected are valid 2025-10-03 10:54:58.264382 INFO::Determining format of input files 2025-10-03 10:54:58.266114 INFO::Input format is data samples as rows and metadata samples as rows 2025-10-03 10:54:58.274187 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject) 2025-10-03 10:54:58.275904 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age 2025-10-03 10:54:58.278301 INFO::Filter data based on min abundance and min prevalence 2025-10-03 10:54:58.279603 INFO::Total samples in data: 1595 2025-10-03 10:54:58.280853 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000 2025-10-03 10:54:58.29033 INFO::Total filtered features: 0 2025-10-03 10:54:58.291944 INFO::Filtered feature names from abundance and prevalence filtering: 2025-10-03 10:54:58.319174 INFO::Total filtered features with variance filtering: 0 2025-10-03 10:54:58.320819 INFO::Filtered feature names from variance filtering: 2025-10-03 10:54:58.322105 INFO::Running selected normalization method: NONE 2025-10-03 10:54:58.323295 INFO::Bypass z-score application to metadata 2025-10-03 10:54:58.32448 INFO::Running selected transform method: AST 2025-10-03 10:54:58.34743 INFO::Running selected analysis method: LM 2025-10-03 10:54:58.349524 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis 2025-10-03 10:54:58.566902 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum 2025-10-03 10:54:58.784421 INFO::Fitting model to feature number 3, Bifidobacterium.longum 2025-10-03 10:54:58.996874 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum 2025-10-03 10:54:59.229499 INFO::Fitting model to feature number 5, Collinsella.aerofaciens 2025-10-03 10:54:59.4483 INFO::Fitting model to feature number 6, Bacteroides.caccae 2025-10-03 10:54:59.683905 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus 2025-10-03 10:54:59.917785 INFO::Fitting model to feature number 8, Bacteroides.dorei 2025-10-03 10:55:00.15065 INFO::Fitting model to feature number 9, Bacteroides.eggerthii 2025-10-03 10:55:00.339604 WARNING::Fitting problem for feature 9 a warning was issued 2025-10-03 10:55:00.603836 INFO::Fitting model to feature number 10, Bacteroides.faecis 2025-10-03 10:55:00.825297 INFO::Fitting model to feature number 11, Bacteroides.finegoldii 2025-10-03 10:55:01.057687 INFO::Fitting model to feature number 12, Bacteroides.fragilis 2025-10-03 10:55:01.269164 INFO::Fitting model to feature number 13, Bacteroides.intestinalis 2025-10-03 10:55:01.449282 WARNING::Fitting problem for feature 13 a warning was issued 2025-10-03 10:55:01.677207 INFO::Fitting model to feature number 14, Bacteroides.massiliensis 2025-10-03 10:55:01.904294 INFO::Fitting model to feature number 15, Bacteroides.ovatus 2025-10-03 10:55:02.157064 INFO::Fitting model to feature number 16, Bacteroides.salyersiae 2025-10-03 10:55:02.337534 WARNING::Fitting problem for feature 16 a warning was issued 2025-10-03 10:55:02.56588 INFO::Fitting model to feature number 17, Bacteroides.stercoris 2025-10-03 10:55:02.791013 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron 2025-10-03 10:55:03.025202 INFO::Fitting model to feature number 19, Bacteroides.uniformis 2025-10-03 10:55:03.248711 INFO::Fitting model to feature number 20, Bacteroides.vulgatus 2025-10-03 10:55:03.461318 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens 2025-10-03 10:55:03.679194 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8 2025-10-03 10:55:03.910134 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis 2025-10-03 10:55:04.117807 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus 2025-10-03 10:55:04.335074 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus 2025-10-03 10:55:04.553925 INFO::Fitting model to feature number 26, Parabacteroides.distasonis 2025-10-03 10:55:04.781539 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii 2025-10-03 10:55:05.001067 INFO::Fitting model to feature number 28, Parabacteroides.merdae 2025-10-03 10:55:05.21628 INFO::Fitting model to feature number 29, Parabacteroides.unclassified 2025-10-03 10:55:05.428723 INFO::Fitting model to feature number 30, Paraprevotella.clara 2025-10-03 10:55:05.642022 INFO::Fitting model to feature number 31, Paraprevotella.unclassified 2025-10-03 10:55:05.878545 INFO::Fitting model to feature number 32, Prevotella.copri 2025-10-03 10:55:06.114767 INFO::Fitting model to feature number 33, Alistipes.finegoldii 2025-10-03 10:55:06.329178 INFO::Fitting model to feature number 34, Alistipes.onderdonkii 2025-10-03 10:55:06.549606 INFO::Fitting model to feature number 35, Alistipes.putredinis 2025-10-03 10:55:06.773067 INFO::Fitting model to feature number 36, Alistipes.shahii 2025-10-03 10:55:06.992225 INFO::Fitting model to feature number 37, Alistipes.unclassified 2025-10-03 10:55:07.20683 INFO::Fitting model to feature number 38, Streptococcus.salivarius 2025-10-03 10:55:07.422226 INFO::Fitting model to feature number 39, Clostridium.bolteae 2025-10-03 10:55:07.669818 INFO::Fitting model to feature number 40, Clostridium.citroniae 2025-10-03 10:55:07.882014 INFO::Fitting model to feature number 41, Clostridium.clostridioforme 2025-10-03 10:55:08.103358 INFO::Fitting model to feature number 42, Clostridium.hathewayi 2025-10-03 10:55:08.327393 INFO::Fitting model to feature number 43, Clostridium.leptum 2025-10-03 10:55:08.564726 INFO::Fitting model to feature number 44, Clostridium.nexile 2025-10-03 10:55:08.78544 INFO::Fitting model to feature number 45, Clostridium.symbiosum 2025-10-03 10:55:09.00143 INFO::Fitting model to feature number 46, Flavonifractor.plautii 2025-10-03 10:55:09.227808 INFO::Fitting model to feature number 47, Eubacterium.eligens 2025-10-03 10:55:09.453084 INFO::Fitting model to feature number 48, Eubacterium.hallii 2025-10-03 10:55:09.673244 INFO::Fitting model to feature number 49, Eubacterium.rectale 2025-10-03 10:55:09.889022 INFO::Fitting model to feature number 50, Eubacterium.siraeum 2025-10-03 10:55:10.09852 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31 2025-10-03 10:55:10.338212 INFO::Fitting model to feature number 52, Eubacterium.ventriosum 2025-10-03 10:55:10.542817 INFO::Fitting model to feature number 53, Ruminococcus.gnavus 2025-10-03 10:55:10.743314 INFO::Fitting model to feature number 54, Ruminococcus.obeum 2025-10-03 10:55:10.951289 INFO::Fitting model to feature number 55, Ruminococcus.torques 2025-10-03 10:55:11.172328 INFO::Fitting model to feature number 56, Coprococcus.comes 2025-10-03 10:55:11.388677 INFO::Fitting model to feature number 57, Dorea.longicatena 2025-10-03 10:55:11.600661 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA 2025-10-03 10:55:11.812727 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA 2025-10-03 10:55:12.04121 INFO::Fitting model to feature number 60, Roseburia.hominis 2025-10-03 10:55:12.254869 INFO::Fitting model to feature number 61, Roseburia.intestinalis 2025-10-03 10:55:12.470033 INFO::Fitting model to feature number 62, Roseburia.inulinivorans 2025-10-03 10:55:12.689448 INFO::Fitting model to feature number 63, Roseburia.unclassified 2025-10-03 10:55:12.90061 INFO::Fitting model to feature number 64, Oscillibacter.unclassified 2025-10-03 10:55:13.110024 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified 2025-10-03 10:55:13.320247 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii 2025-10-03 10:55:13.554619 INFO::Fitting model to feature number 67, Ruminococcus.bromii 2025-10-03 10:55:13.782328 INFO::Fitting model to feature number 68, Ruminococcus.callidus 2025-10-03 10:55:14.003946 INFO::Fitting model to feature number 69, Ruminococcus.lactaris 2025-10-03 10:55:14.563074 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified 2025-10-03 10:55:14.798387 INFO::Fitting model to feature number 71, Coprobacillus.unclassified 2025-10-03 10:55:15.016292 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified 2025-10-03 10:55:15.090233 WARNING::Fitting problem for feature 72 a warning was issued 2025-10-03 10:55:15.301056 INFO::Fitting model to feature number 73, Dialister.invisus 2025-10-03 10:55:15.529124 INFO::Fitting model to feature number 74, Veillonella.atypica 2025-10-03 10:55:15.748156 INFO::Fitting model to feature number 75, Veillonella.dispar 2025-10-03 10:55:15.96632 INFO::Fitting model to feature number 76, Veillonella.parvula 2025-10-03 10:55:16.184408 INFO::Fitting model to feature number 77, Veillonella.unclassified 2025-10-03 10:55:16.408397 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47 2025-10-03 10:55:16.625731 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis 2025-10-03 10:55:16.852118 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis 2025-10-03 10:55:17.065433 INFO::Fitting model to feature number 81, Bilophila.unclassified 2025-10-03 10:55:17.300084 INFO::Fitting model to feature number 82, Escherichia.coli 2025-10-03 10:55:17.517936 INFO::Fitting model to feature number 83, Escherichia.unclassified 2025-10-03 10:55:17.73096 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae 2025-10-03 10:55:17.94763 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae 2025-10-03 10:55:18.185122 INFO::Fitting model to feature number 86, Akkermansia.muciniphila 2025-10-03 10:55:18.406489 INFO::Fitting model to feature number 87, C2likevirus.unclassified 2025-10-03 10:55:18.668553 INFO::Counting total values for each feature 2025-10-03 10:55:18.706234 INFO::Writing filtered data to file output2/features/filtered_data.tsv 2025-10-03 10:55:18.822235 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv 2025-10-03 10:55:18.938063 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv 2025-10-03 10:55:19.06038 INFO::Writing residuals to file output2/fits/residuals.rds 2025-10-03 10:55:19.135478 INFO::Writing fitted values to file output2/fits/fitted.rds 2025-10-03 10:55:19.207217 INFO::Writing extracted random effects to file output2/fits/ranef.rds 2025-10-03 10:55:19.214027 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv 2025-10-03 10:55:19.219824 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 5 | SKIP 0 | PASS 12 ] [ FAIL 0 | WARN 5 | SKIP 0 | PASS 12 ] > > > proc.time() user system elapsed 46.828 0.522 47.447
Maaslin2.Rcheck/Maaslin2-Ex.timings
name | user | system | elapsed | |
Maaslin2 | 123.015 | 1.101 | 124.460 | |