Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-11 11:40 -0400 (Thu, 11 Sep 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" | 4824 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4606 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4547 |
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 | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 1.22.0 |
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_1.22.0.tar.gz |
StartedAt: 2025-09-10 01:14:53 -0400 (Wed, 10 Sep 2025) |
EndedAt: 2025-09-10 01:17:46 -0400 (Wed, 10 Sep 2025) |
EllapsedTime: 172.4 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_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Maaslin2.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 13.7.5 * 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 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 91.732 1.787 94.306 * 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-3.21-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-arm64/Resources/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 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(Maaslin2) > > test_check("Maaslin2") [1] "Creating output folder" [1] "Creating output feature tables folder" [1] "Creating output fits folder" 2025-09-10 01:17:01.773406 INFO::Writing function arguments to log file 2025-09-10 01:17:01.82148 INFO::Verifying options selected are valid 2025-09-10 01:17:01.861475 INFO::Determining format of input files 2025-09-10 01:17:01.863585 INFO::Input format is data samples as rows and metadata samples as rows 2025-09-10 01:17:01.870663 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject) 2025-09-10 01:17:01.87235 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age 2025-09-10 01:17:01.874819 INFO::Filter data based on min abundance and min prevalence 2025-09-10 01:17:01.875835 INFO::Total samples in data: 1595 2025-09-10 01:17:01.876675 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000 2025-09-10 01:17:01.888321 INFO::Total filtered features: 0 2025-09-10 01:17:01.88987 INFO::Filtered feature names from abundance and prevalence filtering: 2025-09-10 01:17:01.898327 INFO::Total filtered features with variance filtering: 0 2025-09-10 01:17:01.899608 INFO::Filtered feature names from variance filtering: 2025-09-10 01:17:01.900456 INFO::Running selected normalization method: TSS 2025-09-10 01:17:03.083023 INFO::Bypass z-score application to metadata 2025-09-10 01:17:03.08483 INFO::Running selected transform method: AST 2025-09-10 01:17:03.10322 INFO::Running selected analysis method: LM 2025-09-10 01:17:03.808322 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis 2025-09-10 01:17:04.3262 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum 2025-09-10 01:17:04.501191 INFO::Fitting model to feature number 3, Bifidobacterium.longum 2025-09-10 01:17:04.702342 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum 2025-09-10 01:17:04.88643 INFO::Fitting model to feature number 5, Collinsella.aerofaciens 2025-09-10 01:17:05.065893 INFO::Fitting model to feature number 6, Bacteroides.caccae 2025-09-10 01:17:05.242819 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus 2025-09-10 01:17:05.426985 INFO::Fitting model to feature number 8, Bacteroides.dorei 2025-09-10 01:17:05.606138 INFO::Fitting model to feature number 9, Bacteroides.eggerthii 2025-09-10 01:17:05.748282 WARNING::Fitting problem for feature 9 a warning was issued 2025-09-10 01:17:05.94533 INFO::Fitting model to feature number 10, Bacteroides.faecis 2025-09-10 01:17:06.113073 INFO::Fitting model to feature number 11, Bacteroides.finegoldii 2025-09-10 01:17:06.286493 INFO::Fitting model to feature number 12, Bacteroides.fragilis 2025-09-10 01:17:06.500075 INFO::Fitting model to feature number 13, Bacteroides.intestinalis 2025-09-10 01:17:06.673415 INFO::Fitting model to feature number 14, Bacteroides.massiliensis 2025-09-10 01:17:06.844664 INFO::Fitting model to feature number 15, Bacteroides.ovatus 2025-09-10 01:17:07.024244 INFO::Fitting model to feature number 16, Bacteroides.salyersiae 2025-09-10 01:17:07.208829 INFO::Fitting model to feature number 17, Bacteroides.stercoris 2025-09-10 01:17:07.393947 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron 2025-09-10 01:17:07.578666 INFO::Fitting model to feature number 19, Bacteroides.uniformis 2025-09-10 01:17:07.768684 INFO::Fitting model to feature number 20, Bacteroides.vulgatus 2025-09-10 01:17:07.943837 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens 2025-09-10 01:17:08.115214 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8 2025-09-10 01:17:08.29596 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis 2025-09-10 01:17:08.459658 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus 2025-09-10 01:17:08.635814 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus 2025-09-10 01:17:08.809686 INFO::Fitting model to feature number 26, Parabacteroides.distasonis 2025-09-10 01:17:08.990129 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii 2025-09-10 01:17:09.175749 INFO::Fitting model to feature number 28, Parabacteroides.merdae 2025-09-10 01:17:09.351626 INFO::Fitting model to feature number 29, Parabacteroides.unclassified 2025-09-10 01:17:09.542086 INFO::Fitting model to feature number 30, Paraprevotella.clara 2025-09-10 01:17:09.710515 INFO::Fitting model to feature number 31, Paraprevotella.unclassified 2025-09-10 01:17:09.890599 INFO::Fitting model to feature number 32, Prevotella.copri 2025-09-10 01:17:10.081956 INFO::Fitting model to feature number 33, Alistipes.finegoldii 2025-09-10 01:17:10.270089 INFO::Fitting model to feature number 34, Alistipes.onderdonkii 2025-09-10 01:17:10.436474 INFO::Fitting model to feature number 35, Alistipes.putredinis 2025-09-10 01:17:10.629092 INFO::Fitting model to feature number 36, Alistipes.shahii 2025-09-10 01:17:10.811756 INFO::Fitting model to feature number 37, Alistipes.unclassified 2025-09-10 01:17:11.000769 INFO::Fitting model to feature number 38, Streptococcus.salivarius 2025-09-10 01:17:11.174556 INFO::Fitting model to feature number 39, Clostridium.bolteae 2025-09-10 01:17:11.345314 INFO::Fitting model to feature number 40, Clostridium.citroniae 2025-09-10 01:17:11.54055 INFO::Fitting model to feature number 41, Clostridium.clostridioforme 2025-09-10 01:17:11.721332 INFO::Fitting model to feature number 42, Clostridium.hathewayi 2025-09-10 01:17:11.905013 INFO::Fitting model to feature number 43, Clostridium.leptum 2025-09-10 01:17:12.088898 INFO::Fitting model to feature number 44, Clostridium.nexile 2025-09-10 01:17:12.261046 INFO::Fitting model to feature number 45, Clostridium.symbiosum 2025-09-10 01:17:12.449888 INFO::Fitting model to feature number 46, Flavonifractor.plautii 2025-09-10 01:17:12.627662 INFO::Fitting model to feature number 47, Eubacterium.eligens 2025-09-10 01:17:12.814013 INFO::Fitting model to feature number 48, Eubacterium.hallii 2025-09-10 01:17:12.999538 INFO::Fitting model to feature number 49, Eubacterium.rectale 2025-09-10 01:17:13.169316 INFO::Fitting model to feature number 50, Eubacterium.siraeum 2025-09-10 01:17:13.339448 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31 2025-09-10 01:17:13.503287 INFO::Fitting model to feature number 52, Eubacterium.ventriosum 2025-09-10 01:17:13.685088 INFO::Fitting model to feature number 53, Ruminococcus.gnavus 2025-09-10 01:17:13.865033 INFO::Fitting model to feature number 54, Ruminococcus.obeum 2025-09-10 01:17:14.039113 INFO::Fitting model to feature number 55, Ruminococcus.torques 2025-09-10 01:17:14.215066 INFO::Fitting model to feature number 56, Coprococcus.comes 2025-09-10 01:17:14.407585 INFO::Fitting model to feature number 57, Dorea.longicatena 2025-09-10 01:17:14.57093 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA 2025-09-10 01:17:14.759385 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA 2025-09-10 01:17:14.930903 INFO::Fitting model to feature number 60, Roseburia.hominis 2025-09-10 01:17:15.115754 INFO::Fitting model to feature number 61, Roseburia.intestinalis 2025-09-10 01:17:15.300833 INFO::Fitting model to feature number 62, Roseburia.inulinivorans 2025-09-10 01:17:15.485733 INFO::Fitting model to feature number 63, Roseburia.unclassified 2025-09-10 01:17:15.667715 INFO::Fitting model to feature number 64, Oscillibacter.unclassified 2025-09-10 01:17:15.87485 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified 2025-09-10 01:17:16.039401 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii 2025-09-10 01:17:16.212058 INFO::Fitting model to feature number 67, Ruminococcus.bromii 2025-09-10 01:17:16.37932 INFO::Fitting model to feature number 68, Ruminococcus.callidus 2025-09-10 01:17:16.845695 INFO::Fitting model to feature number 69, Ruminococcus.lactaris 2025-09-10 01:17:17.025918 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified 2025-09-10 01:17:17.199786 INFO::Fitting model to feature number 71, Coprobacillus.unclassified 2025-09-10 01:17:17.376832 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified 2025-09-10 01:17:17.548029 INFO::Fitting model to feature number 73, Dialister.invisus 2025-09-10 01:17:17.724859 INFO::Fitting model to feature number 74, Veillonella.atypica 2025-09-10 01:17:18.184011 INFO::Fitting model to feature number 75, Veillonella.dispar 2025-09-10 01:17:18.354716 INFO::Fitting model to feature number 76, Veillonella.parvula 2025-09-10 01:17:18.532038 INFO::Fitting model to feature number 77, Veillonella.unclassified 2025-09-10 01:17:18.717359 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47 2025-09-10 01:17:18.915938 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis 2025-09-10 01:17:19.096074 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis 2025-09-10 01:17:19.263482 INFO::Fitting model to feature number 81, Bilophila.unclassified 2025-09-10 01:17:19.441349 INFO::Fitting model to feature number 82, Escherichia.coli 2025-09-10 01:17:19.624411 INFO::Fitting model to feature number 83, Escherichia.unclassified 2025-09-10 01:17:19.785678 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae 2025-09-10 01:17:19.961925 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae 2025-09-10 01:17:20.139025 INFO::Fitting model to feature number 86, Akkermansia.muciniphila 2025-09-10 01:17:20.315118 INFO::Fitting model to feature number 87, C2likevirus.unclassified 2025-09-10 01:17:20.52985 INFO::Counting total values for each feature 2025-09-10 01:17:20.567612 INFO::Writing filtered data to file output/features/filtered_data.tsv 2025-09-10 01:17:20.714585 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv 2025-09-10 01:17:20.887218 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv 2025-09-10 01:17:21.06352 INFO::Writing residuals to file output/fits/residuals.rds 2025-09-10 01:17:21.145227 INFO::Writing fitted values to file output/fits/fitted.rds 2025-09-10 01:17:21.189616 INFO::Writing extracted random effects to file output/fits/ranef.rds 2025-09-10 01:17:21.199256 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv 2025-09-10 01:17:21.20826 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" 2025-09-10 01:17:21.224455 INFO::Writing function arguments to log file 2025-09-10 01:17:21.230857 INFO::Verifying options selected are valid 2025-09-10 01:17:21.232012 INFO::Determining format of input files 2025-09-10 01:17:21.233308 INFO::Input format is data samples as rows and metadata samples as rows 2025-09-10 01:17:21.239654 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject) 2025-09-10 01:17:21.240911 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age 2025-09-10 01:17:21.242577 INFO::Filter data based on min abundance and min prevalence 2025-09-10 01:17:21.243485 INFO::Total samples in data: 1595 2025-09-10 01:17:21.24429 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000 2025-09-10 01:17:21.248572 INFO::Total filtered features: 0 2025-09-10 01:17:21.249802 INFO::Filtered feature names from abundance and prevalence filtering: 2025-09-10 01:17:21.271171 INFO::Total filtered features with variance filtering: 0 2025-09-10 01:17:21.272876 INFO::Filtered feature names from variance filtering: 2025-09-10 01:17:21.273845 INFO::Running selected normalization method: NONE 2025-09-10 01:17:21.274727 INFO::Bypass z-score application to metadata 2025-09-10 01:17:21.275549 INFO::Running selected transform method: AST 2025-09-10 01:17:21.29172 INFO::Running selected analysis method: LM 2025-09-10 01:17:21.293775 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis 2025-09-10 01:17:21.457914 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum 2025-09-10 01:17:21.623478 INFO::Fitting model to feature number 3, Bifidobacterium.longum 2025-09-10 01:17:21.787745 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum 2025-09-10 01:17:21.968809 INFO::Fitting model to feature number 5, Collinsella.aerofaciens 2025-09-10 01:17:22.133279 INFO::Fitting model to feature number 6, Bacteroides.caccae 2025-09-10 01:17:22.312952 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus 2025-09-10 01:17:22.485315 INFO::Fitting model to feature number 8, Bacteroides.dorei 2025-09-10 01:17:22.665221 INFO::Fitting model to feature number 9, Bacteroides.eggerthii 2025-09-10 01:17:22.833926 INFO::Fitting model to feature number 10, Bacteroides.faecis 2025-09-10 01:17:22.999441 INFO::Fitting model to feature number 11, Bacteroides.finegoldii 2025-09-10 01:17:23.138076 WARNING::Fitting problem for feature 11 a warning was issued 2025-09-10 01:17:23.328467 INFO::Fitting model to feature number 12, Bacteroides.fragilis 2025-09-10 01:17:23.485753 INFO::Fitting model to feature number 13, Bacteroides.intestinalis 2025-09-10 01:17:23.621217 WARNING::Fitting problem for feature 13 a warning was issued 2025-09-10 01:17:23.792164 INFO::Fitting model to feature number 14, Bacteroides.massiliensis 2025-09-10 01:17:23.963306 INFO::Fitting model to feature number 15, Bacteroides.ovatus 2025-09-10 01:17:24.127773 INFO::Fitting model to feature number 16, Bacteroides.salyersiae 2025-09-10 01:17:24.285661 INFO::Fitting model to feature number 17, Bacteroides.stercoris 2025-09-10 01:17:24.45297 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron 2025-09-10 01:17:24.623658 INFO::Fitting model to feature number 19, Bacteroides.uniformis 2025-09-10 01:17:24.77672 INFO::Fitting model to feature number 20, Bacteroides.vulgatus 2025-09-10 01:17:24.947752 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens 2025-09-10 01:17:25.127634 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8 2025-09-10 01:17:25.296915 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis 2025-09-10 01:17:25.457248 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus 2025-09-10 01:17:25.62974 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus 2025-09-10 01:17:26.107639 INFO::Fitting model to feature number 26, Parabacteroides.distasonis 2025-09-10 01:17:26.272071 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii 2025-09-10 01:17:26.438282 INFO::Fitting model to feature number 28, Parabacteroides.merdae 2025-09-10 01:17:26.594667 INFO::Fitting model to feature number 29, Parabacteroides.unclassified 2025-09-10 01:17:26.767148 INFO::Fitting model to feature number 30, Paraprevotella.clara 2025-09-10 01:17:26.928481 INFO::Fitting model to feature number 31, Paraprevotella.unclassified 2025-09-10 01:17:27.091529 INFO::Fitting model to feature number 32, Prevotella.copri 2025-09-10 01:17:27.259188 INFO::Fitting model to feature number 33, Alistipes.finegoldii 2025-09-10 01:17:27.451372 INFO::Fitting model to feature number 34, Alistipes.onderdonkii 2025-09-10 01:17:27.612054 INFO::Fitting model to feature number 35, Alistipes.putredinis 2025-09-10 01:17:27.780978 INFO::Fitting model to feature number 36, Alistipes.shahii 2025-09-10 01:17:27.954753 INFO::Fitting model to feature number 37, Alistipes.unclassified 2025-09-10 01:17:28.138637 INFO::Fitting model to feature number 38, Streptococcus.salivarius 2025-09-10 01:17:28.300774 INFO::Fitting model to feature number 39, Clostridium.bolteae 2025-09-10 01:17:28.461625 INFO::Fitting model to feature number 40, Clostridium.citroniae 2025-09-10 01:17:28.616952 INFO::Fitting model to feature number 41, Clostridium.clostridioforme 2025-09-10 01:17:28.790817 INFO::Fitting model to feature number 42, Clostridium.hathewayi 2025-09-10 01:17:28.947935 INFO::Fitting model to feature number 43, Clostridium.leptum 2025-09-10 01:17:29.113351 INFO::Fitting model to feature number 44, Clostridium.nexile 2025-09-10 01:17:29.278696 INFO::Fitting model to feature number 45, Clostridium.symbiosum 2025-09-10 01:17:29.45371 INFO::Fitting model to feature number 46, Flavonifractor.plautii 2025-09-10 01:17:29.619702 INFO::Fitting model to feature number 47, Eubacterium.eligens 2025-09-10 01:17:29.774543 INFO::Fitting model to feature number 48, Eubacterium.hallii 2025-09-10 01:17:29.939358 INFO::Fitting model to feature number 49, Eubacterium.rectale 2025-09-10 01:17:30.099644 INFO::Fitting model to feature number 50, Eubacterium.siraeum 2025-09-10 01:17:30.260371 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31 2025-09-10 01:17:30.425274 INFO::Fitting model to feature number 52, Eubacterium.ventriosum 2025-09-10 01:17:30.576932 INFO::Fitting model to feature number 53, Ruminococcus.gnavus 2025-09-10 01:17:30.729022 INFO::Fitting model to feature number 54, Ruminococcus.obeum 2025-09-10 01:17:30.901429 INFO::Fitting model to feature number 55, Ruminococcus.torques 2025-09-10 01:17:31.064784 INFO::Fitting model to feature number 56, Coprococcus.comes 2025-09-10 01:17:31.230109 INFO::Fitting model to feature number 57, Dorea.longicatena 2025-09-10 01:17:31.389243 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA 2025-09-10 01:17:31.559877 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA 2025-09-10 01:17:31.722696 INFO::Fitting model to feature number 60, Roseburia.hominis 2025-09-10 01:17:31.876275 INFO::Fitting model to feature number 61, Roseburia.intestinalis 2025-09-10 01:17:32.034118 INFO::Fitting model to feature number 62, Roseburia.inulinivorans 2025-09-10 01:17:32.204191 INFO::Fitting model to feature number 63, Roseburia.unclassified 2025-09-10 01:17:32.360697 INFO::Fitting model to feature number 64, Oscillibacter.unclassified 2025-09-10 01:17:32.517722 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified 2025-09-10 01:17:32.678037 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii 2025-09-10 01:17:32.84732 INFO::Fitting model to feature number 67, Ruminococcus.bromii 2025-09-10 01:17:33.009143 INFO::Fitting model to feature number 68, Ruminococcus.callidus 2025-09-10 01:17:33.165588 INFO::Fitting model to feature number 69, Ruminococcus.lactaris 2025-09-10 01:17:33.336702 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified 2025-09-10 01:17:33.534688 INFO::Fitting model to feature number 71, Coprobacillus.unclassified 2025-09-10 01:17:33.698552 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified 2025-09-10 01:17:33.758207 WARNING::Fitting problem for feature 72 a warning was issued 2025-09-10 01:17:33.929031 INFO::Fitting model to feature number 73, Dialister.invisus 2025-09-10 01:17:34.091905 INFO::Fitting model to feature number 74, Veillonella.atypica 2025-09-10 01:17:34.270065 INFO::Fitting model to feature number 75, Veillonella.dispar 2025-09-10 01:17:34.4314 INFO::Fitting model to feature number 76, Veillonella.parvula 2025-09-10 01:17:34.606826 INFO::Fitting model to feature number 77, Veillonella.unclassified 2025-09-10 01:17:34.769987 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47 2025-09-10 01:17:34.94939 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis 2025-09-10 01:17:35.121232 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis 2025-09-10 01:17:35.292219 INFO::Fitting model to feature number 81, Bilophila.unclassified 2025-09-10 01:17:35.477175 INFO::Fitting model to feature number 82, Escherichia.coli 2025-09-10 01:17:35.656373 INFO::Fitting model to feature number 83, Escherichia.unclassified 2025-09-10 01:17:35.807311 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae 2025-09-10 01:17:35.96449 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae 2025-09-10 01:17:36.123506 INFO::Fitting model to feature number 86, Akkermansia.muciniphila 2025-09-10 01:17:36.304853 INFO::Fitting model to feature number 87, C2likevirus.unclassified 2025-09-10 01:17:36.491089 INFO::Counting total values for each feature 2025-09-10 01:17:36.518547 INFO::Writing filtered data to file output2/features/filtered_data.tsv 2025-09-10 01:17:36.663373 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv 2025-09-10 01:17:36.808865 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv 2025-09-10 01:17:36.992249 INFO::Writing residuals to file output2/fits/residuals.rds 2025-09-10 01:17:37.104273 INFO::Writing fitted values to file output2/fits/fitted.rds 2025-09-10 01:17:37.21017 INFO::Writing extracted random effects to file output2/fits/ranef.rds 2025-09-10 01:17:37.219568 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv 2025-09-10 01:17:37.226676 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 35.956 0.801 36.802
Maaslin2.Rcheck/Maaslin2-Ex.timings
name | user | system | elapsed | |
Maaslin2 | 91.732 | 1.787 | 94.306 | |