Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-11 12:03 -0400 (Thu, 11 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4539 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4474 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4519 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4544 |
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 1149/2322 | 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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Maaslin2_1.23.0.tar.gz |
StartedAt: 2025-09-11 02:03:15 -0400 (Thu, 11 Sep 2025) |
EndedAt: 2025-09-11 02:07:38 -0400 (Thu, 11 Sep 2025) |
EllapsedTime: 263.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Maaslin2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Maaslin2_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Maaslin2.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * 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 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 90.242 0.802 91.067 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.22-bioc/meat/Maaslin2.Rcheck/00check.log’ for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 Patched (2025-08-23 r88802) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(Maaslin2) > > test_check("Maaslin2") [1] "Creating output folder" [1] "Creating output feature tables folder" [1] "Creating output fits folder" 2025-09-11 02:05:16.864333 INFO::Writing function arguments to log file 2025-09-11 02:05:16.912032 INFO::Verifying options selected are valid 2025-09-11 02:05:16.945566 INFO::Determining format of input files 2025-09-11 02:05:16.947122 INFO::Input format is data samples as rows and metadata samples as rows 2025-09-11 02:05:16.952261 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject) 2025-09-11 02:05:16.953574 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age 2025-09-11 02:05:16.955986 INFO::Filter data based on min abundance and min prevalence 2025-09-11 02:05:16.956884 INFO::Total samples in data: 1595 2025-09-11 02:05:16.957706 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000 2025-09-11 02:05:16.969241 INFO::Total filtered features: 0 2025-09-11 02:05:16.970468 INFO::Filtered feature names from abundance and prevalence filtering: 2025-09-11 02:05:16.977247 INFO::Total filtered features with variance filtering: 0 2025-09-11 02:05:16.978304 INFO::Filtered feature names from variance filtering: 2025-09-11 02:05:16.979186 INFO::Running selected normalization method: TSS 2025-09-11 02:05:18.207938 INFO::Bypass z-score application to metadata 2025-09-11 02:05:18.209268 INFO::Running selected transform method: AST 2025-09-11 02:05:18.229567 INFO::Running selected analysis method: LM 2025-09-11 02:05:18.883693 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis 2025-09-11 02:05:19.373641 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum 2025-09-11 02:05:19.546526 INFO::Fitting model to feature number 3, Bifidobacterium.longum 2025-09-11 02:05:19.738408 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum 2025-09-11 02:05:19.899215 INFO::Fitting model to feature number 5, Collinsella.aerofaciens 2025-09-11 02:05:20.05421 INFO::Fitting model to feature number 6, Bacteroides.caccae 2025-09-11 02:05:20.261665 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus 2025-09-11 02:05:20.452906 INFO::Fitting model to feature number 8, Bacteroides.dorei 2025-09-11 02:05:20.576555 WARNING::Fitting problem for feature 8 a warning was issued 2025-09-11 02:05:20.748291 INFO::Fitting model to feature number 9, Bacteroides.eggerthii 2025-09-11 02:05:20.888873 WARNING::Fitting problem for feature 9 a warning was issued 2025-09-11 02:05:21.079837 INFO::Fitting model to feature number 10, Bacteroides.faecis 2025-09-11 02:05:21.229368 INFO::Fitting model to feature number 11, Bacteroides.finegoldii 2025-09-11 02:05:21.434918 INFO::Fitting model to feature number 12, Bacteroides.fragilis 2025-09-11 02:05:21.593992 INFO::Fitting model to feature number 13, Bacteroides.intestinalis 2025-09-11 02:05:21.7133 WARNING::Fitting problem for feature 13 a warning was issued 2025-09-11 02:05:21.884322 INFO::Fitting model to feature number 14, Bacteroides.massiliensis 2025-09-11 02:05:22.075234 INFO::Fitting model to feature number 15, Bacteroides.ovatus 2025-09-11 02:05:22.236986 INFO::Fitting model to feature number 16, Bacteroides.salyersiae 2025-09-11 02:05:22.388278 INFO::Fitting model to feature number 17, Bacteroides.stercoris 2025-09-11 02:05:22.588016 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron 2025-09-11 02:05:22.756547 INFO::Fitting model to feature number 19, Bacteroides.uniformis 2025-09-11 02:05:22.891935 INFO::Fitting model to feature number 20, Bacteroides.vulgatus 2025-09-11 02:05:23.054933 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens 2025-09-11 02:05:23.201507 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8 2025-09-11 02:05:23.346485 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis 2025-09-11 02:05:23.523299 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus 2025-09-11 02:05:23.690132 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus 2025-09-11 02:05:23.852236 INFO::Fitting model to feature number 26, Parabacteroides.distasonis 2025-09-11 02:05:23.995243 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii 2025-09-11 02:05:24.156144 INFO::Fitting model to feature number 28, Parabacteroides.merdae 2025-09-11 02:05:24.337445 INFO::Fitting model to feature number 29, Parabacteroides.unclassified 2025-09-11 02:05:24.527779 INFO::Fitting model to feature number 30, Paraprevotella.clara 2025-09-11 02:05:24.680158 INFO::Fitting model to feature number 31, Paraprevotella.unclassified 2025-09-11 02:05:24.842181 INFO::Fitting model to feature number 32, Prevotella.copri 2025-09-11 02:05:25.000746 INFO::Fitting model to feature number 33, Alistipes.finegoldii 2025-09-11 02:05:25.178265 INFO::Fitting model to feature number 34, Alistipes.onderdonkii 2025-09-11 02:05:25.323905 INFO::Fitting model to feature number 35, Alistipes.putredinis 2025-09-11 02:05:25.479026 INFO::Fitting model to feature number 36, Alistipes.shahii 2025-09-11 02:05:25.623542 INFO::Fitting model to feature number 37, Alistipes.unclassified 2025-09-11 02:05:25.785782 INFO::Fitting model to feature number 38, Streptococcus.salivarius 2025-09-11 02:05:25.938745 INFO::Fitting model to feature number 39, Clostridium.bolteae 2025-09-11 02:05:26.10241 INFO::Fitting model to feature number 40, Clostridium.citroniae 2025-09-11 02:05:26.266937 INFO::Fitting model to feature number 41, Clostridium.clostridioforme 2025-09-11 02:05:26.470542 INFO::Fitting model to feature number 42, Clostridium.hathewayi 2025-09-11 02:05:26.643975 INFO::Fitting model to feature number 43, Clostridium.leptum 2025-09-11 02:05:26.789781 INFO::Fitting model to feature number 44, Clostridium.nexile 2025-09-11 02:05:26.947897 INFO::Fitting model to feature number 45, Clostridium.symbiosum 2025-09-11 02:05:27.1098 INFO::Fitting model to feature number 46, Flavonifractor.plautii 2025-09-11 02:05:27.28164 INFO::Fitting model to feature number 47, Eubacterium.eligens 2025-09-11 02:05:27.448342 INFO::Fitting model to feature number 48, Eubacterium.hallii 2025-09-11 02:05:27.610004 INFO::Fitting model to feature number 49, Eubacterium.rectale 2025-09-11 02:05:27.755597 INFO::Fitting model to feature number 50, Eubacterium.siraeum 2025-09-11 02:05:27.920361 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31 2025-09-11 02:05:28.085744 INFO::Fitting model to feature number 52, Eubacterium.ventriosum 2025-09-11 02:05:28.234418 INFO::Fitting model to feature number 53, Ruminococcus.gnavus 2025-09-11 02:05:28.386517 INFO::Fitting model to feature number 54, Ruminococcus.obeum 2025-09-11 02:05:28.532106 INFO::Fitting model to feature number 55, Ruminococcus.torques 2025-09-11 02:05:28.677732 INFO::Fitting model to feature number 56, Coprococcus.comes 2025-09-11 02:05:28.836325 INFO::Fitting model to feature number 57, Dorea.longicatena 2025-09-11 02:05:28.974422 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA 2025-09-11 02:05:29.128299 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA 2025-09-11 02:05:29.277651 INFO::Fitting model to feature number 60, Roseburia.hominis 2025-09-11 02:05:29.430809 INFO::Fitting model to feature number 61, Roseburia.intestinalis 2025-09-11 02:05:29.576506 INFO::Fitting model to feature number 62, Roseburia.inulinivorans 2025-09-11 02:05:29.736507 INFO::Fitting model to feature number 63, Roseburia.unclassified 2025-09-11 02:05:29.918682 INFO::Fitting model to feature number 64, Oscillibacter.unclassified 2025-09-11 02:05:30.061193 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified 2025-09-11 02:05:30.210164 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii 2025-09-11 02:05:30.382743 INFO::Fitting model to feature number 67, Ruminococcus.bromii 2025-09-11 02:05:30.607507 INFO::Fitting model to feature number 68, Ruminococcus.callidus 2025-09-11 02:05:30.813372 INFO::Fitting model to feature number 69, Ruminococcus.lactaris 2025-09-11 02:05:30.993635 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified 2025-09-11 02:05:31.15366 INFO::Fitting model to feature number 71, Coprobacillus.unclassified 2025-09-11 02:05:31.298474 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified 2025-09-11 02:05:31.444191 INFO::Fitting model to feature number 73, Dialister.invisus 2025-09-11 02:05:31.597995 INFO::Fitting model to feature number 74, Veillonella.atypica 2025-09-11 02:05:31.749754 INFO::Fitting model to feature number 75, Veillonella.dispar 2025-09-11 02:05:31.906693 INFO::Fitting model to feature number 76, Veillonella.parvula 2025-09-11 02:05:32.069092 INFO::Fitting model to feature number 77, Veillonella.unclassified 2025-09-11 02:05:32.225431 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47 2025-09-11 02:05:32.391336 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis 2025-09-11 02:05:32.563129 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis 2025-09-11 02:05:32.711259 INFO::Fitting model to feature number 81, Bilophila.unclassified 2025-09-11 02:05:32.87312 INFO::Fitting model to feature number 82, Escherichia.coli 2025-09-11 02:05:33.028533 INFO::Fitting model to feature number 83, Escherichia.unclassified 2025-09-11 02:05:33.170879 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae 2025-09-11 02:05:33.337356 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae 2025-09-11 02:05:33.522087 INFO::Fitting model to feature number 86, Akkermansia.muciniphila 2025-09-11 02:05:33.699787 INFO::Fitting model to feature number 87, C2likevirus.unclassified 2025-09-11 02:05:33.94259 INFO::Counting total values for each feature 2025-09-11 02:05:33.978631 INFO::Writing filtered data to file output/features/filtered_data.tsv 2025-09-11 02:05:34.072637 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv 2025-09-11 02:05:34.16907 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv 2025-09-11 02:05:34.271909 INFO::Writing residuals to file output/fits/residuals.rds 2025-09-11 02:05:34.320244 INFO::Writing fitted values to file output/fits/fitted.rds 2025-09-11 02:05:34.599949 INFO::Writing extracted random effects to file output/fits/ranef.rds 2025-09-11 02:05:34.606431 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv 2025-09-11 02:05:34.61161 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" 2025-09-11 02:05:34.6239 INFO::Writing function arguments to log file 2025-09-11 02:05:34.629543 INFO::Verifying options selected are valid 2025-09-11 02:05:34.630591 INFO::Determining format of input files 2025-09-11 02:05:34.631844 INFO::Input format is data samples as rows and metadata samples as rows 2025-09-11 02:05:34.636896 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject) 2025-09-11 02:05:34.638016 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age 2025-09-11 02:05:34.639681 INFO::Filter data based on min abundance and min prevalence 2025-09-11 02:05:34.640557 INFO::Total samples in data: 1595 2025-09-11 02:05:34.641404 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000 2025-09-11 02:05:34.645024 INFO::Total filtered features: 0 2025-09-11 02:05:34.645997 INFO::Filtered feature names from abundance and prevalence filtering: 2025-09-11 02:05:34.651893 INFO::Total filtered features with variance filtering: 0 2025-09-11 02:05:34.652883 INFO::Filtered feature names from variance filtering: 2025-09-11 02:05:34.653694 INFO::Running selected normalization method: NONE 2025-09-11 02:05:34.654498 INFO::Bypass z-score application to metadata 2025-09-11 02:05:34.655299 INFO::Running selected transform method: AST 2025-09-11 02:05:34.668902 INFO::Running selected analysis method: LM 2025-09-11 02:05:34.670498 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis 2025-09-11 02:05:34.80966 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum 2025-09-11 02:05:34.99591 INFO::Fitting model to feature number 3, Bifidobacterium.longum 2025-09-11 02:05:35.140994 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum 2025-09-11 02:05:35.292075 INFO::Fitting model to feature number 5, Collinsella.aerofaciens 2025-09-11 02:05:35.446095 INFO::Fitting model to feature number 6, Bacteroides.caccae 2025-09-11 02:05:35.607461 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus 2025-09-11 02:05:35.755383 INFO::Fitting model to feature number 8, Bacteroides.dorei 2025-09-11 02:05:35.900355 INFO::Fitting model to feature number 9, Bacteroides.eggerthii 2025-09-11 02:05:36.060435 INFO::Fitting model to feature number 10, Bacteroides.faecis 2025-09-11 02:05:36.216798 INFO::Fitting model to feature number 11, Bacteroides.finegoldii 2025-09-11 02:05:36.341871 WARNING::Fitting problem for feature 11 a warning was issued 2025-09-11 02:05:36.48989 INFO::Fitting model to feature number 12, Bacteroides.fragilis 2025-09-11 02:05:36.632484 INFO::Fitting model to feature number 13, Bacteroides.intestinalis 2025-09-11 02:05:36.777853 INFO::Fitting model to feature number 14, Bacteroides.massiliensis 2025-09-11 02:05:36.919897 INFO::Fitting model to feature number 15, Bacteroides.ovatus 2025-09-11 02:05:37.072274 INFO::Fitting model to feature number 16, Bacteroides.salyersiae 2025-09-11 02:05:37.184558 WARNING::Fitting problem for feature 16 a warning was issued 2025-09-11 02:05:37.33164 INFO::Fitting model to feature number 17, Bacteroides.stercoris 2025-09-11 02:05:37.487348 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron 2025-09-11 02:05:37.625506 INFO::Fitting model to feature number 19, Bacteroides.uniformis 2025-09-11 02:05:37.763229 INFO::Fitting model to feature number 20, Bacteroides.vulgatus 2025-09-11 02:05:37.923221 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens 2025-09-11 02:05:38.075334 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8 2025-09-11 02:05:38.221434 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis 2025-09-11 02:05:38.367542 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus 2025-09-11 02:05:38.514564 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus 2025-09-11 02:05:38.663417 INFO::Fitting model to feature number 26, Parabacteroides.distasonis 2025-09-11 02:05:38.837014 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii 2025-09-11 02:05:38.991202 INFO::Fitting model to feature number 28, Parabacteroides.merdae 2025-09-11 02:05:39.13289 INFO::Fitting model to feature number 29, Parabacteroides.unclassified 2025-09-11 02:05:39.289076 INFO::Fitting model to feature number 30, Paraprevotella.clara 2025-09-11 02:05:39.431929 INFO::Fitting model to feature number 31, Paraprevotella.unclassified 2025-09-11 02:05:39.881868 INFO::Fitting model to feature number 32, Prevotella.copri 2025-09-11 02:05:40.020502 INFO::Fitting model to feature number 33, Alistipes.finegoldii 2025-09-11 02:05:40.163209 INFO::Fitting model to feature number 34, Alistipes.onderdonkii 2025-09-11 02:05:40.307218 INFO::Fitting model to feature number 35, Alistipes.putredinis 2025-09-11 02:05:40.456414 INFO::Fitting model to feature number 36, Alistipes.shahii 2025-09-11 02:05:40.597982 INFO::Fitting model to feature number 37, Alistipes.unclassified 2025-09-11 02:05:40.746649 INFO::Fitting model to feature number 38, Streptococcus.salivarius 2025-09-11 02:05:40.890503 INFO::Fitting model to feature number 39, Clostridium.bolteae 2025-09-11 02:05:41.039412 INFO::Fitting model to feature number 40, Clostridium.citroniae 2025-09-11 02:05:41.175191 INFO::Fitting model to feature number 41, Clostridium.clostridioforme 2025-09-11 02:05:41.313178 INFO::Fitting model to feature number 42, Clostridium.hathewayi 2025-09-11 02:05:41.465808 INFO::Fitting model to feature number 43, Clostridium.leptum 2025-09-11 02:05:41.612684 INFO::Fitting model to feature number 44, Clostridium.nexile 2025-09-11 02:05:41.754776 INFO::Fitting model to feature number 45, Clostridium.symbiosum 2025-09-11 02:05:41.89528 INFO::Fitting model to feature number 46, Flavonifractor.plautii 2025-09-11 02:05:42.04895 INFO::Fitting model to feature number 47, Eubacterium.eligens 2025-09-11 02:05:42.186835 INFO::Fitting model to feature number 48, Eubacterium.hallii 2025-09-11 02:05:42.335978 INFO::Fitting model to feature number 49, Eubacterium.rectale 2025-09-11 02:05:42.474754 INFO::Fitting model to feature number 50, Eubacterium.siraeum 2025-09-11 02:05:42.612496 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31 2025-09-11 02:05:42.753915 INFO::Fitting model to feature number 52, Eubacterium.ventriosum 2025-09-11 02:05:42.883936 INFO::Fitting model to feature number 53, Ruminococcus.gnavus 2025-09-11 02:05:43.024104 INFO::Fitting model to feature number 54, Ruminococcus.obeum 2025-09-11 02:05:43.162283 INFO::Fitting model to feature number 55, Ruminococcus.torques 2025-09-11 02:05:43.318127 INFO::Fitting model to feature number 56, Coprococcus.comes 2025-09-11 02:05:43.461549 INFO::Fitting model to feature number 57, Dorea.longicatena 2025-09-11 02:05:43.625915 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA 2025-09-11 02:05:43.767489 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA 2025-09-11 02:05:43.931734 INFO::Fitting model to feature number 60, Roseburia.hominis 2025-09-11 02:05:44.074816 INFO::Fitting model to feature number 61, Roseburia.intestinalis 2025-09-11 02:05:44.230821 INFO::Fitting model to feature number 62, Roseburia.inulinivorans 2025-09-11 02:05:44.375319 INFO::Fitting model to feature number 63, Roseburia.unclassified 2025-09-11 02:05:44.524458 INFO::Fitting model to feature number 64, Oscillibacter.unclassified 2025-09-11 02:05:44.685307 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified 2025-09-11 02:05:44.835048 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii 2025-09-11 02:05:44.980392 INFO::Fitting model to feature number 67, Ruminococcus.bromii 2025-09-11 02:05:45.101339 WARNING::Fitting problem for feature 67 a warning was issued 2025-09-11 02:05:45.276485 INFO::Fitting model to feature number 68, Ruminococcus.callidus 2025-09-11 02:05:45.42212 INFO::Fitting model to feature number 69, Ruminococcus.lactaris 2025-09-11 02:05:45.575175 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified 2025-09-11 02:05:45.74636 INFO::Fitting model to feature number 71, Coprobacillus.unclassified 2025-09-11 02:05:46.169194 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified 2025-09-11 02:05:46.22371 WARNING::Fitting problem for feature 72 a warning was issued 2025-09-11 02:05:46.366117 INFO::Fitting model to feature number 73, Dialister.invisus 2025-09-11 02:05:46.529182 INFO::Fitting model to feature number 74, Veillonella.atypica 2025-09-11 02:05:46.682871 INFO::Fitting model to feature number 75, Veillonella.dispar 2025-09-11 02:05:46.839137 INFO::Fitting model to feature number 76, Veillonella.parvula 2025-09-11 02:05:46.974751 INFO::Fitting model to feature number 77, Veillonella.unclassified 2025-09-11 02:05:47.116657 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47 2025-09-11 02:05:47.280287 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis 2025-09-11 02:05:47.430324 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis 2025-09-11 02:05:47.588548 INFO::Fitting model to feature number 81, Bilophila.unclassified 2025-09-11 02:05:47.73781 INFO::Fitting model to feature number 82, Escherichia.coli 2025-09-11 02:05:47.902204 INFO::Fitting model to feature number 83, Escherichia.unclassified 2025-09-11 02:05:48.050139 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae 2025-09-11 02:05:48.196731 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae 2025-09-11 02:05:48.347908 INFO::Fitting model to feature number 86, Akkermansia.muciniphila 2025-09-11 02:05:48.491997 INFO::Fitting model to feature number 87, C2likevirus.unclassified 2025-09-11 02:05:48.664379 INFO::Counting total values for each feature 2025-09-11 02:05:48.686508 INFO::Writing filtered data to file output2/features/filtered_data.tsv 2025-09-11 02:05:48.789409 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv 2025-09-11 02:05:48.904375 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv 2025-09-11 02:05:49.009195 INFO::Writing residuals to file output2/fits/residuals.rds 2025-09-11 02:05:49.072971 INFO::Writing fitted values to file output2/fits/fitted.rds 2025-09-11 02:05:49.134423 INFO::Writing extracted random effects to file output2/fits/ranef.rds 2025-09-11 02:05:49.139675 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv 2025-09-11 02:05:49.143755 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 7 | SKIP 0 | PASS 12 ] [ FAIL 0 | WARN 7 | SKIP 0 | PASS 12 ] > > > proc.time() user system elapsed 32.925 0.501 33.427
Maaslin2.Rcheck/Maaslin2-Ex.timings
name | user | system | elapsed | |
Maaslin2 | 90.242 | 0.802 | 91.067 | |