Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-01-20 11:40 -0500 (Mon, 20 Jan 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4777 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4502 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4461 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4416 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4403 |
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 1128/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Maaslin2 1.21.0 (landing page) Lauren McIver
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.21.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Maaslin2_1.21.0.tar.gz |
StartedAt: 2025-01-19 23:30:47 -0500 (Sun, 19 Jan 2025) |
EndedAt: 2025-01-19 23:34:58 -0500 (Sun, 19 Jan 2025) |
EllapsedTime: 250.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Maaslin2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Maaslin2_1.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘Maaslin2/DESCRIPTION’ ... OK * this is package ‘Maaslin2’ version ‘1.21.0’ * 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 88.21 1.511 89.709 * 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-3.21-bioc/meat/Maaslin2.Rcheck/00check.log’ for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘Maaslin2’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning in check_dep_version(dep_pkg = "TMB") : package version mismatch: glmmTMB was built with TMB package version 1.9.15 Current TMB package version is 1.9.16 Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information) ** 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) (2024-10-21 r87258) -- "Unsuffered Consequences" Copyright (C) 2024 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" 2025-01-19 23:32:46.40341 INFO::Writing function arguments to log file 2025-01-19 23:32:46.443619 INFO::Verifying options selected are valid 2025-01-19 23:32:46.475545 INFO::Determining format of input files 2025-01-19 23:32:46.477144 INFO::Input format is data samples as rows and metadata samples as rows 2025-01-19 23:32:46.482014 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject) 2025-01-19 23:32:46.48329 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age 2025-01-19 23:32:46.485557 INFO::Filter data based on min abundance and min prevalence 2025-01-19 23:32:46.486448 INFO::Total samples in data: 1595 2025-01-19 23:32:46.487279 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000 2025-01-19 23:32:46.491113 INFO::Total filtered features: 0 2025-01-19 23:32:46.492115 INFO::Filtered feature names from abundance and prevalence filtering: 2025-01-19 23:32:46.505399 INFO::Total filtered features with variance filtering: 0 2025-01-19 23:32:46.506502 INFO::Filtered feature names from variance filtering: 2025-01-19 23:32:46.507346 INFO::Running selected normalization method: TSS 2025-01-19 23:32:47.584563 INFO::Bypass z-score application to metadata 2025-01-19 23:32:47.585815 INFO::Running selected transform method: AST 2025-01-19 23:32:47.601915 INFO::Running selected analysis method: LM 2025-01-19 23:32:48.084542 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis 2025-01-19 23:32:48.412698 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum 2025-01-19 23:32:48.577746 INFO::Fitting model to feature number 3, Bifidobacterium.longum 2025-01-19 23:32:48.720688 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum 2025-01-19 23:32:48.871596 INFO::Fitting model to feature number 5, Collinsella.aerofaciens 2025-01-19 23:32:49.015307 INFO::Fitting model to feature number 6, Bacteroides.caccae 2025-01-19 23:32:49.389988 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus 2025-01-19 23:32:49.529011 INFO::Fitting model to feature number 8, Bacteroides.dorei 2025-01-19 23:32:49.638582 WARNING::Fitting problem for feature 8 a warning was issued 2025-01-19 23:32:49.803085 INFO::Fitting model to feature number 9, Bacteroides.eggerthii 2025-01-19 23:32:49.934664 WARNING::Fitting problem for feature 9 a warning was issued 2025-01-19 23:32:50.083724 INFO::Fitting model to feature number 10, Bacteroides.faecis 2025-01-19 23:32:50.221121 INFO::Fitting model to feature number 11, Bacteroides.finegoldii 2025-01-19 23:32:50.364283 INFO::Fitting model to feature number 12, Bacteroides.fragilis 2025-01-19 23:32:50.498027 INFO::Fitting model to feature number 13, Bacteroides.intestinalis 2025-01-19 23:32:50.614631 WARNING::Fitting problem for feature 13 a warning was issued 2025-01-19 23:32:50.759701 INFO::Fitting model to feature number 14, Bacteroides.massiliensis 2025-01-19 23:32:50.910822 INFO::Fitting model to feature number 15, Bacteroides.ovatus 2025-01-19 23:32:51.052231 INFO::Fitting model to feature number 16, Bacteroides.salyersiae 2025-01-19 23:32:51.206264 INFO::Fitting model to feature number 17, Bacteroides.stercoris 2025-01-19 23:32:51.371088 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron 2025-01-19 23:32:51.518962 INFO::Fitting model to feature number 19, Bacteroides.uniformis 2025-01-19 23:32:51.660642 INFO::Fitting model to feature number 20, Bacteroides.vulgatus 2025-01-19 23:32:51.801712 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens 2025-01-19 23:32:51.950228 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8 2025-01-19 23:32:52.089488 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis 2025-01-19 23:32:52.228262 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus 2025-01-19 23:32:52.375176 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus 2025-01-19 23:32:52.521427 INFO::Fitting model to feature number 26, Parabacteroides.distasonis 2025-01-19 23:32:52.664213 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii 2025-01-19 23:32:52.831313 INFO::Fitting model to feature number 28, Parabacteroides.merdae 2025-01-19 23:32:52.976611 INFO::Fitting model to feature number 29, Parabacteroides.unclassified 2025-01-19 23:32:53.11846 INFO::Fitting model to feature number 30, Paraprevotella.clara 2025-01-19 23:32:53.262814 INFO::Fitting model to feature number 31, Paraprevotella.unclassified 2025-01-19 23:32:53.406996 INFO::Fitting model to feature number 32, Prevotella.copri 2025-01-19 23:32:53.551303 INFO::Fitting model to feature number 33, Alistipes.finegoldii 2025-01-19 23:32:53.704664 INFO::Fitting model to feature number 34, Alistipes.onderdonkii 2025-01-19 23:32:53.839611 INFO::Fitting model to feature number 35, Alistipes.putredinis 2025-01-19 23:32:53.978776 INFO::Fitting model to feature number 36, Alistipes.shahii 2025-01-19 23:32:54.124378 INFO::Fitting model to feature number 37, Alistipes.unclassified 2025-01-19 23:32:54.265015 INFO::Fitting model to feature number 38, Streptococcus.salivarius 2025-01-19 23:32:54.403151 INFO::Fitting model to feature number 39, Clostridium.bolteae 2025-01-19 23:32:54.572477 INFO::Fitting model to feature number 40, Clostridium.citroniae 2025-01-19 23:32:54.72777 INFO::Fitting model to feature number 41, Clostridium.clostridioforme 2025-01-19 23:32:54.89324 INFO::Fitting model to feature number 42, Clostridium.hathewayi 2025-01-19 23:32:55.037549 INFO::Fitting model to feature number 43, Clostridium.leptum 2025-01-19 23:32:55.181781 INFO::Fitting model to feature number 44, Clostridium.nexile 2025-01-19 23:32:55.327759 INFO::Fitting model to feature number 45, Clostridium.symbiosum 2025-01-19 23:32:55.470703 INFO::Fitting model to feature number 46, Flavonifractor.plautii 2025-01-19 23:32:55.632304 INFO::Fitting model to feature number 47, Eubacterium.eligens 2025-01-19 23:32:55.783981 INFO::Fitting model to feature number 48, Eubacterium.hallii 2025-01-19 23:32:55.931575 INFO::Fitting model to feature number 49, Eubacterium.rectale 2025-01-19 23:32:56.096691 INFO::Fitting model to feature number 50, Eubacterium.siraeum 2025-01-19 23:32:56.249497 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31 2025-01-19 23:32:56.411332 INFO::Fitting model to feature number 52, Eubacterium.ventriosum 2025-01-19 23:32:56.565615 INFO::Fitting model to feature number 53, Ruminococcus.gnavus 2025-01-19 23:32:56.729886 INFO::Fitting model to feature number 54, Ruminococcus.obeum 2025-01-19 23:32:56.864329 INFO::Fitting model to feature number 55, Ruminococcus.torques 2025-01-19 23:32:57.013898 INFO::Fitting model to feature number 56, Coprococcus.comes 2025-01-19 23:32:57.164493 INFO::Fitting model to feature number 57, Dorea.longicatena 2025-01-19 23:32:57.310032 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA 2025-01-19 23:32:57.464081 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA 2025-01-19 23:32:57.616522 INFO::Fitting model to feature number 60, Roseburia.hominis 2025-01-19 23:32:57.75605 INFO::Fitting model to feature number 61, Roseburia.intestinalis 2025-01-19 23:32:57.913996 INFO::Fitting model to feature number 62, Roseburia.inulinivorans 2025-01-19 23:32:58.070165 INFO::Fitting model to feature number 63, Roseburia.unclassified 2025-01-19 23:32:58.210805 INFO::Fitting model to feature number 64, Oscillibacter.unclassified 2025-01-19 23:32:58.352579 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified 2025-01-19 23:32:58.50582 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii 2025-01-19 23:32:58.650733 INFO::Fitting model to feature number 67, Ruminococcus.bromii 2025-01-19 23:32:58.794023 INFO::Fitting model to feature number 68, Ruminococcus.callidus 2025-01-19 23:32:58.94882 INFO::Fitting model to feature number 69, Ruminococcus.lactaris 2025-01-19 23:32:59.110546 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified 2025-01-19 23:32:59.255343 INFO::Fitting model to feature number 71, Coprobacillus.unclassified 2025-01-19 23:32:59.398304 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified 2025-01-19 23:32:59.549176 INFO::Fitting model to feature number 73, Dialister.invisus 2025-01-19 23:32:59.691164 INFO::Fitting model to feature number 74, Veillonella.atypica 2025-01-19 23:32:59.847288 INFO::Fitting model to feature number 75, Veillonella.dispar 2025-01-19 23:33:00.027935 INFO::Fitting model to feature number 76, Veillonella.parvula 2025-01-19 23:33:00.182298 INFO::Fitting model to feature number 77, Veillonella.unclassified 2025-01-19 23:33:00.335433 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47 2025-01-19 23:33:00.498754 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis 2025-01-19 23:33:00.651392 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis 2025-01-19 23:33:00.80521 INFO::Fitting model to feature number 81, Bilophila.unclassified 2025-01-19 23:33:00.973888 INFO::Fitting model to feature number 82, Escherichia.coli 2025-01-19 23:33:01.121437 INFO::Fitting model to feature number 83, Escherichia.unclassified 2025-01-19 23:33:01.266278 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae 2025-01-19 23:33:01.412234 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae 2025-01-19 23:33:01.563887 INFO::Fitting model to feature number 86, Akkermansia.muciniphila 2025-01-19 23:33:01.712118 INFO::Fitting model to feature number 87, C2likevirus.unclassified 2025-01-19 23:33:01.895523 INFO::Counting total values for each feature 2025-01-19 23:33:01.934957 INFO::Writing filtered data to file output/features/filtered_data.tsv 2025-01-19 23:33:02.028968 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv 2025-01-19 23:33:02.124772 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv 2025-01-19 23:33:02.226274 INFO::Writing residuals to file output/fits/residuals.rds 2025-01-19 23:33:02.276429 INFO::Writing fitted values to file output/fits/fitted.rds 2025-01-19 23:33:02.304804 INFO::Writing extracted random effects to file output/fits/ranef.rds 2025-01-19 23:33:02.310702 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv 2025-01-19 23:33:02.317261 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" 2025-01-19 23:33:02.334013 INFO::Writing function arguments to log file 2025-01-19 23:33:02.340574 INFO::Verifying options selected are valid 2025-01-19 23:33:02.341758 INFO::Determining format of input files 2025-01-19 23:33:02.343156 INFO::Input format is data samples as rows and metadata samples as rows 2025-01-19 23:33:02.349243 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject) 2025-01-19 23:33:02.350462 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age 2025-01-19 23:33:02.352215 INFO::Filter data based on min abundance and min prevalence 2025-01-19 23:33:02.353169 INFO::Total samples in data: 1595 2025-01-19 23:33:02.354122 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000 2025-01-19 23:33:02.359257 INFO::Total filtered features: 0 2025-01-19 23:33:02.36036 INFO::Filtered feature names from abundance and prevalence filtering: 2025-01-19 23:33:02.369505 INFO::Total filtered features with variance filtering: 0 2025-01-19 23:33:02.371008 INFO::Filtered feature names from variance filtering: 2025-01-19 23:33:02.371945 INFO::Running selected normalization method: NONE 2025-01-19 23:33:02.372852 INFO::Bypass z-score application to metadata 2025-01-19 23:33:02.373734 INFO::Running selected transform method: AST 2025-01-19 23:33:02.399548 INFO::Running selected analysis method: LM 2025-01-19 23:33:02.40235 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis 2025-01-19 23:33:02.54432 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum 2025-01-19 23:33:02.701293 INFO::Fitting model to feature number 3, Bifidobacterium.longum 2025-01-19 23:33:03.088099 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum 2025-01-19 23:33:03.22313 INFO::Fitting model to feature number 5, Collinsella.aerofaciens 2025-01-19 23:33:03.360371 INFO::Fitting model to feature number 6, Bacteroides.caccae 2025-01-19 23:33:03.502972 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus 2025-01-19 23:33:03.659551 INFO::Fitting model to feature number 8, Bacteroides.dorei 2025-01-19 23:33:03.792436 INFO::Fitting model to feature number 9, Bacteroides.eggerthii 2025-01-19 23:33:03.92679 INFO::Fitting model to feature number 10, Bacteroides.faecis 2025-01-19 23:33:04.069056 INFO::Fitting model to feature number 11, Bacteroides.finegoldii 2025-01-19 23:33:04.195721 WARNING::Fitting problem for feature 11 a warning was issued 2025-01-19 23:33:04.345059 INFO::Fitting model to feature number 12, Bacteroides.fragilis 2025-01-19 23:33:04.481123 INFO::Fitting model to feature number 13, Bacteroides.intestinalis 2025-01-19 23:33:04.622073 INFO::Fitting model to feature number 14, Bacteroides.massiliensis 2025-01-19 23:33:04.767805 INFO::Fitting model to feature number 15, Bacteroides.ovatus 2025-01-19 23:33:04.908525 INFO::Fitting model to feature number 16, Bacteroides.salyersiae 2025-01-19 23:33:05.015555 WARNING::Fitting problem for feature 16 a warning was issued 2025-01-19 23:33:05.16128 INFO::Fitting model to feature number 17, Bacteroides.stercoris 2025-01-19 23:33:05.300238 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron 2025-01-19 23:33:05.438772 INFO::Fitting model to feature number 19, Bacteroides.uniformis 2025-01-19 23:33:05.579847 INFO::Fitting model to feature number 20, Bacteroides.vulgatus 2025-01-19 23:33:05.716586 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens 2025-01-19 23:33:05.854572 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8 2025-01-19 23:33:05.992082 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis 2025-01-19 23:33:06.135899 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus 2025-01-19 23:33:06.286012 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus 2025-01-19 23:33:06.43242 INFO::Fitting model to feature number 26, Parabacteroides.distasonis 2025-01-19 23:33:06.586855 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii 2025-01-19 23:33:06.737478 INFO::Fitting model to feature number 28, Parabacteroides.merdae 2025-01-19 23:33:06.881407 INFO::Fitting model to feature number 29, Parabacteroides.unclassified 2025-01-19 23:33:07.040778 INFO::Fitting model to feature number 30, Paraprevotella.clara 2025-01-19 23:33:07.179566 INFO::Fitting model to feature number 31, Paraprevotella.unclassified 2025-01-19 23:33:07.315157 INFO::Fitting model to feature number 32, Prevotella.copri 2025-01-19 23:33:07.461989 INFO::Fitting model to feature number 33, Alistipes.finegoldii 2025-01-19 23:33:07.600519 INFO::Fitting model to feature number 34, Alistipes.onderdonkii 2025-01-19 23:33:07.739495 INFO::Fitting model to feature number 35, Alistipes.putredinis 2025-01-19 23:33:07.881838 INFO::Fitting model to feature number 36, Alistipes.shahii 2025-01-19 23:33:08.017539 INFO::Fitting model to feature number 37, Alistipes.unclassified 2025-01-19 23:33:08.156161 INFO::Fitting model to feature number 38, Streptococcus.salivarius 2025-01-19 23:33:08.304494 INFO::Fitting model to feature number 39, Clostridium.bolteae 2025-01-19 23:33:08.437887 INFO::Fitting model to feature number 40, Clostridium.citroniae 2025-01-19 23:33:08.567982 INFO::Fitting model to feature number 41, Clostridium.clostridioforme 2025-01-19 23:33:08.705417 INFO::Fitting model to feature number 42, Clostridium.hathewayi 2025-01-19 23:33:08.837146 INFO::Fitting model to feature number 43, Clostridium.leptum 2025-01-19 23:33:08.974248 INFO::Fitting model to feature number 44, Clostridium.nexile 2025-01-19 23:33:09.110249 INFO::Fitting model to feature number 45, Clostridium.symbiosum 2025-01-19 23:33:09.248878 INFO::Fitting model to feature number 46, Flavonifractor.plautii 2025-01-19 23:33:09.385062 INFO::Fitting model to feature number 47, Eubacterium.eligens 2025-01-19 23:33:09.518863 INFO::Fitting model to feature number 48, Eubacterium.hallii 2025-01-19 23:33:09.668262 INFO::Fitting model to feature number 49, Eubacterium.rectale 2025-01-19 23:33:09.798974 INFO::Fitting model to feature number 50, Eubacterium.siraeum 2025-01-19 23:33:09.928431 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31 2025-01-19 23:33:10.065751 INFO::Fitting model to feature number 52, Eubacterium.ventriosum 2025-01-19 23:33:10.199878 INFO::Fitting model to feature number 53, Ruminococcus.gnavus 2025-01-19 23:33:10.323257 INFO::Fitting model to feature number 54, Ruminococcus.obeum 2025-01-19 23:33:10.456368 INFO::Fitting model to feature number 55, Ruminococcus.torques 2025-01-19 23:33:10.847655 INFO::Fitting model to feature number 56, Coprococcus.comes 2025-01-19 23:33:10.981063 INFO::Fitting model to feature number 57, Dorea.longicatena 2025-01-19 23:33:11.139138 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA 2025-01-19 23:33:11.282416 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA 2025-01-19 23:33:11.440743 INFO::Fitting model to feature number 60, Roseburia.hominis 2025-01-19 23:33:11.580049 INFO::Fitting model to feature number 61, Roseburia.intestinalis 2025-01-19 23:33:11.722343 INFO::Fitting model to feature number 62, Roseburia.inulinivorans 2025-01-19 23:33:11.863068 INFO::Fitting model to feature number 63, Roseburia.unclassified 2025-01-19 23:33:12.007751 INFO::Fitting model to feature number 64, Oscillibacter.unclassified 2025-01-19 23:33:12.138084 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified 2025-01-19 23:33:12.277403 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii 2025-01-19 23:33:12.422082 INFO::Fitting model to feature number 67, Ruminococcus.bromii 2025-01-19 23:33:12.54457 WARNING::Fitting problem for feature 67 a warning was issued 2025-01-19 23:33:12.687556 INFO::Fitting model to feature number 68, Ruminococcus.callidus 2025-01-19 23:33:12.81547 INFO::Fitting model to feature number 69, Ruminococcus.lactaris 2025-01-19 23:33:12.952013 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified 2025-01-19 23:33:13.097124 INFO::Fitting model to feature number 71, Coprobacillus.unclassified 2025-01-19 23:33:13.232275 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified 2025-01-19 23:33:13.279367 WARNING::Fitting problem for feature 72 a warning was issued 2025-01-19 23:33:13.41715 INFO::Fitting model to feature number 73, Dialister.invisus 2025-01-19 23:33:13.558134 INFO::Fitting model to feature number 74, Veillonella.atypica 2025-01-19 23:33:13.692011 INFO::Fitting model to feature number 75, Veillonella.dispar 2025-01-19 23:33:13.823921 INFO::Fitting model to feature number 76, Veillonella.parvula 2025-01-19 23:33:13.957113 INFO::Fitting model to feature number 77, Veillonella.unclassified 2025-01-19 23:33:14.095532 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47 2025-01-19 23:33:14.231923 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis 2025-01-19 23:33:14.374116 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis 2025-01-19 23:33:14.510873 INFO::Fitting model to feature number 81, Bilophila.unclassified 2025-01-19 23:33:14.662699 INFO::Fitting model to feature number 82, Escherichia.coli 2025-01-19 23:33:14.792856 INFO::Fitting model to feature number 83, Escherichia.unclassified 2025-01-19 23:33:14.920456 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae 2025-01-19 23:33:15.050839 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae 2025-01-19 23:33:15.195742 INFO::Fitting model to feature number 86, Akkermansia.muciniphila 2025-01-19 23:33:15.335798 INFO::Fitting model to feature number 87, C2likevirus.unclassified 2025-01-19 23:33:15.49498 INFO::Counting total values for each feature 2025-01-19 23:33:15.517254 INFO::Writing filtered data to file output2/features/filtered_data.tsv 2025-01-19 23:33:15.608966 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv 2025-01-19 23:33:15.700523 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv 2025-01-19 23:33:15.797316 INFO::Writing residuals to file output2/fits/residuals.rds 2025-01-19 23:33:15.861139 INFO::Writing fitted values to file output2/fits/fitted.rds 2025-01-19 23:33:15.923041 INFO::Writing extracted random effects to file output2/fits/ranef.rds 2025-01-19 23:33:15.928472 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv 2025-01-19 23:33:15.932892 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 30.042 0.547 30.583
Maaslin2.Rcheck/Maaslin2-Ex.timings
name | user | system | elapsed | |
Maaslin2 | 88.210 | 1.511 | 89.709 | |