Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-12 12:07 -0400 (Tue, 12 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
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 1146/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Maaslin2 1.23.0 (landing page) Lauren McIver
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | 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 | ![]() | ||||||||
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: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings Maaslin2_1.23.0.tar.gz |
StartedAt: 2025-08-12 03:43:57 -0400 (Tue, 12 Aug 2025) |
EndedAt: 2025-08-12 03:47:31 -0400 (Tue, 12 Aug 2025) |
EllapsedTime: 214.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Maaslin2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings Maaslin2_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/Maaslin2.Rcheck' * using R version 4.5.1 (2025-06-13 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'Maaslin2/DESCRIPTION' ... OK * this is package 'Maaslin2' version '1.23.0' * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 23 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking 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 114.61 7.51 123.2 * 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 'F:/biocbuild/bbs-3.22-bioc/meat/Maaslin2.Rcheck/00check.log' for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library' * installing *source* package 'Maaslin2' ... ** this is package 'Maaslin2' version '1.23.0' ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Maaslin2)
Maaslin2.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(Maaslin2) > > test_check("Maaslin2") [1] "Creating output folder" [1] "Creating output feature tables folder" [1] "Creating output fits folder" 2025-08-12 03:46:43.547496 INFO::Writing function arguments to log file 2025-08-12 03:46:43.587568 INFO::Verifying options selected are valid 2025-08-12 03:46:43.622267 INFO::Determining format of input files 2025-08-12 03:46:43.624645 INFO::Input format is data samples as rows and metadata samples as rows 2025-08-12 03:46:43.63986 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject) 2025-08-12 03:46:43.642518 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age 2025-08-12 03:46:43.646145 INFO::Filter data based on min abundance and min prevalence 2025-08-12 03:46:43.648007 INFO::Total samples in data: 1595 2025-08-12 03:46:43.649856 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000 2025-08-12 03:46:43.655369 INFO::Total filtered features: 0 2025-08-12 03:46:43.657473 INFO::Filtered feature names from abundance and prevalence filtering: 2025-08-12 03:46:43.666185 INFO::Total filtered features with variance filtering: 0 2025-08-12 03:46:43.668207 INFO::Filtered feature names from variance filtering: 2025-08-12 03:46:43.669879 INFO::Running selected normalization method: TSS 2025-08-12 03:46:45.026645 INFO::Bypass z-score application to metadata 2025-08-12 03:46:45.029796 INFO::Running selected transform method: AST 2025-08-12 03:46:45.058439 INFO::Running selected analysis method: LM 2025-08-12 03:46:45.720983 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis 2025-08-12 03:46:46.310973 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum 2025-08-12 03:46:46.537041 INFO::Fitting model to feature number 3, Bifidobacterium.longum 2025-08-12 03:46:46.765378 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum 2025-08-12 03:46:46.991843 INFO::Fitting model to feature number 5, Collinsella.aerofaciens 2025-08-12 03:46:47.214268 INFO::Fitting model to feature number 6, Bacteroides.caccae 2025-08-12 03:46:47.447586 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus 2025-08-12 03:46:47.668225 INFO::Fitting model to feature number 8, Bacteroides.dorei 2025-08-12 03:46:47.863309 INFO::Fitting model to feature number 9, Bacteroides.eggerthii 2025-08-12 03:46:48.084618 INFO::Fitting model to feature number 10, Bacteroides.faecis 2025-08-12 03:46:48.247771 INFO::Fitting model to feature number 11, Bacteroides.finegoldii 2025-08-12 03:46:48.403744 INFO::Fitting model to feature number 12, Bacteroides.fragilis 2025-08-12 03:46:48.542441 INFO::Fitting model to feature number 13, Bacteroides.intestinalis 2025-08-12 03:46:48.697739 WARNING::Fitting problem for feature 13 a warning was issued 2025-08-12 03:46:48.892754 INFO::Fitting model to feature number 14, Bacteroides.massiliensis 2025-08-12 03:46:49.078943 INFO::Fitting model to feature number 15, Bacteroides.ovatus 2025-08-12 03:46:49.251337 INFO::Fitting model to feature number 16, Bacteroides.salyersiae 2025-08-12 03:46:49.441851 INFO::Fitting model to feature number 17, Bacteroides.stercoris 2025-08-12 03:46:49.654718 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron 2025-08-12 03:46:49.870292 INFO::Fitting model to feature number 19, Bacteroides.uniformis 2025-08-12 03:46:50.088598 INFO::Fitting model to feature number 20, Bacteroides.vulgatus 2025-08-12 03:46:50.303209 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens 2025-08-12 03:46:50.495223 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8 2025-08-12 03:46:50.656485 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis 2025-08-12 03:46:50.831134 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus 2025-08-12 03:46:51.048072 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus 2025-08-12 03:46:51.221417 INFO::Fitting model to feature number 26, Parabacteroides.distasonis 2025-08-12 03:46:51.405627 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii 2025-08-12 03:46:51.594331 INFO::Fitting model to feature number 28, Parabacteroides.merdae 2025-08-12 03:46:51.772982 INFO::Fitting model to feature number 29, Parabacteroides.unclassified 2025-08-12 03:46:51.949514 INFO::Fitting model to feature number 30, Paraprevotella.clara 2025-08-12 03:46:52.07918 INFO::Fitting model to feature number 31, Paraprevotella.unclassified 2025-08-12 03:46:52.316636 INFO::Fitting model to feature number 32, Prevotella.copri 2025-08-12 03:46:52.488283 INFO::Fitting model to feature number 33, Alistipes.finegoldii 2025-08-12 03:46:52.704312 INFO::Fitting model to feature number 34, Alistipes.onderdonkii 2025-08-12 03:46:52.921115 INFO::Fitting model to feature number 35, Alistipes.putredinis 2025-08-12 03:46:53.127724 INFO::Fitting model to feature number 36, Alistipes.shahii 2025-08-12 03:46:53.269425 INFO::Fitting model to feature number 37, Alistipes.unclassified 2025-08-12 03:46:53.47058 INFO::Fitting model to feature number 38, Streptococcus.salivarius 2025-08-12 03:46:53.618627 INFO::Fitting model to feature number 39, Clostridium.bolteae 2025-08-12 03:46:53.757539 INFO::Fitting model to feature number 40, Clostridium.citroniae 2025-08-12 03:46:53.944016 INFO::Fitting model to feature number 41, Clostridium.clostridioforme 2025-08-12 03:46:54.116108 INFO::Fitting model to feature number 42, Clostridium.hathewayi 2025-08-12 03:46:54.342988 INFO::Fitting model to feature number 43, Clostridium.leptum 2025-08-12 03:46:54.548388 INFO::Fitting model to feature number 44, Clostridium.nexile 2025-08-12 03:46:55.03522 INFO::Fitting model to feature number 45, Clostridium.symbiosum 2025-08-12 03:46:55.208078 INFO::Fitting model to feature number 46, Flavonifractor.plautii 2025-08-12 03:46:55.390506 INFO::Fitting model to feature number 47, Eubacterium.eligens 2025-08-12 03:46:55.590931 INFO::Fitting model to feature number 48, Eubacterium.hallii 2025-08-12 03:46:55.813175 INFO::Fitting model to feature number 49, Eubacterium.rectale 2025-08-12 03:46:56.021811 INFO::Fitting model to feature number 50, Eubacterium.siraeum 2025-08-12 03:46:56.22961 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31 2025-08-12 03:46:56.453127 INFO::Fitting model to feature number 52, Eubacterium.ventriosum 2025-08-12 03:46:56.660467 INFO::Fitting model to feature number 53, Ruminococcus.gnavus 2025-08-12 03:46:56.899787 INFO::Fitting model to feature number 54, Ruminococcus.obeum 2025-08-12 03:46:57.096349 INFO::Fitting model to feature number 55, Ruminococcus.torques 2025-08-12 03:46:57.286632 INFO::Fitting model to feature number 56, Coprococcus.comes 2025-08-12 03:46:57.507022 INFO::Fitting model to feature number 57, Dorea.longicatena 2025-08-12 03:46:57.654941 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA 2025-08-12 03:46:57.829637 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA 2025-08-12 03:46:57.998032 INFO::Fitting model to feature number 60, Roseburia.hominis 2025-08-12 03:46:58.202302 INFO::Fitting model to feature number 61, Roseburia.intestinalis 2025-08-12 03:46:58.409378 INFO::Fitting model to feature number 62, Roseburia.inulinivorans 2025-08-12 03:46:58.603521 INFO::Fitting model to feature number 63, Roseburia.unclassified 2025-08-12 03:46:58.807759 INFO::Fitting model to feature number 64, Oscillibacter.unclassified 2025-08-12 03:46:58.980163 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified 2025-08-12 03:46:59.167126 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii 2025-08-12 03:46:59.361628 INFO::Fitting model to feature number 67, Ruminococcus.bromii 2025-08-12 03:46:59.51507 INFO::Fitting model to feature number 68, Ruminococcus.callidus 2025-08-12 03:46:59.718407 INFO::Fitting model to feature number 69, Ruminococcus.lactaris 2025-08-12 03:46:59.888131 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified 2025-08-12 03:47:00.029853 INFO::Fitting model to feature number 71, Coprobacillus.unclassified 2025-08-12 03:47:00.235974 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified 2025-08-12 03:47:00.446802 INFO::Fitting model to feature number 73, Dialister.invisus 2025-08-12 03:47:00.61776 INFO::Fitting model to feature number 74, Veillonella.atypica 2025-08-12 03:47:00.756572 INFO::Fitting model to feature number 75, Veillonella.dispar 2025-08-12 03:47:00.95802 INFO::Fitting model to feature number 76, Veillonella.parvula 2025-08-12 03:47:01.183538 INFO::Fitting model to feature number 77, Veillonella.unclassified 2025-08-12 03:47:01.368794 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47 2025-08-12 03:47:01.555738 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis 2025-08-12 03:47:01.764885 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis 2025-08-12 03:47:01.958161 INFO::Fitting model to feature number 81, Bilophila.unclassified 2025-08-12 03:47:02.157083 INFO::Fitting model to feature number 82, Escherichia.coli 2025-08-12 03:47:02.31669 INFO::Fitting model to feature number 83, Escherichia.unclassified 2025-08-12 03:47:02.521372 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae 2025-08-12 03:47:02.721154 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae 2025-08-12 03:47:02.942019 INFO::Fitting model to feature number 86, Akkermansia.muciniphila 2025-08-12 03:47:03.134328 INFO::Fitting model to feature number 87, C2likevirus.unclassified 2025-08-12 03:47:03.366228 INFO::Counting total values for each feature 2025-08-12 03:47:03.411247 INFO::Writing filtered data to file output/features/filtered_data.tsv 2025-08-12 03:47:03.801688 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv 2025-08-12 03:47:04.315922 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv 2025-08-12 03:47:04.863806 INFO::Writing residuals to file output/fits/residuals.rds 2025-08-12 03:47:04.919541 INFO::Writing fitted values to file output/fits/fitted.rds 2025-08-12 03:47:04.943732 INFO::Writing extracted random effects to file output/fits/ranef.rds 2025-08-12 03:47:04.949931 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv 2025-08-12 03:47:04.966611 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output/significant_results.tsv [1] "Creating output folder" [1] "Creating output feature tables folder" [1] "Creating output fits folder" 2025-08-12 03:47:05.031057 INFO::Writing function arguments to log file 2025-08-12 03:47:05.045351 INFO::Verifying options selected are valid 2025-08-12 03:47:05.047144 INFO::Determining format of input files 2025-08-12 03:47:05.049292 INFO::Input format is data samples as rows and metadata samples as rows 2025-08-12 03:47:05.058273 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject) 2025-08-12 03:47:05.061003 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age 2025-08-12 03:47:05.064533 INFO::Filter data based on min abundance and min prevalence 2025-08-12 03:47:05.066988 INFO::Total samples in data: 1595 2025-08-12 03:47:05.06946 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000 2025-08-12 03:47:05.078129 INFO::Total filtered features: 0 2025-08-12 03:47:05.080927 INFO::Filtered feature names from abundance and prevalence filtering: 2025-08-12 03:47:05.094519 INFO::Total filtered features with variance filtering: 0 2025-08-12 03:47:05.098069 INFO::Filtered feature names from variance filtering: 2025-08-12 03:47:05.099907 INFO::Running selected normalization method: NONE 2025-08-12 03:47:05.101621 INFO::Bypass z-score application to metadata 2025-08-12 03:47:05.103318 INFO::Running selected transform method: AST 2025-08-12 03:47:05.126463 INFO::Running selected analysis method: LM 2025-08-12 03:47:05.129487 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis 2025-08-12 03:47:05.273202 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum 2025-08-12 03:47:05.428419 INFO::Fitting model to feature number 3, Bifidobacterium.longum 2025-08-12 03:47:05.585211 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum 2025-08-12 03:47:05.797748 INFO::Fitting model to feature number 5, Collinsella.aerofaciens 2025-08-12 03:47:05.942062 INFO::Fitting model to feature number 6, Bacteroides.caccae 2025-08-12 03:47:06.145604 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus 2025-08-12 03:47:06.618547 INFO::Fitting model to feature number 8, Bacteroides.dorei 2025-08-12 03:47:06.789556 INFO::Fitting model to feature number 9, Bacteroides.eggerthii 2025-08-12 03:47:06.95759 WARNING::Fitting problem for feature 9 a warning was issued 2025-08-12 03:47:07.132402 INFO::Fitting model to feature number 10, Bacteroides.faecis 2025-08-12 03:47:07.294816 INFO::Fitting model to feature number 11, Bacteroides.finegoldii 2025-08-12 03:47:07.40618 WARNING::Fitting problem for feature 11 a warning was issued 2025-08-12 03:47:07.580847 INFO::Fitting model to feature number 12, Bacteroides.fragilis 2025-08-12 03:47:07.765946 INFO::Fitting model to feature number 13, Bacteroides.intestinalis 2025-08-12 03:47:07.918545 INFO::Fitting model to feature number 14, Bacteroides.massiliensis 2025-08-12 03:47:08.09523 INFO::Fitting model to feature number 15, Bacteroides.ovatus 2025-08-12 03:47:08.250638 INFO::Fitting model to feature number 16, Bacteroides.salyersiae 2025-08-12 03:47:08.411841 WARNING::Fitting problem for feature 16 a warning was issued 2025-08-12 03:47:08.641699 INFO::Fitting model to feature number 17, Bacteroides.stercoris 2025-08-12 03:47:08.843191 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron 2025-08-12 03:47:09.012952 INFO::Fitting model to feature number 19, Bacteroides.uniformis 2025-08-12 03:47:09.234072 INFO::Fitting model to feature number 20, Bacteroides.vulgatus 2025-08-12 03:47:09.439144 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens 2025-08-12 03:47:09.633623 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8 2025-08-12 03:47:09.796221 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis 2025-08-12 03:47:09.979106 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus 2025-08-12 03:47:10.178231 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus 2025-08-12 03:47:10.359559 INFO::Fitting model to feature number 26, Parabacteroides.distasonis 2025-08-12 03:47:10.528378 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii 2025-08-12 03:47:10.714596 INFO::Fitting model to feature number 28, Parabacteroides.merdae 2025-08-12 03:47:10.887191 INFO::Fitting model to feature number 29, Parabacteroides.unclassified 2025-08-12 03:47:11.051489 INFO::Fitting model to feature number 30, Paraprevotella.clara 2025-08-12 03:47:11.251629 INFO::Fitting model to feature number 31, Paraprevotella.unclassified 2025-08-12 03:47:11.435826 INFO::Fitting model to feature number 32, Prevotella.copri 2025-08-12 03:47:11.638316 INFO::Fitting model to feature number 33, Alistipes.finegoldii 2025-08-12 03:47:11.83173 INFO::Fitting model to feature number 34, Alistipes.onderdonkii 2025-08-12 03:47:12.011411 INFO::Fitting model to feature number 35, Alistipes.putredinis 2025-08-12 03:47:12.197748 INFO::Fitting model to feature number 36, Alistipes.shahii 2025-08-12 03:47:12.363775 INFO::Fitting model to feature number 37, Alistipes.unclassified 2025-08-12 03:47:12.512897 INFO::Fitting model to feature number 38, Streptococcus.salivarius 2025-08-12 03:47:12.693592 INFO::Fitting model to feature number 39, Clostridium.bolteae 2025-08-12 03:47:12.828305 INFO::Fitting model to feature number 40, Clostridium.citroniae 2025-08-12 03:47:12.989629 INFO::Fitting model to feature number 41, Clostridium.clostridioforme 2025-08-12 03:47:13.199151 INFO::Fitting model to feature number 42, Clostridium.hathewayi 2025-08-12 03:47:13.374151 INFO::Fitting model to feature number 43, Clostridium.leptum 2025-08-12 03:47:13.580815 INFO::Fitting model to feature number 44, Clostridium.nexile 2025-08-12 03:47:13.747926 INFO::Fitting model to feature number 45, Clostridium.symbiosum 2025-08-12 03:47:13.912426 INFO::Fitting model to feature number 46, Flavonifractor.plautii 2025-08-12 03:47:14.344746 INFO::Fitting model to feature number 47, Eubacterium.eligens 2025-08-12 03:47:14.534241 INFO::Fitting model to feature number 48, Eubacterium.hallii 2025-08-12 03:47:14.69368 INFO::Fitting model to feature number 49, Eubacterium.rectale 2025-08-12 03:47:14.893346 INFO::Fitting model to feature number 50, Eubacterium.siraeum 2025-08-12 03:47:15.013719 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31 2025-08-12 03:47:15.198471 INFO::Fitting model to feature number 52, Eubacterium.ventriosum 2025-08-12 03:47:15.341757 INFO::Fitting model to feature number 53, Ruminococcus.gnavus 2025-08-12 03:47:15.504936 INFO::Fitting model to feature number 54, Ruminococcus.obeum 2025-08-12 03:47:15.626844 INFO::Fitting model to feature number 55, Ruminococcus.torques 2025-08-12 03:47:15.783153 INFO::Fitting model to feature number 56, Coprococcus.comes 2025-08-12 03:47:15.969563 INFO::Fitting model to feature number 57, Dorea.longicatena 2025-08-12 03:47:16.153674 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA 2025-08-12 03:47:16.314706 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA 2025-08-12 03:47:16.523117 INFO::Fitting model to feature number 60, Roseburia.hominis 2025-08-12 03:47:16.728848 INFO::Fitting model to feature number 61, Roseburia.intestinalis 2025-08-12 03:47:16.921086 INFO::Fitting model to feature number 62, Roseburia.inulinivorans 2025-08-12 03:47:17.114125 INFO::Fitting model to feature number 63, Roseburia.unclassified 2025-08-12 03:47:17.329818 INFO::Fitting model to feature number 64, Oscillibacter.unclassified 2025-08-12 03:47:17.483698 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified 2025-08-12 03:47:17.637693 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii 2025-08-12 03:47:17.794629 INFO::Fitting model to feature number 67, Ruminococcus.bromii 2025-08-12 03:47:17.950121 INFO::Fitting model to feature number 68, Ruminococcus.callidus 2025-08-12 03:47:18.129335 INFO::Fitting model to feature number 69, Ruminococcus.lactaris 2025-08-12 03:47:18.277665 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified 2025-08-12 03:47:18.443903 INFO::Fitting model to feature number 71, Coprobacillus.unclassified 2025-08-12 03:47:18.625894 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified 2025-08-12 03:47:18.709097 WARNING::Fitting problem for feature 72 a warning was issued 2025-08-12 03:47:18.903331 INFO::Fitting model to feature number 73, Dialister.invisus 2025-08-12 03:47:19.091608 INFO::Fitting model to feature number 74, Veillonella.atypica 2025-08-12 03:47:19.290901 INFO::Fitting model to feature number 75, Veillonella.dispar 2025-08-12 03:47:19.481251 INFO::Fitting model to feature number 76, Veillonella.parvula 2025-08-12 03:47:19.686 INFO::Fitting model to feature number 77, Veillonella.unclassified 2025-08-12 03:47:20.08306 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47 2025-08-12 03:47:20.28313 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis 2025-08-12 03:47:20.436473 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis 2025-08-12 03:47:20.637382 INFO::Fitting model to feature number 81, Bilophila.unclassified 2025-08-12 03:47:20.777782 INFO::Fitting model to feature number 82, Escherichia.coli 2025-08-12 03:47:20.900438 INFO::Fitting model to feature number 83, Escherichia.unclassified 2025-08-12 03:47:21.019955 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae 2025-08-12 03:47:21.159725 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae 2025-08-12 03:47:21.344087 INFO::Fitting model to feature number 86, Akkermansia.muciniphila 2025-08-12 03:47:21.530726 INFO::Fitting model to feature number 87, C2likevirus.unclassified 2025-08-12 03:47:21.729792 INFO::Counting total values for each feature 2025-08-12 03:47:21.766681 INFO::Writing filtered data to file output2/features/filtered_data.tsv 2025-08-12 03:47:22.21613 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv 2025-08-12 03:47:22.571469 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv 2025-08-12 03:47:23.059753 INFO::Writing residuals to file output2/fits/residuals.rds 2025-08-12 03:47:23.132278 INFO::Writing fitted values to file output2/fits/fitted.rds 2025-08-12 03:47:23.20455 INFO::Writing extracted random effects to file output2/fits/ranef.rds 2025-08-12 03:47:23.21373 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv 2025-08-12 03:47:23.233469 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 40.25 0.92 41.25
Maaslin2.Rcheck/Maaslin2-Ex.timings
name | user | system | elapsed | |
Maaslin2 | 114.61 | 7.51 | 123.20 | |