Sagun Maharjan
| Snapshot Date: 2026-05-05 13:45 -0400 (Tue, 05 May 2026) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: devel |
| git_last_commit: 6335054 |
| git_last_commit_date: 2026-04-28 08:50:35 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-06 11:34 -0400 (Wed, 06 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4878 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4663 |
| 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 1174/2366 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.27.0 (landing page) Sagun Maharjan
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
| See other builds for Maaslin2 in R Universe. | ||||||||||||||
|
To the developers/maintainers of the Maaslin2 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Maaslin2.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: Maaslin2 |
| Version: 1.27.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Maaslin2_1.27.0.tar.gz |
| StartedAt: 2026-05-05 11:33:55 -0000 (Tue, 05 May 2026) |
| EndedAt: 2026-05-05 11:38:16 -0000 (Tue, 05 May 2026) |
| EllapsedTime: 261.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Maaslin2_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/Maaslin2.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.27.0’
* 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: no visible binding for global variable ‘var’
maaslin2_association_plots: no visible binding for global variable
‘xnames’
Undefined global functions or variables:
var xnames
Consider adding
importFrom("stats", "var")
to your NAMESPACE file.
* 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 171.268 1.109 172.833
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.24-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘Maaslin2’ ... ** this is package ‘Maaslin2’ version ‘1.27.0’ ** 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 1.9.17 Current TMB package version is 1.9.18 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 version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(Maaslin2)
>
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2026-05-05 11:37:30.060508 INFO::Writing function arguments to log file
2026-05-05 11:37:30.114545 INFO::Verifying options selected are valid
2026-05-05 11:37:30.159835 INFO::Determining format of input files
2026-05-05 11:37:30.161787 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-05 11:37:30.16898 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-05-05 11:37:30.170894 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2026-05-05 11:37:30.174504 INFO::Filter data based on min abundance and min prevalence
2026-05-05 11:37:30.175894 INFO::Total samples in data: 1595
2026-05-05 11:37:30.177112 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-05-05 11:37:30.185331 INFO::Total filtered features: 0
2026-05-05 11:37:30.195532 INFO::Filtered feature names from abundance and prevalence filtering:
2026-05-05 11:37:30.221766 INFO::Total filtered features with variance filtering: 0
2026-05-05 11:37:30.22333 INFO::Filtered feature names from variance filtering:
2026-05-05 11:37:30.224577 INFO::Running selected normalization method: TSS
2026-05-05 11:37:31.523918 INFO::Bypass z-score application to metadata
2026-05-05 11:37:31.525435 INFO::Running selected transform method: AST
2026-05-05 11:37:31.546057 INFO::Running selected analysis method: LM
2026-05-05 11:37:32.236742 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-05-05 11:37:33.121573 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-05-05 11:37:33.360247 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-05-05 11:37:33.580418 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-05-05 11:37:33.808665 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-05-05 11:37:34.035594 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-05-05 11:37:34.250824 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-05-05 11:37:34.461546 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-05-05 11:37:34.67826 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-05-05 11:37:34.909059 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-05-05 11:37:35.13129 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-05-05 11:37:35.407677 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-05-05 11:37:35.62004 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-05-05 11:37:35.798042 WARNING::Fitting problem for feature 13 a warning was issued
2026-05-05 11:37:36.033979 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-05-05 11:37:36.247426 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-05-05 11:37:36.471316 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-05-05 11:37:36.692026 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-05-05 11:37:36.912328 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-05-05 11:37:37.136806 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-05-05 11:37:37.360226 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-05-05 11:37:37.585482 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-05-05 11:37:37.814055 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-05-05 11:37:38.039411 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-05-05 11:37:38.251092 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-05-05 11:37:38.465894 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-05-05 11:37:38.689629 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-05-05 11:37:38.896986 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-05-05 11:37:39.368369 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-05-05 11:37:39.579614 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-05-05 11:37:39.819876 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-05-05 11:37:40.030458 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-05-05 11:37:40.278515 INFO::Fitting model to feature number 32, Prevotella.copri
2026-05-05 11:37:40.514247 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-05-05 11:37:40.749241 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-05-05 11:37:40.974438 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-05-05 11:37:41.188931 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-05-05 11:37:41.405217 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-05-05 11:37:41.630709 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-05-05 11:37:41.835491 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-05-05 11:37:42.0438 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-05-05 11:37:42.260186 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-05-05 11:37:42.482423 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-05-05 11:37:42.709748 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-05-05 11:37:42.92458 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-05-05 11:37:43.145299 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-05-05 11:37:43.353948 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-05-05 11:37:43.568607 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-05-05 11:37:43.78636 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-05-05 11:37:44.004489 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-05-05 11:37:44.217736 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-05-05 11:37:44.425735 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-05-05 11:37:44.642756 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-05-05 11:37:44.851695 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-05-05 11:37:45.0753 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-05-05 11:37:45.289541 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-05-05 11:37:45.504935 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-05-05 11:37:45.732229 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-05-05 11:37:45.944391 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-05-05 11:37:46.187667 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-05-05 11:37:46.408294 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-05-05 11:37:46.62429 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-05-05 11:37:46.850357 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-05-05 11:37:47.068632 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-05-05 11:37:47.283684 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-05-05 11:37:47.505034 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-05-05 11:37:47.708138 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-05-05 11:37:47.928387 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-05-05 11:37:48.132491 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-05-05 11:37:48.357729 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-05-05 11:37:48.581354 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-05-05 11:37:48.800863 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-05-05 11:37:49.025053 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-05-05 11:37:49.228049 INFO::Fitting model to feature number 73, Dialister.invisus
2026-05-05 11:37:49.438505 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-05-05 11:37:49.67632 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-05-05 11:37:49.892944 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-05-05 11:37:50.112791 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-05-05 11:37:50.336223 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-05-05 11:37:50.574872 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-05-05 11:37:50.7986 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-05-05 11:37:51.012132 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-05-05 11:37:51.252856 INFO::Fitting model to feature number 82, Escherichia.coli
2026-05-05 11:37:51.474561 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-05-05 11:37:51.683819 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-05-05 11:37:51.913786 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-05-05 11:37:52.125808 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-05-05 11:37:52.345214 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-05-05 11:37:52.635911 INFO::Counting total values for each feature
2026-05-05 11:37:52.680376 INFO::Writing filtered data to file output/features/filtered_data.tsv
2026-05-05 11:37:52.797557 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2026-05-05 11:37:52.917306 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2026-05-05 11:37:53.03921 INFO::Writing residuals to file output/fits/residuals.rds
2026-05-05 11:37:53.095778 INFO::Writing fitted values to file output/fits/fitted.rds
2026-05-05 11:37:53.126322 INFO::Writing extracted random effects to file output/fits/ranef.rds
2026-05-05 11:37:53.13315 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2026-05-05 11:37:53.14035 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"
2026-05-05 11:37:53.158881 INFO::Writing function arguments to log file
2026-05-05 11:37:53.167384 INFO::Verifying options selected are valid
2026-05-05 11:37:53.168829 INFO::Determining format of input files
2026-05-05 11:37:53.170558 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-05 11:37:53.178026 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-05-05 11:37:53.179816 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2026-05-05 11:37:53.182335 INFO::Filter data based on min abundance and min prevalence
2026-05-05 11:37:53.183848 INFO::Total samples in data: 1595
2026-05-05 11:37:53.185201 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-05-05 11:37:53.194018 INFO::Total filtered features: 0
2026-05-05 11:37:53.195744 INFO::Filtered feature names from abundance and prevalence filtering:
2026-05-05 11:37:53.221898 INFO::Total filtered features with variance filtering: 0
2026-05-05 11:37:53.223616 INFO::Filtered feature names from variance filtering:
2026-05-05 11:37:53.224907 INFO::Running selected normalization method: NONE
2026-05-05 11:37:53.226183 INFO::Bypass z-score application to metadata
2026-05-05 11:37:53.227466 INFO::Running selected transform method: AST
2026-05-05 11:37:53.246762 INFO::Running selected analysis method: LM
2026-05-05 11:37:53.248971 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-05-05 11:37:53.472323 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-05-05 11:37:53.686672 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-05-05 11:37:53.907252 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-05-05 11:37:54.141856 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-05-05 11:37:54.353116 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-05-05 11:37:54.58611 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-05-05 11:37:54.804302 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-05-05 11:37:55.016261 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-05-05 11:37:55.190018 WARNING::Fitting problem for feature 9 a warning was issued
2026-05-05 11:37:55.426529 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-05-05 11:37:55.655232 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-05-05 11:37:55.864956 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-05-05 11:37:56.071893 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-05-05 11:37:56.254062 WARNING::Fitting problem for feature 13 a warning was issued
2026-05-05 11:37:56.496352 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-05-05 11:37:56.704529 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-05-05 11:37:56.919449 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-05-05 11:37:57.085368 WARNING::Fitting problem for feature 16 a warning was issued
2026-05-05 11:37:57.304165 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-05-05 11:37:57.514471 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-05-05 11:37:57.721129 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-05-05 11:37:57.935282 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-05-05 11:37:58.149191 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-05-05 11:37:58.371086 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-05-05 11:37:58.617181 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-05-05 11:37:58.826284 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-05-05 11:37:59.038862 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-05-05 11:37:59.24824 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-05-05 11:37:59.465246 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-05-05 11:37:59.671868 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-05-05 11:37:59.870237 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-05-05 11:38:00.078821 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-05-05 11:38:00.275985 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-05-05 11:38:00.477074 INFO::Fitting model to feature number 32, Prevotella.copri
2026-05-05 11:38:00.701514 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-05-05 11:38:00.901933 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-05-05 11:38:01.106252 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-05-05 11:38:01.320717 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-05-05 11:38:01.562138 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-05-05 11:38:01.788271 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-05-05 11:38:02.00001 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-05-05 11:38:02.207545 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-05-05 11:38:02.408123 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-05-05 11:38:02.614503 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-05-05 11:38:02.825742 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-05-05 11:38:03.038023 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-05-05 11:38:03.245557 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-05-05 11:38:03.460447 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-05-05 11:38:03.668792 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-05-05 11:38:04.106143 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-05-05 11:38:04.347589 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-05-05 11:38:04.566335 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-05-05 11:38:04.761 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-05-05 11:38:04.983974 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-05-05 11:38:05.17255 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-05-05 11:38:05.359605 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-05-05 11:38:05.57322 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-05-05 11:38:05.777358 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-05-05 11:38:05.982042 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-05-05 11:38:06.181485 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-05-05 11:38:06.389961 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-05-05 11:38:06.598018 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-05-05 11:38:06.79365 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-05-05 11:38:07.254938 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-05-05 11:38:07.450917 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-05-05 11:38:07.653032 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-05-05 11:38:07.85918 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-05-05 11:38:08.085499 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-05-05 11:38:08.305474 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-05-05 11:38:08.51738 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-05-05 11:38:08.718898 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-05-05 11:38:08.925163 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-05-05 11:38:09.137775 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-05-05 11:38:09.342068 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-05-05 11:38:09.412164 WARNING::Fitting problem for feature 72 a warning was issued
2026-05-05 11:38:09.623196 INFO::Fitting model to feature number 73, Dialister.invisus
2026-05-05 11:38:09.829938 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-05-05 11:38:10.030457 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-05-05 11:38:10.262038 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-05-05 11:38:10.498198 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-05-05 11:38:10.734316 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-05-05 11:38:10.934556 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-05-05 11:38:11.153267 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-05-05 11:38:11.352718 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-05-05 11:38:11.566902 INFO::Fitting model to feature number 82, Escherichia.coli
2026-05-05 11:38:11.774697 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-05-05 11:38:11.968619 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-05-05 11:38:12.168447 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-05-05 11:38:12.37857 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-05-05 11:38:12.608671 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-05-05 11:38:12.858343 INFO::Counting total values for each feature
2026-05-05 11:38:12.891702 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2026-05-05 11:38:13.008155 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2026-05-05 11:38:13.124609 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2026-05-05 11:38:13.246847 INFO::Writing residuals to file output2/fits/residuals.rds
2026-05-05 11:38:13.322933 INFO::Writing fitted values to file output2/fits/fitted.rds
2026-05-05 11:38:13.395258 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2026-05-05 11:38:13.40194 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2026-05-05 11:38:13.407726 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
44.184 0.535 44.816
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 171.268 | 1.109 | 172.833 | |