Sagun Maharjan
| Snapshot Date: 2026-05-20 13:40 -0400 (Wed, 20 May 2026) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: RELEASE_3_23 |
| git_last_commit: 0616fc9 |
| git_last_commit_date: 2026-04-28 08:50:35 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-21 11:32 -0400 (Thu, 21 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4995 |
| 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 1199/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.26.0 (landing page) Sagun Maharjan
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | 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. |
| Package: Maaslin2 |
| Version: 1.26.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings Maaslin2_1.26.0.tar.gz |
| StartedAt: 2026-05-21 01:37:24 -0400 (Thu, 21 May 2026) |
| EndedAt: 2026-05-21 01:42:55 -0400 (Thu, 21 May 2026) |
| EllapsedTime: 331.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings Maaslin2_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/Maaslin2.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-21 05:37:24 UTC
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.26.0’
* 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 129.842 1.185 132.679
* 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-3.23-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘Maaslin2’ ... ** this is package ‘Maaslin2’ version ‘1.26.0’ ** 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 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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"
2026-05-21 01:40:07.503756 INFO::Writing function arguments to log file
2026-05-21 01:40:07.529501 INFO::Verifying options selected are valid
2026-05-21 01:40:07.562002 INFO::Determining format of input files
2026-05-21 01:40:07.563555 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-21 01:40:07.574458 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-05-21 01:40:07.575989 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2026-05-21 01:40:07.578374 INFO::Filter data based on min abundance and min prevalence
2026-05-21 01:40:07.579325 INFO::Total samples in data: 1595
2026-05-21 01:40:07.580205 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-05-21 01:40:07.583952 INFO::Total filtered features: 0
2026-05-21 01:40:07.585009 INFO::Filtered feature names from abundance and prevalence filtering:
2026-05-21 01:40:07.590972 INFO::Total filtered features with variance filtering: 0
2026-05-21 01:40:07.591995 INFO::Filtered feature names from variance filtering:
2026-05-21 01:40:07.592883 INFO::Running selected normalization method: TSS
2026-05-21 01:40:08.627424 INFO::Bypass z-score application to metadata
2026-05-21 01:40:08.628866 INFO::Running selected transform method: AST
2026-05-21 01:40:08.646722 INFO::Running selected analysis method: LM
2026-05-21 01:40:09.311752 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-05-21 01:40:09.913985 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-05-21 01:40:10.082618 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-05-21 01:40:10.225691 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-05-21 01:40:10.368958 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-05-21 01:40:10.523441 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-05-21 01:40:10.665223 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-05-21 01:40:10.812272 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-05-21 01:40:10.932953 WARNING::Fitting problem for feature 8 a warning was issued
2026-05-21 01:40:11.077596 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-05-21 01:40:11.190071 WARNING::Fitting problem for feature 9 a warning was issued
2026-05-21 01:40:11.407766 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-05-21 01:40:11.555866 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-05-21 01:40:11.699388 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-05-21 01:40:11.833767 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-05-21 01:40:11.955735 WARNING::Fitting problem for feature 13 a warning was issued
2026-05-21 01:40:12.103501 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-05-21 01:40:12.244085 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-05-21 01:40:12.395194 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-05-21 01:40:12.532204 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-05-21 01:40:12.700192 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-05-21 01:40:12.872365 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-05-21 01:40:13.019206 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-05-21 01:40:13.156524 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-05-21 01:40:13.307487 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-05-21 01:40:13.451931 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-05-21 01:40:13.588482 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-05-21 01:40:13.736501 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-05-21 01:40:13.877365 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-05-21 01:40:14.012424 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-05-21 01:40:14.164333 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-05-21 01:40:14.306997 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-05-21 01:40:14.459569 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-05-21 01:40:14.598803 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-05-21 01:40:14.745784 INFO::Fitting model to feature number 32, Prevotella.copri
2026-05-21 01:40:14.902386 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-05-21 01:40:15.053274 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-05-21 01:40:15.201052 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-05-21 01:40:15.353213 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-05-21 01:40:15.498363 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-05-21 01:40:15.647473 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-05-21 01:40:15.781868 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-05-21 01:40:15.930214 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-05-21 01:40:16.074752 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-05-21 01:40:16.228986 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-05-21 01:40:16.374938 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-05-21 01:40:16.521964 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-05-21 01:40:16.659388 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-05-21 01:40:16.80446 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-05-21 01:40:16.946756 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-05-21 01:40:17.101542 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-05-21 01:40:17.244367 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-05-21 01:40:17.395096 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-05-21 01:40:17.541079 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-05-21 01:40:17.711384 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-05-21 01:40:17.873334 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-05-21 01:40:18.032816 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-05-21 01:40:18.164951 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-05-21 01:40:18.341263 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-05-21 01:40:18.495093 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-05-21 01:40:18.639515 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-05-21 01:40:18.791366 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-05-21 01:40:18.929629 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-05-21 01:40:19.06613 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-05-21 01:40:19.443038 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-05-21 01:40:19.579401 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-05-21 01:40:19.713819 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-05-21 01:40:19.850714 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-05-21 01:40:19.990029 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-05-21 01:40:20.127049 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-05-21 01:40:20.254728 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-05-21 01:40:20.420983 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-05-21 01:40:20.575532 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-05-21 01:40:20.731561 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-05-21 01:40:20.872066 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-05-21 01:40:21.019848 INFO::Fitting model to feature number 73, Dialister.invisus
2026-05-21 01:40:21.158524 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-05-21 01:40:21.298961 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-05-21 01:40:21.442934 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-05-21 01:40:21.578926 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-05-21 01:40:21.719686 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-05-21 01:40:21.868796 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-05-21 01:40:22.022879 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-05-21 01:40:22.157734 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-05-21 01:40:22.30058 INFO::Fitting model to feature number 82, Escherichia.coli
2026-05-21 01:40:22.442397 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-05-21 01:40:22.582656 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-05-21 01:40:22.719504 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-05-21 01:40:22.852803 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-05-21 01:40:22.998366 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-05-21 01:40:23.179009 INFO::Counting total values for each feature
2026-05-21 01:40:23.208873 INFO::Writing filtered data to file output/features/filtered_data.tsv
2026-05-21 01:40:23.303538 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2026-05-21 01:40:23.399914 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2026-05-21 01:40:23.498673 INFO::Writing residuals to file output/fits/residuals.rds
2026-05-21 01:40:23.547727 INFO::Writing fitted values to file output/fits/fitted.rds
2026-05-21 01:40:23.57552 INFO::Writing extracted random effects to file output/fits/ranef.rds
2026-05-21 01:40:23.581021 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2026-05-21 01:40:23.586288 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"
2026-05-21 01:40:23.59939 INFO::Writing function arguments to log file
2026-05-21 01:40:23.605545 INFO::Verifying options selected are valid
2026-05-21 01:40:23.60655 INFO::Determining format of input files
2026-05-21 01:40:23.607779 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-21 01:40:23.613046 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-05-21 01:40:23.614196 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2026-05-21 01:40:23.615919 INFO::Filter data based on min abundance and min prevalence
2026-05-21 01:40:23.616853 INFO::Total samples in data: 1595
2026-05-21 01:40:23.617784 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-05-21 01:40:23.621615 INFO::Total filtered features: 0
2026-05-21 01:40:23.622605 INFO::Filtered feature names from abundance and prevalence filtering:
2026-05-21 01:40:23.636074 INFO::Total filtered features with variance filtering: 0
2026-05-21 01:40:23.637295 INFO::Filtered feature names from variance filtering:
2026-05-21 01:40:23.638199 INFO::Running selected normalization method: NONE
2026-05-21 01:40:23.639084 INFO::Bypass z-score application to metadata
2026-05-21 01:40:23.639937 INFO::Running selected transform method: AST
2026-05-21 01:40:23.654185 INFO::Running selected analysis method: LM
2026-05-21 01:40:23.655753 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-05-21 01:40:23.78499 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-05-21 01:40:23.91839 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-05-21 01:40:24.053513 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-05-21 01:40:24.184066 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-05-21 01:40:24.314878 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-05-21 01:40:24.458251 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-05-21 01:40:24.589388 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-05-21 01:40:24.717081 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-05-21 01:40:24.849436 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-05-21 01:40:24.990558 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-05-21 01:40:25.100067 WARNING::Fitting problem for feature 11 a warning was issued
2026-05-21 01:40:25.24157 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-05-21 01:40:25.371843 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-05-21 01:40:25.510646 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-05-21 01:40:25.655839 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-05-21 01:40:25.810984 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-05-21 01:40:25.936195 WARNING::Fitting problem for feature 16 a warning was issued
2026-05-21 01:40:26.070609 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-05-21 01:40:26.215673 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-05-21 01:40:26.36099 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-05-21 01:40:26.487783 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-05-21 01:40:26.619561 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-05-21 01:40:26.760983 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-05-21 01:40:26.894478 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-05-21 01:40:27.022204 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-05-21 01:40:27.164549 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-05-21 01:40:27.293771 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-05-21 01:40:27.423544 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-05-21 01:40:27.566724 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-05-21 01:40:27.69585 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-05-21 01:40:27.822929 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-05-21 01:40:27.964548 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-05-21 01:40:28.096895 INFO::Fitting model to feature number 32, Prevotella.copri
2026-05-21 01:40:28.228197 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-05-21 01:40:28.360694 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-05-21 01:40:28.495623 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-05-21 01:40:28.633252 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-05-21 01:40:28.762634 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-05-21 01:40:28.898134 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-05-21 01:40:29.054127 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-05-21 01:40:29.178565 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-05-21 01:40:29.317854 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-05-21 01:40:29.472773 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-05-21 01:40:29.602795 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-05-21 01:40:29.743364 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-05-21 01:40:29.883866 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-05-21 01:40:30.030064 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-05-21 01:40:30.163487 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-05-21 01:40:30.295372 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-05-21 01:40:30.439148 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-05-21 01:40:30.582731 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-05-21 01:40:30.702246 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-05-21 01:40:30.838654 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-05-21 01:40:30.962091 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-05-21 01:40:31.091398 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-05-21 01:40:31.215396 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-05-21 01:40:31.349489 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-05-21 01:40:31.4924 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-05-21 01:40:31.621711 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-05-21 01:40:31.748915 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-05-21 01:40:31.881968 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-05-21 01:40:32.01882 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-05-21 01:40:32.152901 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-05-21 01:40:32.282902 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-05-21 01:40:32.419878 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-05-21 01:40:32.561945 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-05-21 01:40:32.695288 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-05-21 01:40:32.827413 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-05-21 01:40:32.94079 WARNING::Fitting problem for feature 67 a warning was issued
2026-05-21 01:40:33.091151 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-05-21 01:40:33.222949 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-05-21 01:40:33.364964 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-05-21 01:40:33.514487 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-05-21 01:40:33.647098 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-05-21 01:40:33.695641 WARNING::Fitting problem for feature 72 a warning was issued
2026-05-21 01:40:33.830698 INFO::Fitting model to feature number 73, Dialister.invisus
2026-05-21 01:40:33.969899 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-05-21 01:40:34.102103 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-05-21 01:40:34.232124 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-05-21 01:40:34.372053 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-05-21 01:40:34.5153 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-05-21 01:40:34.656811 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-05-21 01:40:34.794763 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-05-21 01:40:34.937766 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-05-21 01:40:35.08399 INFO::Fitting model to feature number 82, Escherichia.coli
2026-05-21 01:40:35.21283 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-05-21 01:40:35.351015 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-05-21 01:40:35.478447 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-05-21 01:40:35.609834 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-05-21 01:40:35.757579 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-05-21 01:40:35.921209 INFO::Counting total values for each feature
2026-05-21 01:40:35.944129 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2026-05-21 01:40:36.038189 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2026-05-21 01:40:36.132925 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2026-05-21 01:40:36.238201 INFO::Writing residuals to file output2/fits/residuals.rds
2026-05-21 01:40:36.303272 INFO::Writing fitted values to file output2/fits/fitted.rds
2026-05-21 01:40:36.36603 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2026-05-21 01:40:36.371665 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2026-05-21 01:40:36.376199 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
29.471 0.537 29.998
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 129.842 | 1.185 | 132.679 | |