Sagun Maharjan
| Snapshot Date: 2026-05-07 13:40 -0400 (Thu, 07 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 Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-08 11:33 -0400 (Fri, 08 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" | 4992 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There" | 4725 |
| 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 | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| 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: 2026-05-08 01:32:32 -0400 (Fri, 08 May 2026) |
| EndedAt: 2026-05-08 01:37:59 -0400 (Fri, 08 May 2026) |
| EllapsedTime: 327.4 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: 2026-05-08 05:32:32 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 118.769 1.012 119.78
* 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"
2026-05-08 01:35:02.563733 INFO::Writing function arguments to log file
2026-05-08 01:35:02.589907 INFO::Verifying options selected are valid
2026-05-08 01:35:02.622573 INFO::Determining format of input files
2026-05-08 01:35:02.624094 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-08 01:35:02.635006 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-05-08 01:35:02.636485 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2026-05-08 01:35:02.638799 INFO::Filter data based on min abundance and min prevalence
2026-05-08 01:35:02.639734 INFO::Total samples in data: 1595
2026-05-08 01:35:02.640592 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-05-08 01:35:02.644279 INFO::Total filtered features: 0
2026-05-08 01:35:02.645354 INFO::Filtered feature names from abundance and prevalence filtering:
2026-05-08 01:35:02.651294 INFO::Total filtered features with variance filtering: 0
2026-05-08 01:35:02.652336 INFO::Filtered feature names from variance filtering:
2026-05-08 01:35:02.653253 INFO::Running selected normalization method: TSS
2026-05-08 01:35:03.676485 INFO::Bypass z-score application to metadata
2026-05-08 01:35:03.677886 INFO::Running selected transform method: AST
2026-05-08 01:35:03.695482 INFO::Running selected analysis method: LM
2026-05-08 01:35:04.33095 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-05-08 01:35:04.94671 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-05-08 01:35:05.115935 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-05-08 01:35:05.254203 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-05-08 01:35:05.397342 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-05-08 01:35:05.548988 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-05-08 01:35:05.688931 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-05-08 01:35:05.832065 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-05-08 01:35:05.951701 WARNING::Fitting problem for feature 8 a warning was issued
2026-05-08 01:35:06.100947 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-05-08 01:35:06.212427 WARNING::Fitting problem for feature 9 a warning was issued
2026-05-08 01:35:06.416417 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-05-08 01:35:06.555618 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-05-08 01:35:06.692143 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-05-08 01:35:06.827055 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-05-08 01:35:06.950067 WARNING::Fitting problem for feature 13 a warning was issued
2026-05-08 01:35:07.097735 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-05-08 01:35:07.23834 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-05-08 01:35:07.424055 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-05-08 01:35:07.570791 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-05-08 01:35:07.720447 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-05-08 01:35:07.866494 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-05-08 01:35:07.998169 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-05-08 01:35:08.135366 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-05-08 01:35:08.282201 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-05-08 01:35:08.427857 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-05-08 01:35:08.564713 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-05-08 01:35:08.711592 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-05-08 01:35:08.853156 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-05-08 01:35:08.992597 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-05-08 01:35:09.148499 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-05-08 01:35:09.288689 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-05-08 01:35:09.440127 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-05-08 01:35:09.578011 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-05-08 01:35:09.722324 INFO::Fitting model to feature number 32, Prevotella.copri
2026-05-08 01:35:09.866104 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-05-08 01:35:10.011547 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-05-08 01:35:10.162832 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-05-08 01:35:10.314279 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-05-08 01:35:10.4641 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-05-08 01:35:10.635939 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-05-08 01:35:10.784097 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-05-08 01:35:10.944713 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-05-08 01:35:11.085197 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-05-08 01:35:11.761078 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-05-08 01:35:12.396236 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-05-08 01:35:13.076882 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-05-08 01:35:13.58339 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-05-08 01:35:14.535168 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-05-08 01:35:14.998997 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-05-08 01:35:15.213796 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-05-08 01:35:15.353752 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-05-08 01:35:15.49889 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-05-08 01:35:15.636908 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-05-08 01:35:15.776671 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-05-08 01:35:15.920593 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-05-08 01:35:16.070816 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-05-08 01:35:16.204311 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-05-08 01:35:16.384369 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-05-08 01:35:16.5364 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-05-08 01:35:16.681983 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-05-08 01:35:16.833245 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-05-08 01:35:16.971274 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-05-08 01:35:17.106923 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-05-08 01:35:17.552436 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-05-08 01:35:17.690145 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-05-08 01:35:17.825487 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-05-08 01:35:17.961544 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-05-08 01:35:18.101474 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-05-08 01:35:18.239794 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-05-08 01:35:18.365786 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-05-08 01:35:18.515546 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-05-08 01:35:18.66201 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-05-08 01:35:18.808062 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-05-08 01:35:18.942405 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-05-08 01:35:19.087622 INFO::Fitting model to feature number 73, Dialister.invisus
2026-05-08 01:35:19.219261 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-05-08 01:35:19.355241 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-05-08 01:35:19.498055 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-05-08 01:35:19.638796 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-05-08 01:35:19.78646 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-05-08 01:35:19.936719 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-05-08 01:35:20.095249 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-05-08 01:35:20.235902 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-05-08 01:35:20.38146 INFO::Fitting model to feature number 82, Escherichia.coli
2026-05-08 01:35:20.527658 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-05-08 01:35:20.677095 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-05-08 01:35:20.819773 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-05-08 01:35:20.957385 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-05-08 01:35:21.109592 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-05-08 01:35:21.293109 INFO::Counting total values for each feature
2026-05-08 01:35:21.323096 INFO::Writing filtered data to file output/features/filtered_data.tsv
2026-05-08 01:35:21.419246 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2026-05-08 01:35:21.518993 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2026-05-08 01:35:21.619201 INFO::Writing residuals to file output/fits/residuals.rds
2026-05-08 01:35:21.668302 INFO::Writing fitted values to file output/fits/fitted.rds
2026-05-08 01:35:21.695836 INFO::Writing extracted random effects to file output/fits/ranef.rds
2026-05-08 01:35:21.701327 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2026-05-08 01:35:21.706623 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"
2026-05-08 01:35:21.719532 INFO::Writing function arguments to log file
2026-05-08 01:35:21.725664 INFO::Verifying options selected are valid
2026-05-08 01:35:21.726662 INFO::Determining format of input files
2026-05-08 01:35:21.72787 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-08 01:35:21.732955 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-05-08 01:35:21.734047 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2026-05-08 01:35:21.735711 INFO::Filter data based on min abundance and min prevalence
2026-05-08 01:35:21.736607 INFO::Total samples in data: 1595
2026-05-08 01:35:21.737536 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-05-08 01:35:21.741325 INFO::Total filtered features: 0
2026-05-08 01:35:21.742311 INFO::Filtered feature names from abundance and prevalence filtering:
2026-05-08 01:35:21.756074 INFO::Total filtered features with variance filtering: 0
2026-05-08 01:35:21.757245 INFO::Filtered feature names from variance filtering:
2026-05-08 01:35:21.758125 INFO::Running selected normalization method: NONE
2026-05-08 01:35:21.758997 INFO::Bypass z-score application to metadata
2026-05-08 01:35:21.759864 INFO::Running selected transform method: AST
2026-05-08 01:35:21.774162 INFO::Running selected analysis method: LM
2026-05-08 01:35:21.775757 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-05-08 01:35:21.904673 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-05-08 01:35:22.037927 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-05-08 01:35:22.171016 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-05-08 01:35:22.30476 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-05-08 01:35:22.440737 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-05-08 01:35:22.583434 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-05-08 01:35:22.715076 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-05-08 01:35:22.842758 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-05-08 01:35:22.975219 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-05-08 01:35:23.116123 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-05-08 01:35:23.22397 WARNING::Fitting problem for feature 11 a warning was issued
2026-05-08 01:35:23.362161 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-05-08 01:35:23.489264 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-05-08 01:35:23.626975 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-05-08 01:35:23.753345 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-05-08 01:35:23.88917 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-05-08 01:35:24.000808 WARNING::Fitting problem for feature 16 a warning was issued
2026-05-08 01:35:24.13205 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-05-08 01:35:24.269237 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-05-08 01:35:24.408946 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-05-08 01:35:24.535606 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-05-08 01:35:24.668844 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-05-08 01:35:24.814442 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-05-08 01:35:24.951459 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-05-08 01:35:25.080124 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-05-08 01:35:25.22539 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-05-08 01:35:25.355617 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-05-08 01:35:25.484251 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-05-08 01:35:25.633175 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-05-08 01:35:25.760633 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-05-08 01:35:25.883913 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-05-08 01:35:26.019652 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-05-08 01:35:26.151198 INFO::Fitting model to feature number 32, Prevotella.copri
2026-05-08 01:35:26.284918 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-05-08 01:35:26.420543 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-05-08 01:35:26.553979 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-05-08 01:35:26.691039 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-05-08 01:35:26.82352 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-05-08 01:35:26.958742 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-05-08 01:35:27.117542 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-05-08 01:35:27.246668 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-05-08 01:35:27.37618 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-05-08 01:35:27.515794 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-05-08 01:35:27.642341 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-05-08 01:35:27.778934 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-05-08 01:35:27.916899 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-05-08 01:35:28.061482 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-05-08 01:35:28.196537 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-05-08 01:35:28.326691 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-05-08 01:35:28.462234 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-05-08 01:35:28.599901 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-05-08 01:35:28.720171 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-05-08 01:35:28.859125 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-05-08 01:35:28.984521 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-05-08 01:35:29.114023 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-05-08 01:35:29.237791 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-05-08 01:35:29.367666 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-05-08 01:35:29.511631 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-05-08 01:35:29.644456 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-05-08 01:35:29.774967 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-05-08 01:35:29.909246 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-05-08 01:35:30.048284 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-05-08 01:35:30.183385 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-05-08 01:35:30.317106 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-05-08 01:35:30.447472 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-05-08 01:35:30.58675 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-05-08 01:35:30.735709 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-05-08 01:35:30.888422 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-05-08 01:35:31.005021 WARNING::Fitting problem for feature 67 a warning was issued
2026-05-08 01:35:31.165401 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-05-08 01:35:31.30009 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-05-08 01:35:31.440779 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-05-08 01:35:31.592395 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-05-08 01:35:31.723917 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-05-08 01:35:31.771055 WARNING::Fitting problem for feature 72 a warning was issued
2026-05-08 01:35:31.905404 INFO::Fitting model to feature number 73, Dialister.invisus
2026-05-08 01:35:32.044248 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-05-08 01:35:32.172246 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-05-08 01:35:32.300818 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-05-08 01:35:32.43156 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-05-08 01:35:32.570921 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-05-08 01:35:32.70422 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-05-08 01:35:32.838017 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-05-08 01:35:32.973895 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-05-08 01:35:33.112275 INFO::Fitting model to feature number 82, Escherichia.coli
2026-05-08 01:35:33.242281 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-05-08 01:35:33.376452 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-05-08 01:35:33.500388 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-05-08 01:35:33.628155 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-05-08 01:35:33.772038 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-05-08 01:35:33.944476 INFO::Counting total values for each feature
2026-05-08 01:35:33.969555 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2026-05-08 01:35:34.065399 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2026-05-08 01:35:34.165219 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2026-05-08 01:35:34.276706 INFO::Writing residuals to file output2/fits/residuals.rds
2026-05-08 01:35:34.3417 INFO::Writing fitted values to file output2/fits/fitted.rds
2026-05-08 01:35:34.404484 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2026-05-08 01:35:34.410321 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2026-05-08 01:35:34.41515 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
31.086 0.591 32.946
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 118.769 | 1.012 | 119.780 | |