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This page was generated on 2025-08-11 11:44 -0400 (Mon, 11 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 1154/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.22.0  (landing page)
Lauren McIver
Snapshot Date: 2025-08-07 13:40 -0400 (Thu, 07 Aug 2025)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_21
git_last_commit: fcec85e
git_last_commit_date: 2025-04-15 11:48:14 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for Maaslin2 on merida1

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.

raw results


Summary

Package: Maaslin2
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.22.0.tar.gz
StartedAt: 2025-08-08 05:36:53 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 05:42:32 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 339.1 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.22.0’
* 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 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 185.924  2.721 200.993
* 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
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘Maaslin2’ ...
** this is package ‘Maaslin2’ version ‘1.22.0’
** 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)

Tests output

Maaslin2.Rcheck/tests/testthat.Rout


R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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"
2025-08-08 05:41:15.833301 INFO::Writing function arguments to log file
2025-08-08 05:41:15.935738 INFO::Verifying options selected are valid
2025-08-08 05:41:16.012898 INFO::Determining format of input files
2025-08-08 05:41:16.016863 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-08 05:41:16.03264 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-08-08 05:41:16.036171 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-08-08 05:41:16.042845 INFO::Filter data based on min abundance and min prevalence
2025-08-08 05:41:16.045449 INFO::Total samples in data: 1595
2025-08-08 05:41:16.047947 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-08-08 05:41:16.070055 INFO::Total filtered features: 0
2025-08-08 05:41:16.073096 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-08 05:41:16.094271 INFO::Total filtered features with variance filtering: 0
2025-08-08 05:41:16.096969 INFO::Filtered feature names from variance filtering:
2025-08-08 05:41:16.099324 INFO::Running selected normalization method: TSS
2025-08-08 05:41:18.442598 INFO::Bypass z-score application to metadata
2025-08-08 05:41:18.445384 INFO::Running selected transform method: AST
2025-08-08 05:41:18.482069 INFO::Running selected analysis method: LM
2025-08-08 05:41:19.723833 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-08-08 05:41:20.884671 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-08-08 05:41:21.235175 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-08-08 05:41:21.600484 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-08-08 05:41:21.93557 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-08-08 05:41:22.260079 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-08-08 05:41:22.595557 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-08-08 05:41:22.932723 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-08-08 05:41:23.254336 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-08-08 05:41:23.565264 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-08-08 05:41:23.879436 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-08-08 05:41:24.228608 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-08-08 05:41:24.548422 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-08-08 05:41:24.892194 WARNING::Fitting problem for feature 13 a warning was issued
2025-08-08 05:41:25.279865 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-08-08 05:41:25.634626 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-08-08 05:41:25.990548 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-08-08 05:41:26.331203 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-08-08 05:41:26.65172 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-08-08 05:41:26.97151 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-08-08 05:41:27.313039 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-08-08 05:41:27.647072 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-08-08 05:41:27.967538 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-08-08 05:41:28.275628 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-08-08 05:41:28.582387 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-08-08 05:41:28.891744 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-08-08 05:41:29.214628 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-08-08 05:41:29.509147 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-08-08 05:41:29.82505 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-08-08 05:41:30.148955 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-08-08 05:41:30.461892 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-08-08 05:41:30.763444 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-08-08 05:41:31.091198 INFO::Fitting model to feature number 32, Prevotella.copri
2025-08-08 05:41:31.398632 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-08-08 05:41:31.727857 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-08-08 05:41:32.034114 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-08-08 05:41:32.349142 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-08-08 05:41:32.675626 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-08-08 05:41:32.99716 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-08-08 05:41:33.306936 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-08-08 05:41:33.645264 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-08-08 05:41:33.986993 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-08-08 05:41:34.353613 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-08-08 05:41:34.67827 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-08-08 05:41:35.034804 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-08-08 05:41:35.352332 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-08-08 05:41:35.685317 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-08-08 05:41:36.00797 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-08-08 05:41:36.377085 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-08-08 05:41:36.701015 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-08-08 05:41:37.025058 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-08-08 05:41:37.345608 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-08-08 05:41:37.686364 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-08-08 05:41:38.03321 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-08-08 05:41:38.370857 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-08-08 05:41:38.686729 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-08-08 05:41:39.019425 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-08-08 05:41:39.355367 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-08-08 05:41:39.680443 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-08-08 05:41:40.003462 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-08-08 05:41:40.317789 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-08-08 05:41:40.641782 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-08-08 05:41:40.960539 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-08-08 05:41:41.287159 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-08-08 05:41:41.612622 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-08-08 05:41:41.917122 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-08-08 05:41:42.237373 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-08-08 05:41:42.540342 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-08-08 05:41:42.821547 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-08-08 05:41:43.159478 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-08-08 05:41:43.501077 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-08-08 05:41:43.872584 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-08-08 05:41:44.180182 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-08-08 05:41:44.496899 INFO::Fitting model to feature number 73, Dialister.invisus
2025-08-08 05:41:44.803216 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-08-08 05:41:45.407157 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-08-08 05:41:45.729775 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-08-08 05:41:46.03906 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-08-08 05:41:46.354706 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-08-08 05:41:46.752897 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-08-08 05:41:47.084157 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-08-08 05:41:47.408215 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-08-08 05:41:47.733985 INFO::Fitting model to feature number 82, Escherichia.coli
2025-08-08 05:41:48.065823 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-08-08 05:41:48.371446 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-08-08 05:41:48.69103 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-08-08 05:41:49.000511 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-08-08 05:41:49.326468 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-08-08 05:41:49.769918 INFO::Counting total values for each feature
2025-08-08 05:41:49.867582 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-08-08 05:41:50.154985 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-08-08 05:41:50.500674 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-08-08 05:41:50.852501 INFO::Writing residuals to file output/fits/residuals.rds
2025-08-08 05:41:50.944289 INFO::Writing fitted values to file output/fits/fitted.rds
2025-08-08 05:41:50.997995 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-08-08 05:41:51.008635 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-08-08 05:41:51.024355 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"
2025-08-08 05:41:51.055539 INFO::Writing function arguments to log file
2025-08-08 05:41:51.07148 INFO::Verifying options selected are valid
2025-08-08 05:41:51.074007 INFO::Determining format of input files
2025-08-08 05:41:51.076983 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-08 05:41:51.134617 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-08-08 05:41:51.137701 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-08-08 05:41:51.142126 INFO::Filter data based on min abundance and min prevalence
2025-08-08 05:41:51.144672 INFO::Total samples in data: 1595
2025-08-08 05:41:51.147086 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-08-08 05:41:51.15628 INFO::Total filtered features: 0
2025-08-08 05:41:51.159688 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-08 05:41:51.178198 INFO::Total filtered features with variance filtering: 0
2025-08-08 05:41:51.181032 INFO::Filtered feature names from variance filtering:
2025-08-08 05:41:51.183522 INFO::Running selected normalization method: NONE
2025-08-08 05:41:51.186453 INFO::Bypass z-score application to metadata
2025-08-08 05:41:51.18899 INFO::Running selected transform method: AST
2025-08-08 05:41:51.23966 INFO::Running selected analysis method: LM
2025-08-08 05:41:51.243098 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-08-08 05:41:51.546497 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-08-08 05:41:51.851316 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-08-08 05:41:52.152427 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-08-08 05:41:52.483808 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-08-08 05:41:52.786533 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-08-08 05:41:53.109635 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-08-08 05:41:53.418267 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-08-08 05:41:53.728345 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-08-08 05:41:54.023496 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-08-08 05:41:54.326563 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-08-08 05:41:54.642293 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-08-08 05:41:54.949555 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-08-08 05:41:55.227537 WARNING::Fitting problem for feature 13 a warning was issued
2025-08-08 05:41:55.562562 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-08-08 05:41:55.872366 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-08-08 05:41:56.174754 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-08-08 05:41:56.476676 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-08-08 05:41:56.802126 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-08-08 05:41:57.096827 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-08-08 05:41:57.390479 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-08-08 05:41:57.701333 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-08-08 05:41:58.007916 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-08-08 05:41:58.303255 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-08-08 05:41:58.589806 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-08-08 05:41:58.911009 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-08-08 05:41:59.212485 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-08-08 05:41:59.513939 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-08-08 05:41:59.838628 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-08-08 05:42:00.121199 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-08-08 05:42:00.394504 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-08-08 05:42:00.689334 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-08-08 05:42:00.979738 INFO::Fitting model to feature number 32, Prevotella.copri
2025-08-08 05:42:01.301657 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-08-08 05:42:01.605462 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-08-08 05:42:01.920321 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-08-08 05:42:02.216691 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-08-08 05:42:02.535011 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-08-08 05:42:02.821076 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-08-08 05:42:03.12778 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-08-08 05:42:03.440581 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-08-08 05:42:03.716389 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-08-08 05:42:04.010728 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-08-08 05:42:04.42664 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-08-08 05:42:04.768796 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-08-08 05:42:05.082942 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-08-08 05:42:05.377478 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-08-08 05:42:05.822893 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-08-08 05:42:06.137795 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-08-08 05:42:06.518853 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-08-08 05:42:06.92416 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-08-08 05:42:07.292132 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-08-08 05:42:07.615979 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-08-08 05:42:07.910375 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-08-08 05:42:08.202664 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-08-08 05:42:08.539612 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-08-08 05:42:08.822957 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-08-08 05:42:09.123903 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-08-08 05:42:09.427407 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-08-08 05:42:09.749602 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-08-08 05:42:10.070654 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-08-08 05:42:10.356901 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-08-08 05:42:10.665036 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-08-08 05:42:10.970911 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-08-08 05:42:11.283724 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-08-08 05:42:11.577298 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-08-08 05:42:11.890741 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-08-08 05:42:12.19972 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-08-08 05:42:12.457422 WARNING::Fitting problem for feature 67 a warning was issued
2025-08-08 05:42:12.770694 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-08-08 05:42:13.064045 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-08-08 05:42:13.416724 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-08-08 05:42:13.742712 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-08-08 05:42:14.04169 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-08-08 05:42:14.145187 WARNING::Fitting problem for feature 72 a warning was issued
2025-08-08 05:42:14.462723 INFO::Fitting model to feature number 73, Dialister.invisus
2025-08-08 05:42:14.781273 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-08-08 05:42:15.088397 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-08-08 05:42:15.386549 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-08-08 05:42:15.701542 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-08-08 05:42:16.027119 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-08-08 05:42:16.322377 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-08-08 05:42:16.633681 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-08-08 05:42:16.944169 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-08-08 05:42:17.272083 INFO::Fitting model to feature number 82, Escherichia.coli
2025-08-08 05:42:17.566552 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-08-08 05:42:17.847564 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-08-08 05:42:18.153569 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-08-08 05:42:18.459848 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-08-08 05:42:18.769396 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-08-08 05:42:19.169538 INFO::Counting total values for each feature
2025-08-08 05:42:19.235059 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-08-08 05:42:19.50021 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-08-08 05:42:19.775585 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-08-08 05:42:20.123005 INFO::Writing residuals to file output2/fits/residuals.rds
2025-08-08 05:42:20.247566 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-08-08 05:42:20.368239 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-08-08 05:42:20.380678 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-08-08 05:42:20.394019 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 4 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 62.180   1.094  67.206

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2185.924 2.721200.993