Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-01-20 11:40 -0500 (Mon, 20 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4777
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4502
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4461
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4416
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4403
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 1128/2286HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.21.0  (landing page)
Lauren McIver
Snapshot Date: 2025-01-19 13:40 -0500 (Sun, 19 Jan 2025)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: devel
git_last_commit: 3dacd30
git_last_commit_date: 2024-10-29 10:38:48 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for Maaslin2 on nebbiolo1

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: 1.21.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Maaslin2_1.21.0.tar.gz
StartedAt: 2025-01-19 23:30:47 -0500 (Sun, 19 Jan 2025)
EndedAt: 2025-01-19 23:34:58 -0500 (Sun, 19 Jan 2025)
EllapsedTime: 250.4 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Maaslin2_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.21.0’
* 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_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 88.21  1.511  89.709
* 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-3.21-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.


Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘Maaslin2’ ...
** 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 1.9.15
Current TMB package version is 1.9.16
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)

Tests output

Maaslin2.Rcheck/tests/testthat.Rout

R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 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"
2025-01-19 23:32:46.40341 INFO::Writing function arguments to log file
2025-01-19 23:32:46.443619 INFO::Verifying options selected are valid
2025-01-19 23:32:46.475545 INFO::Determining format of input files
2025-01-19 23:32:46.477144 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-19 23:32:46.482014 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-19 23:32:46.48329 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-01-19 23:32:46.485557 INFO::Filter data based on min abundance and min prevalence
2025-01-19 23:32:46.486448 INFO::Total samples in data: 1595
2025-01-19 23:32:46.487279 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-19 23:32:46.491113 INFO::Total filtered features: 0
2025-01-19 23:32:46.492115 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-19 23:32:46.505399 INFO::Total filtered features with variance filtering: 0
2025-01-19 23:32:46.506502 INFO::Filtered feature names from variance filtering:
2025-01-19 23:32:46.507346 INFO::Running selected normalization method: TSS
2025-01-19 23:32:47.584563 INFO::Bypass z-score application to metadata
2025-01-19 23:32:47.585815 INFO::Running selected transform method: AST
2025-01-19 23:32:47.601915 INFO::Running selected analysis method: LM
2025-01-19 23:32:48.084542 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-19 23:32:48.412698 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-19 23:32:48.577746 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-19 23:32:48.720688 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-19 23:32:48.871596 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-19 23:32:49.015307 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-19 23:32:49.389988 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-19 23:32:49.529011 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-19 23:32:49.638582 WARNING::Fitting problem for feature 8 a warning was issued
2025-01-19 23:32:49.803085 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-19 23:32:49.934664 WARNING::Fitting problem for feature 9 a warning was issued
2025-01-19 23:32:50.083724 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-19 23:32:50.221121 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-19 23:32:50.364283 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-19 23:32:50.498027 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-19 23:32:50.614631 WARNING::Fitting problem for feature 13 a warning was issued
2025-01-19 23:32:50.759701 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-19 23:32:50.910822 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-19 23:32:51.052231 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-19 23:32:51.206264 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-19 23:32:51.371088 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-19 23:32:51.518962 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-19 23:32:51.660642 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-19 23:32:51.801712 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-19 23:32:51.950228 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-19 23:32:52.089488 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-19 23:32:52.228262 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-19 23:32:52.375176 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-19 23:32:52.521427 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-19 23:32:52.664213 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-19 23:32:52.831313 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-19 23:32:52.976611 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-19 23:32:53.11846 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-19 23:32:53.262814 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-19 23:32:53.406996 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-19 23:32:53.551303 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-19 23:32:53.704664 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-19 23:32:53.839611 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-19 23:32:53.978776 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-19 23:32:54.124378 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-19 23:32:54.265015 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-19 23:32:54.403151 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-19 23:32:54.572477 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-19 23:32:54.72777 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-19 23:32:54.89324 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-19 23:32:55.037549 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-19 23:32:55.181781 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-19 23:32:55.327759 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-19 23:32:55.470703 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-19 23:32:55.632304 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-19 23:32:55.783981 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-19 23:32:55.931575 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-19 23:32:56.096691 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-19 23:32:56.249497 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-19 23:32:56.411332 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-19 23:32:56.565615 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-19 23:32:56.729886 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-19 23:32:56.864329 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-19 23:32:57.013898 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-19 23:32:57.164493 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-19 23:32:57.310032 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-19 23:32:57.464081 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-19 23:32:57.616522 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-19 23:32:57.75605 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-19 23:32:57.913996 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-19 23:32:58.070165 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-19 23:32:58.210805 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-19 23:32:58.352579 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-19 23:32:58.50582 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-19 23:32:58.650733 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-19 23:32:58.794023 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-19 23:32:58.94882 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-19 23:32:59.110546 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-19 23:32:59.255343 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-19 23:32:59.398304 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-19 23:32:59.549176 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-19 23:32:59.691164 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-19 23:32:59.847288 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-19 23:33:00.027935 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-19 23:33:00.182298 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-19 23:33:00.335433 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-19 23:33:00.498754 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-19 23:33:00.651392 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-19 23:33:00.80521 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-19 23:33:00.973888 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-19 23:33:01.121437 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-19 23:33:01.266278 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-19 23:33:01.412234 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-19 23:33:01.563887 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-19 23:33:01.712118 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-19 23:33:01.895523 INFO::Counting total values for each feature
2025-01-19 23:33:01.934957 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-01-19 23:33:02.028968 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-01-19 23:33:02.124772 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-01-19 23:33:02.226274 INFO::Writing residuals to file output/fits/residuals.rds
2025-01-19 23:33:02.276429 INFO::Writing fitted values to file output/fits/fitted.rds
2025-01-19 23:33:02.304804 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-01-19 23:33:02.310702 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-01-19 23:33:02.317261 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"
2025-01-19 23:33:02.334013 INFO::Writing function arguments to log file
2025-01-19 23:33:02.340574 INFO::Verifying options selected are valid
2025-01-19 23:33:02.341758 INFO::Determining format of input files
2025-01-19 23:33:02.343156 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-19 23:33:02.349243 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-19 23:33:02.350462 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-01-19 23:33:02.352215 INFO::Filter data based on min abundance and min prevalence
2025-01-19 23:33:02.353169 INFO::Total samples in data: 1595
2025-01-19 23:33:02.354122 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-19 23:33:02.359257 INFO::Total filtered features: 0
2025-01-19 23:33:02.36036 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-19 23:33:02.369505 INFO::Total filtered features with variance filtering: 0
2025-01-19 23:33:02.371008 INFO::Filtered feature names from variance filtering:
2025-01-19 23:33:02.371945 INFO::Running selected normalization method: NONE
2025-01-19 23:33:02.372852 INFO::Bypass z-score application to metadata
2025-01-19 23:33:02.373734 INFO::Running selected transform method: AST
2025-01-19 23:33:02.399548 INFO::Running selected analysis method: LM
2025-01-19 23:33:02.40235 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-19 23:33:02.54432 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-19 23:33:02.701293 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-19 23:33:03.088099 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-19 23:33:03.22313 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-19 23:33:03.360371 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-19 23:33:03.502972 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-19 23:33:03.659551 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-19 23:33:03.792436 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-19 23:33:03.92679 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-19 23:33:04.069056 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-19 23:33:04.195721 WARNING::Fitting problem for feature 11 a warning was issued
2025-01-19 23:33:04.345059 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-19 23:33:04.481123 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-19 23:33:04.622073 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-19 23:33:04.767805 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-19 23:33:04.908525 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-19 23:33:05.015555 WARNING::Fitting problem for feature 16 a warning was issued
2025-01-19 23:33:05.16128 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-19 23:33:05.300238 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-19 23:33:05.438772 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-19 23:33:05.579847 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-19 23:33:05.716586 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-19 23:33:05.854572 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-19 23:33:05.992082 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-19 23:33:06.135899 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-19 23:33:06.286012 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-19 23:33:06.43242 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-19 23:33:06.586855 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-19 23:33:06.737478 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-19 23:33:06.881407 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-19 23:33:07.040778 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-19 23:33:07.179566 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-19 23:33:07.315157 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-19 23:33:07.461989 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-19 23:33:07.600519 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-19 23:33:07.739495 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-19 23:33:07.881838 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-19 23:33:08.017539 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-19 23:33:08.156161 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-19 23:33:08.304494 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-19 23:33:08.437887 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-19 23:33:08.567982 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-19 23:33:08.705417 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-19 23:33:08.837146 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-19 23:33:08.974248 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-19 23:33:09.110249 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-19 23:33:09.248878 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-19 23:33:09.385062 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-19 23:33:09.518863 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-19 23:33:09.668262 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-19 23:33:09.798974 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-19 23:33:09.928431 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-19 23:33:10.065751 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-19 23:33:10.199878 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-19 23:33:10.323257 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-19 23:33:10.456368 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-19 23:33:10.847655 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-19 23:33:10.981063 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-19 23:33:11.139138 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-19 23:33:11.282416 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-19 23:33:11.440743 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-19 23:33:11.580049 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-19 23:33:11.722343 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-19 23:33:11.863068 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-19 23:33:12.007751 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-19 23:33:12.138084 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-19 23:33:12.277403 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-19 23:33:12.422082 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-19 23:33:12.54457 WARNING::Fitting problem for feature 67 a warning was issued
2025-01-19 23:33:12.687556 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-19 23:33:12.81547 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-19 23:33:12.952013 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-19 23:33:13.097124 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-19 23:33:13.232275 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-19 23:33:13.279367 WARNING::Fitting problem for feature 72 a warning was issued
2025-01-19 23:33:13.41715 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-19 23:33:13.558134 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-19 23:33:13.692011 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-19 23:33:13.823921 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-19 23:33:13.957113 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-19 23:33:14.095532 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-19 23:33:14.231923 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-19 23:33:14.374116 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-19 23:33:14.510873 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-19 23:33:14.662699 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-19 23:33:14.792856 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-19 23:33:14.920456 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-19 23:33:15.050839 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-19 23:33:15.195742 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-19 23:33:15.335798 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-19 23:33:15.49498 INFO::Counting total values for each feature
2025-01-19 23:33:15.517254 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-01-19 23:33:15.608966 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-01-19 23:33:15.700523 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-01-19 23:33:15.797316 INFO::Writing residuals to file output2/fits/residuals.rds
2025-01-19 23:33:15.861139 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-01-19 23:33:15.923041 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-01-19 23:33:15.928472 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-01-19 23:33:15.932892 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 
 30.042   0.547  30.583 

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin288.210 1.51189.709