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This page was generated on 2025-01-23 12:12 -0500 (Thu, 23 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4746
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4493
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4517
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4469
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4394
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 1130/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.20.0  (landing page)
Lauren McIver
Snapshot Date: 2025-01-20 13:00 -0500 (Mon, 20 Jan 2025)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_20
git_last_commit: 1cacd4c
git_last_commit_date: 2024-10-29 10:38:48 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows 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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for Maaslin2 on taishan

To the developers/maintainers of the Maaslin2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Maaslin2.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: Maaslin2
Version: 1.20.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Maaslin2_1.20.0.tar.gz
StartedAt: 2025-01-21 08:19:20 -0000 (Tue, 21 Jan 2025)
EndedAt: 2025-01-21 08:22:34 -0000 (Tue, 21 Jan 2025)
EllapsedTime: 194.2 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Maaslin2_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.20.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 113.689  1.376 115.338
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.2/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 version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(Maaslin2)
> 
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2025-01-21 08:21:49.926237 INFO::Writing function arguments to log file
2025-01-21 08:21:49.977392 INFO::Verifying options selected are valid
2025-01-21 08:21:50.02073 INFO::Determining format of input files
2025-01-21 08:21:50.02255 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-21 08:21:50.028866 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-21 08:21:50.030666 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-01-21 08:21:50.033925 INFO::Filter data based on min abundance and min prevalence
2025-01-21 08:21:50.035239 INFO::Total samples in data: 1595
2025-01-21 08:21:50.036413 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-21 08:21:50.044254 INFO::Total filtered features: 0
2025-01-21 08:21:50.045802 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-21 08:21:50.073698 INFO::Total filtered features with variance filtering: 0
2025-01-21 08:21:50.075265 INFO::Filtered feature names from variance filtering:
2025-01-21 08:21:50.076468 INFO::Running selected normalization method: TSS
2025-01-21 08:21:51.436843 INFO::Bypass z-score application to metadata
2025-01-21 08:21:51.43839 INFO::Running selected transform method: AST
2025-01-21 08:21:51.457505 INFO::Running selected analysis method: LM
2025-01-21 08:21:52.044135 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-21 08:21:52.489909 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-21 08:21:52.714758 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-21 08:21:52.924722 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-21 08:21:53.146871 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-21 08:21:53.361933 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-21 08:21:53.58278 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-21 08:21:53.796377 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-21 08:21:54.0154 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-21 08:21:54.185826 WARNING::Fitting problem for feature 9 a warning was issued
2025-01-21 08:21:54.395853 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-21 08:21:54.634923 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-21 08:21:54.870465 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-21 08:21:55.09971 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-21 08:21:55.314355 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-21 08:21:55.526398 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-21 08:21:55.73813 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-21 08:21:55.947486 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-21 08:21:56.168804 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-21 08:21:56.386513 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-21 08:21:56.587876 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-21 08:21:56.813323 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-21 08:21:57.039646 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-21 08:21:57.274247 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-21 08:21:57.488714 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-21 08:21:57.721532 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-21 08:21:57.939939 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-21 08:21:58.142913 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-21 08:21:58.387636 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-21 08:21:58.603132 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-21 08:21:58.822006 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-21 08:21:59.017529 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-21 08:21:59.246229 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-21 08:21:59.461915 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-21 08:21:59.724813 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-21 08:21:59.947783 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-21 08:22:00.144772 WARNING::Fitting problem for feature 35 a warning was issued
2025-01-21 08:22:00.386142 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-21 08:22:00.624445 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-21 08:22:00.837352 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-21 08:22:01.244329 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-21 08:22:01.44432 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-21 08:22:01.657109 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-21 08:22:01.874122 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-21 08:22:02.084517 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-21 08:22:02.295817 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-21 08:22:02.526811 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-21 08:22:02.73427 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-21 08:22:02.942165 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-21 08:22:03.160283 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-21 08:22:03.36688 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-21 08:22:03.56414 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-21 08:22:03.766286 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-21 08:22:03.97491 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-21 08:22:04.177828 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-21 08:22:04.408314 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-21 08:22:04.62237 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-21 08:22:04.828578 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-21 08:22:05.050096 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-21 08:22:05.256433 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-21 08:22:05.469809 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-21 08:22:05.683934 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-21 08:22:05.917433 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-21 08:22:06.129885 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-21 08:22:06.370616 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-21 08:22:06.573847 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-21 08:22:06.772414 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-21 08:22:06.976317 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-21 08:22:07.185228 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-21 08:22:07.384254 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-21 08:22:07.597996 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-21 08:22:07.826767 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-21 08:22:08.035011 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-21 08:22:08.233076 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-21 08:22:08.442224 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-21 08:22:08.640432 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-21 08:22:08.837461 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-21 08:22:09.048067 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-21 08:22:09.250163 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-21 08:22:09.460454 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-21 08:22:09.693336 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-21 08:22:09.916831 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-21 08:22:10.137055 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-21 08:22:10.363313 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-21 08:22:10.569938 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-21 08:22:10.775658 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-21 08:22:10.976235 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-21 08:22:11.178825 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-21 08:22:11.388592 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-21 08:22:11.654864 INFO::Counting total values for each feature
2025-01-21 08:22:11.712884 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-01-21 08:22:11.832571 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-01-21 08:22:11.954102 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-01-21 08:22:12.077411 INFO::Writing residuals to file output/fits/residuals.rds
2025-01-21 08:22:12.133718 INFO::Writing fitted values to file output/fits/fitted.rds
2025-01-21 08:22:12.164417 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-01-21 08:22:12.171062 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-01-21 08:22:12.178052 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"
2025-01-21 08:22:12.196311 INFO::Writing function arguments to log file
2025-01-21 08:22:12.204841 INFO::Verifying options selected are valid
2025-01-21 08:22:12.206252 INFO::Determining format of input files
2025-01-21 08:22:12.207871 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-21 08:22:12.215154 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-21 08:22:12.216893 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-01-21 08:22:12.219362 INFO::Filter data based on min abundance and min prevalence
2025-01-21 08:22:12.220786 INFO::Total samples in data: 1595
2025-01-21 08:22:12.222088 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-21 08:22:12.230604 INFO::Total filtered features: 0
2025-01-21 08:22:12.232226 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-21 08:22:12.259268 INFO::Total filtered features with variance filtering: 0
2025-01-21 08:22:12.260833 INFO::Filtered feature names from variance filtering:
2025-01-21 08:22:12.262113 INFO::Running selected normalization method: NONE
2025-01-21 08:22:12.263367 INFO::Bypass z-score application to metadata
2025-01-21 08:22:12.264592 INFO::Running selected transform method: AST
2025-01-21 08:22:12.29297 INFO::Running selected analysis method: LM
2025-01-21 08:22:12.295167 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-21 08:22:12.502942 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-21 08:22:12.718106 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-21 08:22:12.919122 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-21 08:22:13.118071 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-21 08:22:13.310418 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-21 08:22:13.522696 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-21 08:22:13.720173 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-21 08:22:13.937059 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-21 08:22:14.165505 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-21 08:22:14.380527 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-21 08:22:14.591578 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-21 08:22:14.799614 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-21 08:22:14.967995 WARNING::Fitting problem for feature 13 a warning was issued
2025-01-21 08:22:15.175648 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-21 08:22:15.390938 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-21 08:22:15.598581 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-21 08:22:15.809852 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-21 08:22:16.020811 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-21 08:22:16.218005 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-21 08:22:16.419111 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-21 08:22:16.618173 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-21 08:22:16.826999 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-21 08:22:17.025327 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-21 08:22:17.229673 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-21 08:22:17.431607 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-21 08:22:17.634675 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-21 08:22:17.827742 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-21 08:22:18.053168 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-21 08:22:18.244 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-21 08:22:18.444715 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-21 08:22:18.665175 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-21 08:22:18.869502 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-21 08:22:19.080725 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-21 08:22:19.28674 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-21 08:22:19.481656 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-21 08:22:19.68377 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-21 08:22:19.892998 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-21 08:22:20.089086 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-21 08:22:20.302674 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-21 08:22:20.488323 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-21 08:22:20.675139 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-21 08:22:20.881699 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-21 08:22:21.076111 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-21 08:22:21.288939 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-21 08:22:21.494056 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-21 08:22:21.70913 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-21 08:22:21.917927 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-21 08:22:22.127905 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-21 08:22:22.340981 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-21 08:22:22.54439 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-21 08:22:22.72402 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-21 08:22:22.929955 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-21 08:22:23.106499 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-21 08:22:23.258454 WARNING::Fitting problem for feature 53 a warning was issued
2025-01-21 08:22:23.459897 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-21 08:22:23.646336 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-21 08:22:23.834202 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-21 08:22:24.043075 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-21 08:22:24.254986 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-21 08:22:24.465348 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-21 08:22:24.703342 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-21 08:22:24.899898 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-21 08:22:25.113712 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-21 08:22:25.30981 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-21 08:22:25.513348 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-21 08:22:25.721378 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-21 08:22:25.914526 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-21 08:22:26.122642 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-21 08:22:26.28461 WARNING::Fitting problem for feature 67 a warning was issued
2025-01-21 08:22:26.497225 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-21 08:22:26.709489 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-21 08:22:26.919845 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-21 08:22:27.131366 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-21 08:22:27.339813 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-21 08:22:27.409145 WARNING::Fitting problem for feature 72 a warning was issued
2025-01-21 08:22:27.613041 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-21 08:22:27.824464 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-21 08:22:28.023199 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-21 08:22:28.23716 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-21 08:22:28.440479 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-21 08:22:28.651301 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-21 08:22:28.848776 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-21 08:22:29.053447 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-21 08:22:29.478803 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-21 08:22:29.692487 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-21 08:22:29.885259 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-21 08:22:30.08334 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-21 08:22:30.294297 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-21 08:22:30.490154 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-21 08:22:30.699027 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-21 08:22:30.943073 INFO::Counting total values for each feature
2025-01-21 08:22:30.975387 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-01-21 08:22:31.093253 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-01-21 08:22:31.210322 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-01-21 08:22:31.334656 INFO::Writing residuals to file output2/fits/residuals.rds
2025-01-21 08:22:31.409409 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-01-21 08:22:31.480666 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-01-21 08:22:31.487303 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-01-21 08:22:31.493082 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 6 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 42.421   0.463  42.965

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2113.689 1.376115.338