Multiple platform build/check report for BioC 3.21 - CHECK results for Maaslin2 on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4719
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4481
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4492
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4445
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*

CHECK results for Maaslin2 on palomino7

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: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings Maaslin2_1.21.0.tar.gz

StartedAt: 2025-02-13 02:39:05 -0500 (Thu, 13 Feb 2025)

EndedAt: 2025-02-13 02:42:34 -0500 (Thu, 13 Feb 2025)

EllapsedTime: 209.0 seconds

RetCode: 0

Status: OK

CheckDir: Maaslin2.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings Maaslin2_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Maaslin2/DESCRIPTION' ... OK
* this is package 'Maaslin2' version '1.21.0'
* 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 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 111.61   6.95  118.78
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'E:/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'Maaslin2' ...
** this is package 'Maaslin2' version '1.21.0'
** 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 Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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"
2025-02-13 02:41:43.811645 INFO::Writing function arguments to log file
2025-02-13 02:41:43.848947 INFO::Verifying options selected are valid
2025-02-13 02:41:43.894684 INFO::Determining format of input files
2025-02-13 02:41:43.898468 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-13 02:41:43.918856 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-02-13 02:41:43.922388 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-02-13 02:41:43.92723 INFO::Filter data based on min abundance and min prevalence
2025-02-13 02:41:43.929817 INFO::Total samples in data: 1595
2025-02-13 02:41:43.932358 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-02-13 02:41:43.940182 INFO::Total filtered features: 0
2025-02-13 02:41:43.943254 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-13 02:41:43.957293 INFO::Total filtered features with variance filtering: 0
2025-02-13 02:41:43.960374 INFO::Filtered feature names from variance filtering:
2025-02-13 02:41:43.963108 INFO::Running selected normalization method: TSS
2025-02-13 02:41:45.38202 INFO::Bypass z-score application to metadata
2025-02-13 02:41:45.384789 INFO::Running selected transform method: AST
2025-02-13 02:41:45.409915 INFO::Running selected analysis method: LM
2025-02-13 02:41:46.073324 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-02-13 02:41:46.522202 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-02-13 02:41:46.736665 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-02-13 02:41:46.901324 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-02-13 02:41:47.053211 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-02-13 02:41:47.254111 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-02-13 02:41:47.420256 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-02-13 02:41:47.592739 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-02-13 02:41:47.85679 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-02-13 02:41:48.065435 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-02-13 02:41:48.264613 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-02-13 02:41:48.489971 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-02-13 02:41:48.696605 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-02-13 02:41:48.885302 WARNING::Fitting problem for feature 13 a warning was issued
2025-02-13 02:41:49.100316 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-02-13 02:41:49.250969 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-02-13 02:41:49.452705 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-02-13 02:41:49.663433 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-02-13 02:41:49.875519 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-02-13 02:41:50.062531 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-02-13 02:41:50.238972 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-02-13 02:41:50.445148 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-02-13 02:41:50.586626 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-02-13 02:41:50.713104 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-02-13 02:41:50.844083 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-02-13 02:41:50.976073 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-02-13 02:41:51.137569 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-02-13 02:41:51.348027 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-02-13 02:41:51.530259 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-02-13 02:41:51.727639 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-02-13 02:41:51.902773 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-02-13 02:41:52.078838 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-02-13 02:41:52.306972 INFO::Fitting model to feature number 32, Prevotella.copri
2025-02-13 02:41:52.483505 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-02-13 02:41:52.694909 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-02-13 02:41:52.915443 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-02-13 02:41:53.137535 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-02-13 02:41:53.350182 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-02-13 02:41:53.820636 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-02-13 02:41:54.015134 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-02-13 02:41:54.217069 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-02-13 02:41:54.445562 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-02-13 02:41:54.649811 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-02-13 02:41:54.866191 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-02-13 02:41:55.091461 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-02-13 02:41:55.284507 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-02-13 02:41:55.458817 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-02-13 02:41:55.6197 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-02-13 02:41:55.840953 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-02-13 02:41:55.991735 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-02-13 02:41:56.124769 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-02-13 02:41:56.29034 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-02-13 02:41:56.498613 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-02-13 02:41:56.719059 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-02-13 02:41:56.937021 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-02-13 02:41:57.129038 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-02-13 02:41:57.341802 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-02-13 02:41:57.532851 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-02-13 02:41:57.665805 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-02-13 02:41:57.834532 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-02-13 02:41:57.963967 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-02-13 02:41:58.092603 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-02-13 02:41:58.223207 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-02-13 02:41:58.393856 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-02-13 02:41:58.525637 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-02-13 02:41:58.659523 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-02-13 02:41:58.801332 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-02-13 02:41:58.957357 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-02-13 02:41:59.134868 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-02-13 02:41:59.337316 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-02-13 02:41:59.551363 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-02-13 02:41:59.766116 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-02-13 02:41:59.983425 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-02-13 02:42:00.127628 INFO::Fitting model to feature number 73, Dialister.invisus
2025-02-13 02:42:00.259975 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-02-13 02:42:00.455632 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-02-13 02:42:00.625696 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-02-13 02:42:00.751416 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-02-13 02:42:00.888286 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-02-13 02:42:01.029372 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-02-13 02:42:01.246565 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-02-13 02:42:01.454728 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-02-13 02:42:01.595029 INFO::Fitting model to feature number 82, Escherichia.coli
2025-02-13 02:42:01.780117 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-02-13 02:42:01.951602 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-02-13 02:42:02.160121 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-02-13 02:42:02.366394 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-02-13 02:42:02.527803 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-02-13 02:42:02.753709 INFO::Counting total values for each feature
2025-02-13 02:42:02.811339 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-02-13 02:42:03.25836 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-02-13 02:42:03.696325 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-02-13 02:42:04.220596 INFO::Writing residuals to file output/fits/residuals.rds
2025-02-13 02:42:04.280887 INFO::Writing fitted values to file output/fits/fitted.rds
2025-02-13 02:42:04.318064 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-02-13 02:42:04.3275 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-02-13 02:42:04.351043 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"
2025-02-13 02:42:04.409698 INFO::Writing function arguments to log file
2025-02-13 02:42:04.432703 INFO::Verifying options selected are valid
2025-02-13 02:42:04.435469 INFO::Determining format of input files
2025-02-13 02:42:04.438608 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-13 02:42:04.461838 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-02-13 02:42:04.465094 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-02-13 02:42:04.469011 INFO::Filter data based on min abundance and min prevalence
2025-02-13 02:42:04.471649 INFO::Total samples in data: 1595
2025-02-13 02:42:04.474247 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-02-13 02:42:04.481489 INFO::Total filtered features: 0
2025-02-13 02:42:04.484467 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-13 02:42:04.495637 INFO::Total filtered features with variance filtering: 0
2025-02-13 02:42:04.498626 INFO::Filtered feature names from variance filtering:
2025-02-13 02:42:04.50122 INFO::Running selected normalization method: NONE
2025-02-13 02:42:04.503768 INFO::Bypass z-score application to metadata
2025-02-13 02:42:04.506299 INFO::Running selected transform method: AST
2025-02-13 02:42:04.529402 INFO::Running selected analysis method: LM
2025-02-13 02:42:04.533093 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-02-13 02:42:04.718267 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-02-13 02:42:04.894931 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-02-13 02:42:05.088702 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-02-13 02:42:05.25476 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-02-13 02:42:05.448745 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-02-13 02:42:05.61693 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-02-13 02:42:05.788225 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-02-13 02:42:05.954368 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-02-13 02:42:06.103541 WARNING::Fitting problem for feature 9 a warning was issued
2025-02-13 02:42:06.309285 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-02-13 02:42:06.506317 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-02-13 02:42:06.701981 WARNING::Fitting problem for feature 11 a warning was issued
2025-02-13 02:42:06.909618 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-02-13 02:42:07.11091 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-02-13 02:42:07.330096 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-02-13 02:42:07.522118 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-02-13 02:42:07.720896 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-02-13 02:42:07.891641 WARNING::Fitting problem for feature 16 a warning was issued
2025-02-13 02:42:08.092241 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-02-13 02:42:08.29458 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-02-13 02:42:08.510302 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-02-13 02:42:08.694923 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-02-13 02:42:08.912874 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-02-13 02:42:09.107387 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-02-13 02:42:09.247295 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-02-13 02:42:09.410779 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-02-13 02:42:09.599979 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-02-13 02:42:09.799893 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-02-13 02:42:10.002681 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-02-13 02:42:10.200667 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-02-13 02:42:10.360435 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-02-13 02:42:10.501639 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-02-13 02:42:10.639427 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-02-13 02:42:11.021631 INFO::Fitting model to feature number 32, Prevotella.copri
2025-02-13 02:42:11.229678 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-02-13 02:42:11.429298 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-02-13 02:42:11.634362 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-02-13 02:42:11.842364 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-02-13 02:42:12.037997 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-02-13 02:42:12.235867 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-02-13 02:42:12.383682 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-02-13 02:42:12.512691 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-02-13 02:42:12.687222 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-02-13 02:42:12.881725 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-02-13 02:42:13.092777 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-02-13 02:42:13.286449 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-02-13 02:42:13.490289 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-02-13 02:42:13.687301 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-02-13 02:42:13.865379 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-02-13 02:42:13.995428 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-02-13 02:42:14.191069 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-02-13 02:42:14.380994 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-02-13 02:42:14.541911 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-02-13 02:42:14.696232 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-02-13 02:42:14.891356 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-02-13 02:42:15.066961 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-02-13 02:42:15.221547 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-02-13 02:42:15.402563 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-02-13 02:42:15.541823 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-02-13 02:42:15.661795 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-02-13 02:42:15.845757 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-02-13 02:42:16.052255 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-02-13 02:42:16.24764 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-02-13 02:42:16.448488 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-02-13 02:42:16.632837 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-02-13 02:42:16.801002 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-02-13 02:42:16.92304 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-02-13 02:42:17.056091 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-02-13 02:42:17.185643 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-02-13 02:42:17.371344 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-02-13 02:42:17.533084 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-02-13 02:42:17.737428 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-02-13 02:42:17.920933 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-02-13 02:42:18.067441 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-02-13 02:42:18.135385 WARNING::Fitting problem for feature 72 a warning was issued
2025-02-13 02:42:18.288558 INFO::Fitting model to feature number 73, Dialister.invisus
2025-02-13 02:42:18.499639 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-02-13 02:42:18.643858 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-02-13 02:42:18.839617 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-02-13 02:42:19.016097 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-02-13 02:42:19.189071 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-02-13 02:42:19.329606 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-02-13 02:42:19.501158 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-02-13 02:42:19.695468 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-02-13 02:42:19.938485 INFO::Fitting model to feature number 82, Escherichia.coli
2025-02-13 02:42:20.120274 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-02-13 02:42:20.295778 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-02-13 02:42:20.485399 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-02-13 02:42:20.686934 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-02-13 02:42:20.885663 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-02-13 02:42:21.094558 INFO::Counting total values for each feature
2025-02-13 02:42:21.129225 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-02-13 02:42:21.568426 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-02-13 02:42:21.902115 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-02-13 02:42:22.338217 INFO::Writing residuals to file output2/fits/residuals.rds
2025-02-13 02:42:22.405875 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-02-13 02:42:22.47978 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-02-13 02:42:22.489128 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-02-13 02:42:22.507481 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 5 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
  38.95    1.10   40.15

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

name	user	system	elapsed
Maaslin2	111.61	6.95	118.78