Multiple platform build/check report for BioC 3.21 - CHECK results for Maaslin2 on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4760
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4479
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4443
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4398
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4391
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 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: 2025-01-10 23:27:23 -0500 (Fri, 10 Jan 2025)

EndedAt: 2025-01-10 23:31:30 -0500 (Fri, 10 Jan 2025)

EllapsedTime: 246.4 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 86.971  0.927    87.9
* 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"
2025-01-10 23:29:20.367215 INFO::Writing function arguments to log file
2025-01-10 23:29:20.409327 INFO::Verifying options selected are valid
2025-01-10 23:29:20.440036 INFO::Determining format of input files
2025-01-10 23:29:20.441579 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-10 23:29:20.446492 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-10 23:29:20.447727 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-01-10 23:29:20.450042 INFO::Filter data based on min abundance and min prevalence
2025-01-10 23:29:20.450941 INFO::Total samples in data: 1595
2025-01-10 23:29:20.451783 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-10 23:29:20.4555 INFO::Total filtered features: 0
2025-01-10 23:29:20.456534 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-10 23:29:20.469084 INFO::Total filtered features with variance filtering: 0
2025-01-10 23:29:20.470191 INFO::Filtered feature names from variance filtering:
2025-01-10 23:29:20.471035 INFO::Running selected normalization method: TSS
2025-01-10 23:29:21.581057 INFO::Bypass z-score application to metadata
2025-01-10 23:29:21.582597 INFO::Running selected transform method: AST
2025-01-10 23:29:21.599987 INFO::Running selected analysis method: LM
2025-01-10 23:29:22.097098 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-10 23:29:22.421787 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-10 23:29:22.584406 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-10 23:29:22.724256 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-10 23:29:22.877928 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-10 23:29:23.02521 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-10 23:29:23.168382 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-10 23:29:23.315397 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-10 23:29:23.427749 WARNING::Fitting problem for feature 8 a warning was issued
2025-01-10 23:29:23.578927 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-10 23:29:23.694792 WARNING::Fitting problem for feature 9 a warning was issued
2025-01-10 23:29:23.87422 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-10 23:29:24.028396 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-10 23:29:24.194044 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-10 23:29:24.335537 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-10 23:29:24.463146 WARNING::Fitting problem for feature 13 a warning was issued
2025-01-10 23:29:24.616463 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-10 23:29:24.758562 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-10 23:29:24.903193 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-10 23:29:25.04311 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-10 23:29:25.188265 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-10 23:29:25.337316 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-10 23:29:25.476513 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-10 23:29:25.629404 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-10 23:29:25.776762 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-10 23:29:25.929259 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-10 23:29:26.075096 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-10 23:29:26.224678 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-10 23:29:26.378778 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-10 23:29:26.521446 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-10 23:29:26.679723 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-10 23:29:26.832709 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-10 23:29:26.988736 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-10 23:29:27.167716 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-10 23:29:27.334716 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-10 23:29:27.509461 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-10 23:29:27.657277 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-10 23:29:27.805585 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-10 23:29:27.948802 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-10 23:29:28.104803 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-10 23:29:28.254701 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-10 23:29:28.401214 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-10 23:29:28.545213 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-10 23:29:28.721545 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-10 23:29:28.868307 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-10 23:29:29.026676 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-10 23:29:29.180571 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-10 23:29:29.317496 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-10 23:29:29.466789 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-10 23:29:29.911635 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-10 23:29:30.055189 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-10 23:29:30.200096 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-10 23:29:30.356876 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-10 23:29:30.507078 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-10 23:29:30.642994 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-10 23:29:30.794046 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-10 23:29:30.949793 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-10 23:29:31.082614 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-10 23:29:31.223003 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-10 23:29:31.374975 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-10 23:29:31.507108 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-10 23:29:31.655417 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-10 23:29:31.799247 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-10 23:29:31.932496 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-10 23:29:32.072457 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-10 23:29:32.222197 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-10 23:29:32.363935 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-10 23:29:32.528609 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-10 23:29:32.686776 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-10 23:29:32.834099 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-10 23:29:32.97347 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-10 23:29:33.113353 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-10 23:29:33.255243 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-10 23:29:33.400089 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-10 23:29:33.529795 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-10 23:29:33.664662 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-10 23:29:33.80735 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-10 23:29:33.945036 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-10 23:29:34.089497 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-10 23:29:34.223924 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-10 23:29:34.357961 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-10 23:29:34.504491 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-10 23:29:34.642709 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-10 23:29:34.77853 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-10 23:29:34.917415 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-10 23:29:35.068118 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-10 23:29:35.206543 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-10 23:29:35.351798 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-10 23:29:35.486362 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-10 23:29:35.627291 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-10 23:29:35.814128 INFO::Counting total values for each feature
2025-01-10 23:29:35.845744 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-01-10 23:29:35.939639 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-01-10 23:29:36.035822 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-01-10 23:29:36.134163 INFO::Writing residuals to file output/fits/residuals.rds
2025-01-10 23:29:36.516313 INFO::Writing fitted values to file output/fits/fitted.rds
2025-01-10 23:29:36.544413 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-01-10 23:29:36.550126 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-01-10 23:29:36.555702 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"
2025-01-10 23:29:36.567807 INFO::Writing function arguments to log file
2025-01-10 23:29:36.573528 INFO::Verifying options selected are valid
2025-01-10 23:29:36.574512 INFO::Determining format of input files
2025-01-10 23:29:36.57569 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-10 23:29:36.580589 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-10 23:29:36.58163 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-01-10 23:29:36.583166 INFO::Filter data based on min abundance and min prevalence
2025-01-10 23:29:36.584007 INFO::Total samples in data: 1595
2025-01-10 23:29:36.584847 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-10 23:29:36.58863 INFO::Total filtered features: 0
2025-01-10 23:29:36.589549 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-10 23:29:36.596749 INFO::Total filtered features with variance filtering: 0
2025-01-10 23:29:36.597755 INFO::Filtered feature names from variance filtering:
2025-01-10 23:29:36.598577 INFO::Running selected normalization method: NONE
2025-01-10 23:29:36.599403 INFO::Bypass z-score application to metadata
2025-01-10 23:29:36.600213 INFO::Running selected transform method: AST
2025-01-10 23:29:36.614757 INFO::Running selected analysis method: LM
2025-01-10 23:29:36.616339 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-10 23:29:36.753618 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-10 23:29:36.897211 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-10 23:29:37.027097 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-10 23:29:37.165484 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-10 23:29:37.299702 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-10 23:29:37.439022 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-10 23:29:37.569229 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-10 23:29:37.702572 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-10 23:29:37.845589 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-10 23:29:37.983334 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-10 23:29:38.096788 WARNING::Fitting problem for feature 11 a warning was issued
2025-01-10 23:29:38.253533 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-10 23:29:38.393165 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-10 23:29:38.527135 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-10 23:29:38.665916 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-10 23:29:38.802047 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-10 23:29:38.9101 WARNING::Fitting problem for feature 16 a warning was issued
2025-01-10 23:29:39.059982 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-10 23:29:39.209815 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-10 23:29:39.346082 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-10 23:29:39.500611 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-10 23:29:39.673794 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-10 23:29:39.816851 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-10 23:29:39.961028 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-10 23:29:40.104398 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-10 23:29:40.243666 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-10 23:29:40.380852 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-10 23:29:40.530778 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-10 23:29:40.675922 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-10 23:29:40.800394 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-10 23:29:40.928997 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-10 23:29:41.055873 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-10 23:29:41.186549 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-10 23:29:41.589869 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-10 23:29:41.719973 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-10 23:29:41.86239 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-10 23:29:42.004126 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-10 23:29:42.154987 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-10 23:29:42.293435 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-10 23:29:42.435266 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-10 23:29:42.574187 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-10 23:29:42.712592 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-10 23:29:42.853974 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-10 23:29:42.99605 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-10 23:29:43.150571 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-10 23:29:43.281414 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-10 23:29:43.411228 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-10 23:29:43.549235 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-10 23:29:43.680678 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-10 23:29:43.809741 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-10 23:29:43.938093 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-10 23:29:44.067091 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-10 23:29:44.201313 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-10 23:29:44.3236 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-10 23:29:44.455939 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-10 23:29:44.586819 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-10 23:29:44.714676 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-10 23:29:44.845252 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-10 23:29:44.986142 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-10 23:29:45.117 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-10 23:29:45.251664 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-10 23:29:45.389268 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-10 23:29:45.521888 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-10 23:29:45.651152 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-10 23:29:45.795141 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-10 23:29:45.931484 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-10 23:29:46.064766 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-10 23:29:46.201674 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-10 23:29:46.312088 WARNING::Fitting problem for feature 67 a warning was issued
2025-01-10 23:29:46.455378 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-10 23:29:46.58766 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-10 23:29:46.720563 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-10 23:29:46.864617 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-10 23:29:46.998178 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-10 23:29:47.04581 WARNING::Fitting problem for feature 72 a warning was issued
2025-01-10 23:29:47.182318 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-10 23:29:47.327852 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-10 23:29:47.459918 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-10 23:29:47.599325 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-10 23:29:47.733574 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-10 23:29:47.862745 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-10 23:29:48.000468 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-10 23:29:48.137548 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-10 23:29:48.283129 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-10 23:29:48.427143 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-10 23:29:48.562234 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-10 23:29:48.687337 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-10 23:29:48.827582 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-10 23:29:48.963303 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-10 23:29:49.101155 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-10 23:29:49.266585 INFO::Counting total values for each feature
2025-01-10 23:29:49.289618 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-01-10 23:29:49.382571 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-01-10 23:29:49.475106 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-01-10 23:29:49.572526 INFO::Writing residuals to file output2/fits/residuals.rds
2025-01-10 23:29:49.636511 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-01-10 23:29:49.698495 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-01-10 23:29:49.704219 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-01-10 23:29:49.70897 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 
 29.841   0.583  30.416

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

name	user	system	elapsed
Maaslin2	86.971	0.927	87.900