Multiple platform build/check report for BioC 3.21 - CHECK results for Maaslin2 on kunpeng2

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"	4658
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4455
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4408
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 kunpeng2

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: 1.21.0

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_1.21.0.tar.gz

StartedAt: 2025-01-25 08:24:28 -0000 (Sat, 25 Jan 2025)

EndedAt: 2025-01-25 08:27:59 -0000 (Sat, 25 Jan 2025)

EllapsedTime: 211.2 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_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* 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 ‘1.21.0’
* 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 123.059  1.297 124.635
* 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-3.21-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-4.5.0-devel_2024-11-24/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) (2024-11-24 r87369) -- "Unsuffered Consequences"
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"
2025-01-25 08:27:11.45889 INFO::Writing function arguments to log file
2025-01-25 08:27:11.51778 INFO::Verifying options selected are valid
2025-01-25 08:27:11.566372 INFO::Determining format of input files
2025-01-25 08:27:11.568695 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-25 08:27:11.57744 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-25 08:27:11.579668 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-01-25 08:27:11.583787 INFO::Filter data based on min abundance and min prevalence
2025-01-25 08:27:11.585421 INFO::Total samples in data: 1595
2025-01-25 08:27:11.586945 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-25 08:27:11.598058 INFO::Total filtered features: 0
2025-01-25 08:27:11.599989 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-25 08:27:11.639934 INFO::Total filtered features with variance filtering: 0
2025-01-25 08:27:11.64178 INFO::Filtered feature names from variance filtering:
2025-01-25 08:27:11.643363 INFO::Running selected normalization method: TSS
2025-01-25 08:27:13.118752 INFO::Bypass z-score application to metadata
2025-01-25 08:27:13.12026 INFO::Running selected transform method: AST
2025-01-25 08:27:13.14414 INFO::Running selected analysis method: LM
2025-01-25 08:27:13.800889 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-25 08:27:14.284585 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-25 08:27:14.537678 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-25 08:27:14.763242 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-25 08:27:15.00562 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-25 08:27:15.232673 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-25 08:27:15.469887 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-25 08:27:15.700202 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-25 08:27:15.929253 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-25 08:27:16.109564 WARNING::Fitting problem for feature 9 a warning was issued
2025-01-25 08:27:16.433511 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-25 08:27:16.676407 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-25 08:27:16.919119 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-25 08:27:17.15032 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-25 08:27:17.337381 WARNING::Fitting problem for feature 13 a warning was issued
2025-01-25 08:27:17.59826 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-25 08:27:17.826988 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-25 08:27:18.066506 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-25 08:27:18.287876 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-25 08:27:18.535663 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-25 08:27:18.775431 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-25 08:27:19.005421 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-25 08:27:19.24317 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-25 08:27:19.504626 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-25 08:27:19.753112 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-25 08:27:19.972837 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-25 08:27:20.216648 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-25 08:27:20.454129 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-25 08:27:20.677384 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-25 08:27:20.923331 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-25 08:27:21.166728 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-25 08:27:21.430567 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-25 08:27:21.662529 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-25 08:27:21.917059 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-25 08:27:22.160444 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-25 08:27:22.415259 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-25 08:27:22.641422 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-25 08:27:22.886119 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-25 08:27:23.129601 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-25 08:27:23.362196 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-25 08:27:23.591131 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-25 08:27:23.833787 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-25 08:27:24.080306 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-25 08:27:24.334207 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-25 08:27:24.582613 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-25 08:27:24.813341 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-25 08:27:25.32295 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-25 08:27:25.547362 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-25 08:27:25.787264 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-25 08:27:26.029569 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-25 08:27:26.26689 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-25 08:27:26.50146 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-25 08:27:26.724407 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-25 08:27:26.955635 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-25 08:27:27.193884 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-25 08:27:27.450786 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-25 08:27:27.701931 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-25 08:27:27.953842 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-25 08:27:28.207842 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-25 08:27:28.425319 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-25 08:27:28.651958 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-25 08:27:28.866274 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-25 08:27:29.084085 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-25 08:27:29.306414 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-25 08:27:29.531122 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-25 08:27:29.757786 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-25 08:27:29.982577 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-25 08:27:30.196491 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-25 08:27:30.418118 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-25 08:27:30.644389 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-25 08:27:30.874328 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-25 08:27:31.117748 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-25 08:27:31.362507 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-25 08:27:31.581078 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-25 08:27:31.81489 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-25 08:27:32.045925 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-25 08:27:32.266433 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-25 08:27:32.506876 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-25 08:27:32.736061 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-25 08:27:32.966412 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-25 08:27:33.216932 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-25 08:27:33.454729 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-25 08:27:33.688658 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-25 08:27:33.94156 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-25 08:27:34.172917 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-25 08:27:34.386232 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-25 08:27:34.619095 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-25 08:27:34.835984 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-25 08:27:35.053856 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-25 08:27:35.377363 INFO::Counting total values for each feature
2025-01-25 08:27:35.429842 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-01-25 08:27:35.545172 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-01-25 08:27:35.662743 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-01-25 08:27:35.782722 INFO::Writing residuals to file output/fits/residuals.rds
2025-01-25 08:27:35.840045 INFO::Writing fitted values to file output/fits/fitted.rds
2025-01-25 08:27:35.872024 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-01-25 08:27:35.883601 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-01-25 08:27:35.89043 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"
2025-01-25 08:27:35.908613 INFO::Writing function arguments to log file
2025-01-25 08:27:35.917176 INFO::Verifying options selected are valid
2025-01-25 08:27:35.918633 INFO::Determining format of input files
2025-01-25 08:27:35.920399 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-25 08:27:35.93874 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-25 08:27:35.940681 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-01-25 08:27:35.943222 INFO::Filter data based on min abundance and min prevalence
2025-01-25 08:27:35.944534 INFO::Total samples in data: 1595
2025-01-25 08:27:35.945786 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-25 08:27:35.954895 INFO::Total filtered features: 0
2025-01-25 08:27:35.956441 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-25 08:27:35.983525 INFO::Total filtered features with variance filtering: 0
2025-01-25 08:27:35.985118 INFO::Filtered feature names from variance filtering:
2025-01-25 08:27:35.986345 INFO::Running selected normalization method: NONE
2025-01-25 08:27:35.98759 INFO::Bypass z-score application to metadata
2025-01-25 08:27:35.988829 INFO::Running selected transform method: AST
2025-01-25 08:27:36.01183 INFO::Running selected analysis method: LM
2025-01-25 08:27:36.013973 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-25 08:27:36.239703 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-25 08:27:36.465531 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-25 08:27:36.679644 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-25 08:27:36.914622 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-25 08:27:37.124264 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-25 08:27:37.354293 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-25 08:27:37.566986 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-25 08:27:37.79379 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-25 08:27:38.01405 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-25 08:27:38.24874 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-25 08:27:38.467633 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-25 08:27:38.691755 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-25 08:27:38.911256 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-25 08:27:39.143783 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-25 08:27:39.36533 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-25 08:27:39.544379 WARNING::Fitting problem for feature 16 a warning was issued
2025-01-25 08:27:39.781361 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-25 08:27:40.010991 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-25 08:27:40.260054 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-25 08:27:40.476059 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-25 08:27:40.693451 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-25 08:27:40.921041 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-25 08:27:41.143362 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-25 08:27:41.350092 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-25 08:27:41.581415 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-25 08:27:41.80157 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-25 08:27:42.020864 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-25 08:27:42.260099 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-25 08:27:42.464095 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-25 08:27:42.667253 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-25 08:27:42.890534 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-25 08:27:43.110883 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-25 08:27:43.353671 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-25 08:27:43.568942 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-25 08:27:43.789633 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-25 08:27:44.019324 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-25 08:27:44.238774 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-25 08:27:44.474419 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-25 08:27:44.70353 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-25 08:27:44.921777 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-25 08:27:45.137677 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-25 08:27:45.350506 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-25 08:27:45.602525 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-25 08:27:45.832018 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-25 08:27:46.062286 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-25 08:27:46.27572 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-25 08:27:46.507009 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-25 08:27:46.71315 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-25 08:27:46.938258 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-25 08:27:47.144337 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-25 08:27:47.353234 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-25 08:27:47.579391 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-25 08:27:47.772547 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-25 08:27:47.992462 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-25 08:27:48.198419 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-25 08:27:48.411807 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-25 08:27:48.642738 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-25 08:27:48.863165 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-25 08:27:49.082812 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-25 08:27:49.315881 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-25 08:27:49.531176 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-25 08:27:49.749588 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-25 08:27:49.954237 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-25 08:27:50.161088 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-25 08:27:50.377318 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-25 08:27:50.589398 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-25 08:27:50.811232 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-25 08:27:51.033844 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-25 08:27:51.248971 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-25 08:27:51.483948 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-25 08:27:51.704349 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-25 08:27:51.923363 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-25 08:27:51.997126 WARNING::Fitting problem for feature 72 a warning was issued
2025-01-25 08:27:52.205286 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-25 08:27:52.712934 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-25 08:27:52.926672 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-25 08:27:53.134063 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-25 08:27:53.359914 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-25 08:27:53.568829 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-25 08:27:53.781673 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-25 08:27:53.997025 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-25 08:27:54.213615 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-25 08:27:54.434603 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-25 08:27:54.644746 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-25 08:27:54.851415 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-25 08:27:55.067811 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-25 08:27:55.276096 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-25 08:27:55.491065 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-25 08:27:55.738546 INFO::Counting total values for each feature
2025-01-25 08:27:55.7745 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-01-25 08:27:55.890046 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-01-25 08:27:56.006513 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-01-25 08:27:56.135657 INFO::Writing residuals to file output2/fits/residuals.rds
2025-01-25 08:27:56.210641 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-01-25 08:27:56.282188 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-01-25 08:27:56.288783 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-01-25 08:27:56.294397 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output2/significant_results.tsv
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 45.779   0.466  46.333

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

name	user	system	elapsed
Maaslin2	123.059	1.297	124.635