Multiple platform build/check report for BioC 3.20 - CHECK results for Maaslin2 on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4746
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4494
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4517
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4469
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4400
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 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: 2025-01-31 07:41:00 -0000 (Fri, 31 Jan 2025)

EndedAt: 2025-01-31 07:44:13 -0000 (Fri, 31 Jan 2025)

EllapsedTime: 193.3 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 113.819  0.687 114.767
* 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"
2025-01-31 07:43:28.786502 INFO::Writing function arguments to log file
2025-01-31 07:43:28.838612 INFO::Verifying options selected are valid
2025-01-31 07:43:28.883299 INFO::Determining format of input files
2025-01-31 07:43:28.885256 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-31 07:43:28.892176 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-31 07:43:28.894091 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-01-31 07:43:28.897591 INFO::Filter data based on min abundance and min prevalence
2025-01-31 07:43:28.898952 INFO::Total samples in data: 1595
2025-01-31 07:43:28.900268 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-31 07:43:28.908463 INFO::Total filtered features: 0
2025-01-31 07:43:28.910099 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-31 07:43:28.938364 INFO::Total filtered features with variance filtering: 0
2025-01-31 07:43:28.939966 INFO::Filtered feature names from variance filtering:
2025-01-31 07:43:28.941292 INFO::Running selected normalization method: TSS
2025-01-31 07:43:30.36064 INFO::Bypass z-score application to metadata
2025-01-31 07:43:30.362297 INFO::Running selected transform method: AST
2025-01-31 07:43:30.382209 INFO::Running selected analysis method: LM
2025-01-31 07:43:30.998701 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-31 07:43:31.462785 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-31 07:43:31.705963 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-31 07:43:31.927552 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-31 07:43:32.160409 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-31 07:43:32.378336 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-31 07:43:32.611672 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-31 07:43:32.831361 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-31 07:43:33.054289 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-31 07:43:33.238316 WARNING::Fitting problem for feature 9 a warning was issued
2025-01-31 07:43:33.488096 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-31 07:43:33.762186 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-31 07:43:33.986454 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-31 07:43:34.215545 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-31 07:43:34.439783 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-31 07:43:34.660998 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-31 07:43:34.880878 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-31 07:43:35.100321 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-31 07:43:35.322318 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-31 07:43:35.551455 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-31 07:43:35.777471 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-31 07:43:36.039447 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-31 07:43:36.301419 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-31 07:43:36.552188 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-31 07:43:36.765105 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-31 07:43:36.988379 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-31 07:43:37.237065 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-31 07:43:37.454987 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-31 07:43:37.682529 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-31 07:43:37.923362 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-31 07:43:38.191657 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-31 07:43:38.416959 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-31 07:43:38.691166 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-31 07:43:38.930982 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-31 07:43:39.172649 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-31 07:43:39.382862 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-31 07:43:39.564546 WARNING::Fitting problem for feature 35 a warning was issued
2025-01-31 07:43:39.800275 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-31 07:43:40.034044 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-31 07:43:40.264439 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-31 07:43:40.500551 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-31 07:43:40.7183 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-31 07:43:40.963889 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-31 07:43:41.182449 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-31 07:43:41.420294 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-31 07:43:41.648961 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-31 07:43:41.849874 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-31 07:43:42.066166 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-31 07:43:42.291075 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-31 07:43:42.50669 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-31 07:43:42.95967 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-31 07:43:43.174546 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-31 07:43:43.379508 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-31 07:43:43.598145 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-31 07:43:43.806388 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-31 07:43:44.028517 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-31 07:43:44.245774 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-31 07:43:44.461123 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-31 07:43:44.68961 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-31 07:43:45.110828 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-31 07:43:45.316447 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-31 07:43:45.516087 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-31 07:43:45.713697 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-31 07:43:45.926818 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-31 07:43:46.149173 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-31 07:43:46.369129 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-31 07:43:46.590317 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-31 07:43:46.797636 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-31 07:43:47.00959 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-31 07:43:47.220328 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-31 07:43:47.430829 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-31 07:43:47.666941 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-31 07:43:47.911146 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-31 07:43:48.119783 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-31 07:43:48.327243 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-31 07:43:48.545061 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-31 07:43:48.75461 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-31 07:43:48.965259 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-31 07:43:49.188842 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-31 07:43:49.40421 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-31 07:43:49.633805 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-31 07:43:49.855792 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-31 07:43:50.061909 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-31 07:43:50.288701 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-31 07:43:50.496034 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-31 07:43:50.710798 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-31 07:43:50.943131 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-31 07:43:51.157951 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-31 07:43:51.374025 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-31 07:43:51.633116 INFO::Counting total values for each feature
2025-01-31 07:43:51.691579 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-01-31 07:43:51.809665 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-01-31 07:43:51.930058 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-01-31 07:43:52.052577 INFO::Writing residuals to file output/fits/residuals.rds
2025-01-31 07:43:52.109637 INFO::Writing fitted values to file output/fits/fitted.rds
2025-01-31 07:43:52.140625 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-01-31 07:43:52.147181 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-01-31 07:43:52.153995 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"
2025-01-31 07:43:52.17077 INFO::Writing function arguments to log file
2025-01-31 07:43:52.178807 INFO::Verifying options selected are valid
2025-01-31 07:43:52.180161 INFO::Determining format of input files
2025-01-31 07:43:52.181687 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-31 07:43:52.188218 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-31 07:43:52.189818 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-01-31 07:43:52.192086 INFO::Filter data based on min abundance and min prevalence
2025-01-31 07:43:52.19338 INFO::Total samples in data: 1595
2025-01-31 07:43:52.194524 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-31 07:43:52.202537 INFO::Total filtered features: 0
2025-01-31 07:43:52.204058 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-31 07:43:52.239218 INFO::Total filtered features with variance filtering: 0
2025-01-31 07:43:52.24076 INFO::Filtered feature names from variance filtering:
2025-01-31 07:43:52.24199 INFO::Running selected normalization method: NONE
2025-01-31 07:43:52.243135 INFO::Bypass z-score application to metadata
2025-01-31 07:43:52.244275 INFO::Running selected transform method: AST
2025-01-31 07:43:52.262684 INFO::Running selected analysis method: LM
2025-01-31 07:43:52.264846 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-31 07:43:52.466944 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-31 07:43:52.691972 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-31 07:43:52.879658 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-31 07:43:53.076513 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-31 07:43:53.289438 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-31 07:43:53.498984 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-31 07:43:53.714256 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-31 07:43:53.929753 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-31 07:43:54.128071 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-31 07:43:54.334721 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-31 07:43:54.559223 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-31 07:43:54.761354 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-31 07:43:54.937803 WARNING::Fitting problem for feature 13 a warning was issued
2025-01-31 07:43:55.152431 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-31 07:43:55.348204 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-31 07:43:55.576405 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-31 07:43:55.784619 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-31 07:43:55.98614 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-31 07:43:56.192603 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-31 07:43:56.398229 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-31 07:43:56.623878 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-31 07:43:56.822551 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-31 07:43:57.02104 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-31 07:43:57.229836 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-31 07:43:57.423939 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-31 07:43:57.624978 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-31 07:43:57.841818 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-31 07:43:58.055446 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-31 07:43:58.242704 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-31 07:43:58.436093 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-31 07:43:58.622911 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-31 07:43:58.824728 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-31 07:43:59.022593 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-31 07:43:59.217918 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-31 07:43:59.420424 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-31 07:43:59.618819 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-31 07:43:59.827128 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-31 07:44:00.021644 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-31 07:44:00.22865 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-31 07:44:00.410221 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-31 07:44:00.613726 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-31 07:44:00.820454 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-31 07:44:01.024095 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-31 07:44:01.255867 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-31 07:44:01.451103 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-31 07:44:01.65422 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-31 07:44:01.865284 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-31 07:44:02.050742 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-31 07:44:02.254563 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-31 07:44:02.442626 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-31 07:44:02.635 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-31 07:44:02.834226 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-31 07:44:03.026042 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-31 07:44:03.191855 WARNING::Fitting problem for feature 53 a warning was issued
2025-01-31 07:44:03.385444 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-31 07:44:03.581124 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-31 07:44:03.814793 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-31 07:44:04.022364 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-31 07:44:04.226784 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-31 07:44:04.435781 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-31 07:44:04.630663 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-31 07:44:04.833574 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-31 07:44:05.02906 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-31 07:44:05.225169 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-31 07:44:05.439 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-31 07:44:05.633585 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-31 07:44:05.845574 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-31 07:44:06.03371 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-31 07:44:06.204369 WARNING::Fitting problem for feature 67 a warning was issued
2025-01-31 07:44:06.407052 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-31 07:44:06.611253 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-31 07:44:06.811479 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-31 07:44:07.020928 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-31 07:44:07.238586 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-31 07:44:07.307978 WARNING::Fitting problem for feature 72 a warning was issued
2025-01-31 07:44:07.507298 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-31 07:44:07.72456 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-31 07:44:07.927686 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-31 07:44:08.129886 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-31 07:44:08.35915 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-31 07:44:08.553439 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-31 07:44:08.768861 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-31 07:44:08.97317 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-31 07:44:09.184841 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-31 07:44:09.392716 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-31 07:44:09.604152 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-31 07:44:09.792614 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-31 07:44:09.994634 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-31 07:44:10.189043 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-31 07:44:10.612674 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-31 07:44:10.840987 INFO::Counting total values for each feature
2025-01-31 07:44:10.87393 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-01-31 07:44:10.990597 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-01-31 07:44:11.107332 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-01-31 07:44:11.22997 INFO::Writing residuals to file output2/fits/residuals.rds
2025-01-31 07:44:11.303759 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-01-31 07:44:11.37411 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-01-31 07:44:11.380845 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-01-31 07:44:11.386792 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 
 43.067   0.815  43.984

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

name	user	system	elapsed
Maaslin2	113.819	0.687	114.767