Lauren McIver
| Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: RELEASE_3_21 |
| git_last_commit: fcec85e |
| git_last_commit_date: 2025-04-15 11:48:14 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-22 13:13 -0400 (Tue, 22 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1154/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.22.0 (landing page) Lauren McIver
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| Package: Maaslin2 |
| Version: 1.22.0 |
| 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_1.22.0.tar.gz |
| StartedAt: 2025-04-21 23:43:52 -0400 (Mon, 21 Apr 2025) |
| EndedAt: 2025-04-21 23:47:59 -0400 (Mon, 21 Apr 2025) |
| EllapsedTime: 247.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.22.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.22.0’
* 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 87.435 1.277 88.716
* 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.
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’ ... ** this is package ‘Maaslin2’ version ‘1.22.0’ ** 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)
Maaslin2.Rcheck/tests/testthat.Rout
R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 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"
2025-04-21 23:45:49.824719 INFO::Writing function arguments to log file
2025-04-21 23:45:49.863849 INFO::Verifying options selected are valid
2025-04-21 23:45:49.897399 INFO::Determining format of input files
2025-04-21 23:45:49.898902 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-21 23:45:49.904039 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-04-21 23:45:49.905304 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-04-21 23:45:49.907653 INFO::Filter data based on min abundance and min prevalence
2025-04-21 23:45:49.908621 INFO::Total samples in data: 1595
2025-04-21 23:45:49.909542 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-04-21 23:45:49.919872 INFO::Total filtered features: 0
2025-04-21 23:45:49.921038 INFO::Filtered feature names from abundance and prevalence filtering:
2025-04-21 23:45:49.927374 INFO::Total filtered features with variance filtering: 0
2025-04-21 23:45:49.928376 INFO::Filtered feature names from variance filtering:
2025-04-21 23:45:49.929233 INFO::Running selected normalization method: TSS
2025-04-21 23:45:51.038187 INFO::Bypass z-score application to metadata
2025-04-21 23:45:51.039509 INFO::Running selected transform method: AST
2025-04-21 23:45:51.054716 INFO::Running selected analysis method: LM
2025-04-21 23:45:51.534948 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-04-21 23:45:51.868316 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-04-21 23:45:52.015595 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-04-21 23:45:52.163288 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-04-21 23:45:52.317266 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-04-21 23:45:52.460203 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-04-21 23:45:52.604639 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-04-21 23:45:52.75631 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-04-21 23:45:52.869172 WARNING::Fitting problem for feature 8 a warning was issued
2025-04-21 23:45:53.016021 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-04-21 23:45:53.129825 WARNING::Fitting problem for feature 9 a warning was issued
2025-04-21 23:45:53.289272 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-04-21 23:45:53.425397 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-04-21 23:45:53.567026 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-04-21 23:45:53.734159 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-04-21 23:45:53.852797 WARNING::Fitting problem for feature 13 a warning was issued
2025-04-21 23:45:54.000496 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-04-21 23:45:54.148671 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-04-21 23:45:54.293175 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-04-21 23:45:54.431669 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-04-21 23:45:54.593597 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-04-21 23:45:54.770143 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-04-21 23:45:54.919306 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-04-21 23:45:55.06839 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-04-21 23:45:55.222765 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-04-21 23:45:55.372684 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-04-21 23:45:55.524292 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-04-21 23:45:55.673811 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-04-21 23:45:55.821565 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-04-21 23:45:55.965456 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-04-21 23:45:56.127279 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-04-21 23:45:56.275476 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-04-21 23:45:56.427078 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-04-21 23:45:56.585728 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-04-21 23:45:56.740409 INFO::Fitting model to feature number 32, Prevotella.copri
2025-04-21 23:45:56.886146 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-04-21 23:45:57.041356 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-04-21 23:45:57.183755 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-04-21 23:45:57.327508 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-04-21 23:45:57.481731 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-04-21 23:45:57.631712 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-04-21 23:45:57.786453 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-04-21 23:45:57.962003 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-04-21 23:45:58.125256 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-04-21 23:45:58.2907 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-04-21 23:45:58.438891 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-04-21 23:45:58.584727 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-04-21 23:45:58.72313 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-04-21 23:45:58.874409 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-04-21 23:45:59.021918 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-04-21 23:45:59.175865 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-04-21 23:45:59.316978 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-04-21 23:45:59.463858 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-04-21 23:45:59.602222 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-04-21 23:45:59.751748 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-04-21 23:45:59.907257 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-04-21 23:46:00.077828 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-04-21 23:46:00.224338 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-04-21 23:46:00.383789 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-04-21 23:46:00.546106 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-04-21 23:46:00.682897 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-04-21 23:46:00.834954 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-04-21 23:46:00.980443 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-04-21 23:46:01.150822 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-04-21 23:46:01.298774 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-04-21 23:46:01.457453 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-04-21 23:46:01.892592 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-04-21 23:46:02.033004 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-04-21 23:46:02.175938 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-04-21 23:46:02.317832 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-04-21 23:46:02.459913 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-04-21 23:46:02.601597 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-04-21 23:46:02.747266 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-04-21 23:46:02.90027 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-04-21 23:46:03.035207 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-04-21 23:46:03.171788 INFO::Fitting model to feature number 73, Dialister.invisus
2025-04-21 23:46:03.34811 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-04-21 23:46:03.495394 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-04-21 23:46:03.648894 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-04-21 23:46:03.799341 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-04-21 23:46:03.938996 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-04-21 23:46:04.086709 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-04-21 23:46:04.240443 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-04-21 23:46:04.387425 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-04-21 23:46:04.529558 INFO::Fitting model to feature number 82, Escherichia.coli
2025-04-21 23:46:04.681346 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-04-21 23:46:04.825433 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-04-21 23:46:04.972166 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-04-21 23:46:05.112296 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-04-21 23:46:05.254051 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-04-21 23:46:05.456565 INFO::Counting total values for each feature
2025-04-21 23:46:05.489793 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-04-21 23:46:05.58805 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-04-21 23:46:05.692901 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-04-21 23:46:05.795012 INFO::Writing residuals to file output/fits/residuals.rds
2025-04-21 23:46:05.843857 INFO::Writing fitted values to file output/fits/fitted.rds
2025-04-21 23:46:05.87117 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-04-21 23:46:05.876824 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-04-21 23:46:05.882431 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"
2025-04-21 23:46:05.89564 INFO::Writing function arguments to log file
2025-04-21 23:46:05.901574 INFO::Verifying options selected are valid
2025-04-21 23:46:05.902644 INFO::Determining format of input files
2025-04-21 23:46:05.903901 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-21 23:46:05.919673 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-04-21 23:46:05.920871 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2025-04-21 23:46:05.922598 INFO::Filter data based on min abundance and min prevalence
2025-04-21 23:46:05.923535 INFO::Total samples in data: 1595
2025-04-21 23:46:05.924583 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-04-21 23:46:05.928713 INFO::Total filtered features: 0
2025-04-21 23:46:05.929683 INFO::Filtered feature names from abundance and prevalence filtering:
2025-04-21 23:46:05.93598 INFO::Total filtered features with variance filtering: 0
2025-04-21 23:46:05.937041 INFO::Filtered feature names from variance filtering:
2025-04-21 23:46:05.937913 INFO::Running selected normalization method: NONE
2025-04-21 23:46:05.938802 INFO::Bypass z-score application to metadata
2025-04-21 23:46:05.939641 INFO::Running selected transform method: AST
2025-04-21 23:46:05.954016 INFO::Running selected analysis method: LM
2025-04-21 23:46:05.95571 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-04-21 23:46:06.098103 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-04-21 23:46:06.235983 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-04-21 23:46:06.375955 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-04-21 23:46:06.511104 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-04-21 23:46:06.649392 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-04-21 23:46:06.791996 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-04-21 23:46:06.934885 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-04-21 23:46:07.066247 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-04-21 23:46:07.21051 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-04-21 23:46:07.351546 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-04-21 23:46:07.471123 WARNING::Fitting problem for feature 11 a warning was issued
2025-04-21 23:46:07.623582 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-04-21 23:46:07.754575 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-04-21 23:46:07.912354 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-04-21 23:46:08.043204 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-04-21 23:46:08.188132 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-04-21 23:46:08.303726 WARNING::Fitting problem for feature 16 a warning was issued
2025-04-21 23:46:08.440599 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-04-21 23:46:08.584198 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-04-21 23:46:08.727944 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-04-21 23:46:08.868488 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-04-21 23:46:09.013928 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-04-21 23:46:09.164187 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-04-21 23:46:09.312585 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-04-21 23:46:09.462255 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-04-21 23:46:09.609503 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-04-21 23:46:09.752169 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-04-21 23:46:10.116398 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-04-21 23:46:10.255505 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-04-21 23:46:10.387652 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-04-21 23:46:10.531783 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-04-21 23:46:10.660852 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-04-21 23:46:10.796413 INFO::Fitting model to feature number 32, Prevotella.copri
2025-04-21 23:46:10.937797 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-04-21 23:46:11.076994 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-04-21 23:46:11.211014 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-04-21 23:46:11.345079 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-04-21 23:46:11.489507 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-04-21 23:46:11.63536 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-04-21 23:46:11.770299 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-04-21 23:46:11.89993 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-04-21 23:46:12.04227 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-04-21 23:46:12.172338 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-04-21 23:46:12.303926 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-04-21 23:46:12.442677 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-04-21 23:46:12.587596 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-04-21 23:46:12.720129 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-04-21 23:46:12.860632 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-04-21 23:46:13.001762 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-04-21 23:46:13.147686 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-04-21 23:46:13.2841 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-04-21 23:46:13.41845 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-04-21 23:46:13.552833 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-04-21 23:46:13.679292 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-04-21 23:46:13.811927 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-04-21 23:46:13.941785 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-04-21 23:46:14.077126 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-04-21 23:46:14.224578 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-04-21 23:46:14.36253 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-04-21 23:46:14.493052 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-04-21 23:46:14.66512 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-04-21 23:46:14.802444 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-04-21 23:46:14.947247 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-04-21 23:46:15.091686 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-04-21 23:46:15.233101 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-04-21 23:46:15.373869 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-04-21 23:46:15.514852 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-04-21 23:46:15.647483 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-04-21 23:46:16.007856 WARNING::Fitting problem for feature 67 a warning was issued
2025-04-21 23:46:16.154189 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-04-21 23:46:16.283053 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-04-21 23:46:16.422066 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-04-21 23:46:16.574544 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-04-21 23:46:16.707565 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-04-21 23:46:16.756435 WARNING::Fitting problem for feature 72 a warning was issued
2025-04-21 23:46:16.890951 INFO::Fitting model to feature number 73, Dialister.invisus
2025-04-21 23:46:17.026562 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-04-21 23:46:17.168591 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-04-21 23:46:17.303526 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-04-21 23:46:17.438767 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-04-21 23:46:17.574689 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-04-21 23:46:17.72956 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-04-21 23:46:17.868189 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-04-21 23:46:18.001426 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-04-21 23:46:18.143546 INFO::Fitting model to feature number 82, Escherichia.coli
2025-04-21 23:46:18.287306 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-04-21 23:46:18.417248 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-04-21 23:46:18.54842 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-04-21 23:46:18.682657 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-04-21 23:46:18.827983 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-04-21 23:46:18.987763 INFO::Counting total values for each feature
2025-04-21 23:46:19.010039 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-04-21 23:46:19.105975 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-04-21 23:46:19.201418 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-04-21 23:46:19.301431 INFO::Writing residuals to file output2/fits/residuals.rds
2025-04-21 23:46:19.365943 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-04-21 23:46:19.428256 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-04-21 23:46:19.433891 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-04-21 23:46:19.438538 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
30.123 0.591 30.705
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 87.435 | 1.277 | 88.716 | |