Lauren McIver
| Snapshot Date: 2025-03-25 13:40 -0400 (Tue, 25 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: devel |
| git_last_commit: 3dacd30 |
| git_last_commit_date: 2024-10-29 10:38:48 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-26 11:42 -0400 (Wed, 26 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4783 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4552 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4581 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4533 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4463 |
| 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 1142/2315 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.21.0 (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: 1.21.0 |
| 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: 2025-03-25 23:42:48 -0400 (Tue, 25 Mar 2025) |
| EndedAt: 2025-03-25 23:46:53 -0400 (Tue, 25 Mar 2025) |
| EllapsedTime: 244.4 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_1.21.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* 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 ‘1.21.0’
* 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 85.312 0.746 86.056
* 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 ‘1.21.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Maaslin2)
Maaslin2.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"
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"
2025-03-25 23:44:43.403558 INFO::Writing function arguments to log file
2025-03-25 23:44:43.441887 INFO::Verifying options selected are valid
2025-03-25 23:44:43.473786 INFO::Determining format of input files
2025-03-25 23:44:43.475296 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-25 23:44:43.48025 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-25 23:44:43.481524 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-03-25 23:44:43.483833 INFO::Filter data based on min abundance and min prevalence
2025-03-25 23:44:43.484729 INFO::Total samples in data: 1595
2025-03-25 23:44:43.48559 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-25 23:44:43.49492 INFO::Total filtered features: 0
2025-03-25 23:44:43.496132 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-25 23:44:43.50248 INFO::Total filtered features with variance filtering: 0
2025-03-25 23:44:43.503566 INFO::Filtered feature names from variance filtering:
2025-03-25 23:44:43.504453 INFO::Running selected normalization method: TSS
2025-03-25 23:44:44.574573 INFO::Bypass z-score application to metadata
2025-03-25 23:44:44.575845 INFO::Running selected transform method: AST
2025-03-25 23:44:44.591206 INFO::Running selected analysis method: LM
2025-03-25 23:44:45.082662 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-25 23:44:45.409534 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-25 23:44:45.560665 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-25 23:44:45.71137 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-25 23:44:45.863471 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-25 23:44:46.006311 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-25 23:44:46.147826 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-25 23:44:46.295419 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-25 23:44:46.410196 WARNING::Fitting problem for feature 8 a warning was issued
2025-03-25 23:44:46.559043 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-25 23:44:46.681334 WARNING::Fitting problem for feature 9 a warning was issued
2025-03-25 23:44:46.834351 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-25 23:44:46.972742 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-25 23:44:47.112821 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-25 23:44:47.278746 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-25 23:44:47.402809 WARNING::Fitting problem for feature 13 a warning was issued
2025-03-25 23:44:47.55283 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-25 23:44:47.699348 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-25 23:44:47.843222 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-25 23:44:47.981924 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-25 23:44:48.14616 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-25 23:44:48.294003 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-25 23:44:48.43221 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-25 23:44:48.584951 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-25 23:44:48.761135 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-25 23:44:48.915009 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-25 23:44:49.063586 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-25 23:44:49.220933 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-25 23:44:49.367196 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-25 23:44:49.510479 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-25 23:44:49.6695 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-25 23:44:49.817978 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-25 23:44:49.966583 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-25 23:44:50.113164 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-25 23:44:50.262653 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-25 23:44:50.404679 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-25 23:44:50.556439 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-25 23:44:50.69452 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-25 23:44:50.840152 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-25 23:44:50.994494 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-25 23:44:51.139549 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-25 23:44:51.281669 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-25 23:44:51.428403 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-25 23:44:51.580949 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-25 23:44:51.731226 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-25 23:44:51.883403 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-25 23:44:52.029267 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-25 23:44:52.16938 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-25 23:44:52.313195 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-25 23:44:52.467236 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-25 23:44:52.61715 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-25 23:44:52.768462 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-25 23:44:52.910391 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-25 23:44:53.057059 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-25 23:44:53.198523 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-25 23:44:53.347449 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-25 23:44:53.510422 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-25 23:44:53.673646 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-25 23:44:53.823392 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-25 23:44:53.976831 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-25 23:44:54.116956 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-25 23:44:54.260765 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-25 23:44:54.405295 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-25 23:44:54.784807 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-25 23:44:54.924772 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-25 23:44:55.069056 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-25 23:44:55.211236 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-25 23:44:55.352114 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-25 23:44:55.485821 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-25 23:44:55.625119 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-25 23:44:55.760962 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-25 23:44:55.901013 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-25 23:44:56.04918 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-25 23:44:56.413659 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-25 23:44:56.551632 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-25 23:44:56.697913 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-25 23:44:56.846001 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-25 23:44:56.988198 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-25 23:44:57.13372 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-25 23:44:57.28175 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-25 23:44:57.423463 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-25 23:44:57.576761 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-25 23:44:57.72684 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-25 23:44:57.86544 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-25 23:44:58.010566 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-25 23:44:58.159015 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-25 23:44:58.294672 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-25 23:44:58.434706 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-25 23:44:58.581768 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-25 23:44:58.718142 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-25 23:44:58.904267 INFO::Counting total values for each feature
2025-03-25 23:44:58.933725 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-03-25 23:44:59.027163 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-03-25 23:44:59.122368 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-03-25 23:44:59.219003 INFO::Writing residuals to file output/fits/residuals.rds
2025-03-25 23:44:59.267088 INFO::Writing fitted values to file output/fits/fitted.rds
2025-03-25 23:44:59.293911 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-03-25 23:44:59.299284 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-03-25 23:44:59.304425 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"
2025-03-25 23:44:59.31618 INFO::Writing function arguments to log file
2025-03-25 23:44:59.321899 INFO::Verifying options selected are valid
2025-03-25 23:44:59.322858 INFO::Determining format of input files
2025-03-25 23:44:59.32404 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-25 23:44:59.328882 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-25 23:44:59.329915 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2025-03-25 23:44:59.331449 INFO::Filter data based on min abundance and min prevalence
2025-03-25 23:44:59.33231 INFO::Total samples in data: 1595
2025-03-25 23:44:59.333168 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-25 23:44:59.342813 INFO::Total filtered features: 0
2025-03-25 23:44:59.344178 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-25 23:44:59.349954 INFO::Total filtered features with variance filtering: 0
2025-03-25 23:44:59.350933 INFO::Filtered feature names from variance filtering:
2025-03-25 23:44:59.351754 INFO::Running selected normalization method: NONE
2025-03-25 23:44:59.352599 INFO::Bypass z-score application to metadata
2025-03-25 23:44:59.353421 INFO::Running selected transform method: AST
2025-03-25 23:44:59.367363 INFO::Running selected analysis method: LM
2025-03-25 23:44:59.368898 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-25 23:44:59.507234 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-25 23:44:59.640283 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-25 23:44:59.769885 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-25 23:44:59.910852 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-25 23:45:00.043031 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-25 23:45:00.1888 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-25 23:45:00.323664 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-25 23:45:00.466549 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-25 23:45:00.602785 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-25 23:45:00.74798 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-25 23:45:00.86945 WARNING::Fitting problem for feature 11 a warning was issued
2025-03-25 23:45:01.019843 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-25 23:45:01.150185 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-25 23:45:01.292305 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-25 23:45:01.426419 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-25 23:45:01.591997 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-25 23:45:01.724612 WARNING::Fitting problem for feature 16 a warning was issued
2025-03-25 23:45:01.867171 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-25 23:45:02.014935 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-25 23:45:02.170402 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-25 23:45:02.304081 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-25 23:45:02.451587 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-25 23:45:02.604782 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-25 23:45:02.74545 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-25 23:45:02.883947 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-25 23:45:03.030259 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-25 23:45:03.168889 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-25 23:45:03.308107 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-25 23:45:03.454035 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-25 23:45:03.584954 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-25 23:45:03.729985 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-25 23:45:03.867545 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-25 23:45:04.00354 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-25 23:45:04.14749 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-25 23:45:04.27774 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-25 23:45:04.411876 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-25 23:45:04.551573 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-25 23:45:04.688206 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-25 23:45:04.836859 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-25 23:45:04.977897 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-25 23:45:05.113827 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-25 23:45:05.265836 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-25 23:45:05.400438 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-25 23:45:05.542997 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-25 23:45:05.680646 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-25 23:45:05.819043 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-25 23:45:05.961001 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-25 23:45:06.099724 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-25 23:45:06.23868 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-25 23:45:06.37204 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-25 23:45:06.511972 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-25 23:45:06.63578 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-25 23:45:06.777714 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-25 23:45:06.901259 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-25 23:45:07.031084 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-25 23:45:07.159047 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-25 23:45:07.295506 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-25 23:45:07.431364 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-25 23:45:07.56125 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-25 23:45:07.698704 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-25 23:45:07.832117 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-25 23:45:07.975689 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-25 23:45:08.113856 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-25 23:45:08.269893 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-25 23:45:08.411337 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-25 23:45:08.552644 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-25 23:45:08.92914 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-25 23:45:09.060342 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-25 23:45:09.179698 WARNING::Fitting problem for feature 67 a warning was issued
2025-03-25 23:45:09.33132 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-25 23:45:09.476094 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-25 23:45:09.617128 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-25 23:45:09.76046 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-25 23:45:09.898898 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-25 23:45:09.947215 WARNING::Fitting problem for feature 72 a warning was issued
2025-03-25 23:45:10.092351 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-25 23:45:10.23605 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-25 23:45:10.384351 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-25 23:45:10.517114 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-25 23:45:10.662637 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-25 23:45:10.793333 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-25 23:45:10.929172 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-25 23:45:11.074039 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-25 23:45:11.216134 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-25 23:45:11.357603 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-25 23:45:11.489888 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-25 23:45:11.618626 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-25 23:45:11.750941 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-25 23:45:11.890099 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-25 23:45:12.032592 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-25 23:45:12.190881 INFO::Counting total values for each feature
2025-03-25 23:45:12.213171 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-03-25 23:45:12.305975 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-03-25 23:45:12.398876 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-03-25 23:45:12.496707 INFO::Writing residuals to file output2/fits/residuals.rds
2025-03-25 23:45:12.5608 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-03-25 23:45:12.622718 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-03-25 23:45:12.628173 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-03-25 23:45:12.632531 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
29.763 0.519 30.272
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 85.312 | 0.746 | 86.056 | |