Lauren McIver
| Snapshot Date: 2025-01-02 13:00 -0500 (Thu, 02 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: RELEASE_3_20 |
| git_last_commit: 1cacd4c |
| git_last_commit_date: 2024-10-29 10:38:48 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-09 12:05 -0500 (Thu, 09 Jan 2025).
| 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" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4358 |
| 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 1130/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.20.0 (landing page) Lauren McIver
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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: 1.20.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Maaslin2_1.20.0.tar.gz |
| StartedAt: 2025-01-02 23:33:47 -0500 (Thu, 02 Jan 2025) |
| EndedAt: 2025-01-02 23:37:46 -0500 (Thu, 02 Jan 2025) |
| EllapsedTime: 238.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --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: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.20.0’
* 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 82.574 0.738 83.294
* 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-3.20-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘Maaslin2’ ... ** 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(Maaslin2)
>
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2025-01-02 23:35:40.626426 INFO::Writing function arguments to log file
2025-01-02 23:35:40.664248 INFO::Verifying options selected are valid
2025-01-02 23:35:40.697193 INFO::Determining format of input files
2025-01-02 23:35:40.698667 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-02 23:35:40.703306 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-02 23:35:40.70448 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-01-02 23:35:40.706735 INFO::Filter data based on min abundance and min prevalence
2025-01-02 23:35:40.707558 INFO::Total samples in data: 1595
2025-01-02 23:35:40.708339 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-02 23:35:40.711847 INFO::Total filtered features: 0
2025-01-02 23:35:40.712773 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-02 23:35:40.719846 INFO::Total filtered features with variance filtering: 0
2025-01-02 23:35:40.720791 INFO::Filtered feature names from variance filtering:
2025-01-02 23:35:40.721597 INFO::Running selected normalization method: TSS
2025-01-02 23:35:41.812107 INFO::Bypass z-score application to metadata
2025-01-02 23:35:41.813458 INFO::Running selected transform method: AST
2025-01-02 23:35:41.830741 INFO::Running selected analysis method: LM
2025-01-02 23:35:42.33304 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-02 23:35:42.651078 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-02 23:35:42.803747 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-02 23:35:42.941172 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-02 23:35:43.085377 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-02 23:35:43.223823 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-02 23:35:43.365899 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-02 23:35:43.505937 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-02 23:35:43.612864 WARNING::Fitting problem for feature 8 a warning was issued
2025-01-02 23:35:43.761304 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-02 23:35:43.870249 WARNING::Fitting problem for feature 9 a warning was issued
2025-01-02 23:35:44.068995 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-02 23:35:44.213848 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-02 23:35:44.378471 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-02 23:35:44.517313 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-02 23:35:44.639778 WARNING::Fitting problem for feature 13 a warning was issued
2025-01-02 23:35:44.804014 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-02 23:35:44.950609 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-02 23:35:45.09889 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-02 23:35:45.233995 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-02 23:35:45.412225 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-02 23:35:45.577159 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-02 23:35:46.037452 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-02 23:35:46.177046 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-02 23:35:46.33554 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-02 23:35:46.493696 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-02 23:35:46.630513 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-02 23:35:46.773215 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-02 23:35:46.922523 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-02 23:35:47.078917 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-02 23:35:47.227374 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-02 23:35:47.380092 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-02 23:35:47.530671 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-02 23:35:47.663404 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-02 23:35:47.811259 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-02 23:35:47.954194 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-02 23:35:48.09907 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-02 23:35:48.230274 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-02 23:35:48.368658 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-02 23:35:48.516531 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-02 23:35:48.657676 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-02 23:35:48.818052 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-02 23:35:48.970729 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-02 23:35:49.119445 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-02 23:35:49.264764 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-02 23:35:49.41374 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-02 23:35:49.545273 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-02 23:35:49.67964 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-02 23:35:49.826445 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-02 23:35:49.966664 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-02 23:35:50.107676 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-02 23:35:50.245206 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-02 23:35:50.381224 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-02 23:35:50.524567 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-02 23:35:50.665105 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-02 23:35:50.807988 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-02 23:35:50.962227 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-02 23:35:51.092535 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-02 23:35:51.236877 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-02 23:35:51.383178 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-02 23:35:51.513467 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-02 23:35:51.657803 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-02 23:35:51.79457 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-02 23:35:51.93592 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-02 23:35:52.074356 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-02 23:35:52.21856 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-02 23:35:52.353923 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-02 23:35:52.493798 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-02 23:35:52.623067 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-02 23:35:52.762892 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-02 23:35:52.886764 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-02 23:35:53.247181 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-02 23:35:53.386781 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-02 23:35:53.530986 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-02 23:35:53.670813 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-02 23:35:53.806496 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-02 23:35:53.942751 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-02 23:35:54.101221 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-02 23:35:54.250564 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-02 23:35:54.399446 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-02 23:35:54.552909 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-02 23:35:54.694885 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-02 23:35:54.832802 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-02 23:35:54.970171 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-02 23:35:55.10618 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-02 23:35:55.24207 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-02 23:35:55.379259 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-02 23:35:55.513904 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-02 23:35:55.654741 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-02 23:35:55.795275 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-02 23:35:55.977386 INFO::Counting total values for each feature
2025-01-02 23:35:56.019603 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-01-02 23:35:56.116265 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-01-02 23:35:56.215065 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-01-02 23:35:56.314662 INFO::Writing residuals to file output/fits/residuals.rds
2025-01-02 23:35:56.362211 INFO::Writing fitted values to file output/fits/fitted.rds
2025-01-02 23:35:56.388833 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-01-02 23:35:56.394124 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-01-02 23:35:56.399234 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"
2025-01-02 23:35:56.411191 INFO::Writing function arguments to log file
2025-01-02 23:35:56.416679 INFO::Verifying options selected are valid
2025-01-02 23:35:56.417626 INFO::Determining format of input files
2025-01-02 23:35:56.418685 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-02 23:35:56.423335 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-02 23:35:56.424326 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2025-01-02 23:35:56.425858 INFO::Filter data based on min abundance and min prevalence
2025-01-02 23:35:56.426662 INFO::Total samples in data: 1595
2025-01-02 23:35:56.42744 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-02 23:35:56.431626 INFO::Total filtered features: 0
2025-01-02 23:35:56.432512 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-02 23:35:56.439437 INFO::Total filtered features with variance filtering: 0
2025-01-02 23:35:56.440337 INFO::Filtered feature names from variance filtering:
2025-01-02 23:35:56.441098 INFO::Running selected normalization method: NONE
2025-01-02 23:35:56.441849 INFO::Bypass z-score application to metadata
2025-01-02 23:35:56.442605 INFO::Running selected transform method: AST
2025-01-02 23:35:56.461758 INFO::Running selected analysis method: LM
2025-01-02 23:35:56.463387 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-02 23:35:56.601412 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-02 23:35:56.739872 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-02 23:35:56.868078 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-02 23:35:56.994937 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-02 23:35:57.13216 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-02 23:35:57.265151 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-02 23:35:57.396446 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-02 23:35:57.530726 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-02 23:35:57.657707 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-02 23:35:57.789259 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-02 23:35:57.905458 WARNING::Fitting problem for feature 11 a warning was issued
2025-01-02 23:35:58.043512 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-02 23:35:58.170739 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-02 23:35:58.309788 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-02 23:35:58.434866 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-02 23:35:58.566019 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-02 23:35:58.674312 WARNING::Fitting problem for feature 16 a warning was issued
2025-01-02 23:35:58.809819 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-02 23:35:58.951815 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-02 23:35:59.081936 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-02 23:35:59.207531 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-02 23:35:59.345275 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-02 23:35:59.476699 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-02 23:35:59.615528 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-02 23:35:59.73954 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-02 23:35:59.877421 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-02 23:36:00.006209 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-02 23:36:00.140244 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-02 23:36:00.273214 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-02 23:36:00.402636 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-02 23:36:00.524338 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-02 23:36:00.666664 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-02 23:36:00.792145 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-02 23:36:00.925616 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-02 23:36:01.060232 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-02 23:36:01.189848 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-02 23:36:01.320103 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-02 23:36:01.455405 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-02 23:36:01.583435 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-02 23:36:01.715616 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-02 23:36:01.847142 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-02 23:36:01.971402 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-02 23:36:02.10794 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-02 23:36:02.233151 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-02 23:36:02.365853 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-02 23:36:02.503602 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-02 23:36:02.631699 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-02 23:36:02.766266 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-02 23:36:02.898163 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-02 23:36:03.032974 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-02 23:36:03.170866 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-02 23:36:03.292134 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-02 23:36:03.43099 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-02 23:36:03.547058 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-02 23:36:03.671988 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-02 23:36:03.794474 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-02 23:36:03.91732 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-02 23:36:04.051101 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-02 23:36:04.176443 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-02 23:36:04.307753 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-02 23:36:04.436497 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-02 23:36:04.56616 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-02 23:36:04.698829 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-02 23:36:04.828869 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-02 23:36:04.964206 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-02 23:36:05.091841 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-02 23:36:05.234431 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-02 23:36:05.360489 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-02 23:36:05.487633 WARNING::Fitting problem for feature 67 a warning was issued
2025-01-02 23:36:05.652913 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-02 23:36:05.782483 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-02 23:36:05.918544 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-02 23:36:06.063734 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-02 23:36:06.19112 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-02 23:36:06.236735 WARNING::Fitting problem for feature 72 a warning was issued
2025-01-02 23:36:06.373045 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-02 23:36:06.503139 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-02 23:36:06.642399 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-02 23:36:06.771271 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-02 23:36:06.902239 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-02 23:36:07.037841 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-02 23:36:07.164821 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-02 23:36:07.304766 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-02 23:36:07.430566 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-02 23:36:07.580156 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-02 23:36:07.709084 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-02 23:36:07.838491 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-02 23:36:07.971006 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-02 23:36:08.096746 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-02 23:36:08.238156 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-02 23:36:08.390586 INFO::Counting total values for each feature
2025-01-02 23:36:08.417193 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-01-02 23:36:08.512736 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-01-02 23:36:08.606279 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-01-02 23:36:08.714179 INFO::Writing residuals to file output2/fits/residuals.rds
2025-01-02 23:36:08.778561 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-01-02 23:36:08.8407 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-01-02 23:36:08.846341 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-01-02 23:36:08.851167 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
28.833 0.512 29.335
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 82.574 | 0.738 | 83.294 | |