Lauren McIver
| Snapshot Date: 2025-01-20 13:40 -0500 (Mon, 20 Jan 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 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-21 11:47 -0500 (Tue, 21 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4777 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4502 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4467 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4422 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4406 |
| 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 1128/2286 | 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 22.03 LTS-SP1) / 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: Maaslin2 |
| Version: 1.21.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Maaslin2_1.21.0.tar.gz |
| StartedAt: 2025-01-21 07:55:23 -0000 (Tue, 21 Jan 2025) |
| EndedAt: 2025-01-21 07:58:52 -0000 (Tue, 21 Jan 2025) |
| EllapsedTime: 209.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Maaslin2_1.21.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.21.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Maaslin2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
maaslin2_association_plots: no visible binding for global variable
‘xnames’
Undefined global functions or variables:
xnames
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Maaslin2 122.494 1.557 124.382
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘Maaslin2’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning in check_dep_version(dep_pkg = "TMB") : package version mismatch: glmmTMB was built with TMB package version 1.9.15 Current TMB package version is 1.9.16 Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information) ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Maaslin2)
Maaslin2.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(Maaslin2)
>
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2025-01-21 07:58:04.268282 INFO::Writing function arguments to log file
2025-01-21 07:58:04.325752 INFO::Verifying options selected are valid
2025-01-21 07:58:04.37186 INFO::Determining format of input files
2025-01-21 07:58:04.373949 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-21 07:58:04.381828 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-21 07:58:04.383874 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-01-21 07:58:04.387446 INFO::Filter data based on min abundance and min prevalence
2025-01-21 07:58:04.388881 INFO::Total samples in data: 1595
2025-01-21 07:58:04.390142 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-21 07:58:04.400198 INFO::Total filtered features: 0
2025-01-21 07:58:04.401922 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-21 07:58:04.439987 INFO::Total filtered features with variance filtering: 0
2025-01-21 07:58:04.44156 INFO::Filtered feature names from variance filtering:
2025-01-21 07:58:04.44282 INFO::Running selected normalization method: TSS
2025-01-21 07:58:05.914454 INFO::Bypass z-score application to metadata
2025-01-21 07:58:05.915962 INFO::Running selected transform method: AST
2025-01-21 07:58:05.938859 INFO::Running selected analysis method: LM
2025-01-21 07:58:06.59707 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-21 07:58:07.076907 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-21 07:58:07.331481 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-21 07:58:07.559318 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-21 07:58:07.80156 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-21 07:58:08.032493 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-21 07:58:08.275425 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-21 07:58:08.498518 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-21 07:58:08.726007 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-21 07:58:08.910257 WARNING::Fitting problem for feature 9 a warning was issued
2025-01-21 07:58:09.231315 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-21 07:58:09.462566 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-21 07:58:09.692055 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-21 07:58:09.923221 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-21 07:58:10.108484 WARNING::Fitting problem for feature 13 a warning was issued
2025-01-21 07:58:10.365642 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-21 07:58:10.589862 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-21 07:58:10.83672 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-21 07:58:11.056031 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-21 07:58:11.303133 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-21 07:58:11.536181 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-21 07:58:11.762742 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-21 07:58:11.986646 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-21 07:58:12.223658 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-21 07:58:12.459536 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-21 07:58:12.6751 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-21 07:58:12.92504 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-21 07:58:13.1707 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-21 07:58:13.387602 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-21 07:58:13.628834 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-21 07:58:13.876078 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-21 07:58:14.133304 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-21 07:58:14.381993 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-21 07:58:14.614852 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-21 07:58:14.859434 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-21 07:58:15.092762 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-21 07:58:15.31349 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-21 07:58:15.547241 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-21 07:58:15.775886 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-21 07:58:16.021183 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-21 07:58:16.24238 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-21 07:58:16.474407 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-21 07:58:16.723557 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-21 07:58:16.950879 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-21 07:58:17.198511 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-21 07:58:17.422372 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-21 07:58:17.649149 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-21 07:58:17.881189 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-21 07:58:18.129318 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-21 07:58:18.66321 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-21 07:58:18.886403 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-21 07:58:19.112992 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-21 07:58:19.602479 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-21 07:58:19.818265 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-21 07:58:20.054826 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-21 07:58:20.300833 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-21 07:58:20.539677 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-21 07:58:20.782447 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-21 07:58:21.03063 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-21 07:58:21.26742 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-21 07:58:21.498147 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-21 07:58:21.718752 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-21 07:58:21.950809 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-21 07:58:22.177678 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-21 07:58:22.40546 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-21 07:58:22.644885 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-21 07:58:22.863018 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-21 07:58:23.080355 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-21 07:58:23.30993 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-21 07:58:23.518934 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-21 07:58:23.755709 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-21 07:58:24.02461 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-21 07:58:24.26839 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-21 07:58:24.506549 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-21 07:58:24.729989 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-21 07:58:24.957871 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-21 07:58:25.203266 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-21 07:58:25.43732 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-21 07:58:25.683711 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-21 07:58:25.921708 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-21 07:58:26.16037 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-21 07:58:26.405063 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-21 07:58:26.630793 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-21 07:58:26.875742 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-21 07:58:27.107954 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-21 07:58:27.337203 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-21 07:58:27.571286 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-21 07:58:27.802943 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-21 07:58:28.022438 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-21 07:58:28.357796 INFO::Counting total values for each feature
2025-01-21 07:58:28.410184 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-01-21 07:58:28.530142 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-01-21 07:58:28.649568 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-01-21 07:58:28.782984 INFO::Writing residuals to file output/fits/residuals.rds
2025-01-21 07:58:28.839335 INFO::Writing fitted values to file output/fits/fitted.rds
2025-01-21 07:58:28.870618 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-01-21 07:58:28.877301 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-01-21 07:58:28.884088 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"
2025-01-21 07:58:28.901541 INFO::Writing function arguments to log file
2025-01-21 07:58:28.909751 INFO::Verifying options selected are valid
2025-01-21 07:58:28.91115 INFO::Determining format of input files
2025-01-21 07:58:28.912845 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-21 07:58:28.920635 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-21 07:58:28.922305 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2025-01-21 07:58:28.924608 INFO::Filter data based on min abundance and min prevalence
2025-01-21 07:58:28.92593 INFO::Total samples in data: 1595
2025-01-21 07:58:28.927137 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-21 07:58:28.936565 INFO::Total filtered features: 0
2025-01-21 07:58:28.938105 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-21 07:58:28.974633 INFO::Total filtered features with variance filtering: 0
2025-01-21 07:58:28.976198 INFO::Filtered feature names from variance filtering:
2025-01-21 07:58:28.977467 INFO::Running selected normalization method: NONE
2025-01-21 07:58:28.978627 INFO::Bypass z-score application to metadata
2025-01-21 07:58:28.979792 INFO::Running selected transform method: AST
2025-01-21 07:58:29.018356 INFO::Running selected analysis method: LM
2025-01-21 07:58:29.021559 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-21 07:58:29.233201 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-21 07:58:29.447351 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-21 07:58:29.664627 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-21 07:58:29.875631 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-21 07:58:30.107163 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-21 07:58:30.329584 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-21 07:58:30.545802 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-21 07:58:30.775039 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-21 07:58:30.990368 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-21 07:58:31.212382 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-21 07:58:31.448551 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-21 07:58:31.670997 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-21 07:58:31.883897 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-21 07:58:32.107517 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-21 07:58:32.324665 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-21 07:58:32.493123 WARNING::Fitting problem for feature 16 a warning was issued
2025-01-21 07:58:32.728055 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-21 07:58:32.951038 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-21 07:58:33.168743 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-21 07:58:33.387619 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-21 07:58:33.604769 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-21 07:58:33.822537 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-21 07:58:34.050626 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-21 07:58:34.25572 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-21 07:58:34.478976 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-21 07:58:34.702451 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-21 07:58:34.913244 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-21 07:58:35.14549 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-21 07:58:35.35178 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-21 07:58:35.555161 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-21 07:58:35.777201 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-21 07:58:35.993929 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-21 07:58:36.230681 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-21 07:58:36.440114 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-21 07:58:36.65544 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-21 07:58:36.884833 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-21 07:58:37.102238 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-21 07:58:37.330081 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-21 07:58:37.546105 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-21 07:58:37.767243 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-21 07:58:37.971839 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-21 07:58:38.18536 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-21 07:58:38.432531 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-21 07:58:38.660858 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-21 07:58:38.885485 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-21 07:58:39.114713 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-21 07:58:39.334785 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-21 07:58:39.545664 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-21 07:58:39.773367 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-21 07:58:39.985498 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-21 07:58:40.1942 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-21 07:58:40.406981 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-21 07:58:40.606253 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-21 07:58:40.814332 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-21 07:58:41.019572 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-21 07:58:41.240272 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-21 07:58:41.453007 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-21 07:58:41.660949 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-21 07:58:41.880246 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-21 07:58:42.093637 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-21 07:58:42.600612 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-21 07:58:42.813048 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-21 07:58:43.021037 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-21 07:58:43.232245 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-21 07:58:43.452849 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-21 07:58:43.663002 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-21 07:58:43.873432 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-21 07:58:44.089059 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-21 07:58:44.323841 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-21 07:58:44.546882 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-21 07:58:44.772731 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-21 07:58:44.987105 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-21 07:58:45.074908 WARNING::Fitting problem for feature 72 a warning was issued
2025-01-21 07:58:45.286052 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-21 07:58:45.497952 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-21 07:58:45.71139 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-21 07:58:45.931598 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-21 07:58:46.149488 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-21 07:58:46.359775 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-21 07:58:46.572777 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-21 07:58:46.804173 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-21 07:58:47.017714 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-21 07:58:47.251503 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-21 07:58:47.457782 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-21 07:58:47.669083 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-21 07:58:47.873211 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-21 07:58:48.082692 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-21 07:58:48.301672 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-21 07:58:48.567971 INFO::Counting total values for each feature
2025-01-21 07:58:48.604197 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-01-21 07:58:48.723664 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-01-21 07:58:48.845092 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-01-21 07:58:48.96893 INFO::Writing residuals to file output2/fits/residuals.rds
2025-01-21 07:58:49.044904 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-01-21 07:58:49.116973 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-01-21 07:58:49.123623 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-01-21 07:58:49.129407 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output2/significant_results.tsv
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ]
>
>
> proc.time()
user system elapsed
45.692 0.560 46.368
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 122.494 | 1.557 | 124.382 | |