Lauren McIver
| Snapshot Date: 2025-01-30 13:00 -0500 (Thu, 30 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 2025-02-03 12:10 -0500 (Mon, 03 Feb 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" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4494 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4517 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4469 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4400 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| 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 | 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: 1.20.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.20.0.tar.gz |
| StartedAt: 2025-01-31 23:39:54 -0500 (Fri, 31 Jan 2025) |
| EndedAt: 2025-01-31 23:42:43 -0500 (Fri, 31 Jan 2025) |
| EllapsedTime: 169.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.20.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Maaslin2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 91.591 1.72 93.496
* 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
‘/Users/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(Maaslin2)
>
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2025-01-31 23:42:00.750235 INFO::Writing function arguments to log file
2025-01-31 23:42:00.797154 INFO::Verifying options selected are valid
2025-01-31 23:42:00.841308 INFO::Determining format of input files
2025-01-31 23:42:00.843441 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-31 23:42:00.850377 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-31 23:42:00.852147 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-01-31 23:42:00.854759 INFO::Filter data based on min abundance and min prevalence
2025-01-31 23:42:00.85582 INFO::Total samples in data: 1595
2025-01-31 23:42:00.857653 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-31 23:42:00.863517 INFO::Total filtered features: 0
2025-01-31 23:42:00.865065 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-31 23:42:00.882594 INFO::Total filtered features with variance filtering: 0
2025-01-31 23:42:00.884267 INFO::Filtered feature names from variance filtering:
2025-01-31 23:42:00.885234 INFO::Running selected normalization method: TSS
2025-01-31 23:42:02.203396 INFO::Bypass z-score application to metadata
2025-01-31 23:42:02.205213 INFO::Running selected transform method: AST
2025-01-31 23:42:02.224042 INFO::Running selected analysis method: LM
2025-01-31 23:42:02.802091 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-31 23:42:03.218151 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-31 23:42:03.398124 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-31 23:42:03.572816 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-31 23:42:03.764982 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-31 23:42:03.941391 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-31 23:42:04.116608 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-31 23:42:04.324057 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-31 23:42:04.501171 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-31 23:42:04.674783 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-31 23:42:04.855688 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-31 23:42:05.043828 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-31 23:42:05.212328 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-31 23:42:05.385592 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-31 23:42:05.603856 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-31 23:42:05.777262 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-31 23:42:05.945486 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-31 23:42:06.131255 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-31 23:42:06.340496 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-31 23:42:06.514037 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-31 23:42:06.672185 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-31 23:42:06.776487 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-31 23:42:06.92609 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-31 23:42:07.0851 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-31 23:42:07.282275 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-31 23:42:07.456215 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-31 23:42:07.621249 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-31 23:42:07.799557 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-31 23:42:07.980238 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-31 23:42:08.177489 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-31 23:42:08.343314 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-31 23:42:08.531804 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-31 23:42:08.707445 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-31 23:42:08.907171 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-31 23:42:09.09238 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-31 23:42:09.265073 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-31 23:42:09.440467 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-31 23:42:09.635664 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-31 23:42:09.807779 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-31 23:42:09.976609 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-31 23:42:10.168049 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-31 23:42:10.340558 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-31 23:42:10.519579 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-31 23:42:10.693204 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-31 23:42:10.856396 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-31 23:42:11.023832 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-31 23:42:11.204344 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-31 23:42:11.381578 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-31 23:42:11.559292 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-31 23:42:11.735122 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-31 23:42:11.905339 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-31 23:42:12.087972 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-31 23:42:12.25625 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-31 23:42:12.446844 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-31 23:42:12.609464 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-31 23:42:12.7957 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-31 23:42:12.986474 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-31 23:42:13.155872 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-31 23:42:13.344452 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-31 23:42:13.509612 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-31 23:42:13.680285 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-31 23:42:13.847526 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-31 23:42:14.031773 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-31 23:42:14.210734 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-31 23:42:14.384309 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-31 23:42:14.547901 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-31 23:42:14.723616 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-31 23:42:14.887553 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-31 23:42:15.057228 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-31 23:42:15.245072 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-31 23:42:15.423412 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-31 23:42:15.888012 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-31 23:42:16.054183 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-31 23:42:16.219409 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-31 23:42:16.393142 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-31 23:42:16.563968 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-31 23:42:16.737307 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-31 23:42:16.918135 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-31 23:42:17.09623 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-31 23:42:17.268399 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-31 23:42:17.447176 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-31 23:42:17.623904 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-31 23:42:17.800086 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-31 23:42:17.974886 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-31 23:42:18.149492 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-31 23:42:18.323457 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-31 23:42:18.510303 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-31 23:42:18.732523 INFO::Counting total values for each feature
2025-01-31 23:42:18.781822 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-01-31 23:42:18.928604 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-01-31 23:42:19.101671 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-01-31 23:42:19.274439 INFO::Writing residuals to file output/fits/residuals.rds
2025-01-31 23:42:19.356304 INFO::Writing fitted values to file output/fits/fitted.rds
2025-01-31 23:42:19.401088 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-01-31 23:42:19.410631 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-01-31 23:42:19.419533 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output/significant_results.tsv
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2025-01-31 23:42:19.437828 INFO::Writing function arguments to log file
2025-01-31 23:42:19.444146 INFO::Verifying options selected are valid
2025-01-31 23:42:19.445146 INFO::Determining format of input files
2025-01-31 23:42:19.446284 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-31 23:42:19.452533 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-31 23:42:19.453887 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2025-01-31 23:42:19.455622 INFO::Filter data based on min abundance and min prevalence
2025-01-31 23:42:19.456923 INFO::Total samples in data: 1595
2025-01-31 23:42:19.45807 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-31 23:42:19.463001 INFO::Total filtered features: 0
2025-01-31 23:42:19.464178 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-31 23:42:19.473015 INFO::Total filtered features with variance filtering: 0
2025-01-31 23:42:19.474365 INFO::Filtered feature names from variance filtering:
2025-01-31 23:42:19.475177 INFO::Running selected normalization method: NONE
2025-01-31 23:42:19.475943 INFO::Bypass z-score application to metadata
2025-01-31 23:42:19.47672 INFO::Running selected transform method: AST
2025-01-31 23:42:19.502381 INFO::Running selected analysis method: LM
2025-01-31 23:42:19.504357 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-31 23:42:19.665096 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-31 23:42:19.837808 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-31 23:42:19.996889 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-31 23:42:20.187915 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-31 23:42:20.350552 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-31 23:42:20.523208 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-31 23:42:20.705629 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-31 23:42:20.875966 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-31 23:42:21.041252 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-31 23:42:21.224973 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-31 23:42:21.394796 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-31 23:42:21.55579 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-31 23:42:21.727385 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-31 23:42:21.889439 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-31 23:42:22.059568 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-31 23:42:22.24152 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-31 23:42:22.424065 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-31 23:42:22.606809 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-31 23:42:22.759785 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-31 23:42:22.923587 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-31 23:42:23.099378 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-31 23:42:23.26402 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-31 23:42:23.43279 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-31 23:42:23.596196 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-31 23:42:23.75634 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-31 23:42:23.924411 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-31 23:42:24.091188 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-31 23:42:24.266987 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-31 23:42:24.429655 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-31 23:42:24.59809 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-31 23:42:24.770937 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-31 23:42:24.94454 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-31 23:42:25.113969 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-31 23:42:25.285356 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-31 23:42:25.451301 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-31 23:42:25.611528 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-31 23:42:25.78792 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-31 23:42:25.948708 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-31 23:42:26.10225 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-31 23:42:26.270865 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-31 23:42:26.435376 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-31 23:42:26.599128 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-31 23:42:26.778023 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-31 23:42:26.94006 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-31 23:42:27.378598 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-31 23:42:27.549792 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-31 23:42:27.714151 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-31 23:42:27.887918 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-31 23:42:28.060811 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-31 23:42:28.222234 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-31 23:42:28.388131 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-31 23:42:28.54273 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-31 23:42:28.69545 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-31 23:42:28.865923 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-31 23:42:29.031585 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-31 23:42:29.193603 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-31 23:42:29.355457 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-31 23:42:29.532162 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-31 23:42:29.696337 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-31 23:42:29.851042 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-31 23:42:30.009814 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-31 23:42:30.165811 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-31 23:42:30.340605 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-31 23:42:30.500256 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-31 23:42:30.659321 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-31 23:42:30.821447 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-31 23:42:30.996491 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-31 23:42:31.151209 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-31 23:42:31.319704 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-31 23:42:31.49114 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-31 23:42:31.662409 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-31 23:42:31.718898 WARNING::Fitting problem for feature 72 a warning was issued
2025-01-31 23:42:31.888017 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-31 23:42:32.049617 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-31 23:42:32.215339 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-31 23:42:32.390498 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-31 23:42:32.553329 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-31 23:42:32.711407 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-31 23:42:32.874007 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-31 23:42:33.046763 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-31 23:42:33.211448 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-31 23:42:33.377468 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-31 23:42:33.534536 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-31 23:42:33.689388 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-31 23:42:33.860663 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-31 23:42:34.020149 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-31 23:42:34.188662 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-31 23:42:34.384263 INFO::Counting total values for each feature
2025-01-31 23:42:34.413566 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-01-31 23:42:34.561295 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-01-31 23:42:34.69894 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-01-31 23:42:34.891703 INFO::Writing residuals to file output2/fits/residuals.rds
2025-01-31 23:42:35.00152 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-01-31 23:42:35.066343 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-01-31 23:42:35.070371 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-01-31 23:42:35.073478 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 1 | SKIP 0 | PASS 12 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 12 ]
>
>
> proc.time()
user system elapsed
34.756 0.874 35.683
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 91.591 | 1.720 | 93.496 | |