Lauren McIver
| Snapshot Date: 2025-02-14 13:40 -0500 (Fri, 14 Feb 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 2025-02-15 11:41 -0500 (Sat, 15 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4720 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4482 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4493 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4446 |
| 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 1132/2295 | 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 | | ||||||||
|
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: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings Maaslin2_1.21.0.tar.gz |
| StartedAt: 2025-02-15 02:37:18 -0500 (Sat, 15 Feb 2025) |
| EndedAt: 2025-02-15 02:40:54 -0500 (Sat, 15 Feb 2025) |
| EllapsedTime: 215.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings Maaslin2_1.21.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 ... 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 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 115.37 7.05 123.2
* 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
'E:/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/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) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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"
2025-02-15 02:40:04.105104 INFO::Writing function arguments to log file
2025-02-15 02:40:04.156155 INFO::Verifying options selected are valid
2025-02-15 02:40:04.199847 INFO::Determining format of input files
2025-02-15 02:40:04.203375 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-15 02:40:04.215023 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-02-15 02:40:04.228489 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-02-15 02:40:04.233664 INFO::Filter data based on min abundance and min prevalence
2025-02-15 02:40:04.23633 INFO::Total samples in data: 1595
2025-02-15 02:40:04.239117 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-02-15 02:40:04.247093 INFO::Total filtered features: 0
2025-02-15 02:40:04.250285 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-15 02:40:04.264303 INFO::Total filtered features with variance filtering: 0
2025-02-15 02:40:04.267479 INFO::Filtered feature names from variance filtering:
2025-02-15 02:40:04.270261 INFO::Running selected normalization method: TSS
2025-02-15 02:40:05.568049 INFO::Bypass z-score application to metadata
2025-02-15 02:40:05.570086 INFO::Running selected transform method: AST
2025-02-15 02:40:05.587394 INFO::Running selected analysis method: LM
2025-02-15 02:40:06.285825 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-02-15 02:40:06.741521 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-02-15 02:40:06.943609 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-02-15 02:40:07.148272 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-02-15 02:40:07.383674 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-02-15 02:40:07.590372 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-02-15 02:40:07.818808 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-02-15 02:40:07.972011 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-02-15 02:40:08.101479 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-02-15 02:40:08.3389 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-02-15 02:40:08.493277 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-02-15 02:40:08.697024 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-02-15 02:40:08.838413 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-02-15 02:40:08.955418 WARNING::Fitting problem for feature 13 a warning was issued
2025-02-15 02:40:09.092203 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-02-15 02:40:09.293347 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-02-15 02:40:09.52038 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-02-15 02:40:09.736365 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-02-15 02:40:09.940386 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-02-15 02:40:10.098704 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-02-15 02:40:10.277344 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-02-15 02:40:10.475173 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-02-15 02:40:10.701275 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-02-15 02:40:10.910135 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-02-15 02:40:11.127191 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-02-15 02:40:11.353101 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-02-15 02:40:11.570867 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-02-15 02:40:11.77771 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-02-15 02:40:11.938141 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-02-15 02:40:12.188623 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-02-15 02:40:12.403846 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-02-15 02:40:12.61998 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-02-15 02:40:12.843715 INFO::Fitting model to feature number 32, Prevotella.copri
2025-02-15 02:40:13.070988 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-02-15 02:40:13.285542 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-02-15 02:40:13.507867 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-02-15 02:40:13.71445 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-02-15 02:40:13.93973 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-02-15 02:40:14.151836 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-02-15 02:40:14.36032 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-02-15 02:40:14.533002 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-02-15 02:40:14.701503 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-02-15 02:40:14.92761 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-02-15 02:40:15.14661 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-02-15 02:40:15.371678 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-02-15 02:40:15.565508 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-02-15 02:40:16.024074 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-02-15 02:40:16.186031 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-02-15 02:40:16.317338 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-02-15 02:40:16.476702 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-02-15 02:40:16.647564 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-02-15 02:40:16.802937 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-02-15 02:40:17.003803 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-02-15 02:40:17.18277 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-02-15 02:40:17.383458 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-02-15 02:40:17.575967 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-02-15 02:40:17.771075 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-02-15 02:40:17.944045 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-02-15 02:40:18.070829 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-02-15 02:40:18.218783 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-02-15 02:40:18.372539 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-02-15 02:40:18.51648 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-02-15 02:40:18.683176 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-02-15 02:40:18.860854 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-02-15 02:40:19.05321 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-02-15 02:40:19.24033 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-02-15 02:40:19.431455 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-02-15 02:40:19.64351 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-02-15 02:40:19.839378 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-02-15 02:40:20.03023 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-02-15 02:40:20.239397 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-02-15 02:40:20.440546 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-02-15 02:40:20.583093 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-02-15 02:40:20.754159 INFO::Fitting model to feature number 73, Dialister.invisus
2025-02-15 02:40:20.902118 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-02-15 02:40:21.082289 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-02-15 02:40:21.289641 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-02-15 02:40:21.511516 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-02-15 02:40:21.720141 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-02-15 02:40:21.949036 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-02-15 02:40:22.15949 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-02-15 02:40:22.370043 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-02-15 02:40:22.575289 INFO::Fitting model to feature number 82, Escherichia.coli
2025-02-15 02:40:22.781021 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-02-15 02:40:22.903483 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-02-15 02:40:23.035291 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-02-15 02:40:23.186772 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-02-15 02:40:23.359111 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-02-15 02:40:23.63175 INFO::Counting total values for each feature
2025-02-15 02:40:23.687833 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-02-15 02:40:24.156459 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-02-15 02:40:24.704774 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-02-15 02:40:25.151437 INFO::Writing residuals to file output/fits/residuals.rds
2025-02-15 02:40:25.205779 INFO::Writing fitted values to file output/fits/fitted.rds
2025-02-15 02:40:25.237181 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-02-15 02:40:25.245209 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-02-15 02:40:25.266639 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"
2025-02-15 02:40:25.384899 INFO::Writing function arguments to log file
2025-02-15 02:40:25.40316 INFO::Verifying options selected are valid
2025-02-15 02:40:25.405484 INFO::Determining format of input files
2025-02-15 02:40:25.408077 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-15 02:40:25.417098 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-02-15 02:40:25.419905 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2025-02-15 02:40:25.423067 INFO::Filter data based on min abundance and min prevalence
2025-02-15 02:40:25.425378 INFO::Total samples in data: 1595
2025-02-15 02:40:25.427503 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-02-15 02:40:25.433827 INFO::Total filtered features: 0
2025-02-15 02:40:25.436183 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-15 02:40:25.472418 INFO::Total filtered features with variance filtering: 0
2025-02-15 02:40:25.475507 INFO::Filtered feature names from variance filtering:
2025-02-15 02:40:25.478115 INFO::Running selected normalization method: NONE
2025-02-15 02:40:25.480427 INFO::Bypass z-score application to metadata
2025-02-15 02:40:25.482627 INFO::Running selected transform method: AST
2025-02-15 02:40:25.503934 INFO::Running selected analysis method: LM
2025-02-15 02:40:25.507281 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-02-15 02:40:25.671997 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-02-15 02:40:25.849832 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-02-15 02:40:26.013725 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-02-15 02:40:26.175472 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-02-15 02:40:26.321935 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-02-15 02:40:26.459029 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-02-15 02:40:26.60354 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-02-15 02:40:27.071501 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-02-15 02:40:27.249172 WARNING::Fitting problem for feature 9 a warning was issued
2025-02-15 02:40:27.486547 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-02-15 02:40:27.692513 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-02-15 02:40:27.867733 WARNING::Fitting problem for feature 11 a warning was issued
2025-02-15 02:40:28.048733 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-02-15 02:40:28.250387 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-02-15 02:40:28.464616 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-02-15 02:40:28.659353 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-02-15 02:40:28.791019 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-02-15 02:40:28.942586 WARNING::Fitting problem for feature 16 a warning was issued
2025-02-15 02:40:29.130003 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-02-15 02:40:29.356974 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-02-15 02:40:29.542935 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-02-15 02:40:29.670473 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-02-15 02:40:29.819858 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-02-15 02:40:29.949291 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-02-15 02:40:30.118681 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-02-15 02:40:30.273445 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-02-15 02:40:30.458486 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-02-15 02:40:30.661948 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-02-15 02:40:30.863487 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-02-15 02:40:31.051142 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-02-15 02:40:31.231399 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-02-15 02:40:31.425162 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-02-15 02:40:31.591369 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-02-15 02:40:31.785036 INFO::Fitting model to feature number 32, Prevotella.copri
2025-02-15 02:40:31.934882 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-02-15 02:40:32.095229 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-02-15 02:40:32.302721 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-02-15 02:40:32.510107 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-02-15 02:40:32.708304 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-02-15 02:40:32.891509 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-02-15 02:40:33.041708 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-02-15 02:40:33.203512 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-02-15 02:40:33.397865 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-02-15 02:40:33.609534 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-02-15 02:40:33.824726 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-02-15 02:40:34.014042 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-02-15 02:40:34.210533 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-02-15 02:40:34.42244 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-02-15 02:40:34.615009 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-02-15 02:40:34.798227 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-02-15 02:40:35.00614 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-02-15 02:40:35.199207 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-02-15 02:40:35.391225 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-02-15 02:40:35.610416 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-02-15 02:40:35.800586 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-02-15 02:40:35.99161 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-02-15 02:40:36.202047 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-02-15 02:40:36.396736 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-02-15 02:40:36.600199 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-02-15 02:40:36.77146 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-02-15 02:40:36.928951 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-02-15 02:40:37.099516 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-02-15 02:40:37.300413 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-02-15 02:40:37.424202 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-02-15 02:40:37.552476 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-02-15 02:40:37.71686 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-02-15 02:40:37.91851 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-02-15 02:40:38.127692 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-02-15 02:40:38.322641 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-02-15 02:40:38.534253 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-02-15 02:40:38.724339 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-02-15 02:40:38.925823 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-02-15 02:40:39.108577 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-02-15 02:40:39.310676 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-02-15 02:40:39.396685 WARNING::Fitting problem for feature 72 a warning was issued
2025-02-15 02:40:39.555189 INFO::Fitting model to feature number 73, Dialister.invisus
2025-02-15 02:40:39.688992 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-02-15 02:40:39.819722 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-02-15 02:40:40.041301 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-02-15 02:40:40.171024 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-02-15 02:40:40.339148 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-02-15 02:40:40.538784 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-02-15 02:40:40.760677 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-02-15 02:40:40.95223 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-02-15 02:40:41.106988 INFO::Fitting model to feature number 82, Escherichia.coli
2025-02-15 02:40:41.31832 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-02-15 02:40:41.510548 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-02-15 02:40:41.704734 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-02-15 02:40:41.890819 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-02-15 02:40:42.028342 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-02-15 02:40:42.195663 INFO::Counting total values for each feature
2025-02-15 02:40:42.22712 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-02-15 02:40:42.575833 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-02-15 02:40:42.93563 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-02-15 02:40:43.379362 INFO::Writing residuals to file output2/fits/residuals.rds
2025-02-15 02:40:43.46364 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-02-15 02:40:43.537432 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-02-15 02:40:43.546419 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-02-15 02:40:43.561054 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 5 | SKIP 0 | PASS 12 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 12 ]
>
>
> proc.time()
user system elapsed
39.95 1.04 41.14
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 115.37 | 7.05 | 123.20 | |