Lauren McIver
| Snapshot Date: 2025-02-12 13:40 -0500 (Wed, 12 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 2025-02-13 11:39 -0500 (Thu, 13 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" | 4719 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4481 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4492 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4445 |
| 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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Maaslin2_1.21.0.tar.gz |
| StartedAt: 2025-02-12 23:42:43 -0500 (Wed, 12 Feb 2025) |
| EndedAt: 2025-02-12 23:46:55 -0500 (Wed, 12 Feb 2025) |
| EllapsedTime: 252.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Maaslin2_1.21.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.21.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Maaslin2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
maaslin2_association_plots: no visible binding for global variable
‘xnames’
Undefined global functions or variables:
xnames
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Maaslin2 88.975 0.796 89.758
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘Maaslin2’ ... ** this is package ‘Maaslin2’ version ‘1.21.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Maaslin2)
Maaslin2.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(Maaslin2)
>
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2025-02-12 23:44:42.667487 INFO::Writing function arguments to log file
2025-02-12 23:44:42.713275 INFO::Verifying options selected are valid
2025-02-12 23:44:42.747816 INFO::Determining format of input files
2025-02-12 23:44:42.749673 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-12 23:44:42.755549 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-02-12 23:44:42.756991 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-02-12 23:44:42.759539 INFO::Filter data based on min abundance and min prevalence
2025-02-12 23:44:42.760523 INFO::Total samples in data: 1595
2025-02-12 23:44:42.761449 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-02-12 23:44:42.773494 INFO::Total filtered features: 0
2025-02-12 23:44:42.774857 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-12 23:44:42.781945 INFO::Total filtered features with variance filtering: 0
2025-02-12 23:44:42.783167 INFO::Filtered feature names from variance filtering:
2025-02-12 23:44:42.78408 INFO::Running selected normalization method: TSS
2025-02-12 23:44:44.015046 INFO::Bypass z-score application to metadata
2025-02-12 23:44:44.016444 INFO::Running selected transform method: AST
2025-02-12 23:44:44.031673 INFO::Running selected analysis method: LM
2025-02-12 23:44:44.584822 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-02-12 23:44:44.946286 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-02-12 23:44:45.102323 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-02-12 23:44:45.250886 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-02-12 23:44:45.407005 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-02-12 23:44:45.551517 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-02-12 23:44:45.692897 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-02-12 23:44:45.840261 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-02-12 23:44:45.954089 WARNING::Fitting problem for feature 8 a warning was issued
2025-02-12 23:44:46.105186 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-02-12 23:44:46.219191 WARNING::Fitting problem for feature 9 a warning was issued
2025-02-12 23:44:46.409027 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-02-12 23:44:46.550387 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-02-12 23:44:46.733207 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-02-12 23:44:46.877174 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-02-12 23:44:46.998043 WARNING::Fitting problem for feature 13 a warning was issued
2025-02-12 23:44:47.152276 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-02-12 23:44:47.316093 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-02-12 23:44:47.514027 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-02-12 23:44:47.673524 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-02-12 23:44:47.835589 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-02-12 23:44:47.997795 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-02-12 23:44:48.139531 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-02-12 23:44:48.281941 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-02-12 23:44:48.435209 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-02-12 23:44:48.591619 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-02-12 23:44:48.733808 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-02-12 23:44:48.889344 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-02-12 23:44:49.055646 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-02-12 23:44:49.207517 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-02-12 23:44:49.377721 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-02-12 23:44:49.536614 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-02-12 23:44:49.684221 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-02-12 23:44:49.830074 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-02-12 23:44:49.991117 INFO::Fitting model to feature number 32, Prevotella.copri
2025-02-12 23:44:50.143771 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-02-12 23:44:50.296736 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-02-12 23:44:50.454245 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-02-12 23:44:50.604566 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-02-12 23:44:50.766736 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-02-12 23:44:51.202625 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-02-12 23:44:51.339704 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-02-12 23:44:51.47748 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-02-12 23:44:51.631587 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-02-12 23:44:51.775284 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-02-12 23:44:51.920076 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-02-12 23:44:52.062766 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-02-12 23:44:52.209656 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-02-12 23:44:52.35341 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-02-12 23:44:52.496433 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-02-12 23:44:52.669247 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-02-12 23:44:52.814879 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-02-12 23:44:52.962494 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-02-12 23:44:53.111021 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-02-12 23:44:53.24817 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-02-12 23:44:53.387143 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-02-12 23:44:53.542522 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-02-12 23:44:53.680549 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-02-12 23:44:53.825773 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-02-12 23:44:53.98889 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-02-12 23:44:54.133027 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-02-12 23:44:54.285111 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-02-12 23:44:54.433237 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-02-12 23:44:54.574303 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-02-12 23:44:54.728788 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-02-12 23:44:54.874699 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-02-12 23:44:55.017762 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-02-12 23:44:55.170767 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-02-12 23:44:55.312735 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-02-12 23:44:55.46003 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-02-12 23:44:55.604693 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-02-12 23:44:55.753597 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-02-12 23:44:55.914283 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-02-12 23:44:56.093733 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-02-12 23:44:56.246816 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-02-12 23:44:56.404363 INFO::Fitting model to feature number 73, Dialister.invisus
2025-02-12 23:44:56.546244 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-02-12 23:44:56.693425 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-02-12 23:44:56.8401 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-02-12 23:44:56.993623 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-02-12 23:44:57.146622 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-02-12 23:44:57.56415 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-02-12 23:44:57.708965 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-02-12 23:44:57.860654 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-02-12 23:44:58.016969 INFO::Fitting model to feature number 82, Escherichia.coli
2025-02-12 23:44:58.182781 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-02-12 23:44:58.322573 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-02-12 23:44:58.473109 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-02-12 23:44:58.625272 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-02-12 23:44:58.794846 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-02-12 23:44:58.97591 INFO::Counting total values for each feature
2025-02-12 23:44:59.007596 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-02-12 23:44:59.100713 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-02-12 23:44:59.196316 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-02-12 23:44:59.294545 INFO::Writing residuals to file output/fits/residuals.rds
2025-02-12 23:44:59.343251 INFO::Writing fitted values to file output/fits/fitted.rds
2025-02-12 23:44:59.37054 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-02-12 23:44:59.376144 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-02-12 23:44:59.3816 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"
2025-02-12 23:44:59.394305 INFO::Writing function arguments to log file
2025-02-12 23:44:59.400307 INFO::Verifying options selected are valid
2025-02-12 23:44:59.401349 INFO::Determining format of input files
2025-02-12 23:44:59.402613 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-12 23:44:59.407892 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-02-12 23:44:59.409016 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2025-02-12 23:44:59.410692 INFO::Filter data based on min abundance and min prevalence
2025-02-12 23:44:59.4116 INFO::Total samples in data: 1595
2025-02-12 23:44:59.412504 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-02-12 23:44:59.417158 INFO::Total filtered features: 0
2025-02-12 23:44:59.418211 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-12 23:44:59.425595 INFO::Total filtered features with variance filtering: 0
2025-02-12 23:44:59.426804 INFO::Filtered feature names from variance filtering:
2025-02-12 23:44:59.427709 INFO::Running selected normalization method: NONE
2025-02-12 23:44:59.428581 INFO::Bypass z-score application to metadata
2025-02-12 23:44:59.429445 INFO::Running selected transform method: AST
2025-02-12 23:44:59.450764 INFO::Running selected analysis method: LM
2025-02-12 23:44:59.452476 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-02-12 23:44:59.592744 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-02-12 23:44:59.731696 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-02-12 23:44:59.869365 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-02-12 23:45:00.010342 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-02-12 23:45:00.142906 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-02-12 23:45:00.284007 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-02-12 23:45:00.425721 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-02-12 23:45:00.573954 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-02-12 23:45:00.712103 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-02-12 23:45:00.855161 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-02-12 23:45:00.990235 WARNING::Fitting problem for feature 11 a warning was issued
2025-02-12 23:45:01.136068 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-02-12 23:45:01.273117 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-02-12 23:45:01.419913 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-02-12 23:45:01.562864 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-02-12 23:45:01.703161 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-02-12 23:45:01.815054 WARNING::Fitting problem for feature 16 a warning was issued
2025-02-12 23:45:01.961139 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-02-12 23:45:02.099941 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-02-12 23:45:02.236042 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-02-12 23:45:02.379174 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-02-12 23:45:02.516749 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-02-12 23:45:02.654665 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-02-12 23:45:02.802027 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-02-12 23:45:02.930846 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-02-12 23:45:03.067805 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-02-12 23:45:03.210562 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-02-12 23:45:03.341716 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-02-12 23:45:03.481327 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-02-12 23:45:03.615124 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-02-12 23:45:03.740911 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-02-12 23:45:03.872056 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-02-12 23:45:04.01197 INFO::Fitting model to feature number 32, Prevotella.copri
2025-02-12 23:45:04.149694 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-02-12 23:45:04.295954 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-02-12 23:45:04.437926 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-02-12 23:45:04.571281 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-02-12 23:45:04.713581 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-02-12 23:45:04.850448 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-02-12 23:45:04.997051 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-02-12 23:45:05.124668 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-02-12 23:45:05.262051 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-02-12 23:45:05.397409 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-02-12 23:45:05.546692 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-02-12 23:45:05.684875 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-02-12 23:45:05.831259 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-02-12 23:45:05.964997 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-02-12 23:45:06.120083 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-02-12 23:45:06.250135 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-02-12 23:45:06.386591 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-02-12 23:45:06.519606 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-02-12 23:45:06.657584 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-02-12 23:45:06.794887 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-02-12 23:45:06.920188 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-02-12 23:45:07.050723 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-02-12 23:45:07.182114 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-02-12 23:45:07.330516 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-02-12 23:45:07.464304 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-02-12 23:45:07.598156 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-02-12 23:45:07.73138 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-02-12 23:45:07.877693 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-02-12 23:45:08.009325 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-02-12 23:45:08.150253 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-02-12 23:45:08.286152 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-02-12 23:45:08.440224 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-02-12 23:45:08.581425 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-02-12 23:45:08.715468 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-02-12 23:45:08.849884 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-02-12 23:45:08.962168 WARNING::Fitting problem for feature 67 a warning was issued
2025-02-12 23:45:09.111223 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-02-12 23:45:09.240933 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-02-12 23:45:09.381274 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-02-12 23:45:09.524587 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-02-12 23:45:09.697884 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-02-12 23:45:09.747903 WARNING::Fitting problem for feature 72 a warning was issued
2025-02-12 23:45:09.892668 INFO::Fitting model to feature number 73, Dialister.invisus
2025-02-12 23:45:10.040119 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-02-12 23:45:10.19498 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-02-12 23:45:10.329817 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-02-12 23:45:10.468132 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-02-12 23:45:10.606663 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-02-12 23:45:10.765053 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-02-12 23:45:10.911144 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-02-12 23:45:11.062754 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-02-12 23:45:11.213621 INFO::Fitting model to feature number 82, Escherichia.coli
2025-02-12 23:45:11.362038 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-02-12 23:45:11.497456 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-02-12 23:45:11.636651 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-02-12 23:45:11.776451 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-02-12 23:45:11.924259 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-02-12 23:45:12.082989 INFO::Counting total values for each feature
2025-02-12 23:45:12.105563 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-02-12 23:45:12.198106 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-02-12 23:45:12.29146 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-02-12 23:45:12.389803 INFO::Writing residuals to file output2/fits/residuals.rds
2025-02-12 23:45:12.73462 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-02-12 23:45:12.797905 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-02-12 23:45:12.80344 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-02-12 23:45:12.8079 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
30.752 0.619 31.367
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 88.975 | 0.796 | 89.758 | |