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This page was generated on 2025-01-02 12:06 -0500 (Thu, 02 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1130/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.20.0  (landing page)
Lauren McIver
Snapshot Date: 2024-12-30 13:00 -0500 (Mon, 30 Dec 2024)
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)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  NO, package depends on 'metagenomeSeq' which is not available
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'metagenomeSeq' which is not available
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'metagenomeSeq' which is not available
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for Maaslin2 on merida1

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.

raw results


Summary

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: 2024-12-31 05:43:38 -0500 (Tue, 31 Dec 2024)
EndedAt: 2024-12-31 05:49:52 -0500 (Tue, 31 Dec 2024)
EllapsedTime: 374.4 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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: x86_64-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 Monterey 12.7.6
* 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 181.139  2.871 222.688
* 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.

Installation output

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-x86_64/Resources/library’
* installing *source* package ‘Maaslin2’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Maaslin2)

Tests output

Maaslin2.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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"
2024-12-31 05:48:29.352187 INFO::Writing function arguments to log file
2024-12-31 05:48:29.531646 INFO::Verifying options selected are valid
2024-12-31 05:48:29.607074 INFO::Determining format of input files
2024-12-31 05:48:29.615219 INFO::Input format is data samples as rows and metadata samples as rows
2024-12-31 05:48:29.629887 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-12-31 05:48:29.635272 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-12-31 05:48:29.642273 INFO::Filter data based on min abundance and min prevalence
2024-12-31 05:48:29.644665 INFO::Total samples in data: 1595
2024-12-31 05:48:29.647026 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-12-31 05:48:29.683609 INFO::Total filtered features: 0
2024-12-31 05:48:29.756017 INFO::Filtered feature names from abundance and prevalence filtering:
2024-12-31 05:48:29.788142 INFO::Total filtered features with variance filtering: 0
2024-12-31 05:48:29.831346 INFO::Filtered feature names from variance filtering:
2024-12-31 05:48:29.871098 INFO::Running selected normalization method: TSS
2024-12-31 05:48:32.556181 INFO::Bypass z-score application to metadata
2024-12-31 05:48:32.684055 INFO::Running selected transform method: AST
2024-12-31 05:48:32.802368 INFO::Running selected analysis method: LM
2024-12-31 05:48:34.010485 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-12-31 05:48:34.861866 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-12-31 05:48:35.277503 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-12-31 05:48:35.715828 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-12-31 05:48:36.154857 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-12-31 05:48:36.540586 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-12-31 05:48:36.887908 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-12-31 05:48:37.339652 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-12-31 05:48:37.779359 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-12-31 05:48:38.155183 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-12-31 05:48:38.527712 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-12-31 05:48:38.883498 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-12-31 05:48:39.218559 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-12-31 05:48:39.519222 WARNING::Fitting problem for feature 13 a warning was issued
2024-12-31 05:48:39.95796 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-12-31 05:48:40.29038 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-12-31 05:48:40.622801 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-12-31 05:48:40.967217 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-12-31 05:48:41.327606 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-12-31 05:48:41.662077 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-12-31 05:48:41.978243 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-12-31 05:48:42.311861 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-12-31 05:48:42.655833 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-12-31 05:48:43.014384 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-12-31 05:48:43.365243 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-12-31 05:48:43.723669 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-12-31 05:48:44.068706 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-12-31 05:48:44.424209 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-12-31 05:48:44.779184 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-12-31 05:48:45.124159 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-12-31 05:48:45.509637 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-12-31 05:48:45.875642 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-12-31 05:48:46.214252 INFO::Fitting model to feature number 32, Prevotella.copri
2024-12-31 05:48:46.565295 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-12-31 05:48:46.897294 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-12-31 05:48:47.242825 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-12-31 05:48:47.587908 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-12-31 05:48:47.99322 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-12-31 05:48:48.345016 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-12-31 05:48:48.704688 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-12-31 05:48:49.066584 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-12-31 05:48:49.406597 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-12-31 05:48:49.796104 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-12-31 05:48:50.154488 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-12-31 05:48:50.503898 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-12-31 05:48:50.828844 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-12-31 05:48:51.197947 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-12-31 05:48:51.561877 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-12-31 05:48:51.912728 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-12-31 05:48:52.246283 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-12-31 05:48:52.617887 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-12-31 05:48:52.974506 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-12-31 05:48:53.314361 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-12-31 05:48:53.678621 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-12-31 05:48:54.046296 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-12-31 05:48:54.410594 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-12-31 05:48:54.790198 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-12-31 05:48:55.137248 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-12-31 05:48:55.509697 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-12-31 05:48:55.855882 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-12-31 05:48:56.224923 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-12-31 05:48:56.55661 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-12-31 05:48:56.939489 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-12-31 05:48:57.280278 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-12-31 05:48:57.650023 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-12-31 05:48:57.993462 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-12-31 05:48:58.326511 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-12-31 05:48:58.740018 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-12-31 05:48:59.099975 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-12-31 05:48:59.453038 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-12-31 05:48:59.8103 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-12-31 05:49:00.15343 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-12-31 05:49:00.480387 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-12-31 05:49:00.801374 INFO::Fitting model to feature number 73, Dialister.invisus
2024-12-31 05:49:01.1798 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-12-31 05:49:01.529449 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-12-31 05:49:02.107991 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-12-31 05:49:02.438607 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-12-31 05:49:02.772123 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-12-31 05:49:03.168339 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-12-31 05:49:03.554899 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-12-31 05:49:03.900872 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-12-31 05:49:04.328639 INFO::Fitting model to feature number 82, Escherichia.coli
2024-12-31 05:49:04.640322 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-12-31 05:49:04.978947 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-12-31 05:49:05.337412 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-12-31 05:49:05.676556 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-12-31 05:49:06.018272 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-12-31 05:49:06.509198 INFO::Counting total values for each feature
2024-12-31 05:49:06.604994 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-12-31 05:49:06.930899 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-12-31 05:49:07.32561 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-12-31 05:49:07.748735 INFO::Writing residuals to file output/fits/residuals.rds
2024-12-31 05:49:07.889554 INFO::Writing fitted values to file output/fits/fitted.rds
2024-12-31 05:49:07.943871 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-12-31 05:49:07.955708 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-12-31 05:49:08.013948 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"
2024-12-31 05:49:08.045313 INFO::Writing function arguments to log file
2024-12-31 05:49:08.192065 INFO::Verifying options selected are valid
2024-12-31 05:49:08.195043 INFO::Determining format of input files
2024-12-31 05:49:08.197864 INFO::Input format is data samples as rows and metadata samples as rows
2024-12-31 05:49:08.21117 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-12-31 05:49:08.214084 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-12-31 05:49:08.218498 INFO::Filter data based on min abundance and min prevalence
2024-12-31 05:49:08.221029 INFO::Total samples in data: 1595
2024-12-31 05:49:08.223417 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-12-31 05:49:08.234158 INFO::Total filtered features: 0
2024-12-31 05:49:08.268977 INFO::Filtered feature names from abundance and prevalence filtering:
2024-12-31 05:49:08.284947 INFO::Total filtered features with variance filtering: 0
2024-12-31 05:49:08.287611 INFO::Filtered feature names from variance filtering:
2024-12-31 05:49:08.290047 INFO::Running selected normalization method: NONE
2024-12-31 05:49:08.292422 INFO::Bypass z-score application to metadata
2024-12-31 05:49:08.294913 INFO::Running selected transform method: AST
2024-12-31 05:49:08.356205 INFO::Running selected analysis method: LM
2024-12-31 05:49:08.359796 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-12-31 05:49:08.725268 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-12-31 05:49:09.072528 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-12-31 05:49:09.410443 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-12-31 05:49:09.743732 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-12-31 05:49:10.029153 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-12-31 05:49:10.365687 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-12-31 05:49:10.685291 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-12-31 05:49:10.981493 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-12-31 05:49:11.27243 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-12-31 05:49:11.588308 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-12-31 05:49:11.883908 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-12-31 05:49:12.171357 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-12-31 05:49:12.422532 WARNING::Fitting problem for feature 13 a warning was issued
2024-12-31 05:49:12.772925 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-12-31 05:49:13.056457 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-12-31 05:49:13.355468 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-12-31 05:49:13.636201 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-12-31 05:49:13.928333 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-12-31 05:49:14.241454 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-12-31 05:49:14.530723 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-12-31 05:49:14.8283 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-12-31 05:49:15.156204 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-12-31 05:49:15.51226 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-12-31 05:49:15.792837 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-12-31 05:49:16.13964 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-12-31 05:49:16.420445 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-12-31 05:49:16.723225 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-12-31 05:49:17.043796 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-12-31 05:49:17.367004 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-12-31 05:49:17.676073 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-12-31 05:49:18.001695 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-12-31 05:49:18.336118 INFO::Fitting model to feature number 32, Prevotella.copri
2024-12-31 05:49:18.656194 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-12-31 05:49:19.027614 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-12-31 05:49:19.343693 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-12-31 05:49:19.697715 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-12-31 05:49:20.025052 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-12-31 05:49:20.334268 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-12-31 05:49:20.649452 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-12-31 05:49:20.951767 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-12-31 05:49:21.281094 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-12-31 05:49:21.605783 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-12-31 05:49:21.933497 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-12-31 05:49:22.314119 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-12-31 05:49:22.653238 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-12-31 05:49:22.963423 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-12-31 05:49:23.286365 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-12-31 05:49:23.616118 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-12-31 05:49:23.942786 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-12-31 05:49:24.260715 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-12-31 05:49:24.569056 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-12-31 05:49:24.925088 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-12-31 05:49:25.227929 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-12-31 05:49:25.525239 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-12-31 05:49:25.846036 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-12-31 05:49:26.181175 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-12-31 05:49:26.489109 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-12-31 05:49:26.823484 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-12-31 05:49:27.125566 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-12-31 05:49:27.448456 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-12-31 05:49:27.769409 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-12-31 05:49:28.116662 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-12-31 05:49:28.410526 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-12-31 05:49:28.758203 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-12-31 05:49:29.087178 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-12-31 05:49:29.386069 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-12-31 05:49:29.741497 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-12-31 05:49:29.997475 WARNING::Fitting problem for feature 67 a warning was issued
2024-12-31 05:49:30.311013 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-12-31 05:49:30.596955 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-12-31 05:49:30.922694 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-12-31 05:49:31.276925 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-12-31 05:49:31.623468 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-12-31 05:49:31.782099 WARNING::Fitting problem for feature 72 a warning was issued
2024-12-31 05:49:32.238097 INFO::Fitting model to feature number 73, Dialister.invisus
2024-12-31 05:49:32.665142 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-12-31 05:49:33.020894 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-12-31 05:49:33.32513 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-12-31 05:49:33.6176 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-12-31 05:49:33.948171 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-12-31 05:49:34.313989 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-12-31 05:49:34.635708 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-12-31 05:49:34.942063 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-12-31 05:49:35.258273 INFO::Fitting model to feature number 82, Escherichia.coli
2024-12-31 05:49:35.56662 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-12-31 05:49:36.139208 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-12-31 05:49:36.435169 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-12-31 05:49:36.742133 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-12-31 05:49:37.056977 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-12-31 05:49:37.497736 INFO::Counting total values for each feature
2024-12-31 05:49:37.595203 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-12-31 05:49:37.904324 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-12-31 05:49:38.231624 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-12-31 05:49:38.60899 INFO::Writing residuals to file output2/fits/residuals.rds
2024-12-31 05:49:38.74656 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-12-31 05:49:38.888596 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-12-31 05:49:38.900528 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-12-31 05:49:38.914486 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 
 61.500   1.138  72.576

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2181.139 2.871222.688