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This page was generated on 2024-06-07 20:25 -0400 (Fri, 07 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4755
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4489
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4520
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
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 1138/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.18.0  (landing page)
Lauren McIver
Snapshot Date: 2024-06-05 14:00:26 -0400 (Wed, 05 Jun 2024)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_19
git_last_commit: 35350f9
git_last_commit_date: 2024-04-30 11:16:06 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for Maaslin2 on palomino3

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: 1.18.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings Maaslin2_1.18.0.tar.gz
StartedAt: 2024-06-06 05:47:22 -0400 (Thu, 06 Jun 2024)
EndedAt: 2024-06-06 05:52:20 -0400 (Thu, 06 Jun 2024)
EllapsedTime: 297.8 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings Maaslin2_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* 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 '1.18.0'
* 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 97.41   7.84  105.64
* 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
  'F:/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 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"
2024-06-06 05:51:29.297633 INFO::Writing function arguments to log file
2024-06-06 05:51:29.369217 INFO::Verifying options selected are valid
2024-06-06 05:51:29.417349 INFO::Determining format of input files
2024-06-06 05:51:29.420889 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-06 05:51:29.436883 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-06 05:51:29.439484 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-06-06 05:51:29.443242 INFO::Filter data based on min abundance and min prevalence
2024-06-06 05:51:29.445236 INFO::Total samples in data: 1595
2024-06-06 05:51:29.44727 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-06 05:51:29.45284 INFO::Total filtered features: 0
2024-06-06 05:51:29.454885 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-06 05:51:29.466095 INFO::Total filtered features with variance filtering: 0
2024-06-06 05:51:29.469548 INFO::Filtered feature names from variance filtering:
2024-06-06 05:51:29.472638 INFO::Running selected normalization method: TSS
2024-06-06 05:51:31.678542 INFO::Bypass z-score application to metadata
2024-06-06 05:51:31.681098 INFO::Running selected transform method: AST
2024-06-06 05:51:31.710333 INFO::Running selected analysis method: LM
2024-06-06 05:51:32.234583 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-06 05:51:32.992482 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-06 05:51:33.206183 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-06 05:51:33.425281 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-06 05:51:33.625393 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-06 05:51:33.84012 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-06 05:51:34.038488 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-06 05:51:34.252337 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-06 05:51:34.399187 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-06 05:51:34.605573 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-06 05:51:34.805735 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-06 05:51:35.018539 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-06 05:51:35.219374 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-06 05:51:35.383841 WARNING::Fitting problem for feature 13 a warning was issued
2024-06-06 05:51:35.54286 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-06 05:51:35.690668 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-06 05:51:35.850069 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-06 05:51:36.029778 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-06 05:51:36.193944 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-06 05:51:36.340122 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-06 05:51:36.476152 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-06 05:51:36.619987 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-06 05:51:36.758696 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-06 05:51:36.897675 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-06 05:51:37.033574 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-06 05:51:37.1919 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-06 05:51:37.3584 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-06 05:51:37.497976 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-06 05:51:37.644265 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-06 05:51:37.814376 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-06 05:51:37.955949 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-06 05:51:38.12518 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-06 05:51:38.309175 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-06 05:51:38.45947 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-06 05:51:38.599374 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-06 05:51:38.751633 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-06 05:51:38.899457 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-06 05:51:39.04567 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-06 05:51:39.189942 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-06 05:51:39.404898 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-06 05:51:39.606838 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-06 05:51:39.809059 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-06 05:51:40.000167 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-06 05:51:40.223312 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-06 05:51:40.586515 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-06 05:51:40.716307 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-06 05:51:40.919027 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-06 05:51:41.079576 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-06 05:51:41.233641 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-06 05:51:41.389976 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-06 05:51:41.578855 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-06 05:51:41.76251 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-06 05:51:41.901081 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-06 05:51:42.031079 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-06 05:51:42.175582 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-06 05:51:42.301592 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-06 05:51:42.458194 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-06 05:51:42.602086 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-06 05:51:42.738317 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-06 05:51:42.876072 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-06 05:51:43.021628 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-06 05:51:43.154694 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-06 05:51:43.284096 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-06 05:51:43.481378 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-06 05:51:43.651652 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-06 05:51:43.832587 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-06 05:51:44.019608 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-06 05:51:44.174032 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-06 05:51:44.36442 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-06 05:51:44.546733 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-06 05:51:44.710429 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-06 05:51:44.910906 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-06 05:51:45.087605 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-06 05:51:45.280087 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-06 05:51:45.435295 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-06 05:51:45.567032 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-06 05:51:45.738258 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-06 05:51:45.923436 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-06 05:51:46.128552 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-06 05:51:46.293102 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-06 05:51:46.517791 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-06 05:51:46.720617 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-06 05:51:46.949906 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-06 05:51:47.128869 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-06 05:51:47.262541 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-06 05:51:47.447181 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-06 05:51:47.663692 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-06 05:51:47.803971 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-06 05:51:48.010555 INFO::Counting total values for each feature
2024-06-06 05:51:48.074374 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-06-06 05:51:48.425508 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-06-06 05:51:48.801139 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-06-06 05:51:49.29657 INFO::Writing residuals to file output/fits/residuals.rds
2024-06-06 05:51:49.360038 INFO::Writing fitted values to file output/fits/fitted.rds
2024-06-06 05:51:49.386198 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-06-06 05:51:49.39286 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-06-06 05:51:49.409968 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"
2024-06-06 05:51:49.447758 INFO::Writing function arguments to log file
2024-06-06 05:51:49.471544 INFO::Verifying options selected are valid
2024-06-06 05:51:49.473503 INFO::Determining format of input files
2024-06-06 05:51:49.475632 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-06 05:51:49.483425 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-06 05:51:49.485425 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-06-06 05:51:49.497807 INFO::Filter data based on min abundance and min prevalence
2024-06-06 05:51:49.500638 INFO::Total samples in data: 1595
2024-06-06 05:51:49.503209 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-06 05:51:49.510409 INFO::Total filtered features: 0
2024-06-06 05:51:49.51292 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-06 05:51:49.52719 INFO::Total filtered features with variance filtering: 0
2024-06-06 05:51:49.530188 INFO::Filtered feature names from variance filtering:
2024-06-06 05:51:49.533173 INFO::Running selected normalization method: NONE
2024-06-06 05:51:49.536474 INFO::Bypass z-score application to metadata
2024-06-06 05:51:49.539429 INFO::Running selected transform method: AST
2024-06-06 05:51:49.590304 INFO::Running selected analysis method: LM
2024-06-06 05:51:49.59436 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-06 05:51:49.811101 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-06 05:51:49.997486 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-06 05:51:50.231609 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-06 05:51:50.436097 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-06 05:51:50.65542 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-06 05:51:50.859322 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-06 05:51:51.065143 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-06 05:51:51.275366 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-06 05:51:51.389753 WARNING::Fitting problem for feature 9 a warning was issued
2024-06-06 05:51:51.526825 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-06 05:51:51.656699 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-06 05:51:51.775053 WARNING::Fitting problem for feature 11 a warning was issued
2024-06-06 05:51:51.909433 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-06 05:51:52.031671 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-06 05:51:52.159542 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-06 05:51:52.276723 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-06 05:51:52.424456 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-06 05:51:52.519677 WARNING::Fitting problem for feature 16 a warning was issued
2024-06-06 05:51:52.647137 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-06 05:51:52.781556 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-06 05:51:52.931308 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-06 05:51:53.089552 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-06 05:51:53.247652 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-06 05:51:53.380873 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-06 05:51:53.510942 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-06 05:51:53.626595 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-06 05:51:53.799126 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-06 05:51:53.983919 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-06 05:51:54.166485 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-06 05:51:54.365738 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-06 05:51:54.550569 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-06 05:51:54.725211 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-06 05:51:54.85521 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-06 05:51:54.994346 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-06 05:51:55.146048 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-06 05:51:55.281641 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-06 05:51:55.419895 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-06 05:51:55.621312 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-06 05:51:55.761625 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-06 05:51:55.934369 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-06 05:51:56.147138 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-06 05:51:56.287258 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-06 05:51:56.444197 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-06 05:51:56.621499 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-06 05:51:56.807047 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-06 05:51:56.998406 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-06 05:51:57.207431 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-06 05:51:57.416204 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-06 05:51:57.632511 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-06 05:51:57.7956 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-06 05:51:57.965008 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-06 05:51:58.108316 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-06 05:51:58.223018 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-06 05:51:58.39307 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-06 05:51:58.577338 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-06 05:51:58.720956 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-06 05:51:58.906979 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-06 05:51:59.033696 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-06 05:51:59.16721 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-06 05:51:59.29964 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-06 05:51:59.462245 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-06 05:51:59.656732 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-06 05:51:59.838688 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-06 05:52:00.028751 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-06 05:52:00.204832 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-06 05:52:00.345722 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-06 05:52:00.775582 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-06 05:52:00.933576 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-06 05:52:01.069617 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-06 05:52:01.203914 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-06 05:52:01.371564 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-06 05:52:01.520644 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-06 05:52:01.737603 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-06 05:52:01.932567 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-06 05:52:02.006544 WARNING::Fitting problem for feature 72 a warning was issued
2024-06-06 05:52:02.218437 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-06 05:52:02.354282 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-06 05:52:02.477917 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-06 05:52:02.610131 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-06 05:52:02.753436 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-06 05:52:02.880736 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-06 05:52:03.006705 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-06 05:52:03.165665 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-06 05:52:03.337955 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-06 05:52:03.470924 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-06 05:52:03.601368 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-06 05:52:03.732229 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-06 05:52:03.886825 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-06 05:52:04.022591 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-06 05:52:04.1668 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-06 05:52:04.335582 INFO::Counting total values for each feature
2024-06-06 05:52:04.359238 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-06-06 05:52:04.672998 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-06-06 05:52:04.967436 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-06-06 05:52:05.306977 INFO::Writing residuals to file output2/fits/residuals.rds
2024-06-06 05:52:05.381746 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-06-06 05:52:05.461126 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-06-06 05:52:05.473976 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-06-06 05:52:05.492112 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 
  35.59    5.32   40.87

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2 97.41 7.84105.64