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This page was generated on 2024-07-06 11:40 -0400 (Sat, 06 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4643
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4414
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4442
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4391
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 3833
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 1108/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.19.0  (landing page)
Lauren McIver
Snapshot Date: 2024-07-05 14:00 -0400 (Fri, 05 Jul 2024)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: devel
git_last_commit: 2f9ea7a
git_last_commit_date: 2024-04-30 11:16:06 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for Maaslin2 on palomino6

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: 1.19.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Maaslin2_1.19.0.tar.gz
StartedAt: 2024-07-06 01:08:57 -0400 (Sat, 06 Jul 2024)
EndedAt: 2024-07-06 01:11:58 -0400 (Sat, 06 Jul 2024)
EllapsedTime: 181.3 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Maaslin2_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck'
* using R version 4.4.1 (2024-06-14 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 '1.19.0'
* 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 95.22  10.05  104.67
* 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
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'Maaslin2' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in checkDepPackageVersion(dep_pkg = "TMB") :
  Package version inconsistency detected.
glmmTMB was built with TMB version 1.9.12
Current TMB version is 1.9.14
Please re-install glmmTMB from source or restore original 'TMB' package (see '?reinstalling' for more information)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Maaslin2)

Tests output

Maaslin2.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
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"
2024-07-06 01:11:17.766005 INFO::Writing function arguments to log file
2024-07-06 01:11:17.811322 INFO::Verifying options selected are valid
2024-07-06 01:11:17.844085 INFO::Determining format of input files
2024-07-06 01:11:17.84653 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-06 01:11:17.861025 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-06 01:11:17.862952 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-07-06 01:11:17.865883 INFO::Filter data based on min abundance and min prevalence
2024-07-06 01:11:17.867453 INFO::Total samples in data: 1595
2024-07-06 01:11:17.868986 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-06 01:11:17.874079 INFO::Total filtered features: 0
2024-07-06 01:11:17.875852 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-06 01:11:17.884716 INFO::Total filtered features with variance filtering: 0
2024-07-06 01:11:17.886403 INFO::Filtered feature names from variance filtering:
2024-07-06 01:11:17.888025 INFO::Running selected normalization method: TSS
2024-07-06 01:11:19.02781 INFO::Bypass z-score application to metadata
2024-07-06 01:11:19.029873 INFO::Running selected transform method: AST
2024-07-06 01:11:19.0454 INFO::Running selected analysis method: LM
2024-07-06 01:11:19.342585 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-06 01:11:21.709357 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-06 01:11:21.840158 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-06 01:11:21.969629 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-06 01:11:22.08176 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-06 01:11:22.215208 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-06 01:11:22.331633 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-06 01:11:22.486407 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-06 01:11:22.593464 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-06 01:11:22.705402 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-06 01:11:22.83026 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-06 01:11:22.950987 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-06 01:11:23.070859 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-06 01:11:23.161546 WARNING::Fitting problem for feature 13 a warning was issued
2024-07-06 01:11:23.2875 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-06 01:11:23.395442 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-06 01:11:23.514323 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-06 01:11:23.627412 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-06 01:11:23.759824 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-06 01:11:23.881815 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-06 01:11:24.000038 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-06 01:11:24.130324 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-06 01:11:24.248101 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-06 01:11:24.367338 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-06 01:11:24.484331 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-06 01:11:24.611201 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-06 01:11:24.749541 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-06 01:11:24.870778 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-06 01:11:24.98887 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-06 01:11:25.109934 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-06 01:11:25.234443 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-06 01:11:25.380917 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-06 01:11:25.495309 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-06 01:11:25.861677 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-06 01:11:25.982165 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-06 01:11:26.096083 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-06 01:11:26.233251 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-06 01:11:26.345706 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-06 01:11:26.466401 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-06 01:11:26.587641 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-06 01:11:26.711081 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-06 01:11:27.958877 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-06 01:11:28.080767 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-06 01:11:28.213601 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-06 01:11:28.334282 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-06 01:11:28.444612 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-06 01:11:28.57077 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-06 01:11:28.696069 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-06 01:11:28.819098 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-06 01:11:28.939593 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-06 01:11:29.048864 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-06 01:11:29.165845 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-06 01:11:29.289629 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-06 01:11:29.409079 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-06 01:11:29.528301 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-06 01:11:29.642678 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-06 01:11:29.769789 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-06 01:11:29.894849 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-06 01:11:30.280772 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-06 01:11:30.401638 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-06 01:11:30.528336 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-06 01:11:30.665052 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-06 01:11:30.779571 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-06 01:11:30.916685 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-06 01:11:31.05577 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-06 01:11:31.180839 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-06 01:11:31.302907 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-06 01:11:31.443256 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-06 01:11:31.549064 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-06 01:11:31.662409 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-06 01:11:31.794601 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-06 01:11:31.916734 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-06 01:11:32.035464 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-06 01:11:32.161706 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-06 01:11:32.270682 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-06 01:11:32.383739 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-06 01:11:32.508522 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-06 01:11:32.625366 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-06 01:11:32.749464 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-06 01:11:32.877867 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-06 01:11:32.998279 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-06 01:11:33.122604 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-06 01:11:33.239933 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-06 01:11:33.356045 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-06 01:11:33.473814 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-06 01:11:33.583759 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-06 01:11:33.700843 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-06 01:11:34.997809 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-06 01:11:35.155454 INFO::Counting total values for each feature
2024-07-06 01:11:35.197684 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-07-06 01:11:35.507847 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-07-06 01:11:35.876096 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-07-06 01:11:36.236045 INFO::Writing residuals to file output/fits/residuals.rds
2024-07-06 01:11:36.275885 INFO::Writing fitted values to file output/fits/fitted.rds
2024-07-06 01:11:36.564709 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-07-06 01:11:36.572237 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-07-06 01:11:36.587868 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"
2024-07-06 01:11:36.614539 INFO::Writing function arguments to log file
2024-07-06 01:11:36.630318 INFO::Verifying options selected are valid
2024-07-06 01:11:36.632187 INFO::Determining format of input files
2024-07-06 01:11:36.634161 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-06 01:11:36.640337 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-06 01:11:36.642229 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-07-06 01:11:36.645546 INFO::Filter data based on min abundance and min prevalence
2024-07-06 01:11:36.647283 INFO::Total samples in data: 1595
2024-07-06 01:11:36.64883 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-06 01:11:36.655032 INFO::Total filtered features: 0
2024-07-06 01:11:36.656935 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-06 01:11:36.665584 INFO::Total filtered features with variance filtering: 0
2024-07-06 01:11:36.667928 INFO::Filtered feature names from variance filtering:
2024-07-06 01:11:36.669657 INFO::Running selected normalization method: NONE
2024-07-06 01:11:36.671249 INFO::Bypass z-score application to metadata
2024-07-06 01:11:36.672911 INFO::Running selected transform method: AST
2024-07-06 01:11:36.688764 INFO::Running selected analysis method: LM
2024-07-06 01:11:36.690836 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-06 01:11:36.801742 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-06 01:11:36.938652 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-06 01:11:37.041534 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-06 01:11:37.158218 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-06 01:11:37.268792 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-06 01:11:37.402121 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-06 01:11:37.51894 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-06 01:11:37.630687 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-06 01:11:37.729837 WARNING::Fitting problem for feature 9 a warning was issued
2024-07-06 01:11:37.865775 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-06 01:11:37.974978 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-06 01:11:38.06606 WARNING::Fitting problem for feature 11 a warning was issued
2024-07-06 01:11:38.19722 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-06 01:11:38.30806 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-06 01:11:38.420471 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-06 01:11:38.536275 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-06 01:11:38.646505 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-06 01:11:38.730767 WARNING::Fitting problem for feature 16 a warning was issued
2024-07-06 01:11:38.852889 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-06 01:11:38.965671 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-06 01:11:39.078024 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-06 01:11:39.189595 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-06 01:11:39.295783 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-06 01:11:39.405441 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-06 01:11:39.521781 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-06 01:11:39.624372 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-06 01:11:39.732593 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-06 01:11:39.851109 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-06 01:11:39.959651 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-06 01:11:40.067063 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-06 01:11:40.204437 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-06 01:11:40.31405 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-06 01:11:40.426141 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-06 01:11:40.534445 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-06 01:11:40.654246 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-06 01:11:40.757518 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-06 01:11:40.865308 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-06 01:11:40.986281 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-06 01:11:41.099153 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-06 01:11:41.214008 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-06 01:11:41.324939 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-06 01:11:41.436777 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-06 01:11:42.393156 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-06 01:11:42.510545 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-06 01:11:42.636709 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-06 01:11:42.751514 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-06 01:11:42.856209 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-06 01:11:42.972455 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-06 01:11:43.083924 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-06 01:11:43.186693 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-06 01:11:43.302805 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-06 01:11:43.411752 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-06 01:11:43.509018 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-06 01:11:43.631533 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-06 01:11:43.73716 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-06 01:11:43.83692 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-06 01:11:43.946808 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-06 01:11:44.049275 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-06 01:11:44.156969 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-06 01:11:44.267396 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-06 01:11:44.369891 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-06 01:11:44.499311 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-06 01:11:44.606299 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-06 01:11:44.725277 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-06 01:11:44.845327 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-06 01:11:44.955955 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-06 01:11:45.081272 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-06 01:11:45.184008 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-06 01:11:45.303209 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-06 01:11:45.425495 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-06 01:11:45.545145 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-06 01:11:45.659801 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-06 01:11:45.787686 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-06 01:11:45.901173 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-06 01:11:45.943306 WARNING::Fitting problem for feature 72 a warning was issued
2024-07-06 01:11:46.073345 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-06 01:11:46.196788 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-06 01:11:46.32051 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-06 01:11:46.447568 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-06 01:11:46.572575 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-06 01:11:46.751595 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-06 01:11:46.87101 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-06 01:11:46.99157 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-06 01:11:47.127488 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-06 01:11:47.235918 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-06 01:11:47.336549 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-06 01:11:47.44924 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-06 01:11:47.554065 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-06 01:11:47.65607 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-06 01:11:47.77925 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-06 01:11:47.914429 INFO::Counting total values for each feature
2024-07-06 01:11:47.943024 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-07-06 01:11:48.255199 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-07-06 01:11:48.564263 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-07-06 01:11:49.919135 INFO::Writing residuals to file output2/fits/residuals.rds
2024-07-06 01:11:49.972898 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-07-06 01:11:50.255186 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-07-06 01:11:50.278225 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-07-06 01:11:50.292572 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 
  32.07    0.95   33.70

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2 95.22 10.05104.67