Multiple platform build/check report for BioC 3.19 - CHECK results for Maaslin2 on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4757
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4491
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*

CHECK results for Maaslin2 on nebbiolo1

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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings Maaslin2_1.18.0.tar.gz

StartedAt: 2024-06-13 00:31:13 -0400 (Thu, 13 Jun 2024)

EndedAt: 2024-06-13 00:35:13 -0400 (Thu, 13 Jun 2024)

EllapsedTime: 240.5 seconds

RetCode: 0

Status: OK

CheckDir: Maaslin2.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings Maaslin2_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 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 84.474  1.077  85.492
* 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-3.19-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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) -- "Puppy Cup"
Copyright (C) 2024 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"
2024-06-13 00:33:09.279009 INFO::Writing function arguments to log file
2024-06-13 00:33:09.316894 INFO::Verifying options selected are valid
2024-06-13 00:33:09.351999 INFO::Determining format of input files
2024-06-13 00:33:09.353447 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-13 00:33:09.358016 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-13 00:33:09.3593 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-06-13 00:33:09.361665 INFO::Filter data based on min abundance and min prevalence
2024-06-13 00:33:09.362512 INFO::Total samples in data: 1595
2024-06-13 00:33:09.363326 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-13 00:33:09.367153 INFO::Total filtered features: 0
2024-06-13 00:33:09.368118 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-13 00:33:09.381577 INFO::Total filtered features with variance filtering: 0
2024-06-13 00:33:09.382553 INFO::Filtered feature names from variance filtering:
2024-06-13 00:33:09.383411 INFO::Running selected normalization method: TSS
2024-06-13 00:33:10.547484 INFO::Bypass z-score application to metadata
2024-06-13 00:33:10.548843 INFO::Running selected transform method: AST
2024-06-13 00:33:10.565043 INFO::Running selected analysis method: LM
2024-06-13 00:33:11.062598 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-13 00:33:11.411219 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-13 00:33:11.554857 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-13 00:33:11.702424 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-13 00:33:11.856465 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-13 00:33:12.005408 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-13 00:33:12.150023 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-13 00:33:12.288488 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-13 00:33:12.401595 WARNING::Fitting problem for feature 8 a warning was issued
2024-06-13 00:33:12.547395 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-13 00:33:12.657197 WARNING::Fitting problem for feature 9 a warning was issued
2024-06-13 00:33:13.042274 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-13 00:33:13.178523 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-13 00:33:13.316543 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-13 00:33:13.455363 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-13 00:33:13.570221 WARNING::Fitting problem for feature 13 a warning was issued
2024-06-13 00:33:13.716685 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-13 00:33:13.855197 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-13 00:33:14.011855 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-13 00:33:14.14592 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-13 00:33:14.302623 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-13 00:33:14.456467 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-13 00:33:14.606639 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-13 00:33:14.746288 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-13 00:33:14.902104 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-13 00:33:15.047338 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-13 00:33:15.177622 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-13 00:33:15.315294 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-13 00:33:15.468705 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-13 00:33:15.604392 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-13 00:33:15.747564 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-13 00:33:15.888587 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-13 00:33:16.03814 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-13 00:33:16.178485 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-13 00:33:16.33031 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-13 00:33:16.482114 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-13 00:33:16.626449 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-13 00:33:16.758642 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-13 00:33:16.902205 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-13 00:33:17.036584 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-13 00:33:17.171859 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-13 00:33:17.309483 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-13 00:33:17.439532 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-13 00:33:17.575892 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-13 00:33:17.716539 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-13 00:33:17.860553 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-13 00:33:17.995187 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-13 00:33:18.132381 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-13 00:33:18.271385 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-13 00:33:18.412441 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-13 00:33:18.556957 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-13 00:33:18.688416 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-13 00:33:18.827486 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-13 00:33:18.975653 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-13 00:33:19.118868 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-13 00:33:19.272739 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-13 00:33:19.417592 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-13 00:33:19.552359 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-13 00:33:19.690431 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-13 00:33:19.841236 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-13 00:33:19.971308 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-13 00:33:20.125364 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-13 00:33:20.260928 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-13 00:33:20.398766 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-13 00:33:20.533708 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-13 00:33:20.680279 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-13 00:33:20.81538 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-13 00:33:20.953718 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-13 00:33:21.089784 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-13 00:33:21.224733 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-13 00:33:21.360115 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-13 00:33:21.505161 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-13 00:33:21.650625 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-13 00:33:22.031734 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-13 00:33:22.163148 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-13 00:33:22.303047 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-13 00:33:22.444022 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-13 00:33:22.578826 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-13 00:33:22.725022 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-13 00:33:22.876243 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-13 00:33:23.012049 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-13 00:33:23.159684 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-13 00:33:23.311585 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-13 00:33:23.449123 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-13 00:33:23.592598 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-13 00:33:23.7446 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-13 00:33:23.878973 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-13 00:33:24.018421 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-13 00:33:24.160357 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-13 00:33:24.29424 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-13 00:33:24.470689 INFO::Counting total values for each feature
2024-06-13 00:33:24.508229 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-06-13 00:33:24.653278 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-06-13 00:33:24.803156 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-06-13 00:33:24.95954 INFO::Writing residuals to file output/fits/residuals.rds
2024-06-13 00:33:25.01814 INFO::Writing fitted values to file output/fits/fitted.rds
2024-06-13 00:33:25.051132 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-06-13 00:33:25.057131 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-06-13 00:33:25.064435 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"
2024-06-13 00:33:25.079823 INFO::Writing function arguments to log file
2024-06-13 00:33:25.086093 INFO::Verifying options selected are valid
2024-06-13 00:33:25.087245 INFO::Determining format of input files
2024-06-13 00:33:25.088493 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-13 00:33:25.093741 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-13 00:33:25.09488 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-06-13 00:33:25.096596 INFO::Filter data based on min abundance and min prevalence
2024-06-13 00:33:25.097489 INFO::Total samples in data: 1595
2024-06-13 00:33:25.098364 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-13 00:33:25.102866 INFO::Total filtered features: 0
2024-06-13 00:33:25.103917 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-13 00:33:25.112064 INFO::Total filtered features with variance filtering: 0
2024-06-13 00:33:25.113202 INFO::Filtered feature names from variance filtering:
2024-06-13 00:33:25.114089 INFO::Running selected normalization method: NONE
2024-06-13 00:33:25.114998 INFO::Bypass z-score application to metadata
2024-06-13 00:33:25.115849 INFO::Running selected transform method: AST
2024-06-13 00:33:25.145149 INFO::Running selected analysis method: LM
2024-06-13 00:33:25.14704 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-13 00:33:25.284336 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-13 00:33:25.427858 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-13 00:33:25.555644 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-13 00:33:25.703842 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-13 00:33:25.835534 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-13 00:33:25.977591 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-13 00:33:26.106008 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-13 00:33:26.240964 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-13 00:33:26.378896 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-13 00:33:26.51794 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-13 00:33:26.649708 WARNING::Fitting problem for feature 11 a warning was issued
2024-06-13 00:33:26.793442 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-13 00:33:26.930516 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-13 00:33:27.069918 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-13 00:33:27.199443 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-13 00:33:27.335547 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-13 00:33:27.447184 WARNING::Fitting problem for feature 16 a warning was issued
2024-06-13 00:33:27.581598 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-13 00:33:27.716645 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-13 00:33:27.857303 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-13 00:33:27.985866 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-13 00:33:28.125932 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-13 00:33:28.260084 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-13 00:33:28.39913 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-13 00:33:28.54135 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-13 00:33:28.681185 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-13 00:33:28.827019 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-13 00:33:28.955016 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-13 00:33:29.08656 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-13 00:33:29.218822 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-13 00:33:29.343697 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-13 00:33:29.478241 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-13 00:33:29.609585 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-13 00:33:29.749131 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-13 00:33:29.878914 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-13 00:33:30.017984 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-13 00:33:30.148672 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-13 00:33:30.304374 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-13 00:33:30.439468 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-13 00:33:30.575865 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-13 00:33:30.713889 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-13 00:33:30.840818 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-13 00:33:30.969491 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-13 00:33:31.106288 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-13 00:33:31.237771 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-13 00:33:31.370721 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-13 00:33:31.508887 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-13 00:33:31.646005 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-13 00:33:31.788913 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-13 00:33:31.922682 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-13 00:33:32.055876 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-13 00:33:32.191099 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-13 00:33:32.324416 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-13 00:33:32.456865 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-13 00:33:32.582288 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-13 00:33:32.728944 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-13 00:33:32.884228 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-13 00:33:33.019012 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-13 00:33:33.157971 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-13 00:33:33.292745 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-13 00:33:33.444008 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-13 00:33:33.568791 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-13 00:33:33.698866 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-13 00:33:33.836757 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-13 00:33:33.967049 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-13 00:33:34.099512 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-13 00:33:34.236881 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-13 00:33:34.362669 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-13 00:33:34.477413 WARNING::Fitting problem for feature 67 a warning was issued
2024-06-13 00:33:34.613162 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-13 00:33:34.73825 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-13 00:33:34.880323 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-13 00:33:35.017183 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-13 00:33:35.154557 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-13 00:33:35.201337 WARNING::Fitting problem for feature 72 a warning was issued
2024-06-13 00:33:35.334027 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-13 00:33:35.475499 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-13 00:33:35.606139 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-13 00:33:35.743359 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-13 00:33:35.874182 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-13 00:33:36.008738 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-13 00:33:36.137735 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-13 00:33:36.278453 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-13 00:33:36.405764 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-13 00:33:36.547239 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-13 00:33:36.673336 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-13 00:33:36.803264 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-13 00:33:36.936336 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-13 00:33:37.064778 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-13 00:33:37.432226 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-13 00:33:37.585702 INFO::Counting total values for each feature
2024-06-13 00:33:37.609299 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-06-13 00:33:37.753288 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-06-13 00:33:37.896714 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-06-13 00:33:38.047432 INFO::Writing residuals to file output2/fits/residuals.rds
2024-06-13 00:33:38.122575 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-06-13 00:33:38.195307 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-06-13 00:33:38.201233 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-06-13 00:33:38.206687 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 
 29.587   0.432  30.008

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

name	user	system	elapsed
Maaslin2	84.474	1.077	85.492