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This page was generated on 2024-10-18 20:41 -0400 (Fri, 18 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4500
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4530
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4480
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: 2024-10-16 14:00 -0400 (Wed, 16 Oct 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
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
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: 1.18.0
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_1.18.0.tar.gz
StartedAt: 2024-10-17 07:32:15 -0400 (Thu, 17 Oct 2024)
EndedAt: 2024-10-17 07:38:57 -0400 (Thu, 17 Oct 2024)
EllapsedTime: 402.1 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_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘1.18.0’
* 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 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 185.582  3.294 234.006
* 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-3.19-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 4.4.1 (2024-06-14) -- "Race for Your Life"
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"
2024-10-17 07:37:24.86779 INFO::Writing function arguments to log file
2024-10-17 07:37:24.988673 INFO::Verifying options selected are valid
2024-10-17 07:37:25.073526 INFO::Determining format of input files
2024-10-17 07:37:25.099436 INFO::Input format is data samples as rows and metadata samples as rows
2024-10-17 07:37:25.114807 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-10-17 07:37:25.118083 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-10-17 07:37:25.168157 INFO::Filter data based on min abundance and min prevalence
2024-10-17 07:37:25.205014 INFO::Total samples in data: 1595
2024-10-17 07:37:25.207719 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-10-17 07:37:25.266407 INFO::Total filtered features: 0
2024-10-17 07:37:25.269335 INFO::Filtered feature names from abundance and prevalence filtering:
2024-10-17 07:37:25.292127 INFO::Total filtered features with variance filtering: 0
2024-10-17 07:37:25.316928 INFO::Filtered feature names from variance filtering:
2024-10-17 07:37:25.319537 INFO::Running selected normalization method: TSS
2024-10-17 07:37:27.978323 INFO::Bypass z-score application to metadata
2024-10-17 07:37:27.981354 INFO::Running selected transform method: AST
2024-10-17 07:37:28.031992 INFO::Running selected analysis method: LM
2024-10-17 07:37:29.309517 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-10-17 07:37:30.105878 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-10-17 07:37:30.479153 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-10-17 07:37:30.848572 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-10-17 07:37:31.250274 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-10-17 07:37:31.601456 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-10-17 07:37:31.972946 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-10-17 07:37:32.340795 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-10-17 07:37:32.710796 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-10-17 07:37:33.103501 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-10-17 07:37:33.458384 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-10-17 07:37:33.832966 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-10-17 07:37:34.218717 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-10-17 07:37:34.58676 WARNING::Fitting problem for feature 13 a warning was issued
2024-10-17 07:37:34.977755 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-10-17 07:37:35.362208 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-10-17 07:37:35.745736 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-10-17 07:37:36.115583 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-10-17 07:37:36.47733 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-10-17 07:37:36.85657 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-10-17 07:37:37.213366 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-10-17 07:37:37.608562 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-10-17 07:37:37.970544 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-10-17 07:37:38.341347 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-10-17 07:37:38.708377 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-10-17 07:37:39.066802 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-10-17 07:37:39.432041 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-10-17 07:37:39.792395 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-10-17 07:37:40.172631 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-10-17 07:37:40.563421 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-10-17 07:37:41.103177 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-10-17 07:37:41.5318 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-10-17 07:37:41.978362 INFO::Fitting model to feature number 32, Prevotella.copri
2024-10-17 07:37:42.433894 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-10-17 07:37:42.939683 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-10-17 07:37:43.28438 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-10-17 07:37:43.667459 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-10-17 07:37:44.043724 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-10-17 07:37:44.454167 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-10-17 07:37:44.797728 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-10-17 07:37:45.161921 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-10-17 07:37:45.517334 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-10-17 07:37:45.850866 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-10-17 07:37:46.237334 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-10-17 07:37:46.631808 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-10-17 07:37:46.974576 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-10-17 07:37:47.353062 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-10-17 07:37:47.830769 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-10-17 07:37:48.490525 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-10-17 07:37:48.824447 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-10-17 07:37:49.174945 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-10-17 07:37:49.954813 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-10-17 07:37:50.385789 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-10-17 07:37:50.733731 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-10-17 07:37:51.148167 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-10-17 07:37:51.48203 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-10-17 07:37:51.871491 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-10-17 07:37:52.23942 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-10-17 07:37:52.608356 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-10-17 07:37:52.994172 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-10-17 07:37:53.359183 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-10-17 07:37:53.78684 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-10-17 07:37:54.157762 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-10-17 07:37:54.52197 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-10-17 07:37:54.880381 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-10-17 07:37:55.277196 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-10-17 07:37:55.613538 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-10-17 07:37:55.983747 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-10-17 07:37:56.31848 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-10-17 07:37:56.656921 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-10-17 07:37:57.023879 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-10-17 07:37:57.375869 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-10-17 07:37:57.745301 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-10-17 07:37:58.164151 INFO::Fitting model to feature number 73, Dialister.invisus
2024-10-17 07:37:58.515781 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-10-17 07:37:58.8792 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-10-17 07:37:59.230204 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-10-17 07:37:59.583428 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-10-17 07:37:59.959553 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-10-17 07:38:00.347497 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-10-17 07:38:00.748194 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-10-17 07:38:01.111542 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-10-17 07:38:01.616733 INFO::Fitting model to feature number 82, Escherichia.coli
2024-10-17 07:38:02.008505 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-10-17 07:38:02.452599 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-10-17 07:38:02.779304 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-10-17 07:38:03.139665 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-10-17 07:38:03.484125 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-10-17 07:38:03.952407 INFO::Counting total values for each feature
2024-10-17 07:38:04.341196 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-10-17 07:38:04.881336 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-10-17 07:38:05.55368 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-10-17 07:38:06.112012 INFO::Writing residuals to file output/fits/residuals.rds
2024-10-17 07:38:06.49508 INFO::Writing fitted values to file output/fits/fitted.rds
2024-10-17 07:38:06.58878 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-10-17 07:38:06.601622 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-10-17 07:38:06.61778 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"
2024-10-17 07:38:06.689009 INFO::Writing function arguments to log file
2024-10-17 07:38:06.764803 INFO::Verifying options selected are valid
2024-10-17 07:38:06.767247 INFO::Determining format of input files
2024-10-17 07:38:06.770029 INFO::Input format is data samples as rows and metadata samples as rows
2024-10-17 07:38:06.784101 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-10-17 07:38:06.789277 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-10-17 07:38:06.793537 INFO::Filter data based on min abundance and min prevalence
2024-10-17 07:38:06.796098 INFO::Total samples in data: 1595
2024-10-17 07:38:06.799324 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-10-17 07:38:06.809501 INFO::Total filtered features: 0
2024-10-17 07:38:06.81227 INFO::Filtered feature names from abundance and prevalence filtering:
2024-10-17 07:38:06.832747 INFO::Total filtered features with variance filtering: 0
2024-10-17 07:38:06.835587 INFO::Filtered feature names from variance filtering:
2024-10-17 07:38:06.838131 INFO::Running selected normalization method: NONE
2024-10-17 07:38:06.841502 INFO::Bypass z-score application to metadata
2024-10-17 07:38:06.844862 INFO::Running selected transform method: AST
2024-10-17 07:38:06.876095 INFO::Running selected analysis method: LM
2024-10-17 07:38:06.919923 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-10-17 07:38:07.385004 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-10-17 07:38:08.009474 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-10-17 07:38:08.364514 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-10-17 07:38:08.685852 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-10-17 07:38:09.106511 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-10-17 07:38:09.475239 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-10-17 07:38:09.834637 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-10-17 07:38:10.16833 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-10-17 07:38:10.48899 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-10-17 07:38:10.841317 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-10-17 07:38:11.220392 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-10-17 07:38:11.559142 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-10-17 07:38:11.838805 WARNING::Fitting problem for feature 13 a warning was issued
2024-10-17 07:38:12.210982 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-10-17 07:38:12.618678 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-10-17 07:38:12.997006 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-10-17 07:38:13.320625 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-10-17 07:38:13.637067 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-10-17 07:38:13.977522 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-10-17 07:38:14.293488 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-10-17 07:38:14.645358 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-10-17 07:38:14.994892 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-10-17 07:38:15.346595 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-10-17 07:38:15.780263 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-10-17 07:38:16.270793 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-10-17 07:38:16.942644 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-10-17 07:38:17.296045 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-10-17 07:38:17.645238 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-10-17 07:38:17.967357 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-10-17 07:38:18.32299 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-10-17 07:38:18.712565 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-10-17 07:38:19.036867 INFO::Fitting model to feature number 32, Prevotella.copri
2024-10-17 07:38:19.672171 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-10-17 07:38:20.212113 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-10-17 07:38:20.551529 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-10-17 07:38:20.863348 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-10-17 07:38:21.200829 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-10-17 07:38:21.56284 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-10-17 07:38:21.884044 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-10-17 07:38:22.20898 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-10-17 07:38:22.552881 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-10-17 07:38:22.882603 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-10-17 07:38:23.228932 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-10-17 07:38:23.562985 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-10-17 07:38:23.947181 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-10-17 07:38:24.251059 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-10-17 07:38:24.864076 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-10-17 07:38:25.553379 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-10-17 07:38:25.903686 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-10-17 07:38:26.234517 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-10-17 07:38:26.696862 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-10-17 07:38:27.053955 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-10-17 07:38:27.364275 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-10-17 07:38:27.740586 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-10-17 07:38:28.399023 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-10-17 07:38:28.713752 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-10-17 07:38:29.146635 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-10-17 07:38:29.684141 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-10-17 07:38:30.013929 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-10-17 07:38:30.356348 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-10-17 07:38:30.69097 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-10-17 07:38:31.021369 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-10-17 07:38:31.339561 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-10-17 07:38:31.652509 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-10-17 07:38:31.941448 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-10-17 07:38:32.25687 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-10-17 07:38:32.580353 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-10-17 07:38:32.902782 WARNING::Fitting problem for feature 67 a warning was issued
2024-10-17 07:38:33.238775 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-10-17 07:38:33.571909 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-10-17 07:38:34.010257 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-10-17 07:38:34.334501 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-10-17 07:38:34.644415 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-10-17 07:38:34.774604 WARNING::Fitting problem for feature 72 a warning was issued
2024-10-17 07:38:35.10385 INFO::Fitting model to feature number 73, Dialister.invisus
2024-10-17 07:38:35.450803 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-10-17 07:38:35.8921 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-10-17 07:38:36.232768 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-10-17 07:38:36.578289 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-10-17 07:38:37.039455 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-10-17 07:38:37.362787 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-10-17 07:38:37.673926 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-10-17 07:38:38.092513 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-10-17 07:38:38.436398 INFO::Fitting model to feature number 82, Escherichia.coli
2024-10-17 07:38:38.735583 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-10-17 07:38:39.154709 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-10-17 07:38:39.52839 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-10-17 07:38:39.960691 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-10-17 07:38:40.360809 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-10-17 07:38:40.788117 INFO::Counting total values for each feature
2024-10-17 07:38:40.862537 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-10-17 07:38:41.252457 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-10-17 07:38:41.566105 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-10-17 07:38:41.981852 INFO::Writing residuals to file output2/fits/residuals.rds
2024-10-17 07:38:42.111365 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-10-17 07:38:42.324354 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-10-17 07:38:42.335712 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-10-17 07:38:42.370759 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 
 62.105   1.169  80.543

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2185.582 3.294234.006