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This page was generated on 2024-06-28 11:39 -0400 (Fri, 28 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4693
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4089
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4407
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4356
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: 2024-06-27 14:00 -0400 (Thu, 27 Jun 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    ERROR  skippedskipped
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) / aarch64see weekly results here

CHECK results for Maaslin2 on lconway

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: /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_1.19.0.tar.gz
StartedAt: 2024-06-27 21:08:28 -0400 (Thu, 27 Jun 2024)
EndedAt: 2024-06-27 21:11:23 -0400 (Thu, 27 Jun 2024)
EllapsedTime: 174.3 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_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.1 RC (2024-06-06 r86719)
* 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 12.7.1
* 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 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 92.381  1.652  94.586
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘Maaslin2’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in checkDepPackageVersion(dep_pkg = "TMB") :
  Package version inconsistency detected.
glmmTMB was built with TMB version 1.9.11
Current TMB version is 1.9.12
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 RC (2024-06-06 r86719) -- "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"
2024-06-27 21:10:42.570075 INFO::Writing function arguments to log file
2024-06-27 21:10:42.616973 INFO::Verifying options selected are valid
2024-06-27 21:10:42.65724 INFO::Determining format of input files
2024-06-27 21:10:42.660458 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-27 21:10:42.669879 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-27 21:10:42.672316 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-06-27 21:10:42.675329 INFO::Filter data based on min abundance and min prevalence
2024-06-27 21:10:42.676745 INFO::Total samples in data: 1595
2024-06-27 21:10:42.678081 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-27 21:10:42.693868 INFO::Total filtered features: 0
2024-06-27 21:10:42.695669 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-27 21:10:42.706983 INFO::Total filtered features with variance filtering: 0
2024-06-27 21:10:42.708785 INFO::Filtered feature names from variance filtering:
2024-06-27 21:10:42.710273 INFO::Running selected normalization method: TSS
2024-06-27 21:10:44.03309 INFO::Bypass z-score application to metadata
2024-06-27 21:10:44.035172 INFO::Running selected transform method: AST
2024-06-27 21:10:44.051199 INFO::Running selected analysis method: LM
2024-06-27 21:10:44.601803 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-27 21:10:44.988397 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-27 21:10:45.178728 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-27 21:10:45.347387 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-27 21:10:45.513643 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-27 21:10:45.664595 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-27 21:10:45.82008 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-27 21:10:45.988106 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-27 21:10:46.146637 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-27 21:10:46.348599 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-27 21:10:46.510411 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-27 21:10:46.67217 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-27 21:10:46.836327 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-27 21:10:46.979076 WARNING::Fitting problem for feature 13 a warning was issued
2024-06-27 21:10:47.156961 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-27 21:10:47.318261 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-27 21:10:47.485471 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-27 21:10:47.623358 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-27 21:10:47.782351 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-27 21:10:47.923781 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-27 21:10:48.05966 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-27 21:10:48.220263 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-27 21:10:48.365978 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-27 21:10:48.518711 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-27 21:10:48.672057 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-27 21:10:48.835008 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-27 21:10:48.990877 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-27 21:10:49.147747 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-27 21:10:49.316666 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-27 21:10:49.486997 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-27 21:10:49.642278 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-27 21:10:49.800273 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-27 21:10:49.953437 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-27 21:10:50.104118 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-27 21:10:50.297823 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-27 21:10:50.449765 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-27 21:10:50.614181 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-27 21:10:50.768663 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-27 21:10:50.927886 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-27 21:10:51.085274 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-27 21:10:51.235125 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-27 21:10:51.399006 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-27 21:10:51.550916 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-27 21:10:51.720199 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-27 21:10:51.878802 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-27 21:10:52.031453 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-27 21:10:52.201349 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-27 21:10:52.356659 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-27 21:10:52.761319 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-27 21:10:52.927905 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-27 21:10:53.116135 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-27 21:10:53.29647 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-27 21:10:53.454897 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-27 21:10:53.613762 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-27 21:10:53.774524 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-27 21:10:53.945316 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-27 21:10:54.109892 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-27 21:10:54.285483 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-27 21:10:54.443135 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-27 21:10:54.607155 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-27 21:10:54.753805 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-27 21:10:54.913776 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-27 21:10:55.068852 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-27 21:10:55.229479 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-27 21:10:55.384366 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-27 21:10:55.532265 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-27 21:10:55.693219 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-27 21:10:55.841124 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-27 21:10:55.992028 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-27 21:10:56.144483 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-27 21:10:56.309169 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-27 21:10:56.454915 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-27 21:10:56.604239 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-27 21:10:56.743187 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-27 21:10:56.907125 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-27 21:10:57.082031 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-27 21:10:57.240224 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-27 21:10:57.409995 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-27 21:10:57.561996 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-27 21:10:57.728078 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-27 21:10:57.880464 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-27 21:10:58.047597 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-27 21:10:58.198223 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-27 21:10:58.365689 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-27 21:10:58.525 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-27 21:10:58.687676 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-27 21:10:58.862691 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-27 21:10:59.017629 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-27 21:10:59.229971 INFO::Counting total values for each feature
2024-06-27 21:10:59.275583 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-06-27 21:10:59.418568 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-06-27 21:10:59.576943 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-06-27 21:10:59.740563 INFO::Writing residuals to file output/fits/residuals.rds
2024-06-27 21:10:59.798457 INFO::Writing fitted values to file output/fits/fitted.rds
2024-06-27 21:10:59.826292 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-06-27 21:10:59.832165 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-06-27 21:10:59.840107 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"
2024-06-27 21:10:59.865678 INFO::Writing function arguments to log file
2024-06-27 21:10:59.876794 INFO::Verifying options selected are valid
2024-06-27 21:10:59.87814 INFO::Determining format of input files
2024-06-27 21:10:59.879958 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-27 21:10:59.887561 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-27 21:10:59.88947 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-06-27 21:10:59.892073 INFO::Filter data based on min abundance and min prevalence
2024-06-27 21:10:59.89348 INFO::Total samples in data: 1595
2024-06-27 21:10:59.894929 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-27 21:10:59.900734 INFO::Total filtered features: 0
2024-06-27 21:10:59.902053 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-27 21:10:59.918715 INFO::Total filtered features with variance filtering: 0
2024-06-27 21:10:59.920654 INFO::Filtered feature names from variance filtering:
2024-06-27 21:10:59.922221 INFO::Running selected normalization method: NONE
2024-06-27 21:10:59.923683 INFO::Bypass z-score application to metadata
2024-06-27 21:10:59.925123 INFO::Running selected transform method: AST
2024-06-27 21:10:59.962707 INFO::Running selected analysis method: LM
2024-06-27 21:10:59.966106 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-27 21:11:00.130561 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-27 21:11:00.280692 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-27 21:11:00.431787 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-27 21:11:00.594831 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-27 21:11:00.765608 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-27 21:11:00.897687 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-27 21:11:01.04729 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-27 21:11:01.211573 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-27 21:11:01.367115 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-27 21:11:01.526955 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-27 21:11:01.677697 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-27 21:11:01.834307 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-27 21:11:01.974129 WARNING::Fitting problem for feature 13 a warning was issued
2024-06-27 21:11:02.138727 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-27 21:11:02.276509 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-27 21:11:02.436747 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-27 21:11:02.586175 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-27 21:11:02.740535 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-27 21:11:02.900333 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-27 21:11:03.056007 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-27 21:11:03.205023 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-27 21:11:03.365924 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-27 21:11:03.538283 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-27 21:11:03.707381 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-27 21:11:03.863679 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-27 21:11:04.008713 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-27 21:11:04.163069 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-27 21:11:04.295664 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-27 21:11:04.439722 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-27 21:11:04.587209 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-27 21:11:04.735571 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-27 21:11:04.890676 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-27 21:11:05.061719 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-27 21:11:05.205991 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-27 21:11:05.374197 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-27 21:11:05.530508 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-27 21:11:05.687298 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-27 21:11:05.859225 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-27 21:11:06.016924 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-27 21:11:06.165348 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-27 21:11:06.327561 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-27 21:11:06.485298 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-27 21:11:06.667312 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-27 21:11:06.817251 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-27 21:11:06.993729 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-27 21:11:07.152002 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-27 21:11:07.322926 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-27 21:11:07.468126 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-27 21:11:07.640167 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-27 21:11:07.788839 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-27 21:11:07.950363 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-27 21:11:08.099407 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-27 21:11:08.241581 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-27 21:11:08.396304 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-27 21:11:08.538944 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-27 21:11:08.717915 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-27 21:11:08.873879 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-27 21:11:09.020473 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-27 21:11:09.182612 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-27 21:11:09.337435 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-27 21:11:09.498736 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-27 21:11:09.643337 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-27 21:11:09.787138 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-27 21:11:09.953579 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-27 21:11:10.099634 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-27 21:11:10.268772 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-27 21:11:10.43462 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-27 21:11:10.566982 WARNING::Fitting problem for feature 67 a warning was issued
2024-06-27 21:11:10.96543 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-27 21:11:11.122774 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-27 21:11:11.285252 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-27 21:11:11.453898 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-27 21:11:11.620763 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-27 21:11:11.675722 WARNING::Fitting problem for feature 72 a warning was issued
2024-06-27 21:11:11.819782 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-27 21:11:11.969167 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-27 21:11:12.13272 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-27 21:11:12.29321 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-27 21:11:12.451856 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-27 21:11:12.580359 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-27 21:11:12.722445 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-27 21:11:12.878422 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-27 21:11:13.019078 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-27 21:11:13.170276 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-27 21:11:13.332796 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-27 21:11:13.489959 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-27 21:11:13.63484 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-27 21:11:13.773489 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-27 21:11:13.934303 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-27 21:11:14.119383 INFO::Counting total values for each feature
2024-06-27 21:11:14.14445 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-06-27 21:11:14.263839 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-06-27 21:11:14.405323 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-06-27 21:11:14.582947 INFO::Writing residuals to file output2/fits/residuals.rds
2024-06-27 21:11:14.656156 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-06-27 21:11:14.725906 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-06-27 21:11:14.733318 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-06-27 21:11:14.738644 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 
 32.718   0.709  33.632

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin292.381 1.65294.586