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This page was generated on 2024-05-04 11:40:42 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_19
git_last_commit: 35350f9
git_last_commit_date: 2024-04-30 11:16:06 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for Maaslin2 on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: Maaslin2
Version: 1.18.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings Maaslin2_1.18.0.tar.gz
StartedAt: 2024-05-04 08:59:44 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 09:03:15 -0000 (Sat, 04 May 2024)
EllapsedTime: 211.4 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --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 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 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 120.533  1.022 121.798
* 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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.


Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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"
2024-05-04 09:02:24.563232 INFO::Writing function arguments to log file
2024-05-04 09:02:24.621368 INFO::Verifying options selected are valid
2024-05-04 09:02:24.669118 INFO::Determining format of input files
2024-05-04 09:02:24.671202 INFO::Input format is data samples as rows and metadata samples as rows
2024-05-04 09:02:24.679457 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-05-04 09:02:24.681532 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-05-04 09:02:24.685403 INFO::Filter data based on min abundance and min prevalence
2024-05-04 09:02:24.686901 INFO::Total samples in data: 1595
2024-05-04 09:02:24.688364 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-05-04 09:02:24.700059 INFO::Total filtered features: 0
2024-05-04 09:02:24.701824 INFO::Filtered feature names from abundance and prevalence filtering:
2024-05-04 09:02:24.745654 INFO::Total filtered features with variance filtering: 0
2024-05-04 09:02:24.747441 INFO::Filtered feature names from variance filtering:
2024-05-04 09:02:24.749027 INFO::Running selected normalization method: TSS
2024-05-04 09:02:26.333635 INFO::Bypass z-score application to metadata
2024-05-04 09:02:26.335254 INFO::Running selected transform method: AST
2024-05-04 09:02:26.360751 INFO::Running selected analysis method: LM
2024-05-04 09:02:27.014241 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-05-04 09:02:27.534368 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-05-04 09:02:27.787664 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-05-04 09:02:28.039517 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-05-04 09:02:28.69689 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-05-04 09:02:29.019024 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-05-04 09:02:29.301363 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-05-04 09:02:29.562304 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-05-04 09:02:29.784803 WARNING::Fitting problem for feature 8 a warning was issued
2024-05-04 09:02:30.156386 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-05-04 09:02:30.371772 WARNING::Fitting problem for feature 9 a warning was issued
2024-05-04 09:02:30.65863 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-05-04 09:02:30.895089 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-05-04 09:02:31.133181 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-05-04 09:02:31.397411 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-05-04 09:02:31.602913 WARNING::Fitting problem for feature 13 a warning was issued
2024-05-04 09:02:31.858848 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-05-04 09:02:32.10394 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-05-04 09:02:32.380121 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-05-04 09:02:32.622991 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-05-04 09:02:32.888067 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-05-04 09:02:33.150475 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-05-04 09:02:33.389702 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-05-04 09:02:33.649612 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-05-04 09:02:33.911869 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-05-04 09:02:34.482216 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-05-04 09:02:34.733394 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-05-04 09:02:34.991633 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-05-04 09:02:35.254581 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-05-04 09:02:35.497226 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-05-04 09:02:35.745163 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-05-04 09:02:36.008234 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-05-04 09:02:36.287221 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-05-04 09:02:36.531 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-05-04 09:02:36.800168 INFO::Fitting model to feature number 32, Prevotella.copri
2024-05-04 09:02:37.060793 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-05-04 09:02:37.321029 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-05-04 09:02:37.567177 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-05-04 09:02:37.794392 WARNING::Fitting problem for feature 35 a warning was issued
2024-05-04 09:02:38.050958 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-05-04 09:02:38.298105 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-05-04 09:02:38.555239 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-05-04 09:02:38.79126 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-05-04 09:02:39.027874 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-05-04 09:02:39.299271 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-05-04 09:02:39.56158 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-05-04 09:02:39.814941 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-05-04 09:02:40.069058 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-05-04 09:02:40.299342 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-05-04 09:02:40.537793 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-05-04 09:02:40.794564 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-05-04 09:02:41.052662 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-05-04 09:02:41.308836 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-05-04 09:02:41.563123 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-05-04 09:02:41.810491 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-05-04 09:02:42.062447 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-05-04 09:02:42.318364 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-05-04 09:02:42.584651 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-05-04 09:02:42.819823 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-05-04 09:02:43.089675 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-05-04 09:02:43.357013 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-05-04 09:02:43.609621 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-05-04 09:02:43.885952 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-05-04 09:02:44.142948 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-05-04 09:02:44.374487 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-05-04 09:02:44.619233 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-05-04 09:02:44.864988 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-05-04 09:02:45.121029 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-05-04 09:02:45.359448 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-05-04 09:02:45.605814 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-05-04 09:02:45.870098 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-05-04 09:02:46.101173 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-05-04 09:02:46.365035 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-05-04 09:02:46.652598 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-05-04 09:02:46.920819 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-05-04 09:02:47.165516 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-05-04 09:02:47.698002 INFO::Fitting model to feature number 73, Dialister.invisus
2024-05-04 09:02:47.935928 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-05-04 09:02:48.180398 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-05-04 09:02:48.438897 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-05-04 09:02:48.70591 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-05-04 09:02:48.958077 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-05-04 09:02:49.221647 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-05-04 09:02:49.782624 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-05-04 09:02:50.030822 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-05-04 09:02:50.298963 INFO::Fitting model to feature number 82, Escherichia.coli
2024-05-04 09:02:50.550933 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-05-04 09:02:50.783706 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-05-04 09:02:51.021106 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-05-04 09:02:51.265549 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-05-04 09:02:51.504432 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-05-04 09:02:51.817256 INFO::Counting total values for each feature
2024-05-04 09:02:51.878011 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-05-04 09:02:52.00472 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-05-04 09:02:52.133166 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-05-04 09:02:52.264161 INFO::Writing residuals to file output/fits/residuals.rds
2024-05-04 09:02:52.314031 INFO::Writing fitted values to file output/fits/fitted.rds
2024-05-04 09:02:52.341157 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-05-04 09:02:52.347329 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-05-04 09:02:52.354384 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"
2024-05-04 09:02:52.372397 INFO::Writing function arguments to log file
2024-05-04 09:02:52.380611 INFO::Verifying options selected are valid
2024-05-04 09:02:52.381948 INFO::Determining format of input files
2024-05-04 09:02:52.383443 INFO::Input format is data samples as rows and metadata samples as rows
2024-05-04 09:02:52.39068 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-05-04 09:02:52.39233 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-05-04 09:02:52.394616 INFO::Filter data based on min abundance and min prevalence
2024-05-04 09:02:52.395944 INFO::Total samples in data: 1595
2024-05-04 09:02:52.397155 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-05-04 09:02:52.40777 INFO::Total filtered features: 0
2024-05-04 09:02:52.409338 INFO::Filtered feature names from abundance and prevalence filtering:
2024-05-04 09:02:52.440566 INFO::Total filtered features with variance filtering: 0
2024-05-04 09:02:52.442082 INFO::Filtered feature names from variance filtering:
2024-05-04 09:02:52.44328 INFO::Running selected normalization method: NONE
2024-05-04 09:02:52.444423 INFO::Bypass z-score application to metadata
2024-05-04 09:02:52.445556 INFO::Running selected transform method: AST
2024-05-04 09:02:52.483405 INFO::Running selected analysis method: LM
2024-05-04 09:02:52.48614 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-05-04 09:02:52.718982 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-05-04 09:02:52.970952 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-05-04 09:02:53.207645 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-05-04 09:02:53.453055 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-05-04 09:02:53.685456 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-05-04 09:02:53.948007 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-05-04 09:02:54.181435 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-05-04 09:02:54.419841 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-05-04 09:02:54.648511 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-05-04 09:02:54.885031 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-05-04 09:02:55.140486 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-05-04 09:02:55.361782 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-05-04 09:02:55.589243 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-05-04 09:02:55.826781 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-05-04 09:02:56.059139 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-05-04 09:02:56.243618 WARNING::Fitting problem for feature 16 a warning was issued
2024-05-04 09:02:56.497797 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-05-04 09:02:56.750842 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-05-04 09:02:56.997983 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-05-04 09:02:57.246145 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-05-04 09:02:57.473143 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-05-04 09:02:57.709052 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-05-04 09:02:57.932239 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-05-04 09:02:58.143827 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-05-04 09:02:58.379288 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-05-04 09:02:58.60044 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-05-04 09:02:58.831282 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-05-04 09:02:59.05852 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-05-04 09:02:59.270446 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-05-04 09:02:59.491869 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-05-04 09:02:59.707952 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-05-04 09:02:59.936157 INFO::Fitting model to feature number 32, Prevotella.copri
2024-05-04 09:03:00.164601 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-05-04 09:03:00.389298 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-05-04 09:03:00.607744 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-05-04 09:03:00.846951 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-05-04 09:03:01.074704 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-05-04 09:03:01.316046 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-05-04 09:03:01.54051 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-05-04 09:03:01.778121 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-05-04 09:03:02.000386 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-05-04 09:03:02.226002 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-05-04 09:03:02.454745 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-05-04 09:03:02.679841 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-05-04 09:03:02.914919 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-05-04 09:03:03.138567 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-05-04 09:03:03.373246 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-05-04 09:03:03.600772 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-05-04 09:03:03.826543 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-05-04 09:03:04.049055 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-05-04 09:03:04.267815 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-05-04 09:03:04.486701 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-05-04 09:03:04.697916 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-05-04 09:03:04.899026 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-05-04 09:03:05.110977 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-05-04 09:03:05.336706 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-05-04 09:03:05.556548 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-05-04 09:03:05.784563 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-05-04 09:03:06.00049 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-05-04 09:03:06.253829 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-05-04 09:03:06.47522 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-05-04 09:03:06.699132 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-05-04 09:03:06.925464 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-05-04 09:03:07.143759 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-05-04 09:03:07.370996 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-05-04 09:03:07.583511 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-05-04 09:03:07.805132 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-05-04 09:03:07.986614 WARNING::Fitting problem for feature 67 a warning was issued
2024-05-04 09:03:08.231581 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-05-04 09:03:08.45249 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-05-04 09:03:08.684165 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-05-04 09:03:08.926576 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-05-04 09:03:09.146637 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-05-04 09:03:09.234055 WARNING::Fitting problem for feature 72 a warning was issued
2024-05-04 09:03:09.452557 INFO::Fitting model to feature number 73, Dialister.invisus
2024-05-04 09:03:09.6952 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-05-04 09:03:09.923838 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-05-04 09:03:10.148099 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-05-04 09:03:10.395314 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-05-04 09:03:10.629071 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-05-04 09:03:10.864593 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-05-04 09:03:11.092763 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-05-04 09:03:11.306287 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-05-04 09:03:11.548676 INFO::Fitting model to feature number 82, Escherichia.coli
2024-05-04 09:03:11.770862 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-05-04 09:03:12.003351 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-05-04 09:03:12.216878 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-05-04 09:03:12.438624 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-05-04 09:03:12.688386 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-05-04 09:03:12.954694 INFO::Counting total values for each feature
2024-05-04 09:03:13.010591 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-05-04 09:03:13.136366 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-05-04 09:03:13.263451 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-05-04 09:03:13.394955 INFO::Writing residuals to file output2/fits/residuals.rds
2024-05-04 09:03:13.461715 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-05-04 09:03:13.527383 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-05-04 09:03:13.534044 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-05-04 09:03:13.540526 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 
 49.562   0.902  50.567 

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2120.533 1.022121.798