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This page was generated on 2024-05-04 11:38:01 -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 palomino3


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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings Maaslin2_1.18.0.tar.gz
StartedAt: 2024-05-04 04:56:41 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 05:00:00 -0400 (Sat, 04 May 2024)
EllapsedTime: 199.4 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings Maaslin2_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck'
* using R version 4.4.0 beta (2024-04-15 r86425 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Maaslin2/DESCRIPTION' ... OK
* this is package 'Maaslin2' version '1.18.0'
* 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 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 108.06   7.37   115.7
* 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
  'F:/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.


Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(Maaslin2)
> 
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2024-05-04 04:59:17.448423 INFO::Writing function arguments to log file
2024-05-04 04:59:17.501077 INFO::Verifying options selected are valid
2024-05-04 04:59:17.533646 INFO::Determining format of input files
2024-05-04 04:59:17.536087 INFO::Input format is data samples as rows and metadata samples as rows
2024-05-04 04:59:17.550917 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-05-04 04:59:17.553497 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-05-04 04:59:17.557045 INFO::Filter data based on min abundance and min prevalence
2024-05-04 04:59:17.558911 INFO::Total samples in data: 1595
2024-05-04 04:59:17.560723 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-05-04 04:59:17.566214 INFO::Total filtered features: 0
2024-05-04 04:59:17.568247 INFO::Filtered feature names from abundance and prevalence filtering:
2024-05-04 04:59:17.579032 INFO::Total filtered features with variance filtering: 0
2024-05-04 04:59:17.581206 INFO::Filtered feature names from variance filtering:
2024-05-04 04:59:17.583092 INFO::Running selected normalization method: TSS
2024-05-04 04:59:18.771195 INFO::Bypass z-score application to metadata
2024-05-04 04:59:18.773571 INFO::Running selected transform method: AST
2024-05-04 04:59:18.792805 INFO::Running selected analysis method: LM
2024-05-04 04:59:19.104805 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-05-04 04:59:19.58093 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-05-04 04:59:19.782982 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-05-04 04:59:19.967442 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-05-04 04:59:20.162389 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-05-04 04:59:20.306304 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-05-04 04:59:20.439259 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-05-04 04:59:20.617041 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-05-04 04:59:20.747669 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-05-04 04:59:20.872389 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-05-04 04:59:21.010618 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-05-04 04:59:21.157095 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-05-04 04:59:21.305116 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-05-04 04:59:21.41443 WARNING::Fitting problem for feature 13 a warning was issued
2024-05-04 04:59:21.566848 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-05-04 04:59:21.767719 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-05-04 04:59:22.009737 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-05-04 04:59:22.226998 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-05-04 04:59:22.442101 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-05-04 04:59:22.583496 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-05-04 04:59:22.720424 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-05-04 04:59:22.864142 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-05-04 04:59:23.0019 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-05-04 04:59:23.15633 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-05-04 04:59:23.302205 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-05-04 04:59:23.473226 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-05-04 04:59:23.620851 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-05-04 04:59:23.764873 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-05-04 04:59:23.916541 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-05-04 04:59:24.09749 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-05-04 04:59:24.240311 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-05-04 04:59:24.434714 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-05-04 04:59:24.659545 INFO::Fitting model to feature number 32, Prevotella.copri
2024-05-04 04:59:24.868901 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-05-04 04:59:25.041887 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-05-04 04:59:25.185842 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-05-04 04:59:25.334488 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-05-04 04:59:25.501031 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-05-04 04:59:25.716637 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-05-04 04:59:25.88366 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-05-04 04:59:26.076833 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-05-04 04:59:26.251147 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-05-04 04:59:26.408355 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-05-04 04:59:26.56793 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-05-04 04:59:26.715249 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-05-04 04:59:26.844198 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-05-04 04:59:27.232443 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-05-04 04:59:27.392564 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-05-04 04:59:27.569849 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-05-04 04:59:27.730908 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-05-04 04:59:27.869649 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-05-04 04:59:28.017359 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-05-04 04:59:28.211832 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-05-04 04:59:28.341744 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-05-04 04:59:28.476266 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-05-04 04:59:28.612097 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-05-04 04:59:28.743299 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-05-04 04:59:28.879407 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-05-04 04:59:29.010759 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-05-04 04:59:29.16251 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-05-04 04:59:29.341712 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-05-04 04:59:29.551189 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-05-04 04:59:29.712862 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-05-04 04:59:29.857165 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-05-04 04:59:29.996201 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-05-04 04:59:30.139716 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-05-04 04:59:30.270006 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-05-04 04:59:30.413135 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-05-04 04:59:30.533461 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-05-04 04:59:30.696135 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-05-04 04:59:31.194951 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-05-04 04:59:31.438764 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-05-04 04:59:31.645756 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-05-04 04:59:31.879959 INFO::Fitting model to feature number 73, Dialister.invisus
2024-05-04 04:59:32.094734 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-05-04 04:59:32.30519 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-05-04 04:59:32.490297 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-05-04 04:59:32.72341 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-05-04 04:59:32.930179 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-05-04 04:59:33.159581 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-05-04 04:59:33.324372 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-05-04 04:59:33.478789 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-05-04 04:59:33.670937 INFO::Fitting model to feature number 82, Escherichia.coli
2024-05-04 04:59:33.835806 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-05-04 04:59:34.043367 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-05-04 04:59:34.215728 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-05-04 04:59:34.405541 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-05-04 04:59:34.547484 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-05-04 04:59:34.750444 INFO::Counting total values for each feature
2024-05-04 04:59:34.803052 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-05-04 04:59:35.22338 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-05-04 04:59:35.704885 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-05-04 04:59:36.055336 INFO::Writing residuals to file output/fits/residuals.rds
2024-05-04 04:59:36.100443 INFO::Writing fitted values to file output/fits/fitted.rds
2024-05-04 04:59:36.125487 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-05-04 04:59:36.134917 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-05-04 04:59:36.154212 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 04:59:36.196859 INFO::Writing function arguments to log file
2024-05-04 04:59:36.223313 INFO::Verifying options selected are valid
2024-05-04 04:59:36.225469 INFO::Determining format of input files
2024-05-04 04:59:36.227624 INFO::Input format is data samples as rows and metadata samples as rows
2024-05-04 04:59:36.236074 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-05-04 04:59:36.238299 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-05-04 04:59:36.24117 INFO::Filter data based on min abundance and min prevalence
2024-05-04 04:59:36.243261 INFO::Total samples in data: 1595
2024-05-04 04:59:36.245122 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-05-04 04:59:36.260608 INFO::Total filtered features: 0
2024-05-04 04:59:36.262927 INFO::Filtered feature names from abundance and prevalence filtering:
2024-05-04 04:59:36.269805 INFO::Total filtered features with variance filtering: 0
2024-05-04 04:59:36.27199 INFO::Filtered feature names from variance filtering:
2024-05-04 04:59:36.273902 INFO::Running selected normalization method: NONE
2024-05-04 04:59:36.275754 INFO::Bypass z-score application to metadata
2024-05-04 04:59:36.277563 INFO::Running selected transform method: AST
2024-05-04 04:59:36.292732 INFO::Running selected analysis method: LM
2024-05-04 04:59:36.295491 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-05-04 04:59:36.463334 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-05-04 04:59:36.590063 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-05-04 04:59:36.752743 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-05-04 04:59:37.027573 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-05-04 04:59:37.174657 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-05-04 04:59:37.323078 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-05-04 04:59:37.456256 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-05-04 04:59:37.588639 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-05-04 04:59:37.690773 WARNING::Fitting problem for feature 9 a warning was issued
2024-05-04 04:59:37.887396 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-05-04 04:59:38.088883 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-05-04 04:59:38.224905 WARNING::Fitting problem for feature 11 a warning was issued
2024-05-04 04:59:38.363673 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-05-04 04:59:38.533455 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-05-04 04:59:38.733281 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-05-04 04:59:38.940018 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-05-04 04:59:39.159365 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-05-04 04:59:39.320421 WARNING::Fitting problem for feature 16 a warning was issued
2024-05-04 04:59:39.498588 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-05-04 04:59:39.639894 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-05-04 04:59:39.76427 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-05-04 04:59:39.885692 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-05-04 04:59:40.020081 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-05-04 04:59:40.15622 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-05-04 04:59:40.329023 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-05-04 04:59:40.538057 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-05-04 04:59:40.74521 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-05-04 04:59:40.947681 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-05-04 04:59:41.1023 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-05-04 04:59:41.250093 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-05-04 04:59:41.409518 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-05-04 04:59:41.527304 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-05-04 04:59:41.659453 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-05-04 04:59:41.785009 INFO::Fitting model to feature number 32, Prevotella.copri
2024-05-04 04:59:41.925488 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-05-04 04:59:42.04955 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-05-04 04:59:42.221529 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-05-04 04:59:42.427201 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-05-04 04:59:42.653305 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-05-04 04:59:42.818612 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-05-04 04:59:42.993655 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-05-04 04:59:43.178579 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-05-04 04:59:43.385676 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-05-04 04:59:43.581471 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-05-04 04:59:43.781828 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-05-04 04:59:43.93051 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-05-04 04:59:44.057315 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-05-04 04:59:44.199248 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-05-04 04:59:44.419218 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-05-04 04:59:44.62689 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-05-04 04:59:44.816452 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-05-04 04:59:44.974645 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-05-04 04:59:45.092433 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-05-04 04:59:45.247331 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-05-04 04:59:45.391324 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-05-04 04:59:45.511484 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-05-04 04:59:45.646908 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-05-04 04:59:45.804743 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-05-04 04:59:45.952005 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-05-04 04:59:46.126205 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-05-04 04:59:46.284131 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-05-04 04:59:46.430875 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-05-04 04:59:46.567595 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-05-04 04:59:46.739542 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-05-04 04:59:46.88452 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-05-04 04:59:47.097243 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-05-04 04:59:47.282484 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-05-04 04:59:47.452453 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-05-04 04:59:47.599139 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-05-04 04:59:47.737218 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-05-04 04:59:47.879724 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-05-04 04:59:48.069988 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-05-04 04:59:48.271188 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-05-04 04:59:48.483753 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-05-04 04:59:48.536024 WARNING::Fitting problem for feature 72 a warning was issued
2024-05-04 04:59:48.659192 INFO::Fitting model to feature number 73, Dialister.invisus
2024-05-04 04:59:48.796619 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-05-04 04:59:48.928697 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-05-04 04:59:49.062011 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-05-04 04:59:49.203092 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-05-04 04:59:49.32386 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-05-04 04:59:49.462356 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-05-04 04:59:49.590613 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-05-04 04:59:49.725043 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-05-04 04:59:49.870649 INFO::Fitting model to feature number 82, Escherichia.coli
2024-05-04 04:59:50.032681 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-05-04 04:59:50.22227 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-05-04 04:59:50.439072 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-05-04 04:59:50.639911 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-05-04 04:59:50.861153 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-05-04 04:59:51.106978 INFO::Counting total values for each feature
2024-05-04 04:59:51.142131 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-05-04 04:59:51.470158 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-05-04 04:59:51.772134 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-05-04 04:59:52.103701 INFO::Writing residuals to file output2/fits/residuals.rds
2024-05-04 04:59:52.179558 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-05-04 04:59:52.472314 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-05-04 04:59:52.482987 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-05-04 04:59:52.503099 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output2/significant_results.tsv
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
  35.45    1.07   36.56 

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2108.06 7.37115.70