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This page was generated on 2024-05-22 11:35:49 -0400 (Wed, 22 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 3444
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: 2024-05-21 14:00:15 -0400 (Tue, 21 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
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: 2024-05-22 03:25:55 -0400 (Wed, 22 May 2024)
EndedAt: 2024-05-22 03:29:15 -0400 (Wed, 22 May 2024)
EllapsedTime: 200.0 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 (2024-04-24 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 104.17   7.13  111.78
* 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 (2024-04-24 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"
2024-05-22 03:28:30.120288 INFO::Writing function arguments to log file
2024-05-22 03:28:30.200567 INFO::Verifying options selected are valid
2024-05-22 03:28:30.253238 INFO::Determining format of input files
2024-05-22 03:28:30.25728 INFO::Input format is data samples as rows and metadata samples as rows
2024-05-22 03:28:30.27945 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-05-22 03:28:30.28329 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-05-22 03:28:30.289654 INFO::Filter data based on min abundance and min prevalence
2024-05-22 03:28:30.292783 INFO::Total samples in data: 1595
2024-05-22 03:28:30.295838 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-05-22 03:28:30.303851 INFO::Total filtered features: 0
2024-05-22 03:28:30.307098 INFO::Filtered feature names from abundance and prevalence filtering:
2024-05-22 03:28:30.320065 INFO::Total filtered features with variance filtering: 0
2024-05-22 03:28:30.323461 INFO::Filtered feature names from variance filtering:
2024-05-22 03:28:30.326617 INFO::Running selected normalization method: TSS
2024-05-22 03:28:31.86277 INFO::Bypass z-score application to metadata
2024-05-22 03:28:31.866234 INFO::Running selected transform method: AST
2024-05-22 03:28:31.896272 INFO::Running selected analysis method: LM
2024-05-22 03:28:32.219642 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-05-22 03:28:32.603652 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-05-22 03:28:32.810269 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-05-22 03:28:33.029298 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-05-22 03:28:33.215691 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-05-22 03:28:33.437869 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-05-22 03:28:33.59229 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-05-22 03:28:33.807269 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-05-22 03:28:33.945178 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-05-22 03:28:34.083229 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-05-22 03:28:34.231592 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-05-22 03:28:34.384246 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-05-22 03:28:34.577591 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-05-22 03:28:34.733061 WARNING::Fitting problem for feature 13 a warning was issued
2024-05-22 03:28:34.977366 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-05-22 03:28:35.193861 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-05-22 03:28:35.415353 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-05-22 03:28:35.559763 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-05-22 03:28:35.70948 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-05-22 03:28:35.841999 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-05-22 03:28:36.028624 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-05-22 03:28:36.174058 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-05-22 03:28:36.304052 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-05-22 03:28:36.468201 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-05-22 03:28:36.604939 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-05-22 03:28:36.743143 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-05-22 03:28:36.932323 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-05-22 03:28:37.129334 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-05-22 03:28:37.300146 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-05-22 03:28:37.55913 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-05-22 03:28:37.72025 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-05-22 03:28:37.951481 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-05-22 03:28:38.168086 INFO::Fitting model to feature number 32, Prevotella.copri
2024-05-22 03:28:38.393452 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-05-22 03:28:38.61276 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-05-22 03:28:38.810898 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-05-22 03:28:38.966308 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-05-22 03:28:39.367146 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-05-22 03:28:39.589835 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-05-22 03:28:39.781603 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-05-22 03:28:40.007813 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-05-22 03:28:40.225677 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-05-22 03:28:40.438212 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-05-22 03:28:40.654219 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-05-22 03:28:40.883063 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-05-22 03:28:41.070736 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-05-22 03:28:41.260837 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-05-22 03:28:41.491197 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-05-22 03:28:41.707423 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-05-22 03:28:41.921871 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-05-22 03:28:42.067525 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-05-22 03:28:42.23039 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-05-22 03:28:42.444077 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-05-22 03:28:42.64498 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-05-22 03:28:42.839201 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-05-22 03:28:43.022782 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-05-22 03:28:43.257289 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-05-22 03:28:43.418597 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-05-22 03:28:43.590705 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-05-22 03:28:43.83176 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-05-22 03:28:44.041173 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-05-22 03:28:44.183039 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-05-22 03:28:44.318941 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-05-22 03:28:44.518416 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-05-22 03:28:44.728263 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-05-22 03:28:44.931054 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-05-22 03:28:45.086994 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-05-22 03:28:45.290688 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-05-22 03:28:45.493883 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-05-22 03:28:45.717373 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-05-22 03:28:45.873144 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-05-22 03:28:46.014561 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-05-22 03:28:46.150207 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-05-22 03:28:46.280719 INFO::Fitting model to feature number 73, Dialister.invisus
2024-05-22 03:28:46.415264 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-05-22 03:28:46.557617 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-05-22 03:28:46.696403 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-05-22 03:28:46.853756 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-05-22 03:28:46.986394 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-05-22 03:28:47.126833 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-05-22 03:28:47.273896 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-05-22 03:28:47.419291 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-05-22 03:28:47.616877 INFO::Fitting model to feature number 82, Escherichia.coli
2024-05-22 03:28:47.84721 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-05-22 03:28:48.042002 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-05-22 03:28:48.199805 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-05-22 03:28:48.331887 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-05-22 03:28:48.508172 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-05-22 03:28:48.691415 INFO::Counting total values for each feature
2024-05-22 03:28:48.734962 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-05-22 03:28:49.102488 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-05-22 03:28:49.467292 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-05-22 03:28:49.801722 INFO::Writing residuals to file output/fits/residuals.rds
2024-05-22 03:28:49.848758 INFO::Writing fitted values to file output/fits/fitted.rds
2024-05-22 03:28:49.876419 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-05-22 03:28:49.883225 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-05-22 03:28:49.906614 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"
2024-05-22 03:28:49.942861 INFO::Writing function arguments to log file
2024-05-22 03:28:49.959713 INFO::Verifying options selected are valid
2024-05-22 03:28:49.96161 INFO::Determining format of input files
2024-05-22 03:28:49.963681 INFO::Input format is data samples as rows and metadata samples as rows
2024-05-22 03:28:49.973542 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-05-22 03:28:49.977073 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-05-22 03:28:49.981281 INFO::Filter data based on min abundance and min prevalence
2024-05-22 03:28:49.983471 INFO::Total samples in data: 1595
2024-05-22 03:28:49.985254 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-05-22 03:28:49.991166 INFO::Total filtered features: 0
2024-05-22 03:28:49.993231 INFO::Filtered feature names from abundance and prevalence filtering:
2024-05-22 03:28:50.003138 INFO::Total filtered features with variance filtering: 0
2024-05-22 03:28:50.006005 INFO::Filtered feature names from variance filtering:
2024-05-22 03:28:50.008519 INFO::Running selected normalization method: NONE
2024-05-22 03:28:50.010989 INFO::Bypass z-score application to metadata
2024-05-22 03:28:50.013507 INFO::Running selected transform method: AST
2024-05-22 03:28:50.037446 INFO::Running selected analysis method: LM
2024-05-22 03:28:50.041235 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-05-22 03:28:50.2014 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-05-22 03:28:50.332776 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-05-22 03:28:50.518163 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-05-22 03:28:50.69075 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-05-22 03:28:50.869348 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-05-22 03:28:51.022175 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-05-22 03:28:51.218786 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-05-22 03:28:51.429553 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-05-22 03:28:51.590657 WARNING::Fitting problem for feature 9 a warning was issued
2024-05-22 03:28:51.800687 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-05-22 03:28:52.019663 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-05-22 03:28:52.188447 WARNING::Fitting problem for feature 11 a warning was issued
2024-05-22 03:28:52.350919 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-05-22 03:28:52.505444 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-05-22 03:28:52.633215 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-05-22 03:28:52.77473 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-05-22 03:28:52.967695 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-05-22 03:28:53.130762 WARNING::Fitting problem for feature 16 a warning was issued
2024-05-22 03:28:53.282618 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-05-22 03:28:53.418205 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-05-22 03:28:53.545697 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-05-22 03:28:53.682669 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-05-22 03:28:53.814891 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-05-22 03:28:53.97465 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-05-22 03:28:54.104569 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-05-22 03:28:54.27403 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-05-22 03:28:54.521168 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-05-22 03:28:54.750829 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-05-22 03:28:54.885572 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-05-22 03:28:55.03723 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-05-22 03:28:55.167885 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-05-22 03:28:55.292517 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-05-22 03:28:55.458872 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-05-22 03:28:55.633383 INFO::Fitting model to feature number 32, Prevotella.copri
2024-05-22 03:28:55.842455 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-05-22 03:28:56.046043 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-05-22 03:28:56.235868 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-05-22 03:28:56.431588 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-05-22 03:28:56.639179 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-05-22 03:28:56.85515 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-05-22 03:28:57.079776 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-05-22 03:28:57.271437 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-05-22 03:28:57.406191 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-05-22 03:28:57.531685 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-05-22 03:28:57.669324 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-05-22 03:28:57.806031 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-05-22 03:28:57.968744 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-05-22 03:28:58.139301 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-05-22 03:28:58.31551 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-05-22 03:28:58.465129 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-05-22 03:28:58.592769 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-05-22 03:28:58.745889 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-05-22 03:28:58.882013 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-05-22 03:28:59.032023 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-05-22 03:28:59.148799 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-05-22 03:28:59.314688 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-05-22 03:28:59.481122 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-05-22 03:28:59.625498 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-05-22 03:28:59.772076 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-05-22 03:28:59.961855 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-05-22 03:29:00.179877 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-05-22 03:29:00.387531 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-05-22 03:29:00.589144 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-05-22 03:29:00.757283 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-05-22 03:29:00.899819 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-05-22 03:29:01.046787 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-05-22 03:29:01.198616 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-05-22 03:29:01.377159 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-05-22 03:29:01.559651 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-05-22 03:29:01.751803 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-05-22 03:29:01.902576 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-05-22 03:29:02.124331 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-05-22 03:29:02.336613 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-05-22 03:29:02.524649 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-05-22 03:29:02.572199 WARNING::Fitting problem for feature 72 a warning was issued
2024-05-22 03:29:02.751432 INFO::Fitting model to feature number 73, Dialister.invisus
2024-05-22 03:29:02.897266 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-05-22 03:29:03.026648 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-05-22 03:29:03.168691 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-05-22 03:29:03.549703 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-05-22 03:29:03.673206 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-05-22 03:29:03.801536 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-05-22 03:29:03.938207 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-05-22 03:29:04.140818 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-05-22 03:29:04.275141 INFO::Fitting model to feature number 82, Escherichia.coli
2024-05-22 03:29:04.439349 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-05-22 03:29:04.583018 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-05-22 03:29:04.720331 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-05-22 03:29:04.842621 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-05-22 03:29:05.003883 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-05-22 03:29:05.238203 INFO::Counting total values for each feature
2024-05-22 03:29:05.261346 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-05-22 03:29:05.572611 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-05-22 03:29:05.879825 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-05-22 03:29:06.240301 INFO::Writing residuals to file output2/fits/residuals.rds
2024-05-22 03:29:06.298652 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-05-22 03:29:06.37939 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-05-22 03:29:06.389463 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-05-22 03:29:06.41159 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 
  36.90    0.96   37.95

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2104.17 7.13111.78