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This page was generated on 2024-07-16 11:45 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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: 2024-07-15 14:00 -0400 (Mon, 15 Jul 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    OK    OK    OK  
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
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

CHECK results for Maaslin2 on palomino8

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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Maaslin2_1.19.0.tar.gz
StartedAt: 2024-07-16 01:42:52 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 01:46:22 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 209.8 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Maaslin2_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck'
* using R version 4.4.1 (2024-06-14 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 '1.19.0'
* 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 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 112.54   7.25  120.17
* 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-3.20-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
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"
2024-07-16 01:45:33.395994 INFO::Writing function arguments to log file
2024-07-16 01:45:33.473532 INFO::Verifying options selected are valid
2024-07-16 01:45:33.580283 INFO::Determining format of input files
2024-07-16 01:45:33.583896 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-16 01:45:33.605249 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-16 01:45:33.609009 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-07-16 01:45:33.61463 INFO::Filter data based on min abundance and min prevalence
2024-07-16 01:45:33.617606 INFO::Total samples in data: 1595
2024-07-16 01:45:33.620397 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-16 01:45:33.628264 INFO::Total filtered features: 0
2024-07-16 01:45:33.630361 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-16 01:45:33.640214 INFO::Total filtered features with variance filtering: 0
2024-07-16 01:45:33.642394 INFO::Filtered feature names from variance filtering:
2024-07-16 01:45:33.64426 INFO::Running selected normalization method: TSS
2024-07-16 01:45:35.495716 INFO::Bypass z-score application to metadata
2024-07-16 01:45:35.497896 INFO::Running selected transform method: AST
2024-07-16 01:45:35.516073 INFO::Running selected analysis method: LM
2024-07-16 01:45:36.593474 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-16 01:45:37.246041 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-16 01:45:37.448784 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-16 01:45:37.657165 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-16 01:45:37.7967 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-16 01:45:37.940553 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-16 01:45:38.10757 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-16 01:45:38.326009 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-16 01:45:38.463319 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-16 01:45:38.664986 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-16 01:45:38.908386 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-16 01:45:39.107819 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-16 01:45:39.315086 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-16 01:45:39.469491 WARNING::Fitting problem for feature 13 a warning was issued
2024-07-16 01:45:39.699408 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-16 01:45:39.914054 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-16 01:45:40.112202 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-16 01:45:40.260314 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-16 01:45:40.434146 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-16 01:45:40.63963 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-16 01:45:40.854383 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-16 01:45:41.060917 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-16 01:45:41.198879 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-16 01:45:41.387824 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-16 01:45:41.602362 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-16 01:45:41.847 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-16 01:45:42.028365 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-16 01:45:42.243714 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-16 01:45:42.463633 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-16 01:45:42.615702 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-16 01:45:42.830188 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-16 01:45:43.07211 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-16 01:45:43.29384 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-16 01:45:43.757629 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-16 01:45:43.917503 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-16 01:45:44.115372 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-16 01:45:44.584715 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-16 01:45:44.727945 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-16 01:45:44.908504 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-16 01:45:45.088632 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-16 01:45:45.266934 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-16 01:45:45.427814 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-16 01:45:45.639702 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-16 01:45:45.85899 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-16 01:45:46.066325 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-16 01:45:46.278819 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-16 01:45:46.513157 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-16 01:45:46.698611 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-16 01:45:46.885275 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-16 01:45:47.024059 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-16 01:45:47.147827 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-16 01:45:47.28073 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-16 01:45:47.766846 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-16 01:45:47.989623 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-16 01:45:48.162918 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-16 01:45:48.291702 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-16 01:45:48.457006 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-16 01:45:48.638196 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-16 01:45:48.810316 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-16 01:45:48.964861 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-16 01:45:49.125781 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-16 01:45:49.297803 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-16 01:45:49.448543 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-16 01:45:49.621848 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-16 01:45:49.753997 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-16 01:45:49.961966 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-16 01:45:50.134943 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-16 01:45:50.317726 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-16 01:45:50.495032 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-16 01:45:50.682054 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-16 01:45:50.863732 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-16 01:45:51.058914 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-16 01:45:51.2013 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-16 01:45:51.348803 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-16 01:45:51.562409 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-16 01:45:51.722479 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-16 01:45:51.8765 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-16 01:45:52.041581 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-16 01:45:52.274083 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-16 01:45:52.495462 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-16 01:45:52.677649 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-16 01:45:52.831482 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-16 01:45:52.971214 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-16 01:45:53.161027 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-16 01:45:53.323904 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-16 01:45:53.46293 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-16 01:45:53.599874 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-16 01:45:53.82424 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-16 01:45:54.094566 INFO::Counting total values for each feature
2024-07-16 01:45:54.153691 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-07-16 01:45:54.620675 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-07-16 01:45:55.135412 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-07-16 01:45:55.531596 INFO::Writing residuals to file output/fits/residuals.rds
2024-07-16 01:45:55.863222 INFO::Writing fitted values to file output/fits/fitted.rds
2024-07-16 01:45:55.898894 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-07-16 01:45:55.909011 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-07-16 01:45:55.935113 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"
2024-07-16 01:45:55.978883 INFO::Writing function arguments to log file
2024-07-16 01:45:56.002223 INFO::Verifying options selected are valid
2024-07-16 01:45:56.005122 INFO::Determining format of input files
2024-07-16 01:45:56.008182 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-16 01:45:56.018712 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-16 01:45:56.021858 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-07-16 01:45:56.025807 INFO::Filter data based on min abundance and min prevalence
2024-07-16 01:45:56.028565 INFO::Total samples in data: 1595
2024-07-16 01:45:56.031297 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-16 01:45:56.038931 INFO::Total filtered features: 0
2024-07-16 01:45:56.041979 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-16 01:45:56.053485 INFO::Total filtered features with variance filtering: 0
2024-07-16 01:45:56.056574 INFO::Filtered feature names from variance filtering:
2024-07-16 01:45:56.059255 INFO::Running selected normalization method: NONE
2024-07-16 01:45:56.062039 INFO::Bypass z-score application to metadata
2024-07-16 01:45:56.064716 INFO::Running selected transform method: AST
2024-07-16 01:45:56.085983 INFO::Running selected analysis method: LM
2024-07-16 01:45:56.08859 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-16 01:45:56.253577 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-16 01:45:56.474786 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-16 01:45:56.668096 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-16 01:45:56.830125 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-16 01:45:57.026366 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-16 01:45:57.223456 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-16 01:45:57.422169 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-16 01:45:57.616539 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-16 01:45:57.792195 WARNING::Fitting problem for feature 9 a warning was issued
2024-07-16 01:45:57.967751 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-16 01:45:58.129698 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-16 01:45:58.32098 WARNING::Fitting problem for feature 11 a warning was issued
2024-07-16 01:45:58.517142 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-16 01:45:58.713282 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-16 01:45:58.926686 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-16 01:45:59.12357 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-16 01:45:59.300946 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-16 01:45:59.46155 WARNING::Fitting problem for feature 16 a warning was issued
2024-07-16 01:45:59.667672 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-16 01:45:59.871605 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-16 01:46:00.087357 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-16 01:46:00.268851 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-16 01:46:00.407374 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-16 01:46:00.546556 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-16 01:46:00.677164 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-16 01:46:00.812994 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-16 01:46:00.941072 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-16 01:46:01.065262 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-16 01:46:01.198911 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-16 01:46:01.356521 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-16 01:46:01.512972 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-16 01:46:01.667132 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-16 01:46:01.85962 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-16 01:46:02.063297 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-16 01:46:02.227312 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-16 01:46:02.438617 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-16 01:46:02.599193 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-16 01:46:02.780859 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-16 01:46:02.97019 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-16 01:46:03.179107 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-16 01:46:03.387944 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-16 01:46:03.576499 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-16 01:46:03.758242 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-16 01:46:03.884436 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-16 01:46:04.076463 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-16 01:46:04.256483 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-16 01:46:04.45649 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-16 01:46:04.621623 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-16 01:46:04.823671 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-16 01:46:05.003612 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-16 01:46:05.132183 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-16 01:46:05.289028 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-16 01:46:05.420703 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-16 01:46:05.544234 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-16 01:46:05.692184 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-16 01:46:05.820129 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-16 01:46:05.971804 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-16 01:46:06.106017 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-16 01:46:06.238903 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-16 01:46:06.366723 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-16 01:46:06.525681 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-16 01:46:06.716624 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-16 01:46:06.884846 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-16 01:46:07.090978 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-16 01:46:07.247373 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-16 01:46:07.406247 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-16 01:46:07.537712 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-16 01:46:07.718595 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-16 01:46:07.884547 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-16 01:46:08.074314 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-16 01:46:08.254744 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-16 01:46:08.41546 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-16 01:46:08.615235 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-16 01:46:08.739045 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-16 01:46:08.793465 WARNING::Fitting problem for feature 72 a warning was issued
2024-07-16 01:46:08.998441 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-16 01:46:09.239065 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-16 01:46:09.427519 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-16 01:46:09.620035 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-16 01:46:09.797604 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-16 01:46:09.932743 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-16 01:46:10.128042 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-16 01:46:10.338332 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-16 01:46:10.538582 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-16 01:46:10.745828 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-16 01:46:10.941214 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-16 01:46:11.117093 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-16 01:46:11.298958 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-16 01:46:11.445164 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-16 01:46:11.631577 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-16 01:46:11.780358 INFO::Counting total values for each feature
2024-07-16 01:46:11.824782 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-07-16 01:46:12.184718 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-07-16 01:46:12.569322 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-07-16 01:46:12.989854 INFO::Writing residuals to file output2/fits/residuals.rds
2024-07-16 01:46:13.052556 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-07-16 01:46:13.110125 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-07-16 01:46:13.116659 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-07-16 01:46:13.129062 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 
  38.81    1.03   41.67

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2112.54 7.25120.17