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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 1106/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.19.0  (landing page)
Lauren McIver
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: devel
git_last_commit: 2f9ea7a
git_last_commit_date: 2024-04-30 11:16:06 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for Maaslin2 on palomino4

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: 2024-06-10 04:39:47 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 04:44:42 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 294.9 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 4.4.0 RC (2024-04-16 r86468 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 95.47   7.84  103.72
* 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 4.4.0 RC (2024-04-16 r86468 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"
2024-06-10 04:43:55.110331 INFO::Writing function arguments to log file
2024-06-10 04:43:55.179553 INFO::Verifying options selected are valid
2024-06-10 04:43:55.22112 INFO::Determining format of input files
2024-06-10 04:43:55.223588 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-10 04:43:55.238177 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-10 04:43:55.240527 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-06-10 04:43:55.24399 INFO::Filter data based on min abundance and min prevalence
2024-06-10 04:43:55.245899 INFO::Total samples in data: 1595
2024-06-10 04:43:55.247865 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-10 04:43:55.25427 INFO::Total filtered features: 0
2024-06-10 04:43:55.257037 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-10 04:43:55.267343 INFO::Total filtered features with variance filtering: 0
2024-06-10 04:43:55.269565 INFO::Filtered feature names from variance filtering:
2024-06-10 04:43:55.271513 INFO::Running selected normalization method: TSS
2024-06-10 04:43:57.28816 INFO::Bypass z-score application to metadata
2024-06-10 04:43:57.290524 INFO::Running selected transform method: AST
2024-06-10 04:43:57.318208 INFO::Running selected analysis method: LM
2024-06-10 04:43:57.722325 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-10 04:43:58.385172 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-10 04:43:58.546103 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-10 04:43:58.687386 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-10 04:43:58.825266 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-10 04:43:58.959466 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-10 04:43:59.086674 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-10 04:43:59.300244 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-10 04:43:59.504821 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-10 04:43:59.708678 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-10 04:43:59.906462 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-10 04:44:00.03351 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-10 04:44:00.173079 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-10 04:44:00.348447 WARNING::Fitting problem for feature 13 a warning was issued
2024-06-10 04:44:00.497001 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-10 04:44:00.64339 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-10 04:44:00.801074 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-10 04:44:00.967857 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-10 04:44:01.200576 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-10 04:44:01.335334 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-10 04:44:01.471227 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-10 04:44:01.598832 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-10 04:44:01.750418 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-10 04:44:01.883237 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-10 04:44:02.01951 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-10 04:44:02.155557 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-10 04:44:02.298528 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-10 04:44:02.427397 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-10 04:44:02.581456 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-10 04:44:02.781381 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-10 04:44:02.999029 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-10 04:44:03.15265 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-10 04:44:03.318176 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-10 04:44:03.457357 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-10 04:44:03.59372 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-10 04:44:03.730996 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-10 04:44:03.85435 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-10 04:44:04.004589 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-10 04:44:04.338334 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-10 04:44:04.464159 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-10 04:44:04.600743 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-10 04:44:04.771242 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-10 04:44:04.895008 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-10 04:44:05.02327 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-10 04:44:05.155874 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-10 04:44:05.282624 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-10 04:44:05.406283 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-10 04:44:05.540884 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-10 04:44:05.685476 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-10 04:44:05.847713 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-10 04:44:05.990205 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-10 04:44:06.155554 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-10 04:44:06.281514 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-10 04:44:06.414729 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-10 04:44:06.555091 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-10 04:44:06.673437 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-10 04:44:06.802424 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-10 04:44:06.962365 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-10 04:44:07.090874 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-10 04:44:07.294779 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-10 04:44:07.483585 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-10 04:44:07.660433 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-10 04:44:07.797401 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-10 04:44:07.983737 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-10 04:44:08.173227 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-10 04:44:08.31115 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-10 04:44:08.506548 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-10 04:44:08.694096 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-10 04:44:08.810017 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-10 04:44:08.955092 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-10 04:44:09.119767 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-10 04:44:09.269408 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-10 04:44:09.431122 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-10 04:44:09.577328 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-10 04:44:09.739974 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-10 04:44:09.90027 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-10 04:44:10.034056 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-10 04:44:10.165953 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-10 04:44:10.302435 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-10 04:44:10.482373 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-10 04:44:10.696204 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-10 04:44:10.911594 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-10 04:44:11.041881 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-10 04:44:11.188188 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-10 04:44:11.308997 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-10 04:44:11.433511 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-10 04:44:11.567248 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-10 04:44:11.708822 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-10 04:44:11.936232 INFO::Counting total values for each feature
2024-06-10 04:44:11.971174 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-06-10 04:44:12.330681 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-06-10 04:44:12.799111 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-06-10 04:44:13.277157 INFO::Writing residuals to file output/fits/residuals.rds
2024-06-10 04:44:13.322377 INFO::Writing fitted values to file output/fits/fitted.rds
2024-06-10 04:44:13.557412 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-06-10 04:44:13.564889 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-06-10 04:44:13.587702 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output/significant_results.tsv
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2024-06-10 04:44:13.629071 INFO::Writing function arguments to log file
2024-06-10 04:44:13.652301 INFO::Verifying options selected are valid
2024-06-10 04:44:13.654226 INFO::Determining format of input files
2024-06-10 04:44:13.656366 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-10 04:44:13.663415 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-10 04:44:13.6655 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-06-10 04:44:13.668138 INFO::Filter data based on min abundance and min prevalence
2024-06-10 04:44:13.67003 INFO::Total samples in data: 1595
2024-06-10 04:44:13.671794 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-10 04:44:13.677192 INFO::Total filtered features: 0
2024-06-10 04:44:13.679096 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-10 04:44:13.690918 INFO::Total filtered features with variance filtering: 0
2024-06-10 04:44:13.694163 INFO::Filtered feature names from variance filtering:
2024-06-10 04:44:13.697063 INFO::Running selected normalization method: NONE
2024-06-10 04:44:13.699934 INFO::Bypass z-score application to metadata
2024-06-10 04:44:13.702782 INFO::Running selected transform method: AST
2024-06-10 04:44:13.728999 INFO::Running selected analysis method: LM
2024-06-10 04:44:13.733041 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-10 04:44:13.913396 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-10 04:44:14.085538 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-10 04:44:14.233819 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-10 04:44:14.364451 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-10 04:44:14.489966 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-10 04:44:14.655899 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-10 04:44:14.796473 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-10 04:44:14.917949 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-10 04:44:15.017841 WARNING::Fitting problem for feature 9 a warning was issued
2024-06-10 04:44:15.159445 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-10 04:44:15.288982 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-10 04:44:15.396828 WARNING::Fitting problem for feature 11 a warning was issued
2024-06-10 04:44:15.538091 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-10 04:44:15.658052 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-10 04:44:15.787498 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-10 04:44:16.137576 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-10 04:44:16.330647 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-10 04:44:16.447604 WARNING::Fitting problem for feature 16 a warning was issued
2024-06-10 04:44:16.574606 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-10 04:44:16.723296 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-10 04:44:16.842266 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-10 04:44:16.95999 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-10 04:44:17.090441 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-10 04:44:17.244094 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-10 04:44:17.386038 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-10 04:44:17.532171 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-10 04:44:17.654412 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-10 04:44:17.78084 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-10 04:44:17.89792 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-10 04:44:18.019666 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-10 04:44:18.13462 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-10 04:44:18.310935 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-10 04:44:18.503219 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-10 04:44:18.702553 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-10 04:44:18.917929 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-10 04:44:19.104288 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-10 04:44:19.302694 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-10 04:44:19.50961 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-10 04:44:19.680222 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-10 04:44:19.850847 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-10 04:44:20.02608 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-10 04:44:20.188154 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-10 04:44:20.320581 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-10 04:44:20.44673 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-10 04:44:20.56788 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-10 04:44:20.706426 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-10 04:44:20.828202 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-10 04:44:20.949032 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-10 04:44:21.074995 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-10 04:44:21.20962 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-10 04:44:21.344139 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-10 04:44:21.475971 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-10 04:44:21.644684 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-10 04:44:21.76782 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-10 04:44:21.880513 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-10 04:44:21.994274 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-10 04:44:22.12077 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-10 04:44:22.259353 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-10 04:44:22.381011 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-10 04:44:22.508632 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-10 04:44:22.624619 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-10 04:44:22.746829 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-10 04:44:22.875531 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-10 04:44:23.010568 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-10 04:44:23.133298 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-10 04:44:23.279409 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-10 04:44:23.40656 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-10 04:44:23.532842 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-10 04:44:23.672136 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-10 04:44:23.863815 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-10 04:44:24.048186 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-10 04:44:24.252269 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-10 04:44:24.405736 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-10 04:44:24.524908 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-10 04:44:24.581455 WARNING::Fitting problem for feature 72 a warning was issued
2024-06-10 04:44:24.711201 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-10 04:44:24.836169 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-10 04:44:24.968839 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-10 04:44:25.098139 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-10 04:44:25.24027 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-10 04:44:25.355642 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-10 04:44:25.472896 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-10 04:44:25.605835 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-10 04:44:25.729262 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-10 04:44:25.860616 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-10 04:44:26.031866 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-10 04:44:26.228212 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-10 04:44:26.343481 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-10 04:44:26.467557 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-10 04:44:26.589768 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-10 04:44:26.761345 INFO::Counting total values for each feature
2024-06-10 04:44:26.792672 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-06-10 04:44:27.091231 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-06-10 04:44:27.414912 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-06-10 04:44:27.854798 INFO::Writing residuals to file output2/fits/residuals.rds
2024-06-10 04:44:27.931375 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-06-10 04:44:28.002196 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-06-10 04:44:28.012222 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-06-10 04:44:28.025889 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 
  32.40    4.68   37.01

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2 95.47 7.84103.72