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This page was generated on 2023-11-02 11:40:52 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
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 1124/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.16.0  (landing page)
Lauren McIver
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_18
git_last_commit: 0ab531d
git_last_commit_date: 2023-10-24 11:15:22 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 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
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for Maaslin2 on kunpeng2


To the developers/maintainers of the Maaslin2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Maaslin2.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: Maaslin2
Version: 1.16.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings Maaslin2_1.16.0.tar.gz
StartedAt: 2023-11-02 11:45:34 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 11:49:07 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 212.9 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings Maaslin2_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/Maaslin2.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.16.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Maaslin2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
maaslin2_association_plots: no visible binding for global variable
  ‘xnames’
Undefined global functions or variables:
  xnames
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
Maaslin2 120.753  3.332 127.846
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘Maaslin2’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in checkMatrixPackageVersion() :
  Package version inconsistency detected.
TMB was built with Matrix version 1.6.0
Current Matrix version is 1.6.1.1
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
** 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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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"
2023-11-02 11:48:20.492179 INFO::Writing function arguments to log file
2023-11-02 11:48:20.544749 INFO::Verifying options selected are valid
2023-11-02 11:48:20.595421 INFO::Determining format of input files
2023-11-02 11:48:20.597169 INFO::Input format is data samples as rows and metadata samples as rows
2023-11-02 11:48:20.604129 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2023-11-02 11:48:20.605835 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2023-11-02 11:48:20.609142 INFO::Filter data based on min abundance and min prevalence
2023-11-02 11:48:20.610368 INFO::Total samples in data: 1595
2023-11-02 11:48:20.611593 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2023-11-02 11:48:20.62114 INFO::Total filtered features: 0
2023-11-02 11:48:20.622587 INFO::Filtered feature names from abundance and prevalence filtering:
2023-11-02 11:48:20.653703 INFO::Total filtered features with variance filtering: 0
2023-11-02 11:48:20.655173 INFO::Filtered feature names from variance filtering:
2023-11-02 11:48:20.656321 INFO::Running selected normalization method: TSS
2023-11-02 11:48:22.187104 INFO::Bypass z-score application to metadata
2023-11-02 11:48:22.188557 INFO::Running selected transform method: AST
2023-11-02 11:48:22.212261 INFO::Running selected analysis method: LM
2023-11-02 11:48:22.979808 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2023-11-02 11:48:23.446046 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2023-11-02 11:48:23.693844 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2023-11-02 11:48:23.915085 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2023-11-02 11:48:24.139857 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2023-11-02 11:48:24.362129 INFO::Fitting model to feature number 6, Bacteroides.caccae
2023-11-02 11:48:24.865937 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2023-11-02 11:48:25.079865 INFO::Fitting model to feature number 8, Bacteroides.dorei
2023-11-02 11:48:25.263207 WARNING::Fitting problem for feature 8 a warning was issued
2023-11-02 11:48:25.511548 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2023-11-02 11:48:25.687842 WARNING::Fitting problem for feature 9 a warning was issued
2023-11-02 11:48:25.925175 INFO::Fitting model to feature number 10, Bacteroides.faecis
2023-11-02 11:48:26.141042 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2023-11-02 11:48:26.393437 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2023-11-02 11:48:26.628004 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2023-11-02 11:48:26.861323 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2023-11-02 11:48:27.09989 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2023-11-02 11:48:27.343807 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2023-11-02 11:48:27.585271 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2023-11-02 11:48:27.828629 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2023-11-02 11:48:28.073393 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2023-11-02 11:48:28.288146 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2023-11-02 11:48:28.515806 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2023-11-02 11:48:28.75797 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2023-11-02 11:48:28.988268 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2023-11-02 11:48:29.209217 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2023-11-02 11:48:29.447464 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2023-11-02 11:48:29.682755 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2023-11-02 11:48:29.905524 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2023-11-02 11:48:30.170449 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2023-11-02 11:48:30.404515 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2023-11-02 11:48:30.64326 INFO::Fitting model to feature number 30, Paraprevotella.clara
2023-11-02 11:48:30.874675 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2023-11-02 11:48:31.112766 INFO::Fitting model to feature number 32, Prevotella.copri
2023-11-02 11:48:31.339244 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2023-11-02 11:48:31.586356 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2023-11-02 11:48:31.808255 INFO::Fitting model to feature number 35, Alistipes.putredinis
2023-11-02 11:48:32.051922 INFO::Fitting model to feature number 36, Alistipes.shahii
2023-11-02 11:48:32.273925 INFO::Fitting model to feature number 37, Alistipes.unclassified
2023-11-02 11:48:32.501078 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2023-11-02 11:48:32.734699 INFO::Fitting model to feature number 39, Clostridium.bolteae
2023-11-02 11:48:32.954419 INFO::Fitting model to feature number 40, Clostridium.citroniae
2023-11-02 11:48:33.18513 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2023-11-02 11:48:33.422712 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2023-11-02 11:48:33.657429 INFO::Fitting model to feature number 43, Clostridium.leptum
2023-11-02 11:48:33.88979 INFO::Fitting model to feature number 44, Clostridium.nexile
2023-11-02 11:48:34.107298 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2023-11-02 11:48:34.347764 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2023-11-02 11:48:34.589035 INFO::Fitting model to feature number 47, Eubacterium.eligens
2023-11-02 11:48:34.830728 INFO::Fitting model to feature number 48, Eubacterium.hallii
2023-11-02 11:48:35.051279 INFO::Fitting model to feature number 49, Eubacterium.rectale
2023-11-02 11:48:35.277353 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2023-11-02 11:48:35.511044 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2023-11-02 11:48:35.737129 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2023-11-02 11:48:35.989302 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2023-11-02 11:48:36.255126 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2023-11-02 11:48:36.496483 INFO::Fitting model to feature number 55, Ruminococcus.torques
2023-11-02 11:48:36.732218 INFO::Fitting model to feature number 56, Coprococcus.comes
2023-11-02 11:48:36.985408 INFO::Fitting model to feature number 57, Dorea.longicatena
2023-11-02 11:48:37.213407 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2023-11-02 11:48:37.446984 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2023-11-02 11:48:37.679796 INFO::Fitting model to feature number 60, Roseburia.hominis
2023-11-02 11:48:37.897222 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2023-11-02 11:48:38.133362 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2023-11-02 11:48:38.389745 INFO::Fitting model to feature number 63, Roseburia.unclassified
2023-11-02 11:48:38.617455 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2023-11-02 11:48:38.843682 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2023-11-02 11:48:39.080427 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2023-11-02 11:48:39.305613 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2023-11-02 11:48:39.482614 WARNING::Fitting problem for feature 67 a warning was issued
2023-11-02 11:48:39.704682 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2023-11-02 11:48:39.951649 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2023-11-02 11:48:40.191644 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2023-11-02 11:48:40.432242 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2023-11-02 11:48:40.665082 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2023-11-02 11:48:40.888094 INFO::Fitting model to feature number 73, Dialister.invisus
2023-11-02 11:48:41.108607 INFO::Fitting model to feature number 74, Veillonella.atypica
2023-11-02 11:48:41.348551 INFO::Fitting model to feature number 75, Veillonella.dispar
2023-11-02 11:48:41.581357 INFO::Fitting model to feature number 76, Veillonella.parvula
2023-11-02 11:48:41.816425 INFO::Fitting model to feature number 77, Veillonella.unclassified
2023-11-02 11:48:42.054388 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2023-11-02 11:48:42.295067 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2023-11-02 11:48:42.539091 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2023-11-02 11:48:42.762288 INFO::Fitting model to feature number 81, Bilophila.unclassified
2023-11-02 11:48:43.00716 INFO::Fitting model to feature number 82, Escherichia.coli
2023-11-02 11:48:43.252189 INFO::Fitting model to feature number 83, Escherichia.unclassified
2023-11-02 11:48:43.478076 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2023-11-02 11:48:43.697017 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2023-11-02 11:48:43.954863 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2023-11-02 11:48:44.186851 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2023-11-02 11:48:44.505111 INFO::Counting total values for each feature
2023-11-02 11:48:44.555639 INFO::Writing filtered data to file output/features/filtered_data.tsv
2023-11-02 11:48:44.680395 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2023-11-02 11:48:44.808122 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2023-11-02 11:48:44.939728 INFO::Writing residuals to file output/fits/residuals.rds
2023-11-02 11:48:44.990136 INFO::Writing fitted values to file output/fits/fitted.rds
2023-11-02 11:48:45.017118 INFO::Writing extracted random effects to file output/fits/ranef.rds
2023-11-02 11:48:45.023501 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2023-11-02 11:48:45.030721 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"
2023-11-02 11:48:45.049338 INFO::Writing function arguments to log file
2023-11-02 11:48:45.057662 INFO::Verifying options selected are valid
2023-11-02 11:48:45.059113 INFO::Determining format of input files
2023-11-02 11:48:45.060658 INFO::Input format is data samples as rows and metadata samples as rows
2023-11-02 11:48:45.068167 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2023-11-02 11:48:45.069813 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2023-11-02 11:48:45.072211 INFO::Filter data based on min abundance and min prevalence
2023-11-02 11:48:45.073509 INFO::Total samples in data: 1595
2023-11-02 11:48:45.074758 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2023-11-02 11:48:45.097105 INFO::Total filtered features: 0
2023-11-02 11:48:45.099001 INFO::Filtered feature names from abundance and prevalence filtering:
2023-11-02 11:48:45.132471 INFO::Total filtered features with variance filtering: 0
2023-11-02 11:48:45.134251 INFO::Filtered feature names from variance filtering:
2023-11-02 11:48:45.135684 INFO::Running selected normalization method: NONE
2023-11-02 11:48:45.136928 INFO::Bypass z-score application to metadata
2023-11-02 11:48:45.138177 INFO::Running selected transform method: AST
2023-11-02 11:48:45.162745 INFO::Running selected analysis method: LM
2023-11-02 11:48:45.164943 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2023-11-02 11:48:45.401039 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2023-11-02 11:48:45.624166 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2023-11-02 11:48:45.855121 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2023-11-02 11:48:46.082293 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2023-11-02 11:48:46.30679 INFO::Fitting model to feature number 6, Bacteroides.caccae
2023-11-02 11:48:46.531215 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2023-11-02 11:48:46.758423 INFO::Fitting model to feature number 8, Bacteroides.dorei
2023-11-02 11:48:46.983233 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2023-11-02 11:48:47.203314 INFO::Fitting model to feature number 10, Bacteroides.faecis
2023-11-02 11:48:47.732583 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2023-11-02 11:48:47.951312 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2023-11-02 11:48:48.161369 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2023-11-02 11:48:48.378013 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2023-11-02 11:48:48.608195 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2023-11-02 11:48:48.832478 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2023-11-02 11:48:49.008506 WARNING::Fitting problem for feature 16 a warning was issued
2023-11-02 11:48:49.234454 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2023-11-02 11:48:49.452984 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2023-11-02 11:48:49.666188 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2023-11-02 11:48:49.831732 WARNING::Fitting problem for feature 19 a warning was issued
2023-11-02 11:48:50.049568 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2023-11-02 11:48:50.261631 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2023-11-02 11:48:50.477255 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2023-11-02 11:48:50.690199 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2023-11-02 11:48:50.903592 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2023-11-02 11:48:51.118526 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2023-11-02 11:48:51.33119 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2023-11-02 11:48:51.550781 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2023-11-02 11:48:51.762712 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2023-11-02 11:48:51.967098 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2023-11-02 11:48:52.16862 INFO::Fitting model to feature number 30, Paraprevotella.clara
2023-11-02 11:48:52.387578 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2023-11-02 11:48:52.598097 INFO::Fitting model to feature number 32, Prevotella.copri
2023-11-02 11:48:52.815648 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2023-11-02 11:48:53.040848 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2023-11-02 11:48:53.250839 INFO::Fitting model to feature number 35, Alistipes.putredinis
2023-11-02 11:48:53.464004 INFO::Fitting model to feature number 36, Alistipes.shahii
2023-11-02 11:48:53.675118 INFO::Fitting model to feature number 37, Alistipes.unclassified
2023-11-02 11:48:53.90632 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2023-11-02 11:48:54.129663 INFO::Fitting model to feature number 39, Clostridium.bolteae
2023-11-02 11:48:54.338625 INFO::Fitting model to feature number 40, Clostridium.citroniae
2023-11-02 11:48:54.570021 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2023-11-02 11:48:54.78837 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2023-11-02 11:48:55.003193 INFO::Fitting model to feature number 43, Clostridium.leptum
2023-11-02 11:48:55.230947 INFO::Fitting model to feature number 44, Clostridium.nexile
2023-11-02 11:48:55.465219 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2023-11-02 11:48:55.679374 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2023-11-02 11:48:55.906674 INFO::Fitting model to feature number 47, Eubacterium.eligens
2023-11-02 11:48:56.125781 INFO::Fitting model to feature number 48, Eubacterium.hallii
2023-11-02 11:48:56.344534 INFO::Fitting model to feature number 49, Eubacterium.rectale
2023-11-02 11:48:56.563683 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2023-11-02 11:48:56.776623 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2023-11-02 11:48:56.992044 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2023-11-02 11:48:57.192886 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2023-11-02 11:48:57.392207 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2023-11-02 11:48:57.610296 INFO::Fitting model to feature number 55, Ruminococcus.torques
2023-11-02 11:48:57.824652 INFO::Fitting model to feature number 56, Coprococcus.comes
2023-11-02 11:48:58.040897 INFO::Fitting model to feature number 57, Dorea.longicatena
2023-11-02 11:48:58.267217 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2023-11-02 11:48:58.486115 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2023-11-02 11:48:58.703041 INFO::Fitting model to feature number 60, Roseburia.hominis
2023-11-02 11:48:58.920311 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2023-11-02 11:48:59.131322 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2023-11-02 11:48:59.351947 INFO::Fitting model to feature number 63, Roseburia.unclassified
2023-11-02 11:48:59.567988 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2023-11-02 11:48:59.786901 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2023-11-02 11:49:00.021048 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2023-11-02 11:49:00.237053 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2023-11-02 11:49:00.456616 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2023-11-02 11:49:00.681856 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2023-11-02 11:49:00.903749 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2023-11-02 11:49:01.12673 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2023-11-02 11:49:01.348245 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2023-11-02 11:49:01.422868 WARNING::Fitting problem for feature 72 a warning was issued
2023-11-02 11:49:01.635108 INFO::Fitting model to feature number 73, Dialister.invisus
2023-11-02 11:49:01.858788 INFO::Fitting model to feature number 74, Veillonella.atypica
2023-11-02 11:49:02.073556 INFO::Fitting model to feature number 75, Veillonella.dispar
2023-11-02 11:49:02.296243 INFO::Fitting model to feature number 76, Veillonella.parvula
2023-11-02 11:49:02.513687 INFO::Fitting model to feature number 77, Veillonella.unclassified
2023-11-02 11:49:02.733738 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2023-11-02 11:49:02.950908 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2023-11-02 11:49:03.175838 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2023-11-02 11:49:03.408525 INFO::Fitting model to feature number 81, Bilophila.unclassified
2023-11-02 11:49:03.635037 INFO::Fitting model to feature number 82, Escherichia.coli
2023-11-02 11:49:03.853503 INFO::Fitting model to feature number 83, Escherichia.unclassified
2023-11-02 11:49:04.054979 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2023-11-02 11:49:04.271559 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2023-11-02 11:49:04.482589 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2023-11-02 11:49:04.715645 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2023-11-02 11:49:04.979094 INFO::Counting total values for each feature
2023-11-02 11:49:05.01588 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2023-11-02 11:49:05.141095 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2023-11-02 11:49:05.265608 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2023-11-02 11:49:05.398026 INFO::Writing residuals to file output2/fits/residuals.rds
2023-11-02 11:49:05.466347 INFO::Writing fitted values to file output2/fits/fitted.rds
2023-11-02 11:49:05.534146 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2023-11-02 11:49:05.540364 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2023-11-02 11:49:05.562181 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 6 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 45.877   0.487  46.622

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2120.753 3.332127.846