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This page was generated on 2024-07-06 11:38 -0400 (Sat, 06 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4643
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4414
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4442
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4391
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 3833
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: 2024-07-05 14:00 -0400 (Fri, 05 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for Maaslin2 on nebbiolo2

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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Maaslin2_1.19.0.tar.gz
StartedAt: 2024-07-06 00:11:33 -0400 (Sat, 06 Jul 2024)
EndedAt: 2024-07-06 00:15:35 -0400 (Sat, 06 Jul 2024)
EllapsedTime: 242.4 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Maaslin2_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 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 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 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 83.573  0.708  84.227
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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"
2024-07-06 00:13:26.77364 INFO::Writing function arguments to log file
2024-07-06 00:13:26.812084 INFO::Verifying options selected are valid
2024-07-06 00:13:26.848973 INFO::Determining format of input files
2024-07-06 00:13:26.850442 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-06 00:13:26.854972 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-06 00:13:26.856251 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-07-06 00:13:26.858698 INFO::Filter data based on min abundance and min prevalence
2024-07-06 00:13:26.85952 INFO::Total samples in data: 1595
2024-07-06 00:13:26.860303 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-06 00:13:26.863982 INFO::Total filtered features: 0
2024-07-06 00:13:26.864947 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-06 00:13:26.880298 INFO::Total filtered features with variance filtering: 0
2024-07-06 00:13:26.881397 INFO::Filtered feature names from variance filtering:
2024-07-06 00:13:26.882207 INFO::Running selected normalization method: TSS
2024-07-06 00:13:28.035165 INFO::Bypass z-score application to metadata
2024-07-06 00:13:28.036456 INFO::Running selected transform method: AST
2024-07-06 00:13:28.052445 INFO::Running selected analysis method: LM
2024-07-06 00:13:28.52692 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-06 00:13:28.871407 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-06 00:13:29.01542 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-06 00:13:29.15917 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-06 00:13:29.328326 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-06 00:13:29.467563 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-06 00:13:29.60666 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-06 00:13:29.745686 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-06 00:13:29.863074 WARNING::Fitting problem for feature 8 a warning was issued
2024-07-06 00:13:30.010835 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-06 00:13:30.120566 WARNING::Fitting problem for feature 9 a warning was issued
2024-07-06 00:13:30.272195 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-06 00:13:30.406505 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-06 00:13:30.546332 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-06 00:13:30.686012 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-06 00:13:30.799969 WARNING::Fitting problem for feature 13 a warning was issued
2024-07-06 00:13:30.9461 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-06 00:13:31.084669 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-06 00:13:31.244074 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-06 00:13:31.379961 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-06 00:13:31.525623 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-06 00:13:31.682478 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-06 00:13:31.828407 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-06 00:13:31.967743 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-06 00:13:32.114124 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-06 00:13:32.267677 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-06 00:13:32.400134 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-06 00:13:32.539029 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-06 00:13:32.68117 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-06 00:13:32.815257 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-06 00:13:32.956576 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-06 00:13:33.102075 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-06 00:13:33.249158 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-06 00:13:33.387712 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-06 00:13:33.541435 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-06 00:13:33.681129 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-06 00:13:33.828542 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-06 00:13:33.980142 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-06 00:13:34.124578 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-06 00:13:34.265337 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-06 00:13:34.413696 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-06 00:13:34.548176 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-06 00:13:34.684598 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-06 00:13:34.833222 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-06 00:13:34.973636 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-06 00:13:35.126912 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-06 00:13:35.263867 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-06 00:13:35.398138 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-06 00:13:35.544611 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-06 00:13:35.6883 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-06 00:13:35.836927 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-06 00:13:35.972691 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-06 00:13:36.114497 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-06 00:13:36.24853 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-06 00:13:36.390464 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-06 00:13:36.549175 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-06 00:13:36.716902 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-06 00:13:36.85184 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-06 00:13:37.000335 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-06 00:13:37.147287 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-06 00:13:37.283337 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-06 00:13:37.423498 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-06 00:13:37.563053 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-06 00:13:37.700632 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-06 00:13:37.836641 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-06 00:13:37.981721 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-06 00:13:38.358718 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-06 00:13:38.491257 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-06 00:13:38.621555 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-06 00:13:38.762805 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-06 00:13:38.888927 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-06 00:13:39.026291 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-06 00:13:39.471817 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-06 00:13:39.625127 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-06 00:13:39.7691 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-06 00:13:39.913943 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-06 00:13:40.061648 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-06 00:13:40.204935 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-06 00:13:40.353496 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-06 00:13:40.501227 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-06 00:13:40.645538 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-06 00:13:40.803771 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-06 00:13:40.961321 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-06 00:13:41.105925 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-06 00:13:41.248897 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-06 00:13:41.398693 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-06 00:13:41.534441 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-06 00:13:41.67015 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-06 00:13:41.813844 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-06 00:13:41.951738 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-06 00:13:42.143303 INFO::Counting total values for each feature
2024-07-06 00:13:42.186463 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-07-06 00:13:42.331883 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-07-06 00:13:42.488214 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-07-06 00:13:42.641294 INFO::Writing residuals to file output/fits/residuals.rds
2024-07-06 00:13:42.698016 INFO::Writing fitted values to file output/fits/fitted.rds
2024-07-06 00:13:42.72987 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-07-06 00:13:42.735657 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-07-06 00:13:42.742612 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"
2024-07-06 00:13:42.758168 INFO::Writing function arguments to log file
2024-07-06 00:13:42.764413 INFO::Verifying options selected are valid
2024-07-06 00:13:42.765625 INFO::Determining format of input files
2024-07-06 00:13:42.766851 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-06 00:13:42.772524 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-06 00:13:42.773666 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-07-06 00:13:42.775475 INFO::Filter data based on min abundance and min prevalence
2024-07-06 00:13:42.776351 INFO::Total samples in data: 1595
2024-07-06 00:13:42.777236 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-06 00:13:42.781807 INFO::Total filtered features: 0
2024-07-06 00:13:42.782812 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-06 00:13:42.790867 INFO::Total filtered features with variance filtering: 0
2024-07-06 00:13:42.791996 INFO::Filtered feature names from variance filtering:
2024-07-06 00:13:42.792899 INFO::Running selected normalization method: NONE
2024-07-06 00:13:42.793745 INFO::Bypass z-score application to metadata
2024-07-06 00:13:42.794617 INFO::Running selected transform method: AST
2024-07-06 00:13:42.827643 INFO::Running selected analysis method: LM
2024-07-06 00:13:42.829734 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-06 00:13:42.973036 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-06 00:13:43.11429 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-06 00:13:43.245307 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-06 00:13:43.385798 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-06 00:13:43.515372 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-06 00:13:43.660988 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-06 00:13:43.80026 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-06 00:13:43.930952 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-06 00:13:44.087535 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-06 00:13:44.222187 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-06 00:13:44.336232 WARNING::Fitting problem for feature 11 a warning was issued
2024-07-06 00:13:44.487865 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-06 00:13:44.618011 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-06 00:13:44.749652 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-06 00:13:44.887361 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-06 00:13:45.020372 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-06 00:13:45.127715 WARNING::Fitting problem for feature 16 a warning was issued
2024-07-06 00:13:45.279556 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-06 00:13:45.419595 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-06 00:13:45.556832 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-06 00:13:45.698323 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-06 00:13:45.835762 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-06 00:13:45.97138 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-06 00:13:46.119498 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-06 00:13:46.245801 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-06 00:13:46.381138 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-06 00:13:46.523396 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-06 00:13:46.656917 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-06 00:13:46.803941 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-06 00:13:46.93006 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-06 00:13:47.057138 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-06 00:13:47.206443 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-06 00:13:47.341223 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-06 00:13:47.477099 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-06 00:13:47.608025 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-06 00:13:47.736955 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-06 00:13:47.873837 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-06 00:13:48.008676 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-06 00:13:48.144794 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-06 00:13:48.273974 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-06 00:13:48.415594 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-06 00:13:48.54754 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-06 00:13:48.683628 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-06 00:13:48.830011 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-06 00:13:48.969506 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-06 00:13:49.111983 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-06 00:13:49.252006 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-06 00:13:49.388237 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-06 00:13:49.515572 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-06 00:13:49.654837 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-06 00:13:49.782082 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-06 00:13:49.912149 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-06 00:13:50.043937 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-06 00:13:50.164993 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-06 00:13:50.291805 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-06 00:13:50.429735 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-06 00:13:50.577622 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-06 00:13:50.709497 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-06 00:13:50.844649 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-06 00:13:50.9718 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-06 00:13:51.110829 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-06 00:13:51.235452 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-06 00:13:51.377479 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-06 00:13:51.503322 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-06 00:13:51.647066 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-06 00:13:51.77349 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-06 00:13:51.907913 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-06 00:13:52.041826 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-06 00:13:52.149393 WARNING::Fitting problem for feature 67 a warning was issued
2024-07-06 00:13:52.298755 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-06 00:13:52.422411 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-06 00:13:52.559038 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-06 00:13:52.708621 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-06 00:13:52.842273 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-06 00:13:52.889154 WARNING::Fitting problem for feature 72 a warning was issued
2024-07-06 00:13:53.027358 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-06 00:13:53.155455 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-06 00:13:53.520789 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-06 00:13:53.649597 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-06 00:13:53.783776 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-06 00:13:53.916327 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-06 00:13:54.056511 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-06 00:13:54.199355 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-06 00:13:54.327366 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-06 00:13:54.466569 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-06 00:13:54.597596 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-06 00:13:54.739899 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-06 00:13:54.871756 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-06 00:13:55.004466 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-06 00:13:55.142185 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-06 00:13:55.312707 INFO::Counting total values for each feature
2024-07-06 00:13:55.33453 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-07-06 00:13:55.478151 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-07-06 00:13:55.624671 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-07-06 00:13:55.776576 INFO::Writing residuals to file output2/fits/residuals.rds
2024-07-06 00:13:55.851017 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-07-06 00:13:55.923044 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-07-06 00:13:55.928608 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-07-06 00:13:55.933699 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 7 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 29.736   0.575  30.300

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin283.573 0.70884.227