Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 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 1124/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.21.0  (landing page)
Lauren McIver
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: devel
git_last_commit: 3dacd30
git_last_commit_date: 2024-10-29 10:38:48 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 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 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: 1.21.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Maaslin2_1.21.0.tar.gz
StartedAt: 2024-12-24 08:10:04 -0000 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 08:13:29 -0000 (Tue, 24 Dec 2024)
EllapsedTime: 205.2 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Maaslin2_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.21.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 119.818  0.826 120.934
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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"
2024-12-24 08:12:41.622796 INFO::Writing function arguments to log file
2024-12-24 08:12:41.677171 INFO::Verifying options selected are valid
2024-12-24 08:12:41.722456 INFO::Determining format of input files
2024-12-24 08:12:41.724454 INFO::Input format is data samples as rows and metadata samples as rows
2024-12-24 08:12:41.731886 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-12-24 08:12:41.733753 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-12-24 08:12:41.737168 INFO::Filter data based on min abundance and min prevalence
2024-12-24 08:12:41.738466 INFO::Total samples in data: 1595
2024-12-24 08:12:41.739743 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-12-24 08:12:41.749096 INFO::Total filtered features: 0
2024-12-24 08:12:41.750679 INFO::Filtered feature names from abundance and prevalence filtering:
2024-12-24 08:12:41.78725 INFO::Total filtered features with variance filtering: 0
2024-12-24 08:12:41.788808 INFO::Filtered feature names from variance filtering:
2024-12-24 08:12:41.790025 INFO::Running selected normalization method: TSS
2024-12-24 08:12:43.244096 INFO::Bypass z-score application to metadata
2024-12-24 08:12:43.24571 INFO::Running selected transform method: AST
2024-12-24 08:12:43.269237 INFO::Running selected analysis method: LM
2024-12-24 08:12:43.9047 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-12-24 08:12:44.404315 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-12-24 08:12:44.663263 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-12-24 08:12:44.903851 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-12-24 08:12:45.15234 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-12-24 08:12:45.390213 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-12-24 08:12:45.624145 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-12-24 08:12:45.865479 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-12-24 08:12:46.090232 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-12-24 08:12:46.285069 WARNING::Fitting problem for feature 9 a warning was issued
2024-12-24 08:12:46.597877 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-12-24 08:12:46.978796 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-12-24 08:12:47.219976 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-12-24 08:12:47.460358 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-12-24 08:12:47.664619 WARNING::Fitting problem for feature 13 a warning was issued
2024-12-24 08:12:48.311126 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-12-24 08:12:48.538077 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-12-24 08:12:48.779621 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-12-24 08:12:49.023035 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-12-24 08:12:49.293068 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-12-24 08:12:49.537614 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-12-24 08:12:49.773197 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-12-24 08:12:50.01438 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-12-24 08:12:50.247211 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-12-24 08:12:50.47536 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-12-24 08:12:50.706271 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-12-24 08:12:50.962516 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-12-24 08:12:51.193467 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-12-24 08:12:51.411971 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-12-24 08:12:51.656645 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-12-24 08:12:51.880809 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-12-24 08:12:52.116964 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-12-24 08:12:52.376606 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-12-24 08:12:52.631335 INFO::Fitting model to feature number 32, Prevotella.copri
2024-12-24 08:12:52.879204 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-12-24 08:12:53.133169 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-12-24 08:12:53.360425 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-12-24 08:12:53.5869 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-12-24 08:12:53.818935 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-12-24 08:12:54.046643 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-12-24 08:12:54.267539 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-12-24 08:12:54.503412 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-12-24 08:12:54.736424 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-12-24 08:12:54.961888 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-12-24 08:12:55.205375 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-12-24 08:12:55.427333 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-12-24 08:12:55.653373 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-12-24 08:12:55.883541 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-12-24 08:12:56.119432 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-12-24 08:12:56.379364 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-12-24 08:12:56.610894 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-12-24 08:12:56.854881 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-12-24 08:12:57.083642 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-12-24 08:12:57.299482 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-12-24 08:12:57.529763 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-12-24 08:12:57.764845 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-12-24 08:12:58.28275 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-12-24 08:12:58.509867 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-12-24 08:12:58.756962 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-12-24 08:12:58.989752 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-12-24 08:12:59.235115 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-12-24 08:12:59.467947 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-12-24 08:12:59.68074 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-12-24 08:12:59.911525 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-12-24 08:13:00.134454 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-12-24 08:13:00.364106 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-12-24 08:13:00.600898 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-12-24 08:13:00.815864 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-12-24 08:13:01.034374 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-12-24 08:13:01.251837 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-12-24 08:13:01.496178 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-12-24 08:13:01.742066 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-12-24 08:13:01.992449 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-12-24 08:13:02.217783 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-12-24 08:13:02.43521 INFO::Fitting model to feature number 73, Dialister.invisus
2024-12-24 08:13:02.665284 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-12-24 08:13:02.887571 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-12-24 08:13:03.143158 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-12-24 08:13:03.367218 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-12-24 08:13:03.596752 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-12-24 08:13:03.838016 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-12-24 08:13:04.080853 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-12-24 08:13:04.305534 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-12-24 08:13:04.542407 INFO::Fitting model to feature number 82, Escherichia.coli
2024-12-24 08:13:05.069334 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-12-24 08:13:05.27956 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-12-24 08:13:05.496733 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-12-24 08:13:05.709602 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-12-24 08:13:05.936911 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-12-24 08:13:06.213578 INFO::Counting total values for each feature
2024-12-24 08:13:06.264299 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-12-24 08:13:06.382979 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-12-24 08:13:06.500903 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-12-24 08:13:06.62191 INFO::Writing residuals to file output/fits/residuals.rds
2024-12-24 08:13:06.678777 INFO::Writing fitted values to file output/fits/fitted.rds
2024-12-24 08:13:06.710027 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-12-24 08:13:06.716806 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-12-24 08:13:06.723735 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"
2024-12-24 08:13:06.740758 INFO::Writing function arguments to log file
2024-12-24 08:13:06.748921 INFO::Verifying options selected are valid
2024-12-24 08:13:06.750247 INFO::Determining format of input files
2024-12-24 08:13:06.751905 INFO::Input format is data samples as rows and metadata samples as rows
2024-12-24 08:13:06.759972 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-12-24 08:13:06.761564 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-12-24 08:13:06.763831 INFO::Filter data based on min abundance and min prevalence
2024-12-24 08:13:06.765092 INFO::Total samples in data: 1595
2024-12-24 08:13:06.76629 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-12-24 08:13:06.775604 INFO::Total filtered features: 0
2024-12-24 08:13:06.777138 INFO::Filtered feature names from abundance and prevalence filtering:
2024-12-24 08:13:06.804518 INFO::Total filtered features with variance filtering: 0
2024-12-24 08:13:06.806053 INFO::Filtered feature names from variance filtering:
2024-12-24 08:13:06.807235 INFO::Running selected normalization method: NONE
2024-12-24 08:13:06.808444 INFO::Bypass z-score application to metadata
2024-12-24 08:13:06.809587 INFO::Running selected transform method: AST
2024-12-24 08:13:06.841529 INFO::Running selected analysis method: LM
2024-12-24 08:13:06.843565 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-12-24 08:13:07.048118 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-12-24 08:13:07.255293 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-12-24 08:13:07.454397 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-12-24 08:13:07.6706 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-12-24 08:13:07.870265 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-12-24 08:13:08.082371 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-12-24 08:13:08.288835 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-12-24 08:13:08.529385 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-12-24 08:13:08.739623 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-12-24 08:13:08.958395 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-12-24 08:13:09.17641 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-12-24 08:13:09.387123 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-12-24 08:13:09.597131 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-12-24 08:13:09.808348 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-12-24 08:13:10.028369 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-12-24 08:13:10.204363 WARNING::Fitting problem for feature 16 a warning was issued
2024-12-24 08:13:10.412959 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-12-24 08:13:10.624863 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-12-24 08:13:10.838163 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-12-24 08:13:11.051661 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-12-24 08:13:11.265044 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-12-24 08:13:11.47595 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-12-24 08:13:11.68637 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-12-24 08:13:11.89405 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-12-24 08:13:12.111845 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-12-24 08:13:12.323751 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-12-24 08:13:12.553267 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-12-24 08:13:12.777535 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-12-24 08:13:12.985121 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-12-24 08:13:13.190481 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-12-24 08:13:13.40354 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-12-24 08:13:13.609133 INFO::Fitting model to feature number 32, Prevotella.copri
2024-12-24 08:13:13.827866 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-12-24 08:13:14.050811 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-12-24 08:13:14.265175 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-12-24 08:13:14.479963 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-12-24 08:13:14.702263 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-12-24 08:13:14.910691 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-12-24 08:13:15.123653 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-12-24 08:13:15.337523 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-12-24 08:13:15.542136 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-12-24 08:13:15.753456 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-12-24 08:13:15.964724 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-12-24 08:13:16.172979 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-12-24 08:13:16.383324 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-12-24 08:13:16.602618 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-12-24 08:13:16.816428 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-12-24 08:13:17.017612 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-12-24 08:13:17.254524 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-12-24 08:13:17.469427 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-12-24 08:13:17.688267 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-12-24 08:13:17.904797 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-12-24 08:13:18.105817 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-12-24 08:13:18.322174 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-12-24 08:13:18.53192 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-12-24 08:13:18.747689 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-12-24 08:13:18.955294 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-12-24 08:13:19.163022 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-12-24 08:13:19.401682 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-12-24 08:13:19.620617 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-12-24 08:13:19.829681 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-12-24 08:13:20.047523 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-12-24 08:13:20.268775 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-12-24 08:13:20.479228 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-12-24 08:13:20.691281 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-12-24 08:13:20.902394 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-12-24 08:13:21.128214 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-12-24 08:13:21.347545 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-12-24 08:13:21.551592 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-12-24 08:13:21.775365 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-12-24 08:13:22.018165 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-12-24 08:13:22.248377 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-12-24 08:13:22.328805 WARNING::Fitting problem for feature 72 a warning was issued
2024-12-24 08:13:22.548167 INFO::Fitting model to feature number 73, Dialister.invisus
2024-12-24 08:13:22.779379 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-12-24 08:13:22.993324 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-12-24 08:13:23.20173 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-12-24 08:13:23.413286 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-12-24 08:13:23.632335 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-12-24 08:13:23.84231 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-12-24 08:13:24.062185 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-12-24 08:13:24.276473 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-12-24 08:13:24.503109 INFO::Fitting model to feature number 82, Escherichia.coli
2024-12-24 08:13:24.706653 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-12-24 08:13:24.9058 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-12-24 08:13:25.105103 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-12-24 08:13:25.321761 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-12-24 08:13:25.537354 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-12-24 08:13:25.785732 INFO::Counting total values for each feature
2024-12-24 08:13:25.824115 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-12-24 08:13:25.941712 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-12-24 08:13:26.05878 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-12-24 08:13:26.181056 INFO::Writing residuals to file output2/fits/residuals.rds
2024-12-24 08:13:26.257992 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-12-24 08:13:26.330347 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-12-24 08:13:26.33698 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-12-24 08:13:26.342625 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 4 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 45.187   0.891  46.186

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2119.818 0.826120.934