Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-05-04 11:36:45 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1138/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.18.0  (landing page)
Lauren McIver
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_19
git_last_commit: 35350f9
git_last_commit_date: 2024-04-30 11:16:06 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for Maaslin2 on nebbiolo1


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: 1.18.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings Maaslin2_1.18.0.tar.gz
StartedAt: 2024-05-04 00:36:13 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 00:40:19 -0400 (Sat, 04 May 2024)
EllapsedTime: 245.7 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings Maaslin2_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* 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 ‘1.18.0’
* 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 84.606  0.888  85.437
* 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-3.19-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.


Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
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"
2024-05-04 00:38:09.420423 INFO::Writing function arguments to log file
2024-05-04 00:38:09.460999 INFO::Verifying options selected are valid
2024-05-04 00:38:09.495731 INFO::Determining format of input files
2024-05-04 00:38:09.497181 INFO::Input format is data samples as rows and metadata samples as rows
2024-05-04 00:38:09.501873 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-05-04 00:38:09.503153 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-05-04 00:38:09.505543 INFO::Filter data based on min abundance and min prevalence
2024-05-04 00:38:09.506404 INFO::Total samples in data: 1595
2024-05-04 00:38:09.507203 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-05-04 00:38:09.510884 INFO::Total filtered features: 0
2024-05-04 00:38:09.511869 INFO::Filtered feature names from abundance and prevalence filtering:
2024-05-04 00:38:09.525228 INFO::Total filtered features with variance filtering: 0
2024-05-04 00:38:09.526393 INFO::Filtered feature names from variance filtering:
2024-05-04 00:38:09.527246 INFO::Running selected normalization method: TSS
2024-05-04 00:38:10.661855 INFO::Bypass z-score application to metadata
2024-05-04 00:38:10.663121 INFO::Running selected transform method: AST
2024-05-04 00:38:10.679425 INFO::Running selected analysis method: LM
2024-05-04 00:38:11.146382 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-05-04 00:38:11.485974 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-05-04 00:38:11.631182 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-05-04 00:38:11.77685 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-05-04 00:38:12.15653 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-05-04 00:38:12.294584 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-05-04 00:38:12.43419 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-05-04 00:38:12.573501 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-05-04 00:38:12.687679 WARNING::Fitting problem for feature 8 a warning was issued
2024-05-04 00:38:12.828265 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-05-04 00:38:12.934793 WARNING::Fitting problem for feature 9 a warning was issued
2024-05-04 00:38:13.088926 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-05-04 00:38:13.226165 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-05-04 00:38:13.369336 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-05-04 00:38:13.508722 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-05-04 00:38:13.62242 WARNING::Fitting problem for feature 13 a warning was issued
2024-05-04 00:38:13.767693 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-05-04 00:38:13.902316 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-05-04 00:38:14.061027 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-05-04 00:38:14.197395 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-05-04 00:38:14.340741 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-05-04 00:38:14.516609 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-05-04 00:38:14.652719 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-05-04 00:38:14.791768 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-05-04 00:38:14.936486 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-05-04 00:38:15.082706 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-05-04 00:38:15.218387 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-05-04 00:38:15.361892 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-05-04 00:38:15.505579 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-05-04 00:38:15.639183 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-05-04 00:38:15.779996 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-05-04 00:38:15.926543 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-05-04 00:38:16.066022 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-05-04 00:38:16.196898 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-05-04 00:38:16.344311 INFO::Fitting model to feature number 32, Prevotella.copri
2024-05-04 00:38:16.482754 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-05-04 00:38:16.63824 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-05-04 00:38:16.78846 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-05-04 00:38:16.926148 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-05-04 00:38:17.063063 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-05-04 00:38:17.214357 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-05-04 00:38:17.353398 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-05-04 00:38:17.49179 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-05-04 00:38:17.639396 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-05-04 00:38:17.775975 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-05-04 00:38:17.921864 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-05-04 00:38:18.054314 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-05-04 00:38:18.182962 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-05-04 00:38:18.32379 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-05-04 00:38:18.468743 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-05-04 00:38:18.625829 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-05-04 00:38:18.763101 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-05-04 00:38:18.906513 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-05-04 00:38:19.040384 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-05-04 00:38:19.191803 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-05-04 00:38:19.353546 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-05-04 00:38:19.507566 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-05-04 00:38:19.645816 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-05-04 00:38:19.788811 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-05-04 00:38:19.94508 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-05-04 00:38:20.089481 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-05-04 00:38:20.234502 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-05-04 00:38:20.379824 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-05-04 00:38:20.511925 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-05-04 00:38:20.657659 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-05-04 00:38:20.796462 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-05-04 00:38:20.942291 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-05-04 00:38:21.082704 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-05-04 00:38:21.216794 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-05-04 00:38:21.371968 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-05-04 00:38:21.505593 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-05-04 00:38:21.653126 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-05-04 00:38:22.091837 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-05-04 00:38:22.239355 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-05-04 00:38:22.38428 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-05-04 00:38:22.533962 INFO::Fitting model to feature number 73, Dialister.invisus
2024-05-04 00:38:22.668813 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-05-04 00:38:22.806421 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-05-04 00:38:22.951325 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-05-04 00:38:23.089217 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-05-04 00:38:23.23737 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-05-04 00:38:23.388767 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-05-04 00:38:23.544064 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-05-04 00:38:23.679917 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-05-04 00:38:23.82199 INFO::Fitting model to feature number 82, Escherichia.coli
2024-05-04 00:38:23.966038 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-05-04 00:38:24.097718 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-05-04 00:38:24.236805 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-05-04 00:38:24.376092 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-05-04 00:38:24.512655 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-05-04 00:38:24.935969 INFO::Counting total values for each feature
2024-05-04 00:38:24.967732 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-05-04 00:38:25.118258 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-05-04 00:38:25.274291 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-05-04 00:38:25.42726 INFO::Writing residuals to file output/fits/residuals.rds
2024-05-04 00:38:25.485268 INFO::Writing fitted values to file output/fits/fitted.rds
2024-05-04 00:38:25.518263 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-05-04 00:38:25.524275 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-05-04 00:38:25.531439 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"
2024-05-04 00:38:25.547696 INFO::Writing function arguments to log file
2024-05-04 00:38:25.554148 INFO::Verifying options selected are valid
2024-05-04 00:38:25.555321 INFO::Determining format of input files
2024-05-04 00:38:25.556543 INFO::Input format is data samples as rows and metadata samples as rows
2024-05-04 00:38:25.561973 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-05-04 00:38:25.563172 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-05-04 00:38:25.565022 INFO::Filter data based on min abundance and min prevalence
2024-05-04 00:38:25.565931 INFO::Total samples in data: 1595
2024-05-04 00:38:25.566843 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-05-04 00:38:25.571393 INFO::Total filtered features: 0
2024-05-04 00:38:25.572383 INFO::Filtered feature names from abundance and prevalence filtering:
2024-05-04 00:38:25.58081 INFO::Total filtered features with variance filtering: 0
2024-05-04 00:38:25.58196 INFO::Filtered feature names from variance filtering:
2024-05-04 00:38:25.582846 INFO::Running selected normalization method: NONE
2024-05-04 00:38:25.583751 INFO::Bypass z-score application to metadata
2024-05-04 00:38:25.58463 INFO::Running selected transform method: AST
2024-05-04 00:38:25.600955 INFO::Running selected analysis method: LM
2024-05-04 00:38:25.603136 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-05-04 00:38:25.767243 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-05-04 00:38:25.906577 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-05-04 00:38:26.034439 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-05-04 00:38:26.1754 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-05-04 00:38:26.310285 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-05-04 00:38:26.45363 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-05-04 00:38:26.58625 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-05-04 00:38:26.717469 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-05-04 00:38:26.853408 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-05-04 00:38:27.003458 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-05-04 00:38:27.121206 WARNING::Fitting problem for feature 11 a warning was issued
2024-05-04 00:38:27.26688 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-05-04 00:38:27.396196 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-05-04 00:38:27.543793 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-05-04 00:38:27.682448 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-05-04 00:38:27.825272 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-05-04 00:38:27.940324 WARNING::Fitting problem for feature 16 a warning was issued
2024-05-04 00:38:28.082671 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-05-04 00:38:28.236654 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-05-04 00:38:28.374598 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-05-04 00:38:28.504437 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-05-04 00:38:28.651336 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-05-04 00:38:28.80325 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-05-04 00:38:28.940906 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-05-04 00:38:29.073908 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-05-04 00:38:29.213036 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-05-04 00:38:29.361785 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-05-04 00:38:29.493629 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-05-04 00:38:29.629487 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-05-04 00:38:29.757692 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-05-04 00:38:29.894987 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-05-04 00:38:30.02382 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-05-04 00:38:30.159084 INFO::Fitting model to feature number 32, Prevotella.copri
2024-05-04 00:38:30.292174 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-05-04 00:38:30.427724 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-05-04 00:38:30.563309 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-05-04 00:38:30.696169 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-05-04 00:38:30.833664 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-05-04 00:38:30.976189 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-05-04 00:38:31.10711 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-05-04 00:38:31.230961 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-05-04 00:38:31.366909 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-05-04 00:38:31.495729 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-05-04 00:38:31.623745 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-05-04 00:38:31.755129 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-05-04 00:38:31.891914 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-05-04 00:38:32.023257 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-05-04 00:38:32.159438 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-05-04 00:38:32.299535 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-05-04 00:38:32.4321 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-05-04 00:38:32.561375 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-05-04 00:38:32.953885 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-05-04 00:38:33.107917 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-05-04 00:38:33.247367 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-05-04 00:38:33.386188 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-05-04 00:38:33.530752 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-05-04 00:38:33.691983 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-05-04 00:38:33.828865 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-05-04 00:38:33.963867 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-05-04 00:38:34.101139 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-05-04 00:38:34.249499 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-05-04 00:38:34.380632 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-05-04 00:38:34.519076 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-05-04 00:38:34.654103 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-05-04 00:38:34.797194 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-05-04 00:38:35.240259 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-05-04 00:38:35.378005 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-05-04 00:38:35.513899 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-05-04 00:38:35.627844 WARNING::Fitting problem for feature 67 a warning was issued
2024-05-04 00:38:35.781305 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-05-04 00:38:35.91206 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-05-04 00:38:36.048862 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-05-04 00:38:36.195297 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-05-04 00:38:36.329509 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-05-04 00:38:36.38722 WARNING::Fitting problem for feature 72 a warning was issued
2024-05-04 00:38:36.528727 INFO::Fitting model to feature number 73, Dialister.invisus
2024-05-04 00:38:36.665653 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-05-04 00:38:36.802358 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-05-04 00:38:36.941242 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-05-04 00:38:37.091413 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-05-04 00:38:37.221976 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-05-04 00:38:37.35672 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-05-04 00:38:37.493566 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-05-04 00:38:37.6446 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-05-04 00:38:37.791502 INFO::Fitting model to feature number 82, Escherichia.coli
2024-05-04 00:38:37.930084 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-05-04 00:38:38.062417 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-05-04 00:38:38.196034 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-05-04 00:38:38.339584 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-05-04 00:38:38.484199 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-05-04 00:38:38.646419 INFO::Counting total values for each feature
2024-05-04 00:38:38.669348 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-05-04 00:38:38.813958 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-05-04 00:38:38.960921 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-05-04 00:38:39.116974 INFO::Writing residuals to file output2/fits/residuals.rds
2024-05-04 00:38:39.192731 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-05-04 00:38:39.266395 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-05-04 00:38:39.272224 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-05-04 00:38:39.277828 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 
 30.539   0.428  30.959 

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin284.606 0.88885.437