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This page was generated on 2024-06-25 17:43 -0400 (Tue, 25 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
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: 2024-06-23 14:00 -0400 (Sun, 23 Jun 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    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for Maaslin2 on kjohnson1

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.18.0.tar.gz
StartedAt: 2024-06-25 00:07:40 -0400 (Tue, 25 Jun 2024)
EndedAt: 2024-06-25 00:10:29 -0400 (Tue, 25 Jun 2024)
EllapsedTime: 169.9 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 91.367  1.747  93.308
* 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘Maaslin2’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in checkDepPackageVersion(dep_pkg = "TMB") :
  Package version inconsistency detected.
glmmTMB was built with TMB version 1.9.11
Current TMB version is 1.9.12
Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information)
** 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 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(Maaslin2)
> 
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2024-06-25 00:09:46.890619 INFO::Writing function arguments to log file
2024-06-25 00:09:46.937321 INFO::Verifying options selected are valid
2024-06-25 00:09:46.978905 INFO::Determining format of input files
2024-06-25 00:09:46.980843 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-25 00:09:46.987241 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-25 00:09:46.989007 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-06-25 00:09:46.991592 INFO::Filter data based on min abundance and min prevalence
2024-06-25 00:09:46.992698 INFO::Total samples in data: 1595
2024-06-25 00:09:46.99358 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-25 00:09:47.007449 INFO::Total filtered features: 0
2024-06-25 00:09:47.008886 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-25 00:09:47.018179 INFO::Total filtered features with variance filtering: 0
2024-06-25 00:09:47.019517 INFO::Filtered feature names from variance filtering:
2024-06-25 00:09:47.020373 INFO::Running selected normalization method: TSS
2024-06-25 00:09:48.304478 INFO::Bypass z-score application to metadata
2024-06-25 00:09:48.306119 INFO::Running selected transform method: AST
2024-06-25 00:09:48.32433 INFO::Running selected analysis method: LM
2024-06-25 00:09:48.907721 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-25 00:09:49.315148 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-25 00:09:49.504601 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-25 00:09:49.674874 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-25 00:09:49.856503 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-25 00:09:50.027859 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-25 00:09:50.199478 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-25 00:09:50.381283 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-25 00:09:50.510997 WARNING::Fitting problem for feature 8 a warning was issued
2024-06-25 00:09:50.729796 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-25 00:09:50.866614 WARNING::Fitting problem for feature 9 a warning was issued
2024-06-25 00:09:51.067403 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-25 00:09:51.230037 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-25 00:09:51.407541 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-25 00:09:51.568223 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-25 00:09:51.738331 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-25 00:09:51.909755 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-25 00:09:52.082563 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-25 00:09:52.255107 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-25 00:09:52.424385 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-25 00:09:52.601237 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-25 00:09:52.753272 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-25 00:09:52.931022 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-25 00:09:53.116141 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-25 00:09:53.294223 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-25 00:09:53.467717 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-25 00:09:53.63725 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-25 00:09:53.821783 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-25 00:09:54.00979 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-25 00:09:54.184895 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-25 00:09:54.387186 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-25 00:09:54.561183 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-25 00:09:54.74242 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-25 00:09:54.919987 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-25 00:09:55.107577 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-25 00:09:55.285351 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-25 00:09:55.464051 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-25 00:09:55.635535 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-25 00:09:56.108062 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-25 00:09:56.277541 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-25 00:09:56.44014 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-25 00:09:56.61562 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-25 00:09:56.804575 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-25 00:09:56.981564 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-25 00:09:57.155018 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-25 00:09:57.324098 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-25 00:09:57.47884 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-25 00:09:57.644609 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-25 00:09:57.830293 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-25 00:09:58.006075 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-25 00:09:58.17131 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-25 00:09:58.34567 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-25 00:09:58.504984 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-25 00:09:58.667123 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-25 00:09:58.846275 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-25 00:09:59.023031 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-25 00:09:59.187246 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-25 00:09:59.376269 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-25 00:09:59.559987 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-25 00:09:59.721232 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-25 00:09:59.896904 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-25 00:10:00.063336 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-25 00:10:00.254027 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-25 00:10:00.422443 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-25 00:10:00.601467 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-25 00:10:00.787758 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-25 00:10:00.97124 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-25 00:10:01.130984 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-25 00:10:01.297049 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-25 00:10:01.459039 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-25 00:10:01.628071 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-25 00:10:01.811292 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-25 00:10:02.001355 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-25 00:10:02.160928 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-25 00:10:02.323219 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-25 00:10:02.496111 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-25 00:10:02.661578 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-25 00:10:02.829562 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-25 00:10:03.005417 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-25 00:10:03.169931 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-25 00:10:03.343173 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-25 00:10:03.528067 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-25 00:10:03.689806 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-25 00:10:03.872698 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-25 00:10:04.040131 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-25 00:10:04.197423 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-25 00:10:04.368379 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-25 00:10:04.527048 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-25 00:10:04.690218 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-25 00:10:04.912525 INFO::Counting total values for each feature
2024-06-25 00:10:04.952733 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-06-25 00:10:05.101085 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-06-25 00:10:05.274531 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-06-25 00:10:05.457061 INFO::Writing residuals to file output/fits/residuals.rds
2024-06-25 00:10:05.539018 INFO::Writing fitted values to file output/fits/fitted.rds
2024-06-25 00:10:05.584052 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-06-25 00:10:05.593938 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-06-25 00:10:05.602312 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output/significant_results.tsv
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2024-06-25 00:10:05.61735 INFO::Writing function arguments to log file
2024-06-25 00:10:05.623677 INFO::Verifying options selected are valid
2024-06-25 00:10:05.624675 INFO::Determining format of input files
2024-06-25 00:10:05.625794 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-25 00:10:05.63144 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-25 00:10:05.632604 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-06-25 00:10:05.634268 INFO::Filter data based on min abundance and min prevalence
2024-06-25 00:10:05.635128 INFO::Total samples in data: 1595
2024-06-25 00:10:05.635932 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-25 00:10:05.641048 INFO::Total filtered features: 0
2024-06-25 00:10:05.642123 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-25 00:10:05.650632 INFO::Total filtered features with variance filtering: 0
2024-06-25 00:10:05.651915 INFO::Filtered feature names from variance filtering:
2024-06-25 00:10:05.652736 INFO::Running selected normalization method: NONE
2024-06-25 00:10:05.653528 INFO::Bypass z-score application to metadata
2024-06-25 00:10:05.654318 INFO::Running selected transform method: AST
2024-06-25 00:10:05.679232 INFO::Running selected analysis method: LM
2024-06-25 00:10:05.681355 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-25 00:10:05.843142 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-25 00:10:06.023914 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-25 00:10:06.180684 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-25 00:10:06.345043 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-25 00:10:06.513412 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-25 00:10:06.676703 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-25 00:10:06.838435 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-25 00:10:07.008797 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-25 00:10:07.170106 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-25 00:10:07.33413 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-25 00:10:07.48456 WARNING::Fitting problem for feature 11 a warning was issued
2024-06-25 00:10:07.66038 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-25 00:10:07.82321 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-25 00:10:07.980614 WARNING::Fitting problem for feature 13 a warning was issued
2024-06-25 00:10:08.159514 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-25 00:10:08.333384 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-25 00:10:08.422354 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-25 00:10:08.476024 WARNING::Fitting problem for feature 16 a warning was issued
2024-06-25 00:10:08.556368 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-25 00:10:08.630354 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-25 00:10:08.734332 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-25 00:10:08.801301 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-25 00:10:08.874682 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-25 00:10:09.019998 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-25 00:10:09.114332 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-25 00:10:09.277515 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-25 00:10:09.430033 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-25 00:10:09.619887 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-25 00:10:09.778254 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-25 00:10:09.945867 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-25 00:10:10.114669 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-25 00:10:10.270317 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-25 00:10:10.43233 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-25 00:10:10.604665 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-25 00:10:10.766539 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-25 00:10:10.922238 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-25 00:10:11.093016 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-25 00:10:11.250312 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-25 00:10:11.428783 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-25 00:10:11.589455 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-25 00:10:11.749651 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-25 00:10:11.915696 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-25 00:10:12.071536 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-25 00:10:12.247845 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-25 00:10:12.40662 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-25 00:10:12.572506 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-25 00:10:12.750785 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-25 00:10:12.911314 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-25 00:10:13.096549 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-25 00:10:13.262093 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-25 00:10:13.438344 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-25 00:10:13.59357 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-25 00:10:13.752149 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-25 00:10:13.911951 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-25 00:10:14.070477 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-25 00:10:14.189347 WARNING::Fitting problem for feature 53 a warning was issued
2024-06-25 00:10:14.353242 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-25 00:10:14.503743 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-25 00:10:14.669288 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-25 00:10:14.851841 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-25 00:10:15.006584 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-25 00:10:15.168361 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-25 00:10:15.367051 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-25 00:10:15.529217 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-25 00:10:15.686594 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-25 00:10:15.86067 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-25 00:10:16.022936 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-25 00:10:16.194292 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-25 00:10:16.359282 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-25 00:10:16.518293 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-25 00:10:16.670412 WARNING::Fitting problem for feature 67 a warning was issued
2024-06-25 00:10:16.83687 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-25 00:10:17.009024 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-25 00:10:17.172106 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-25 00:10:17.344274 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-25 00:10:17.522644 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-25 00:10:17.579104 WARNING::Fitting problem for feature 72 a warning was issued
2024-06-25 00:10:17.752284 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-25 00:10:17.911623 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-25 00:10:18.103729 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-25 00:10:18.266735 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-25 00:10:18.433753 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-25 00:10:18.611355 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-25 00:10:18.773498 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-25 00:10:18.941171 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-25 00:10:19.118723 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-25 00:10:19.28693 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-25 00:10:19.458338 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-25 00:10:19.608442 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-25 00:10:19.767835 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-25 00:10:19.942194 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-25 00:10:20.10982 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-25 00:10:20.306551 INFO::Counting total values for each feature
2024-06-25 00:10:20.333154 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-06-25 00:10:20.479516 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-06-25 00:10:20.624078 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-06-25 00:10:20.793633 INFO::Writing residuals to file output2/fits/residuals.rds
2024-06-25 00:10:21.200689 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-06-25 00:10:21.307996 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-06-25 00:10:21.317394 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-06-25 00:10:21.324399 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 8 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 35.021   0.786  35.854

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin291.367 1.74793.308