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This page was generated on 2024-07-24 11:38 -0400 (Wed, 24 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4688
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4284
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4455
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4404
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 1111/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.19.0  (landing page)
Lauren McIver
Snapshot Date: 2024-07-23 14:00 -0400 (Tue, 23 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
palomino8Windows 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 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

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: 2024-07-24 00:54:04 -0400 (Wed, 24 Jul 2024)
EndedAt: 2024-07-24 00:58:13 -0400 (Wed, 24 Jul 2024)
EllapsedTime: 248.5 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 86.439  1.027  87.402
* 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"
2024-07-24 00:56:02.019935 INFO::Writing function arguments to log file
2024-07-24 00:56:02.060842 INFO::Verifying options selected are valid
2024-07-24 00:56:02.095695 INFO::Determining format of input files
2024-07-24 00:56:02.097102 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-24 00:56:02.101616 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-24 00:56:02.102851 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-07-24 00:56:02.105184 INFO::Filter data based on min abundance and min prevalence
2024-07-24 00:56:02.105994 INFO::Total samples in data: 1595
2024-07-24 00:56:02.106762 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-24 00:56:02.110225 INFO::Total filtered features: 0
2024-07-24 00:56:02.111153 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-24 00:56:02.126338 INFO::Total filtered features with variance filtering: 0
2024-07-24 00:56:02.127453 INFO::Filtered feature names from variance filtering:
2024-07-24 00:56:02.128295 INFO::Running selected normalization method: TSS
2024-07-24 00:56:03.331202 INFO::Bypass z-score application to metadata
2024-07-24 00:56:03.332577 INFO::Running selected transform method: AST
2024-07-24 00:56:03.349224 INFO::Running selected analysis method: LM
2024-07-24 00:56:03.892039 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-24 00:56:04.284367 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-24 00:56:04.451415 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-24 00:56:04.607664 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-24 00:56:04.780299 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-24 00:56:04.937806 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-24 00:56:05.090434 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-24 00:56:05.247778 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-24 00:56:05.368098 WARNING::Fitting problem for feature 8 a warning was issued
2024-07-24 00:56:05.527649 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-24 00:56:05.646217 WARNING::Fitting problem for feature 9 a warning was issued
2024-07-24 00:56:05.822778 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-24 00:56:05.974047 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-24 00:56:06.124397 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-24 00:56:06.315242 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-24 00:56:06.447485 WARNING::Fitting problem for feature 13 a warning was issued
2024-07-24 00:56:06.602574 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-24 00:56:06.750918 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-24 00:56:06.915181 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-24 00:56:07.098741 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-24 00:56:07.269179 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-24 00:56:07.493734 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-24 00:56:07.65485 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-24 00:56:07.794165 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-24 00:56:07.94579 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-24 00:56:08.089139 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-24 00:56:08.234077 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-24 00:56:08.387086 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-24 00:56:08.555202 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-24 00:56:08.70994 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-24 00:56:08.863307 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-24 00:56:09.015181 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-24 00:56:09.162088 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-24 00:56:09.300169 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-24 00:56:09.459499 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-24 00:56:09.666942 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-24 00:56:09.855752 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-24 00:56:10.08578 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-24 00:56:10.241355 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-24 00:56:10.384586 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-24 00:56:10.536871 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-24 00:56:10.679618 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-24 00:56:10.865841 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-24 00:56:11.024877 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-24 00:56:11.177946 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-24 00:56:11.336389 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-24 00:56:11.477184 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-24 00:56:11.612656 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-24 00:56:11.759791 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-24 00:56:11.906296 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-24 00:56:12.060788 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-24 00:56:12.200924 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-24 00:56:12.339052 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-24 00:56:12.48337 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-24 00:56:12.646645 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-24 00:56:13.094647 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-24 00:56:13.242396 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-24 00:56:13.382598 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-24 00:56:13.537619 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-24 00:56:13.688856 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-24 00:56:13.828555 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-24 00:56:13.982337 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-24 00:56:14.12822 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-24 00:56:14.268723 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-24 00:56:14.413061 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-24 00:56:14.569367 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-24 00:56:14.710141 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-24 00:56:14.845498 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-24 00:56:14.98634 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-24 00:56:15.124853 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-24 00:56:15.263298 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-24 00:56:15.407482 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-24 00:56:15.552313 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-24 00:56:15.69763 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-24 00:56:15.844009 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-24 00:56:15.977744 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-24 00:56:16.114023 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-24 00:56:16.257677 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-24 00:56:16.410702 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-24 00:56:16.586146 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-24 00:56:16.736916 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-24 00:56:16.897082 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-24 00:56:17.053131 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-24 00:56:17.203849 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-24 00:56:17.352562 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-24 00:56:17.496444 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-24 00:56:17.643277 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-24 00:56:17.780719 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-24 00:56:17.919383 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-24 00:56:18.06273 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-24 00:56:18.249339 INFO::Counting total values for each feature
2024-07-24 00:56:18.292743 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-07-24 00:56:18.439164 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-07-24 00:56:18.590129 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-07-24 00:56:18.743903 INFO::Writing residuals to file output/fits/residuals.rds
2024-07-24 00:56:18.801606 INFO::Writing fitted values to file output/fits/fitted.rds
2024-07-24 00:56:18.834321 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-07-24 00:56:18.840337 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-07-24 00:56:18.847978 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"
2024-07-24 00:56:18.863285 INFO::Writing function arguments to log file
2024-07-24 00:56:18.869877 INFO::Verifying options selected are valid
2024-07-24 00:56:18.87095 INFO::Determining format of input files
2024-07-24 00:56:18.872148 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-24 00:56:18.87748 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-24 00:56:18.878539 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-07-24 00:56:18.880169 INFO::Filter data based on min abundance and min prevalence
2024-07-24 00:56:18.881018 INFO::Total samples in data: 1595
2024-07-24 00:56:18.881897 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-24 00:56:18.886388 INFO::Total filtered features: 0
2024-07-24 00:56:18.887326 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-24 00:56:18.895203 INFO::Total filtered features with variance filtering: 0
2024-07-24 00:56:18.896535 INFO::Filtered feature names from variance filtering:
2024-07-24 00:56:18.897435 INFO::Running selected normalization method: NONE
2024-07-24 00:56:18.89825 INFO::Bypass z-score application to metadata
2024-07-24 00:56:18.899079 INFO::Running selected transform method: AST
2024-07-24 00:56:18.915481 INFO::Running selected analysis method: LM
2024-07-24 00:56:18.917327 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-24 00:56:19.074437 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-24 00:56:19.221429 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-24 00:56:19.373693 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-24 00:56:19.518219 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-24 00:56:19.65827 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-24 00:56:19.809053 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-24 00:56:19.948946 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-24 00:56:20.099671 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-24 00:56:20.242289 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-24 00:56:20.779274 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-24 00:56:20.900743 WARNING::Fitting problem for feature 11 a warning was issued
2024-07-24 00:56:21.051196 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-24 00:56:21.190527 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-24 00:56:21.343465 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-24 00:56:21.479877 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-24 00:56:21.634851 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-24 00:56:21.75989 WARNING::Fitting problem for feature 16 a warning was issued
2024-07-24 00:56:21.932372 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-24 00:56:22.097231 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-24 00:56:22.244403 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-24 00:56:22.390586 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-24 00:56:22.534073 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-24 00:56:22.672063 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-24 00:56:22.811669 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-24 00:56:22.953091 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-24 00:56:23.099418 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-24 00:56:23.239453 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-24 00:56:23.395332 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-24 00:56:23.541847 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-24 00:56:23.672144 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-24 00:56:23.804977 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-24 00:56:23.943633 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-24 00:56:24.08057 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-24 00:56:24.225782 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-24 00:56:24.37556 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-24 00:56:24.513012 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-24 00:56:24.663788 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-24 00:56:24.824745 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-24 00:56:24.96943 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-24 00:56:25.114008 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-24 00:56:25.26184 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-24 00:56:25.395311 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-24 00:56:25.543468 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-24 00:56:25.702751 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-24 00:56:25.841654 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-24 00:56:25.981167 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-24 00:56:26.123218 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-24 00:56:26.265699 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-24 00:56:26.408491 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-24 00:56:26.548935 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-24 00:56:26.684569 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-24 00:56:26.836158 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-24 00:56:26.979961 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-24 00:56:27.115186 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-24 00:56:27.252308 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-24 00:56:27.407205 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-24 00:56:27.542661 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-24 00:56:27.683811 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-24 00:56:27.828101 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-24 00:56:27.970162 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-24 00:56:28.117244 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-24 00:56:28.270329 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-24 00:56:28.449262 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-24 00:56:28.591359 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-24 00:56:28.739791 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-24 00:56:28.893796 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-24 00:56:29.032015 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-24 00:56:29.169306 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-24 00:56:29.29931 WARNING::Fitting problem for feature 67 a warning was issued
2024-07-24 00:56:29.440778 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-24 00:56:29.582863 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-24 00:56:29.740628 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-24 00:56:29.886743 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-24 00:56:30.023751 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-24 00:56:30.071948 WARNING::Fitting problem for feature 72 a warning was issued
2024-07-24 00:56:30.225783 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-24 00:56:30.365029 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-24 00:56:30.516087 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-24 00:56:30.68494 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-24 00:56:30.82075 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-24 00:56:30.964916 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-24 00:56:31.100486 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-24 00:56:31.2407 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-24 00:56:31.384753 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-24 00:56:31.528659 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-24 00:56:31.680399 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-24 00:56:31.818676 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-24 00:56:31.96471 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-24 00:56:32.106938 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-24 00:56:32.247718 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-24 00:56:32.423191 INFO::Counting total values for each feature
2024-07-24 00:56:32.447576 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-07-24 00:56:32.591751 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-07-24 00:56:32.735415 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-07-24 00:56:32.894358 INFO::Writing residuals to file output2/fits/residuals.rds
2024-07-24 00:56:32.969661 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-07-24 00:56:33.042703 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-07-24 00:56:33.049042 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-07-24 00:56:33.054693 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 
 31.265   0.908  32.165

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin286.439 1.02787.402