Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-12-09 12:07 -0500 (Mon, 09 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4739
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4482
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4510
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4462
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 1130/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.20.0  (landing page)
Lauren McIver
Snapshot Date: 2024-12-05 13:00 -0500 (Thu, 05 Dec 2024)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_20
git_last_commit: 1cacd4c
git_last_commit_date: 2024-10-29 10:38:48 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  NO, package depends on 'metagenomeSeq' which is not available
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'metagenomeSeq' which is not available
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'metagenomeSeq' which is not available
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: 1.20.0
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_1.20.0.tar.gz
StartedAt: 2024-12-06 23:31:41 -0500 (Fri, 06 Dec 2024)
EndedAt: 2024-12-06 23:34:31 -0500 (Fri, 06 Dec 2024)
EllapsedTime: 170.1 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_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.20.0’
* 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 91.67  1.693  93.556
* 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-3.20-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
** 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
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"
2024-12-06 23:33:47.584201 INFO::Writing function arguments to log file
2024-12-06 23:33:47.631612 INFO::Verifying options selected are valid
2024-12-06 23:33:47.673669 INFO::Determining format of input files
2024-12-06 23:33:47.675599 INFO::Input format is data samples as rows and metadata samples as rows
2024-12-06 23:33:47.682197 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-12-06 23:33:47.683944 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-12-06 23:33:47.686522 INFO::Filter data based on min abundance and min prevalence
2024-12-06 23:33:47.687544 INFO::Total samples in data: 1595
2024-12-06 23:33:47.688392 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-12-06 23:33:47.701399 INFO::Total filtered features: 0
2024-12-06 23:33:47.702859 INFO::Filtered feature names from abundance and prevalence filtering:
2024-12-06 23:33:47.712736 INFO::Total filtered features with variance filtering: 0
2024-12-06 23:33:47.714563 INFO::Filtered feature names from variance filtering:
2024-12-06 23:33:47.715738 INFO::Running selected normalization method: TSS
2024-12-06 23:33:49.003491 INFO::Bypass z-score application to metadata
2024-12-06 23:33:49.005229 INFO::Running selected transform method: AST
2024-12-06 23:33:49.023614 INFO::Running selected analysis method: LM
2024-12-06 23:33:49.580338 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-12-06 23:33:49.993601 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-12-06 23:33:50.188414 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-12-06 23:33:50.367561 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-12-06 23:33:50.554185 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-12-06 23:33:50.725706 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-12-06 23:33:50.8994 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-12-06 23:33:51.085989 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-12-06 23:33:51.264509 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-12-06 23:33:51.446957 WARNING::Fitting problem for feature 9 a warning was issued
2024-12-06 23:33:51.620931 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-12-06 23:33:51.793938 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-12-06 23:33:51.960774 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-12-06 23:33:52.127816 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-12-06 23:33:52.306767 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-12-06 23:33:52.487501 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-12-06 23:33:52.662333 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-12-06 23:33:52.842434 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-12-06 23:33:53.023095 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-12-06 23:33:53.200986 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-12-06 23:33:53.356746 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-12-06 23:33:53.544397 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-12-06 23:33:53.726069 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-12-06 23:33:53.900122 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-12-06 23:33:54.076455 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-12-06 23:33:54.257539 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-12-06 23:33:54.440513 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-12-06 23:33:54.634738 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-12-06 23:33:54.811288 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-12-06 23:33:54.984989 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-12-06 23:33:55.172086 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-12-06 23:33:55.337815 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-12-06 23:33:55.532126 INFO::Fitting model to feature number 32, Prevotella.copri
2024-12-06 23:33:55.709293 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-12-06 23:33:55.897163 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-12-06 23:33:56.058955 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-12-06 23:33:56.238107 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-12-06 23:33:56.403379 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-12-06 23:33:56.579732 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-12-06 23:33:56.735623 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-12-06 23:33:56.904228 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-12-06 23:33:57.084428 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-12-06 23:33:57.256289 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-12-06 23:33:57.440083 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-12-06 23:33:57.621103 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-12-06 23:33:57.78268 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-12-06 23:33:57.973016 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-12-06 23:33:58.431989 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-12-06 23:33:58.605869 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-12-06 23:33:58.770608 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-12-06 23:33:59.246689 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-12-06 23:33:59.413026 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-12-06 23:33:59.591233 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-12-06 23:33:59.768477 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-12-06 23:33:59.958453 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-12-06 23:34:00.120711 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-12-06 23:34:00.298788 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-12-06 23:34:00.488741 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-12-06 23:34:00.647888 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-12-06 23:34:00.826795 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-12-06 23:34:01.003585 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-12-06 23:34:01.166398 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-12-06 23:34:01.336107 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-12-06 23:34:01.52063 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-12-06 23:34:01.686929 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-12-06 23:34:01.850301 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-12-06 23:34:02.015975 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-12-06 23:34:02.130178 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-12-06 23:34:02.289294 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-12-06 23:34:02.469827 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-12-06 23:34:02.640656 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-12-06 23:34:02.811897 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-12-06 23:34:02.97888 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-12-06 23:34:03.141666 INFO::Fitting model to feature number 73, Dialister.invisus
2024-12-06 23:34:03.315059 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-12-06 23:34:03.480848 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-12-06 23:34:03.651894 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-12-06 23:34:03.832537 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-12-06 23:34:04.005525 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-12-06 23:34:04.195974 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-12-06 23:34:04.36767 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-12-06 23:34:04.548636 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-12-06 23:34:04.62594 INFO::Fitting model to feature number 82, Escherichia.coli
2024-12-06 23:34:04.713774 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-12-06 23:34:04.823321 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-12-06 23:34:04.937154 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-12-06 23:34:05.042598 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-12-06 23:34:05.207896 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-12-06 23:34:05.327462 INFO::Counting total values for each feature
2024-12-06 23:34:05.353849 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-12-06 23:34:05.502288 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-12-06 23:34:05.675444 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-12-06 23:34:05.853643 INFO::Writing residuals to file output/fits/residuals.rds
2024-12-06 23:34:05.940453 INFO::Writing fitted values to file output/fits/fitted.rds
2024-12-06 23:34:05.989696 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-12-06 23:34:05.999119 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-12-06 23:34:06.00852 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"
2024-12-06 23:34:06.025774 INFO::Writing function arguments to log file
2024-12-06 23:34:06.03288 INFO::Verifying options selected are valid
2024-12-06 23:34:06.034015 INFO::Determining format of input files
2024-12-06 23:34:06.035181 INFO::Input format is data samples as rows and metadata samples as rows
2024-12-06 23:34:06.041021 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-12-06 23:34:06.042345 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-12-06 23:34:06.04414 INFO::Filter data based on min abundance and min prevalence
2024-12-06 23:34:06.045493 INFO::Total samples in data: 1595
2024-12-06 23:34:06.046468 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-12-06 23:34:06.051492 INFO::Total filtered features: 0
2024-12-06 23:34:06.052818 INFO::Filtered feature names from abundance and prevalence filtering:
2024-12-06 23:34:06.069961 INFO::Total filtered features with variance filtering: 0
2024-12-06 23:34:06.071594 INFO::Filtered feature names from variance filtering:
2024-12-06 23:34:06.072462 INFO::Running selected normalization method: NONE
2024-12-06 23:34:06.073261 INFO::Bypass z-score application to metadata
2024-12-06 23:34:06.074059 INFO::Running selected transform method: AST
2024-12-06 23:34:06.113756 INFO::Running selected analysis method: LM
2024-12-06 23:34:06.116926 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-12-06 23:34:06.281965 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-12-06 23:34:06.444264 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-12-06 23:34:06.618517 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-12-06 23:34:06.781213 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-12-06 23:34:06.952183 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-12-06 23:34:07.12094 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-12-06 23:34:07.28234 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-12-06 23:34:07.450215 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-12-06 23:34:07.609794 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-12-06 23:34:07.786858 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-12-06 23:34:07.923527 WARNING::Fitting problem for feature 11 a warning was issued
2024-12-06 23:34:08.136431 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-12-06 23:34:08.301561 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-12-06 23:34:08.436768 WARNING::Fitting problem for feature 13 a warning was issued
2024-12-06 23:34:08.625603 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-12-06 23:34:08.785993 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-12-06 23:34:08.953851 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-12-06 23:34:09.126914 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-12-06 23:34:09.291901 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-12-06 23:34:09.45623 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-12-06 23:34:09.628165 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-12-06 23:34:09.787271 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-12-06 23:34:09.958069 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-12-06 23:34:10.136749 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-12-06 23:34:10.291978 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-12-06 23:34:10.467874 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-12-06 23:34:10.626049 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-12-06 23:34:10.783957 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-12-06 23:34:10.961412 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-12-06 23:34:11.117223 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-12-06 23:34:11.283704 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-12-06 23:34:11.442302 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-12-06 23:34:11.613918 INFO::Fitting model to feature number 32, Prevotella.copri
2024-12-06 23:34:11.780327 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-12-06 23:34:11.952194 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-12-06 23:34:12.120428 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-12-06 23:34:12.296413 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-12-06 23:34:12.462537 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-12-06 23:34:12.647273 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-12-06 23:34:12.807802 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-12-06 23:34:12.97177 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-12-06 23:34:13.140811 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-12-06 23:34:13.298202 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-12-06 23:34:13.477613 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-12-06 23:34:13.640796 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-12-06 23:34:13.805683 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-12-06 23:34:13.986261 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-12-06 23:34:14.149813 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-12-06 23:34:14.310792 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-12-06 23:34:14.486586 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-12-06 23:34:14.643667 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-12-06 23:34:14.79159 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-12-06 23:34:14.966885 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-12-06 23:34:15.112451 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-12-06 23:34:15.274642 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-12-06 23:34:15.430673 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-12-06 23:34:15.590518 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-12-06 23:34:15.772039 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-12-06 23:34:15.930341 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-12-06 23:34:16.105064 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-12-06 23:34:16.27157 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-12-06 23:34:16.423304 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-12-06 23:34:16.592715 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-12-06 23:34:16.744586 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-12-06 23:34:16.91601 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-12-06 23:34:17.073426 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-12-06 23:34:17.254871 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-12-06 23:34:17.413833 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-12-06 23:34:17.576585 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-12-06 23:34:17.749559 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-12-06 23:34:17.916143 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-12-06 23:34:18.090242 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-12-06 23:34:18.268164 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-12-06 23:34:18.325698 WARNING::Fitting problem for feature 72 a warning was issued
2024-12-06 23:34:18.485099 INFO::Fitting model to feature number 73, Dialister.invisus
2024-12-06 23:34:18.660768 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-12-06 23:34:18.821281 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-12-06 23:34:18.999707 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-12-06 23:34:19.166561 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-12-06 23:34:19.323418 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-12-06 23:34:19.497483 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-12-06 23:34:19.66292 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-12-06 23:34:19.834699 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-12-06 23:34:20.003673 INFO::Fitting model to feature number 82, Escherichia.coli
2024-12-06 23:34:20.174259 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-12-06 23:34:20.325938 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-12-06 23:34:20.497505 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-12-06 23:34:20.654101 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-12-06 23:34:20.834952 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-12-06 23:34:21.033449 INFO::Counting total values for each feature
2024-12-06 23:34:21.059982 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-12-06 23:34:21.205283 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-12-06 23:34:21.352225 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-12-06 23:34:21.525991 INFO::Writing residuals to file output2/fits/residuals.rds
2024-12-06 23:34:21.636584 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-12-06 23:34:22.034643 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-12-06 23:34:22.045313 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-12-06 23:34:22.052 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 
 35.038   0.795  35.874 

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin291.670 1.69393.556