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This page was generated on 2024-02-20 13:15:01 -0500 (Tue, 20 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
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Package 1112/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.17.0  (landing page)
Lauren McIver
Snapshot Date: 2024-02-19 14:10:08 -0500 (Mon, 19 Feb 2024)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: devel
git_last_commit: a8d86b0
git_last_commit_date: 2023-10-24 11:15:22 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

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: 1.17.0
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_1.17.0.tar.gz
StartedAt: 2024-02-19 23:35:24 -0500 (Mon, 19 Feb 2024)
EndedAt: 2024-02-19 23:39:35 -0500 (Mon, 19 Feb 2024)
EllapsedTime: 251.0 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_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.17.0’
* 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 R 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 87.558  0.913  88.419
* 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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
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"
2024-02-19 23:37:22.135494 INFO::Writing function arguments to log file
2024-02-19 23:37:22.17581 INFO::Verifying options selected are valid
2024-02-19 23:37:22.213249 INFO::Determining format of input files
2024-02-19 23:37:22.214831 INFO::Input format is data samples as rows and metadata samples as rows
2024-02-19 23:37:22.219791 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-02-19 23:37:22.221165 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-02-19 23:37:22.223651 INFO::Filter data based on min abundance and min prevalence
2024-02-19 23:37:22.224552 INFO::Total samples in data: 1595
2024-02-19 23:37:22.225404 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-02-19 23:37:22.229266 INFO::Total filtered features: 0
2024-02-19 23:37:22.230357 INFO::Filtered feature names from abundance and prevalence filtering:
2024-02-19 23:37:22.245231 INFO::Total filtered features with variance filtering: 0
2024-02-19 23:37:22.246512 INFO::Filtered feature names from variance filtering:
2024-02-19 23:37:22.247448 INFO::Running selected normalization method: TSS
2024-02-19 23:37:23.669596 INFO::Bypass z-score application to metadata
2024-02-19 23:37:23.670936 INFO::Running selected transform method: AST
2024-02-19 23:37:23.688691 INFO::Running selected analysis method: LM
2024-02-19 23:37:24.017816 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-02-19 23:37:24.413136 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-02-19 23:37:24.587998 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-02-19 23:37:24.773026 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-02-19 23:37:24.952822 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-02-19 23:37:25.118503 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-02-19 23:37:25.331042 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-02-19 23:37:25.495403 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-02-19 23:37:25.656744 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-02-19 23:37:25.786066 WARNING::Fitting problem for feature 9 a warning was issued
2024-02-19 23:37:25.974477 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-02-19 23:37:26.119937 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-02-19 23:37:26.267246 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-02-19 23:37:26.423861 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-02-19 23:37:26.566344 WARNING::Fitting problem for feature 13 a warning was issued
2024-02-19 23:37:26.745943 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-02-19 23:37:26.931543 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-02-19 23:37:27.084225 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-02-19 23:37:27.263513 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-02-19 23:37:27.448374 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-02-19 23:37:27.615031 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-02-19 23:37:27.757831 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-02-19 23:37:27.917104 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-02-19 23:37:28.359065 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-02-19 23:37:28.513366 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-02-19 23:37:28.657139 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-02-19 23:37:28.819008 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-02-19 23:37:28.975504 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-02-19 23:37:29.118112 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-02-19 23:37:29.267978 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-02-19 23:37:29.448603 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-02-19 23:37:29.601863 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-02-19 23:37:29.745954 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-02-19 23:37:29.914097 INFO::Fitting model to feature number 32, Prevotella.copri
2024-02-19 23:37:30.057316 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-02-19 23:37:30.208201 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-02-19 23:37:30.366614 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-02-19 23:37:30.514477 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-02-19 23:37:30.659992 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-02-19 23:37:30.810241 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-02-19 23:37:30.946139 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-02-19 23:37:31.090213 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-02-19 23:37:31.248038 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-02-19 23:37:31.402545 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-02-19 23:37:31.559157 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-02-19 23:37:31.718986 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-02-19 23:37:31.858842 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-02-19 23:37:32.00272 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-02-19 23:37:32.1545 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-02-19 23:37:32.300686 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-02-19 23:37:32.448496 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-02-19 23:37:32.603525 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-02-19 23:37:32.747989 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-02-19 23:37:32.897314 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-02-19 23:37:33.037607 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-02-19 23:37:33.200764 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-02-19 23:37:33.340633 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-02-19 23:37:33.503894 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-02-19 23:37:33.681708 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-02-19 23:37:33.815578 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-02-19 23:37:33.937143 WARNING::Fitting problem for feature 58 a warning was issued
2024-02-19 23:37:34.105093 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-02-19 23:37:34.271462 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-02-19 23:37:34.417833 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-02-19 23:37:34.569557 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-02-19 23:37:34.729185 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-02-19 23:37:34.873337 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-02-19 23:37:35.01175 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-02-19 23:37:35.156857 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-02-19 23:37:35.297547 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-02-19 23:37:35.44162 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-02-19 23:37:35.601113 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-02-19 23:37:35.7523 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-02-19 23:37:35.918091 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-02-19 23:37:36.057402 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-02-19 23:37:36.195593 INFO::Fitting model to feature number 73, Dialister.invisus
2024-02-19 23:37:36.575519 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-02-19 23:37:36.720055 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-02-19 23:37:36.864443 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-02-19 23:37:37.010404 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-02-19 23:37:37.175929 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-02-19 23:37:37.348695 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-02-19 23:37:37.511496 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-02-19 23:37:37.667089 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-02-19 23:37:37.844863 INFO::Fitting model to feature number 82, Escherichia.coli
2024-02-19 23:37:37.992133 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-02-19 23:37:38.129491 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-02-19 23:37:38.273402 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-02-19 23:37:38.420395 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-02-19 23:37:38.557547 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-02-19 23:37:38.738538 INFO::Counting total values for each feature
2024-02-19 23:37:38.77122 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-02-19 23:37:38.916096 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-02-19 23:37:39.066814 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-02-19 23:37:39.218431 INFO::Writing residuals to file output/fits/residuals.rds
2024-02-19 23:37:39.277207 INFO::Writing fitted values to file output/fits/fitted.rds
2024-02-19 23:37:39.309991 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-02-19 23:37:39.316215 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-02-19 23:37:39.323277 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"
2024-02-19 23:37:39.338643 INFO::Writing function arguments to log file
2024-02-19 23:37:39.345059 INFO::Verifying options selected are valid
2024-02-19 23:37:39.346182 INFO::Determining format of input files
2024-02-19 23:37:39.34734 INFO::Input format is data samples as rows and metadata samples as rows
2024-02-19 23:37:39.352325 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-02-19 23:37:39.353376 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-02-19 23:37:39.355223 INFO::Filter data based on min abundance and min prevalence
2024-02-19 23:37:39.356193 INFO::Total samples in data: 1595
2024-02-19 23:37:39.357099 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-02-19 23:37:39.390061 INFO::Total filtered features: 0
2024-02-19 23:37:39.391858 INFO::Filtered feature names from abundance and prevalence filtering:
2024-02-19 23:37:39.399113 INFO::Total filtered features with variance filtering: 0
2024-02-19 23:37:39.400221 INFO::Filtered feature names from variance filtering:
2024-02-19 23:37:39.401086 INFO::Running selected normalization method: NONE
2024-02-19 23:37:39.401973 INFO::Bypass z-score application to metadata
2024-02-19 23:37:39.402806 INFO::Running selected transform method: AST
2024-02-19 23:37:39.417954 INFO::Running selected analysis method: LM
2024-02-19 23:37:39.419631 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-02-19 23:37:39.557121 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-02-19 23:37:39.698227 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-02-19 23:37:39.839314 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-02-19 23:37:39.981455 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-02-19 23:37:40.111843 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-02-19 23:37:40.253053 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-02-19 23:37:40.391077 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-02-19 23:37:40.530843 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-02-19 23:37:40.668117 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-02-19 23:37:40.805842 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-02-19 23:37:40.949572 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-02-19 23:37:41.087587 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-02-19 23:37:41.198966 WARNING::Fitting problem for feature 13 a warning was issued
2024-02-19 23:37:41.343612 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-02-19 23:37:41.48461 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-02-19 23:37:41.637481 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-02-19 23:37:41.788129 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-02-19 23:37:41.937678 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-02-19 23:37:42.079591 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-02-19 23:37:42.217589 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-02-19 23:37:42.372033 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-02-19 23:37:42.509261 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-02-19 23:37:42.645379 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-02-19 23:37:42.776024 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-02-19 23:37:42.925212 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-02-19 23:37:43.061651 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-02-19 23:37:43.201859 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-02-19 23:37:43.343053 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-02-19 23:37:43.483605 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-02-19 23:37:43.610873 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-02-19 23:37:43.745606 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-02-19 23:37:43.880544 INFO::Fitting model to feature number 32, Prevotella.copri
2024-02-19 23:37:44.02935 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-02-19 23:37:44.16595 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-02-19 23:37:44.30914 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-02-19 23:37:44.458075 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-02-19 23:37:44.6066 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-02-19 23:37:44.741323 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-02-19 23:37:44.877066 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-02-19 23:37:45.008483 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-02-19 23:37:45.148041 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-02-19 23:37:45.284668 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-02-19 23:37:45.419001 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-02-19 23:37:45.565621 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-02-19 23:37:45.702733 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-02-19 23:37:45.836816 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-02-19 23:37:45.976858 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-02-19 23:37:46.113568 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-02-19 23:37:46.249783 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-02-19 23:37:46.385761 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-02-19 23:37:46.519694 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-02-19 23:37:46.660647 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-02-19 23:37:46.792211 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-02-19 23:37:46.934259 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-02-19 23:37:47.072402 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-02-19 23:37:47.205362 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-02-19 23:37:47.375867 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-02-19 23:37:47.521519 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-02-19 23:37:47.668124 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-02-19 23:37:47.817093 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-02-19 23:37:47.950093 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-02-19 23:37:48.082757 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-02-19 23:37:48.226121 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-02-19 23:37:48.361767 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-02-19 23:37:48.497641 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-02-19 23:37:48.638163 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-02-19 23:37:48.769584 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-02-19 23:37:48.891727 WARNING::Fitting problem for feature 67 a warning was issued
2024-02-19 23:37:49.037915 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-02-19 23:37:49.172636 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-02-19 23:37:49.319472 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-02-19 23:37:49.469775 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-02-19 23:37:49.635091 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-02-19 23:37:49.685439 WARNING::Fitting problem for feature 72 a warning was issued
2024-02-19 23:37:49.823179 INFO::Fitting model to feature number 73, Dialister.invisus
2024-02-19 23:37:49.957205 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-02-19 23:37:50.097334 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-02-19 23:37:50.248556 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-02-19 23:37:50.392018 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-02-19 23:37:50.529615 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-02-19 23:37:50.673419 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-02-19 23:37:50.837455 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-02-19 23:37:50.971276 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-02-19 23:37:51.112506 INFO::Fitting model to feature number 82, Escherichia.coli
2024-02-19 23:37:51.243199 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-02-19 23:37:51.383197 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-02-19 23:37:51.51423 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-02-19 23:37:51.650159 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-02-19 23:37:51.797601 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-02-19 23:37:51.979616 INFO::Counting total values for each feature
2024-02-19 23:37:52.002958 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-02-19 23:37:52.147161 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-02-19 23:37:52.292571 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-02-19 23:37:52.445741 INFO::Writing residuals to file output2/fits/residuals.rds
2024-02-19 23:37:52.520302 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-02-19 23:37:52.592421 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-02-19 23:37:52.598206 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-02-19 23:37:52.603547 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 6 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 30.907   0.749  31.644 

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin287.558 0.91388.419