Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2025-01-02 12:05 -0500 (Thu, 02 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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: 2024-12-30 13:00 -0500 (Mon, 30 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 palomino8

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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Maaslin2_1.20.0.tar.gz
StartedAt: 2024-12-31 02:51:36 -0500 (Tue, 31 Dec 2024)
EndedAt: 2024-12-31 02:55:04 -0500 (Tue, 31 Dec 2024)
EllapsedTime: 208.5 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Maaslin2_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 112.59   7.66  120.58
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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"
2024-12-31 02:54:17.727752 INFO::Writing function arguments to log file
2024-12-31 02:54:17.795968 INFO::Verifying options selected are valid
2024-12-31 02:54:17.84335 INFO::Determining format of input files
2024-12-31 02:54:17.846843 INFO::Input format is data samples as rows and metadata samples as rows
2024-12-31 02:54:17.858058 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-12-31 02:54:17.861359 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-12-31 02:54:17.866535 INFO::Filter data based on min abundance and min prevalence
2024-12-31 02:54:17.86932 INFO::Total samples in data: 1595
2024-12-31 02:54:17.882617 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-12-31 02:54:17.890931 INFO::Total filtered features: 0
2024-12-31 02:54:17.894005 INFO::Filtered feature names from abundance and prevalence filtering:
2024-12-31 02:54:17.906077 INFO::Total filtered features with variance filtering: 0
2024-12-31 02:54:17.908142 INFO::Filtered feature names from variance filtering:
2024-12-31 02:54:17.909962 INFO::Running selected normalization method: TSS
2024-12-31 02:54:19.327452 INFO::Bypass z-score application to metadata
2024-12-31 02:54:19.329526 INFO::Running selected transform method: AST
2024-12-31 02:54:19.347094 INFO::Running selected analysis method: LM
2024-12-31 02:54:19.653262 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-12-31 02:54:20.12956 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-12-31 02:54:20.351832 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-12-31 02:54:20.54919 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-12-31 02:54:20.701196 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-12-31 02:54:20.859311 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-12-31 02:54:21.010031 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-12-31 02:54:21.222297 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-12-31 02:54:21.370623 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-12-31 02:54:21.575229 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-12-31 02:54:21.720863 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-12-31 02:54:21.859989 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-12-31 02:54:22.069508 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-12-31 02:54:22.231896 WARNING::Fitting problem for feature 13 a warning was issued
2024-12-31 02:54:22.38531 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-12-31 02:54:22.565981 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-12-31 02:54:23.029448 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-12-31 02:54:23.16045 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-12-31 02:54:23.322681 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-12-31 02:54:23.509146 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-12-31 02:54:23.64928 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-12-31 02:54:23.799309 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-12-31 02:54:23.938226 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-12-31 02:54:24.087714 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-12-31 02:54:24.232481 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-12-31 02:54:24.385272 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-12-31 02:54:24.569582 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-12-31 02:54:24.711784 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-12-31 02:54:24.879431 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-12-31 02:54:25.014908 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-12-31 02:54:25.161483 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-12-31 02:54:25.325361 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-12-31 02:54:25.474026 INFO::Fitting model to feature number 32, Prevotella.copri
2024-12-31 02:54:25.699946 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-12-31 02:54:25.907337 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-12-31 02:54:26.099648 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-12-31 02:54:26.295163 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-12-31 02:54:26.501026 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-12-31 02:54:26.716446 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-12-31 02:54:26.943888 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-12-31 02:54:27.154984 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-12-31 02:54:27.354486 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-12-31 02:54:27.575216 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-12-31 02:54:27.774036 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-12-31 02:54:27.970904 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-12-31 02:54:28.165978 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-12-31 02:54:28.34108 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-12-31 02:54:28.491304 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-12-31 02:54:28.650763 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-12-31 02:54:28.855376 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-12-31 02:54:29.053194 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-12-31 02:54:29.223718 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-12-31 02:54:29.381022 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-12-31 02:54:29.576941 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-12-31 02:54:29.775157 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-12-31 02:54:29.949103 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-12-31 02:54:30.107487 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-12-31 02:54:30.273579 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-12-31 02:54:30.431397 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-12-31 02:54:30.652048 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-12-31 02:54:30.849546 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-12-31 02:54:31.056264 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-12-31 02:54:31.25998 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-12-31 02:54:31.485404 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-12-31 02:54:31.695229 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-12-31 02:54:31.910522 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-12-31 02:54:32.107537 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-12-31 02:54:32.316173 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-12-31 02:54:32.554744 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-12-31 02:54:32.772188 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-12-31 02:54:32.971681 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-12-31 02:54:33.180536 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-12-31 02:54:33.369977 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-12-31 02:54:33.540947 INFO::Fitting model to feature number 73, Dialister.invisus
2024-12-31 02:54:33.742978 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-12-31 02:54:33.944018 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-12-31 02:54:34.105493 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-12-31 02:54:34.260137 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-12-31 02:54:34.454455 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-12-31 02:54:34.650801 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-12-31 02:54:34.877937 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-12-31 02:54:35.097953 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-12-31 02:54:35.295975 INFO::Fitting model to feature number 82, Escherichia.coli
2024-12-31 02:54:35.49758 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-12-31 02:54:35.71659 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-12-31 02:54:35.924123 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-12-31 02:54:36.095911 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-12-31 02:54:36.266115 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-12-31 02:54:36.533102 INFO::Counting total values for each feature
2024-12-31 02:54:36.603054 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-12-31 02:54:37.072471 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-12-31 02:54:37.600219 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-12-31 02:54:38.114865 INFO::Writing residuals to file output/fits/residuals.rds
2024-12-31 02:54:38.159123 INFO::Writing fitted values to file output/fits/fitted.rds
2024-12-31 02:54:38.191964 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-12-31 02:54:38.200749 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-12-31 02:54:38.224525 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"
2024-12-31 02:54:38.268547 INFO::Writing function arguments to log file
2024-12-31 02:54:38.287861 INFO::Verifying options selected are valid
2024-12-31 02:54:38.289593 INFO::Determining format of input files
2024-12-31 02:54:38.291503 INFO::Input format is data samples as rows and metadata samples as rows
2024-12-31 02:54:38.299037 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-12-31 02:54:38.301054 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-12-31 02:54:38.303572 INFO::Filter data based on min abundance and min prevalence
2024-12-31 02:54:38.305316 INFO::Total samples in data: 1595
2024-12-31 02:54:38.30695 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-12-31 02:54:38.312992 INFO::Total filtered features: 0
2024-12-31 02:54:38.315039 INFO::Filtered feature names from abundance and prevalence filtering:
2024-12-31 02:54:38.325074 INFO::Total filtered features with variance filtering: 0
2024-12-31 02:54:38.328148 INFO::Filtered feature names from variance filtering:
2024-12-31 02:54:38.330849 INFO::Running selected normalization method: NONE
2024-12-31 02:54:38.333479 INFO::Bypass z-score application to metadata
2024-12-31 02:54:38.336028 INFO::Running selected transform method: AST
2024-12-31 02:54:38.369803 INFO::Running selected analysis method: LM
2024-12-31 02:54:38.373181 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-12-31 02:54:38.528643 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-12-31 02:54:38.679943 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-12-31 02:54:38.798884 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-12-31 02:54:38.943182 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-12-31 02:54:39.084955 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-12-31 02:54:39.247777 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-12-31 02:54:39.736452 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-12-31 02:54:39.882131 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-12-31 02:54:40.040904 WARNING::Fitting problem for feature 9 a warning was issued
2024-12-31 02:54:40.209366 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-12-31 02:54:40.388153 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-12-31 02:54:40.540459 WARNING::Fitting problem for feature 11 a warning was issued
2024-12-31 02:54:40.717914 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-12-31 02:54:40.913201 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-12-31 02:54:41.122054 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-12-31 02:54:41.300763 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-12-31 02:54:41.500505 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-12-31 02:54:41.668589 WARNING::Fitting problem for feature 16 a warning was issued
2024-12-31 02:54:41.888667 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-12-31 02:54:42.092728 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-12-31 02:54:42.252039 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-12-31 02:54:42.48547 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-12-31 02:54:42.634054 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-12-31 02:54:42.832139 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-12-31 02:54:42.985847 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-12-31 02:54:43.174033 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-12-31 02:54:43.376229 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-12-31 02:54:43.56333 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-12-31 02:54:43.748966 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-12-31 02:54:43.883777 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-12-31 02:54:44.042396 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-12-31 02:54:44.209447 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-12-31 02:54:44.352889 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-12-31 02:54:44.53542 INFO::Fitting model to feature number 32, Prevotella.copri
2024-12-31 02:54:44.670538 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-12-31 02:54:44.794248 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-12-31 02:54:44.947671 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-12-31 02:54:45.125284 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-12-31 02:54:45.343955 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-12-31 02:54:45.544428 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-12-31 02:54:45.722846 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-12-31 02:54:45.857347 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-12-31 02:54:46.022948 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-12-31 02:54:46.170501 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-12-31 02:54:46.312207 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-12-31 02:54:46.475489 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-12-31 02:54:46.601415 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-12-31 02:54:46.751296 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-12-31 02:54:46.892466 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-12-31 02:54:47.032076 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-12-31 02:54:47.229981 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-12-31 02:54:47.419669 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-12-31 02:54:47.552034 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-12-31 02:54:47.745724 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-12-31 02:54:47.898084 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-12-31 02:54:48.058178 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-12-31 02:54:48.258104 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-12-31 02:54:48.441329 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-12-31 02:54:48.631136 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-12-31 02:54:48.832523 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-12-31 02:54:49.017898 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-12-31 02:54:49.207591 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-12-31 02:54:49.407989 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-12-31 02:54:49.597999 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-12-31 02:54:49.745933 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-12-31 02:54:49.89943 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-12-31 02:54:50.051537 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-12-31 02:54:50.228523 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-12-31 02:54:50.355574 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-12-31 02:54:50.48926 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-12-31 02:54:50.6104 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-12-31 02:54:50.742261 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-12-31 02:54:50.866955 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-12-31 02:54:51.309758 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-12-31 02:54:51.389416 WARNING::Fitting problem for feature 72 a warning was issued
2024-12-31 02:54:51.562693 INFO::Fitting model to feature number 73, Dialister.invisus
2024-12-31 02:54:51.690538 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-12-31 02:54:51.820404 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-12-31 02:54:51.963009 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-12-31 02:54:52.094229 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-12-31 02:54:52.21486 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-12-31 02:54:52.341176 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-12-31 02:54:52.542759 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-12-31 02:54:52.703515 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-12-31 02:54:52.832162 INFO::Fitting model to feature number 82, Escherichia.coli
2024-12-31 02:54:52.996188 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-12-31 02:54:53.14351 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-12-31 02:54:53.277912 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-12-31 02:54:53.433703 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-12-31 02:54:53.639525 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-12-31 02:54:53.8448 INFO::Counting total values for each feature
2024-12-31 02:54:53.868258 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-12-31 02:54:54.205146 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-12-31 02:54:54.57431 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-12-31 02:54:55.096156 INFO::Writing residuals to file output2/fits/residuals.rds
2024-12-31 02:54:55.169561 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-12-31 02:54:55.240293 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-12-31 02:54:55.249378 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-12-31 02:54:55.268357 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 5 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
  37.78    1.15   39.17

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2112.59 7.66120.58