Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-01-24 11:40 -0500 (Fri, 24 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4609
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4393
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 3839
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 3835
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4408
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 1128/2286HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.21.0  (landing page)
Lauren McIver
Snapshot Date: 2025-01-23 13:40 -0500 (Thu, 23 Jan 2025)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: devel
git_last_commit: 3dacd30
git_last_commit_date: 2024-10-29 10:38:48 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  ERROR    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for Maaslin2 on palomino7

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: 1.21.0
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings Maaslin2_1.21.0.tar.gz
StartedAt: 2025-01-24 02:32:52 -0500 (Fri, 24 Jan 2025)
EndedAt: 2025-01-24 02:36:22 -0500 (Fri, 24 Jan 2025)
EllapsedTime: 210.3 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings Maaslin2_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 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 '1.21.0'
* 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 112.97   7.64  120.98
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'Maaslin2' ...
** this is package 'Maaslin2' version '1.21.0'
** 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) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 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"
2025-01-24 02:35:34.428515 INFO::Writing function arguments to log file
2025-01-24 02:35:34.480341 INFO::Verifying options selected are valid
2025-01-24 02:35:34.522982 INFO::Determining format of input files
2025-01-24 02:35:34.526493 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-24 02:35:34.545337 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-24 02:35:34.548076 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-01-24 02:35:34.551662 INFO::Filter data based on min abundance and min prevalence
2025-01-24 02:35:34.553656 INFO::Total samples in data: 1595
2025-01-24 02:35:34.55547 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-24 02:35:34.560878 INFO::Total filtered features: 0
2025-01-24 02:35:34.563814 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-24 02:35:34.576514 INFO::Total filtered features with variance filtering: 0
2025-01-24 02:35:34.579381 INFO::Filtered feature names from variance filtering:
2025-01-24 02:35:34.581869 INFO::Running selected normalization method: TSS
2025-01-24 02:35:36.036904 INFO::Bypass z-score application to metadata
2025-01-24 02:35:36.039973 INFO::Running selected transform method: AST
2025-01-24 02:35:36.066745 INFO::Running selected analysis method: LM
2025-01-24 02:35:36.437185 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-24 02:35:36.822756 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-24 02:35:37.040745 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-24 02:35:37.232078 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-24 02:35:37.369739 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-24 02:35:37.504799 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-24 02:35:37.64123 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-24 02:35:37.80555 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-24 02:35:38.041664 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-24 02:35:38.25645 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-24 02:35:38.469762 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-24 02:35:38.685028 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-24 02:35:38.853688 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-24 02:35:38.961701 WARNING::Fitting problem for feature 13 a warning was issued
2025-01-24 02:35:39.109691 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-24 02:35:39.323887 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-24 02:35:39.540588 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-24 02:35:39.729937 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-24 02:35:39.953674 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-24 02:35:40.176783 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-24 02:35:40.374878 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-24 02:35:40.579002 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-24 02:35:40.775906 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-24 02:35:41.002677 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-24 02:35:41.150959 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-24 02:35:41.346332 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-24 02:35:41.558547 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-24 02:35:41.707283 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-24 02:35:41.97881 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-24 02:35:42.197559 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-24 02:35:42.660533 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-24 02:35:42.861611 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-24 02:35:43.080776 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-24 02:35:43.32865 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-24 02:35:43.528242 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-24 02:35:43.708197 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-24 02:35:43.892744 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-24 02:35:44.032977 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-24 02:35:44.212193 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-24 02:35:44.352605 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-24 02:35:44.521902 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-24 02:35:44.711753 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-24 02:35:44.918629 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-24 02:35:45.122535 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-24 02:35:45.250653 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-24 02:35:45.430221 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-24 02:35:45.651664 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-24 02:35:45.780713 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-24 02:35:45.935934 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-24 02:35:46.08433 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-24 02:35:46.207573 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-24 02:35:46.334552 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-24 02:35:46.518741 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-24 02:35:46.711653 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-24 02:35:46.90023 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-24 02:35:47.108442 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-24 02:35:47.314676 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-24 02:35:47.517358 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-24 02:35:47.718633 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-24 02:35:47.938986 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-24 02:35:48.41525 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-24 02:35:48.603387 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-24 02:35:48.811891 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-24 02:35:49.022094 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-24 02:35:49.223715 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-24 02:35:49.369105 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-24 02:35:49.540775 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-24 02:35:49.694554 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-24 02:35:49.841902 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-24 02:35:50.01157 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-24 02:35:50.16284 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-24 02:35:50.310297 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-24 02:35:50.503842 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-24 02:35:50.653797 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-24 02:35:50.777799 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-24 02:35:50.958163 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-24 02:35:51.16739 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-24 02:35:51.373236 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-24 02:35:51.615165 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-24 02:35:51.836485 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-24 02:35:52.007559 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-24 02:35:52.215284 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-24 02:35:52.419761 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-24 02:35:52.58262 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-24 02:35:52.807753 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-24 02:35:52.999972 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-24 02:35:53.141718 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-24 02:35:53.275611 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-24 02:35:53.514119 INFO::Counting total values for each feature
2025-01-24 02:35:53.572024 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-01-24 02:35:54.031355 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-01-24 02:35:54.512891 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-01-24 02:35:54.959952 INFO::Writing residuals to file output/fits/residuals.rds
2025-01-24 02:35:55.018127 INFO::Writing fitted values to file output/fits/fitted.rds
2025-01-24 02:35:55.052974 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-01-24 02:35:55.062245 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-01-24 02:35:55.087019 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"
2025-01-24 02:35:55.148463 INFO::Writing function arguments to log file
2025-01-24 02:35:55.168594 INFO::Verifying options selected are valid
2025-01-24 02:35:55.170471 INFO::Determining format of input files
2025-01-24 02:35:55.172704 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-24 02:35:55.182333 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-24 02:35:55.185359 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-01-24 02:35:55.189203 INFO::Filter data based on min abundance and min prevalence
2025-01-24 02:35:55.19182 INFO::Total samples in data: 1595
2025-01-24 02:35:55.194418 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-24 02:35:55.202519 INFO::Total filtered features: 0
2025-01-24 02:35:55.205261 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-24 02:35:55.218364 INFO::Total filtered features with variance filtering: 0
2025-01-24 02:35:55.221434 INFO::Filtered feature names from variance filtering:
2025-01-24 02:35:55.224094 INFO::Running selected normalization method: NONE
2025-01-24 02:35:55.226688 INFO::Bypass z-score application to metadata
2025-01-24 02:35:55.229174 INFO::Running selected transform method: AST
2025-01-24 02:35:55.264122 INFO::Running selected analysis method: LM
2025-01-24 02:35:55.268523 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-24 02:35:55.408209 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-24 02:35:55.542285 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-24 02:35:55.658334 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-24 02:35:55.857055 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-24 02:35:55.98567 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-24 02:35:56.123024 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-24 02:35:56.312008 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-24 02:35:56.457613 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-24 02:35:56.57531 WARNING::Fitting problem for feature 9 a warning was issued
2025-01-24 02:35:56.780985 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-24 02:35:56.931845 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-24 02:35:57.046727 WARNING::Fitting problem for feature 11 a warning was issued
2025-01-24 02:35:57.228202 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-24 02:35:57.401991 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-24 02:35:57.555998 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-24 02:35:57.682703 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-24 02:35:57.806482 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-24 02:35:57.91646 WARNING::Fitting problem for feature 16 a warning was issued
2025-01-24 02:35:58.100697 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-24 02:35:58.303928 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-24 02:35:58.506627 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-24 02:35:58.654681 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-24 02:35:58.864985 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-24 02:35:59.063336 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-24 02:35:59.220199 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-24 02:35:59.350998 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-24 02:35:59.512145 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-24 02:35:59.679977 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-24 02:35:59.875829 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-24 02:36:00.086171 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-24 02:36:00.236023 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-24 02:36:00.383693 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-24 02:36:00.562995 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-24 02:36:00.706195 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-24 02:36:00.832387 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-24 02:36:00.962723 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-24 02:36:01.160733 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-24 02:36:01.361577 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-24 02:36:01.526019 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-24 02:36:01.677638 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-24 02:36:01.832521 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-24 02:36:01.964916 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-24 02:36:02.159688 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-24 02:36:02.374471 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-24 02:36:02.575388 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-24 02:36:02.786429 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-24 02:36:02.97658 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-24 02:36:03.141762 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-24 02:36:03.345369 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-24 02:36:03.534074 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-24 02:36:03.74345 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-24 02:36:03.920837 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-24 02:36:04.082829 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-24 02:36:04.259775 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-24 02:36:04.46044 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-24 02:36:04.646056 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-24 02:36:04.802469 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-24 02:36:04.927562 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-24 02:36:05.085228 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-24 02:36:05.258714 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-24 02:36:05.422418 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-24 02:36:05.594863 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-24 02:36:05.755629 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-24 02:36:05.952668 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-24 02:36:06.140185 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-24 02:36:06.346882 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-24 02:36:06.536892 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-24 02:36:06.705703 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-24 02:36:06.869721 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-24 02:36:07.009886 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-24 02:36:07.129665 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-24 02:36:07.343297 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-24 02:36:07.529046 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-24 02:36:07.693743 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-24 02:36:07.760303 WARNING::Fitting problem for feature 72 a warning was issued
2025-01-24 02:36:07.948597 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-24 02:36:08.184642 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-24 02:36:08.35815 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-24 02:36:08.578943 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-24 02:36:08.751189 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-24 02:36:08.915941 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-24 02:36:09.061409 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-24 02:36:09.226147 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-24 02:36:09.423596 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-24 02:36:09.618545 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-24 02:36:09.779726 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-24 02:36:09.925302 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-24 02:36:10.051085 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-24 02:36:10.232837 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-24 02:36:10.428912 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-24 02:36:10.636929 INFO::Counting total values for each feature
2025-01-24 02:36:10.661182 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-01-24 02:36:11.139353 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-01-24 02:36:11.519926 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-01-24 02:36:11.986818 INFO::Writing residuals to file output2/fits/residuals.rds
2025-01-24 02:36:12.057921 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-01-24 02:36:12.116192 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-01-24 02:36:12.125139 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-01-24 02:36:12.138158 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 
  38.10    1.21   40.36

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2112.97 7.64120.98