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This page was generated on 2024-07-06 11:44 -0400 (Sat, 06 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4643
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4414
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4442
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4391
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 3833
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 1108/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.19.0  (landing page)
Lauren McIver
Snapshot Date: 2024-07-05 14:00 -0400 (Fri, 05 Jul 2024)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: devel
git_last_commit: 2f9ea7a
git_last_commit_date: 2024-04-30 11:16:06 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for Maaslin2 on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: Maaslin2
Version: 1.19.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Maaslin2_1.19.0.tar.gz
StartedAt: 2024-07-06 06:04:04 -0000 (Sat, 06 Jul 2024)
EndedAt: 2024-07-06 06:07:28 -0000 (Sat, 06 Jul 2024)
EllapsedTime: 203.3 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Maaslin2_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.19.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Maaslin2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
maaslin2_association_plots: no visible binding for global variable
  ‘xnames’
Undefined global functions or variables:
  xnames
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
Maaslin2 118.843  0.799 119.904
* 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
  ‘/home/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘Maaslin2’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Maaslin2)

Tests output

Maaslin2.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(Maaslin2)
> 
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2024-07-06 06:06:40.707757 INFO::Writing function arguments to log file
2024-07-06 06:06:40.762357 INFO::Verifying options selected are valid
2024-07-06 06:06:40.806787 INFO::Determining format of input files
2024-07-06 06:06:40.808657 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-06 06:06:40.815768 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-06 06:06:40.817618 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-07-06 06:06:40.820974 INFO::Filter data based on min abundance and min prevalence
2024-07-06 06:06:40.82225 INFO::Total samples in data: 1595
2024-07-06 06:06:40.823509 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-06 06:06:40.833452 INFO::Total filtered features: 0
2024-07-06 06:06:40.835099 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-06 06:06:40.875034 INFO::Total filtered features with variance filtering: 0
2024-07-06 06:06:40.876556 INFO::Filtered feature names from variance filtering:
2024-07-06 06:06:40.877754 INFO::Running selected normalization method: TSS
2024-07-06 06:06:42.327129 INFO::Bypass z-score application to metadata
2024-07-06 06:06:42.328783 INFO::Running selected transform method: AST
2024-07-06 06:06:42.353291 INFO::Running selected analysis method: LM
2024-07-06 06:06:42.966855 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-06 06:06:43.426145 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-06 06:06:43.653826 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-06 06:06:43.887641 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-06 06:06:44.12966 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-06 06:06:44.354109 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-06 06:06:44.573288 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-06 06:06:44.79814 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-06 06:06:44.972735 WARNING::Fitting problem for feature 8 a warning was issued
2024-07-06 06:06:45.205405 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-06 06:06:45.391093 WARNING::Fitting problem for feature 9 a warning was issued
2024-07-06 06:06:45.650811 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-06 06:06:45.929422 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-06 06:06:46.188835 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-06 06:06:46.520551 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-06 06:06:46.732176 WARNING::Fitting problem for feature 13 a warning was issued
2024-07-06 06:06:46.989014 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-06 06:06:47.223116 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-06 06:06:47.482826 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-06 06:06:47.711012 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-06 06:06:47.948068 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-06 06:06:48.206158 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-06 06:06:48.445746 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-06 06:06:48.712815 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-06 06:06:48.992187 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-06 06:06:49.226439 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-06 06:06:49.44594 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-06 06:06:49.695383 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-06 06:06:49.954674 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-06 06:06:50.183246 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-06 06:06:50.438619 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-06 06:06:50.685766 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-06 06:06:50.927084 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-06 06:06:51.144463 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-06 06:06:51.394797 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-06 06:06:51.636715 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-06 06:06:51.889519 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-06 06:06:52.132888 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-06 06:06:52.323167 WARNING::Fitting problem for feature 35 a warning was issued
2024-07-06 06:06:52.5512 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-06 06:06:52.794493 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-06 06:06:53.022143 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-06 06:06:53.257565 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-06 06:06:53.47707 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-06 06:06:53.707715 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-06 06:06:53.943241 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-06 06:06:54.186924 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-06 06:06:54.414884 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-06 06:06:54.666862 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-06 06:06:54.894067 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-06 06:06:55.131752 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-06 06:06:55.365028 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-06 06:06:55.601951 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-06 06:06:55.832153 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-06 06:06:56.066012 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-06 06:06:56.302725 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-06 06:06:56.523229 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-06 06:06:56.770634 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-06 06:06:56.984822 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-06 06:06:57.227982 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-06 06:06:57.485621 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-06 06:06:57.726555 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-06 06:06:57.962865 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-06 06:06:58.194574 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-06 06:06:58.419665 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-06 06:06:58.664473 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-06 06:06:58.902792 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-06 06:06:59.129741 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-06 06:06:59.390656 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-06 06:06:59.619106 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-06 06:06:59.853675 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-06 06:07:00.084683 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-06 06:07:00.314705 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-06 06:07:00.548714 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-06 06:07:00.79163 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-06 06:07:01.010568 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-06 06:07:01.228069 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-06 06:07:01.443377 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-06 06:07:01.672441 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-06 06:07:01.920484 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-06 06:07:02.160736 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-06 06:07:02.42063 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-06 06:07:02.672029 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-06 06:07:02.925648 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-06 06:07:03.163674 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-06 06:07:03.399842 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-06 06:07:03.643855 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-06 06:07:03.864379 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-06 06:07:04.094888 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-06 06:07:04.334686 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-06 06:07:04.557271 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-06 06:07:04.851615 INFO::Counting total values for each feature
2024-07-06 06:07:04.902614 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-07-06 06:07:05.029014 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-07-06 06:07:05.155079 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-07-06 06:07:05.286228 INFO::Writing residuals to file output/fits/residuals.rds
2024-07-06 06:07:05.336348 INFO::Writing fitted values to file output/fits/fitted.rds
2024-07-06 06:07:05.363365 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-07-06 06:07:05.369635 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-07-06 06:07:05.376825 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output/significant_results.tsv
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2024-07-06 06:07:05.394655 INFO::Writing function arguments to log file
2024-07-06 06:07:05.403109 INFO::Verifying options selected are valid
2024-07-06 06:07:05.404536 INFO::Determining format of input files
2024-07-06 06:07:05.406099 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-06 06:07:05.413935 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-06 06:07:05.415757 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-07-06 06:07:05.418254 INFO::Filter data based on min abundance and min prevalence
2024-07-06 06:07:05.41976 INFO::Total samples in data: 1595
2024-07-06 06:07:05.421089 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-06 06:07:05.432043 INFO::Total filtered features: 0
2024-07-06 06:07:05.433585 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-06 06:07:05.475393 INFO::Total filtered features with variance filtering: 0
2024-07-06 06:07:05.477087 INFO::Filtered feature names from variance filtering:
2024-07-06 06:07:05.478439 INFO::Running selected normalization method: NONE
2024-07-06 06:07:05.479644 INFO::Bypass z-score application to metadata
2024-07-06 06:07:05.480772 INFO::Running selected transform method: AST
2024-07-06 06:07:05.503698 INFO::Running selected analysis method: LM
2024-07-06 06:07:05.505753 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-06 06:07:05.725796 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-06 06:07:05.936411 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-06 06:07:06.153955 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-06 06:07:06.36918 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-06 06:07:06.885209 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-06 06:07:07.102401 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-06 06:07:07.310735 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-06 06:07:07.541171 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-06 06:07:07.777073 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-06 06:07:08.001491 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-06 06:07:08.223715 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-06 06:07:08.431364 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-06 06:07:08.661865 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-06 06:07:08.876954 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-06 06:07:09.099103 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-06 06:07:09.267871 WARNING::Fitting problem for feature 16 a warning was issued
2024-07-06 06:07:09.494153 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-06 06:07:09.711034 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-06 06:07:09.920673 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-06 06:07:10.135713 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-06 06:07:10.350816 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-06 06:07:10.562218 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-06 06:07:10.788144 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-06 06:07:11.012484 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-06 06:07:11.239053 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-06 06:07:11.465147 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-06 06:07:11.700479 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-06 06:07:11.919154 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-06 06:07:12.123795 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-06 06:07:12.33882 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-06 06:07:12.547677 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-06 06:07:12.752511 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-06 06:07:12.981928 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-06 06:07:13.184466 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-06 06:07:13.394951 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-06 06:07:13.621074 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-06 06:07:13.837844 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-06 06:07:14.046482 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-06 06:07:14.276035 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-06 06:07:14.476792 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-06 06:07:14.687231 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-06 06:07:14.919136 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-06 06:07:15.155528 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-06 06:07:15.389606 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-06 06:07:15.630294 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-06 06:07:15.859759 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-06 06:07:16.081004 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-06 06:07:16.289941 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-06 06:07:16.515982 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-06 06:07:16.735162 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-06 06:07:16.931628 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-06 06:07:17.146124 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-06 06:07:17.35266 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-06 06:07:17.547964 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-06 06:07:17.7524 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-06 06:07:17.96886 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-06 06:07:18.179162 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-06 06:07:18.384359 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-06 06:07:18.592081 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-06 06:07:18.827417 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-06 06:07:19.038042 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-06 06:07:19.24782 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-06 06:07:19.474056 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-06 06:07:19.693958 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-06 06:07:19.907654 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-06 06:07:20.136131 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-06 06:07:20.349726 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-06 06:07:20.545306 WARNING::Fitting problem for feature 67 a warning was issued
2024-07-06 06:07:20.784229 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-06 06:07:21.009291 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-06 06:07:21.244532 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-06 06:07:21.465101 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-06 06:07:21.673906 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-06 06:07:21.756178 WARNING::Fitting problem for feature 72 a warning was issued
2024-07-06 06:07:21.961589 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-06 06:07:22.176867 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-06 06:07:22.40472 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-06 06:07:22.614888 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-06 06:07:22.840701 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-06 06:07:23.049578 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-06 06:07:23.277339 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-06 06:07:23.494768 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-06 06:07:23.722493 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-06 06:07:23.942233 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-06 06:07:24.168281 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-06 06:07:24.386398 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-06 06:07:24.615932 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-06 06:07:24.824908 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-06 06:07:25.056877 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-06 06:07:25.317399 INFO::Counting total values for each feature
2024-07-06 06:07:25.353106 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-07-06 06:07:25.476004 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-07-06 06:07:25.60026 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-07-06 06:07:25.749125 INFO::Writing residuals to file output2/fits/residuals.rds
2024-07-06 06:07:25.816219 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-07-06 06:07:25.88099 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-07-06 06:07:25.887454 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-07-06 06:07:25.893706 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output2/significant_results.tsv
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 45.867   0.698  46.659

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2118.843 0.799119.904