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This page was generated on 2025-02-04 11:43 -0500 (Tue, 04 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4716
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4478
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4489
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4442
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 1133/2295HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 0.99.4  (landing page)
William Nickols
Snapshot Date: 2025-02-03 13:40 -0500 (Mon, 03 Feb 2025)
git_url: https://git.bioconductor.org/packages/maaslin3
git_branch: devel
git_last_commit: 05599a9
git_last_commit_date: 2025-01-31 13:14:26 -0500 (Fri, 31 Jan 2025)
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  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for maaslin3 on lconway

To the developers/maintainers of the maaslin3 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.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: maaslin3
Version: 0.99.4
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_0.99.4.tar.gz
StartedAt: 2025-02-03 21:24:54 -0500 (Mon, 03 Feb 2025)
EndedAt: 2025-02-03 21:34:14 -0500 (Mon, 03 Feb 2025)
EllapsedTime: 560.2 seconds
RetCode: 0
Status:   OK  
CheckDir: maaslin3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_0.99.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2025-01-22 r87618)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘0.99.4’
* 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 ‘maaslin3’ 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 ... OK
* 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
maaslin_plot_results               40.283  1.218  41.812
maaslin_plot_results_from_output   39.795  1.235  41.372
maaslin3                           21.573  0.994  22.778
maaslin_contrast_test              19.683  0.990  20.874
maaslin_write_results_lefse_format 17.666  0.810  18.590
maaslin_write_results              15.525  0.558  16.211
maaslin_fit                        14.144  0.717  14.966
* 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: OK

Installation output

maaslin3.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL maaslin3
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘maaslin3’ ...
** this is package ‘maaslin3’ version ‘0.99.4’
** 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 (maaslin3)

Tests output

maaslin3.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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

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

> library(testthat)
> library(maaslin3)
> 
> test_check("maaslin3")
2025-02-03 21:31:26.890543 WARNING::Fitting problem for feature 50 returning NA
2025-02-03 21:31:27.671398 WARNING::Fitting problem for feature 62 returning NA
2025-02-03 21:31:27.77824 WARNING::Fitting problem for feature 74 returning NA
2025-02-03 21:31:27.807806 WARNING::Fitting problem for feature 78 returning NA
2025-02-03 21:31:27.851391 WARNING::Fitting problem for feature 84 returning NA
2025-02-03 21:31:27.972604 WARNING::Fitting problem for feature 96 returning NA
2025-02-03 21:31:27.980513 WARNING::Fitting problem for feature 97 returning NA
2025-02-03 21:31:27.998036 WARNING::Fitting problem for feature 99 returning NA
2025-02-03 21:31:28.125351 WARNING::Fitting problem for feature 114 returning NA
2025-02-03 21:31:28.132573 WARNING::Fitting problem for feature 115 returning NA
2025-02-03 21:31:28.212121 WARNING::Fitting problem for feature 123 returning NA
2025-02-03 21:31:28.269675 WARNING::Fitting problem for feature 130 returning NA
2025-02-03 21:31:28.286189 WARNING::Fitting problem for feature 132 returning NA
2025-02-03 21:31:28.338687 WARNING::Fitting problem for feature 139 returning NA
2025-02-03 21:31:28.424654 WARNING::Fitting problem for feature 150 returning NA
2025-02-03 21:31:45.956733 WARNING::Fitting problem for feature 50 returning NA
2025-02-03 21:31:46.048784 WARNING::Fitting problem for feature 62 returning NA
2025-02-03 21:31:46.144908 WARNING::Fitting problem for feature 74 returning NA
2025-02-03 21:31:46.170572 WARNING::Fitting problem for feature 78 returning NA
2025-02-03 21:31:46.205407 WARNING::Fitting problem for feature 84 returning NA
2025-02-03 21:31:46.292213 WARNING::Fitting problem for feature 96 returning NA
2025-02-03 21:31:46.29801 WARNING::Fitting problem for feature 97 returning NA
2025-02-03 21:31:46.313449 WARNING::Fitting problem for feature 99 returning NA
2025-02-03 21:31:46.425171 WARNING::Fitting problem for feature 114 returning NA
2025-02-03 21:31:46.431576 WARNING::Fitting problem for feature 115 returning NA
2025-02-03 21:31:46.493217 WARNING::Fitting problem for feature 123 returning NA
2025-02-03 21:31:46.550055 WARNING::Fitting problem for feature 130 returning NA
2025-02-03 21:31:46.566339 WARNING::Fitting problem for feature 132 returning NA
2025-02-03 21:31:46.620807 WARNING::Fitting problem for feature 139 returning NA
2025-02-03 21:31:46.723883 WARNING::Fitting problem for feature 150 returning NA
2025-02-03 21:31:50.125 R[93260:83135171] XType: com.apple.fonts is not accessible.
2025-02-03 21:31:50.126 R[93260:83135171] XType: XTFontStaticRegistry is enabled.
2025-02-03 21:32:06.455016 WARNING::Fitting problem for feature 50 returning NA
2025-02-03 21:32:06.594167 WARNING::Fitting problem for feature 62 returning NA
2025-02-03 21:32:06.684829 WARNING::Fitting problem for feature 74 returning NA
2025-02-03 21:32:06.71324 WARNING::Fitting problem for feature 78 returning NA
2025-02-03 21:32:06.757204 WARNING::Fitting problem for feature 84 returning NA
2025-02-03 21:32:06.847853 WARNING::Fitting problem for feature 96 returning NA
2025-02-03 21:32:06.855821 WARNING::Fitting problem for feature 97 returning NA
2025-02-03 21:32:06.869612 WARNING::Fitting problem for feature 99 returning NA
2025-02-03 21:32:06.991255 WARNING::Fitting problem for feature 114 returning NA
2025-02-03 21:32:07.000417 WARNING::Fitting problem for feature 115 returning NA
2025-02-03 21:32:07.987886 WARNING::Fitting problem for feature 123 returning NA
2025-02-03 21:32:08.038781 WARNING::Fitting problem for feature 130 returning NA
2025-02-03 21:32:08.054813 WARNING::Fitting problem for feature 132 returning NA
2025-02-03 21:32:08.11154 WARNING::Fitting problem for feature 139 returning NA
2025-02-03 21:32:08.20262 WARNING::Fitting problem for feature 150 returning NA
2025-02-03 21:32:22.252253 WARNING::Fitting problem for feature 50 returning NA
2025-02-03 21:32:22.35434 WARNING::Fitting problem for feature 62 returning NA
2025-02-03 21:32:22.454757 WARNING::Fitting problem for feature 74 returning NA
2025-02-03 21:32:22.486639 WARNING::Fitting problem for feature 78 returning NA
2025-02-03 21:32:22.52976 WARNING::Fitting problem for feature 84 returning NA
2025-02-03 21:32:22.662463 WARNING::Fitting problem for feature 96 returning NA
2025-02-03 21:32:22.669887 WARNING::Fitting problem for feature 97 returning NA
2025-02-03 21:32:22.685517 WARNING::Fitting problem for feature 99 returning NA
2025-02-03 21:32:22.812302 WARNING::Fitting problem for feature 114 returning NA
2025-02-03 21:32:22.82073 WARNING::Fitting problem for feature 115 returning NA
2025-02-03 21:32:22.886403 WARNING::Fitting problem for feature 123 returning NA
2025-02-03 21:32:22.936464 WARNING::Fitting problem for feature 130 returning NA
2025-02-03 21:32:22.951173 WARNING::Fitting problem for feature 132 returning NA
2025-02-03 21:32:23.002582 WARNING::Fitting problem for feature 139 returning NA
2025-02-03 21:32:23.084421 WARNING::Fitting problem for feature 150 returning NA
2025-02-03 21:32:23.330322 WARNING::Deleting existing residuals file: /tmp/RtmpsvavP2/file16c4c7fa067f4/fits/residuals_linear.rds
2025-02-03 21:32:23.397181 WARNING::Deleting existing fitted file: /tmp/RtmpsvavP2/file16c4c7fa067f4/fits/fitted_linear.rds
2025-02-03 21:32:23.471466 WARNING::Deleting existing residuals file: /tmp/RtmpsvavP2/file16c4c7fa067f4/fits/residuals_logistic.rds
2025-02-03 21:32:23.821924 WARNING::Deleting existing fitted file: /tmp/RtmpsvavP2/file16c4c7fa067f4/fits/fitted_logistic.rds
2025-02-03 21:32:42.654675 WARNING::Fitting problem for feature 50 returning NA
2025-02-03 21:32:42.747383 WARNING::Fitting problem for feature 62 returning NA
2025-02-03 21:32:42.841485 WARNING::Fitting problem for feature 74 returning NA
2025-02-03 21:32:42.871667 WARNING::Fitting problem for feature 78 returning NA
2025-02-03 21:32:42.917619 WARNING::Fitting problem for feature 84 returning NA
2025-02-03 21:32:43.011796 WARNING::Fitting problem for feature 96 returning NA
2025-02-03 21:32:43.017947 WARNING::Fitting problem for feature 97 returning NA
2025-02-03 21:32:43.033659 WARNING::Fitting problem for feature 99 returning NA
2025-02-03 21:32:43.153863 WARNING::Fitting problem for feature 114 returning NA
2025-02-03 21:32:43.159991 WARNING::Fitting problem for feature 115 returning NA
2025-02-03 21:32:43.218946 WARNING::Fitting problem for feature 123 returning NA
2025-02-03 21:32:43.274716 WARNING::Fitting problem for feature 130 returning NA
2025-02-03 21:32:43.292973 WARNING::Fitting problem for feature 132 returning NA
2025-02-03 21:32:43.339461 WARNING::Fitting problem for feature 139 returning NA
2025-02-03 21:32:43.424704 WARNING::Fitting problem for feature 150 returning NA
2025-02-03 21:32:57.598142 WARNING::Fitting problem for feature 50 returning NA
2025-02-03 21:32:57.697487 WARNING::Fitting problem for feature 62 returning NA
2025-02-03 21:32:57.80386 WARNING::Fitting problem for feature 74 returning NA
2025-02-03 21:32:57.835592 WARNING::Fitting problem for feature 78 returning NA
2025-02-03 21:32:57.883758 WARNING::Fitting problem for feature 84 returning NA
2025-02-03 21:32:57.975261 WARNING::Fitting problem for feature 96 returning NA
2025-02-03 21:32:57.981242 WARNING::Fitting problem for feature 97 returning NA
2025-02-03 21:32:57.994323 WARNING::Fitting problem for feature 99 returning NA
2025-02-03 21:32:58.111973 WARNING::Fitting problem for feature 114 returning NA
2025-02-03 21:32:58.118011 WARNING::Fitting problem for feature 115 returning NA
2025-02-03 21:32:58.184552 WARNING::Fitting problem for feature 123 returning NA
2025-02-03 21:32:58.237557 WARNING::Fitting problem for feature 130 returning NA
2025-02-03 21:32:58.252412 WARNING::Fitting problem for feature 132 returning NA
2025-02-03 21:32:58.304695 WARNING::Fitting problem for feature 139 returning NA
2025-02-03 21:32:58.391004 WARNING::Fitting problem for feature 150 returning NA
2025-02-03 21:32:58.644451 WARNING::Deleting existing residuals file: /tmp/RtmpsvavP2/file16c4c7fa067f4/fits/residuals_linear.rds
2025-02-03 21:32:58.711707 WARNING::Deleting existing fitted file: /tmp/RtmpsvavP2/file16c4c7fa067f4/fits/fitted_linear.rds
2025-02-03 21:32:58.781869 WARNING::Deleting existing residuals file: /tmp/RtmpsvavP2/file16c4c7fa067f4/fits/residuals_logistic.rds
2025-02-03 21:32:59.12768 WARNING::Deleting existing fitted file: /tmp/RtmpsvavP2/file16c4c7fa067f4/fits/fitted_logistic.rds
2025-02-03 21:33:18.547757 WARNING::Fitting problem for feature 50 returning NA
2025-02-03 21:33:18.64023 WARNING::Fitting problem for feature 62 returning NA
2025-02-03 21:33:18.741405 WARNING::Fitting problem for feature 74 returning NA
2025-02-03 21:33:18.77575 WARNING::Fitting problem for feature 78 returning NA
2025-02-03 21:33:18.825008 WARNING::Fitting problem for feature 84 returning NA
2025-02-03 21:33:18.919106 WARNING::Fitting problem for feature 96 returning NA
2025-02-03 21:33:18.925309 WARNING::Fitting problem for feature 97 returning NA
2025-02-03 21:33:18.938078 WARNING::Fitting problem for feature 99 returning NA
2025-02-03 21:33:19.063408 WARNING::Fitting problem for feature 114 returning NA
2025-02-03 21:33:19.072188 WARNING::Fitting problem for feature 115 returning NA
2025-02-03 21:33:19.141711 WARNING::Fitting problem for feature 123 returning NA
2025-02-03 21:33:19.195932 WARNING::Fitting problem for feature 130 returning NA
2025-02-03 21:33:19.211702 WARNING::Fitting problem for feature 132 returning NA
2025-02-03 21:33:19.262567 WARNING::Fitting problem for feature 139 returning NA
2025-02-03 21:33:19.352811 WARNING::Fitting problem for feature 150 returning NA
2025-02-03 21:33:31.717864 WARNING::Fitting problem for feature 50 returning NA
2025-02-03 21:33:31.808197 WARNING::Fitting problem for feature 62 returning NA
2025-02-03 21:33:31.90431 WARNING::Fitting problem for feature 74 returning NA
2025-02-03 21:33:31.932397 WARNING::Fitting problem for feature 78 returning NA
2025-02-03 21:33:31.973401 WARNING::Fitting problem for feature 84 returning NA
2025-02-03 21:33:32.066487 WARNING::Fitting problem for feature 96 returning NA
2025-02-03 21:33:32.073852 WARNING::Fitting problem for feature 97 returning NA
2025-02-03 21:33:32.089423 WARNING::Fitting problem for feature 99 returning NA
2025-02-03 21:33:32.207926 WARNING::Fitting problem for feature 114 returning NA
2025-02-03 21:33:32.21384 WARNING::Fitting problem for feature 115 returning NA
2025-02-03 21:33:32.277033 WARNING::Fitting problem for feature 123 returning NA
2025-02-03 21:33:32.354493 WARNING::Fitting problem for feature 130 returning NA
2025-02-03 21:33:32.371513 WARNING::Fitting problem for feature 132 returning NA
2025-02-03 21:33:32.420337 WARNING::Fitting problem for feature 139 returning NA
2025-02-03 21:33:32.501627 WARNING::Fitting problem for feature 150 returning NA
2025-02-03 21:33:32.718326 WARNING::Deleting existing residuals file: /tmp/RtmpsvavP2/file16c4c7fa067f4/fits/residuals_linear.rds
2025-02-03 21:33:32.786892 WARNING::Deleting existing fitted file: /tmp/RtmpsvavP2/file16c4c7fa067f4/fits/fitted_linear.rds
2025-02-03 21:33:32.856565 WARNING::Deleting existing residuals file: /tmp/RtmpsvavP2/file16c4c7fa067f4/fits/residuals_logistic.rds
2025-02-03 21:33:33.192398 WARNING::Deleting existing fitted file: /tmp/RtmpsvavP2/file16c4c7fa067f4/fits/fitted_logistic.rds
2025-02-03 21:33:51.593036 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-02-03 21:33:51.608312 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-02-03 21:33:51.615436 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-02-03 21:33:51.675625 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-02-03 21:33:51.688471 ERROR::Effect name not found in metadata: d
2025-02-03 21:33:51.693924 ERROR::No user formula provided
2025-02-03 21:33:51.722562 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-02-03 21:33:51.730981 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-02-03 21:33:54.744122 INFO::Writing function arguments to log file
2025-02-03 21:33:54.767322 INFO::Verifying options selected are valid
2025-02-03 21:33:56.735806 INFO::Writing function arguments to log file
2025-02-03 21:33:56.753932 INFO::Verifying options selected are valid
2025-02-03 21:33:56.755504 INFO::Determining format of input files
2025-02-03 21:33:56.756841 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-03 21:33:56.759532 INFO::Running selected normalization method: TSS
2025-02-03 21:33:56.761102 INFO::Creating output feature tables folder
2025-02-03 21:33:56.762356 INFO::Writing normalized data to file /tmp/RtmpsvavP2/file16c4c6079bed8/features/data_norm.tsv
2025-02-03 21:33:56.764845 INFO::Filter data based on min abundance and min prevalence
2025-02-03 21:33:56.765866 INFO::Total samples in data: 16
2025-02-03 21:33:56.76685 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-02-03 21:33:56.770386 INFO::Total filtered features: 0
2025-02-03 21:33:56.772342 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-03 21:33:56.774064 INFO::Total features filtered by non-zero variance filtering: 0
2025-02-03 21:33:56.775614 INFO::Filtered feature names from variance filtering:
2025-02-03 21:33:56.777222 INFO::Writing filtered data to file /tmp/RtmpsvavP2/file16c4c6079bed8/features/filtered_data.tsv
2025-02-03 21:33:56.779788 INFO::Running selected transform method: LOG
2025-02-03 21:33:56.781186 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpsvavP2/file16c4c6079bed8/features/data_transformed.tsv
2025-02-03 21:33:56.783589 INFO::Applying z-score to standardize continuous metadata
2025-02-03 21:33:56.789588 INFO::Running the linear model component
2025-02-03 21:33:56.793703 INFO::Fitting model to feature number 1, a
2025-02-03 21:33:56.800415 INFO::Fitting model to feature number 2, b
2025-02-03 21:33:56.80756 INFO::Fitting model to feature number 3, c
2025-02-03 21:33:56.815688 INFO::Counting total values for each feature
2025-02-03 21:33:56.818752 INFO::Running the logistic model component
2025-02-03 21:33:56.824305 INFO::Fitting model to feature number 1, a
2025-02-03 21:33:56.831863 INFO::Fitting model to feature number 2, b
2025-02-03 21:33:56.840873 INFO::Fitting model to feature number 3, c
2025-02-03 21:33:56.850378 INFO::Counting total values for each feature
2025-02-03 21:33:56.853425 INFO::Re-running abundances for warn_prevalence
2025-02-03 21:33:56.855234 INFO::Running selected normalization method: TSS
2025-02-03 21:33:56.857521 INFO::Running selected transform method: LOG
2025-02-03 21:33:56.860672 INFO::Fitting model to feature number 1, a
2025-02-03 21:33:56.865031 INFO::Fitting model to feature number 2, b
2025-02-03 21:33:56.869242 INFO::Fitting model to feature number 3, c
2025-02-03 21:33:56.976884 INFO::Creating fits folder
2025-02-03 21:33:56.979054 INFO::Writing residuals to file /tmp/RtmpsvavP2/file16c4c6079bed8/fits/residuals_linear.rds
2025-02-03 21:33:56.981219 INFO::Writing fitted values to file /tmp/RtmpsvavP2/file16c4c6079bed8/fits/fitted_linear.rds
2025-02-03 21:33:56.983114 INFO::Writing residuals to file /tmp/RtmpsvavP2/file16c4c6079bed8/fits/residuals_logistic.rds
2025-02-03 21:33:56.984644 INFO::Writing fitted values to file /tmp/RtmpsvavP2/file16c4c6079bed8/fits/fitted_logistic.rds
2025-02-03 21:33:56.988867 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpsvavP2/file16c4c6079bed8/all_results.tsv
2025-02-03 21:33:56.992126 INFO::Writing the significant results without errors (those which have joint q-values less than or equal to the threshold of 0.100000 ) to file (ordered by increasing individual q-values): /tmp/RtmpsvavP2/file16c4c6079bed8/significant_results.tsv
2025-02-03 21:33:56.99498 INFO::Creating output figures folder
2025-02-03 21:33:56.997475 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpsvavP2/file16c4c6079bed8/figures/summary_plot.pdf
2025-02-03 21:33:58.570349 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpsvavP2/file16c4c6079bed8/figures
2025-02-03 21:33:58.572962 INFO::Plotting associations from most to least significant, grouped by metadata
2025-02-03 21:33:58.58084 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-02-03 21:33:59.015576 INFO::Writing summary plot of
                        significant results to file: /tmp/RtmpsvavP2/file16c4c6079bed8/figures/summary_plot.pdf
2025-02-03 21:34:00.377388 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpsvavP2/file16c4c6079bed8/figures
2025-02-03 21:34:00.378996 INFO::Plotting associations from most to least significant, grouped by metadata
2025-02-03 21:34:00.384815 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-02-03 21:34:00.837053 INFO::Running the linear model component
2025-02-03 21:34:00.84146 INFO::Fitting model to feature number 1, a
2025-02-03 21:34:00.847821 INFO::Fitting model to feature number 2, b
2025-02-03 21:34:00.852996 INFO::Fitting model to feature number 3, c
2025-02-03 21:34:00.86038 INFO::Counting total values for each feature
2025-02-03 21:34:00.862331 INFO::Running the logistic model component
2025-02-03 21:34:00.865017 INFO::Fitting model to feature number 1, a
2025-02-03 21:34:00.871721 INFO::Fitting model to feature number 2, b
2025-02-03 21:34:00.880386 INFO::Fitting model to feature number 3, c
2025-02-03 21:34:00.889553 INFO::Counting total values for each feature
2025-02-03 21:34:00.891951 INFO::Re-running abundances for warn_prevalence
2025-02-03 21:34:00.893342 INFO::Running selected normalization method: TSS
2025-02-03 21:34:00.895489 INFO::Running selected transform method: LOG
2025-02-03 21:34:00.898702 INFO::Fitting model to feature number 1, a
2025-02-03 21:34:00.90308 INFO::Fitting model to feature number 2, b
2025-02-03 21:34:00.908938 INFO::Fitting model to feature number 3, c
2025-02-03 21:34:01.015751 INFO::Creating output folder
2025-02-03 21:34:01.016919 INFO::Creating output figures folder
2025-02-03 21:34:01.018506 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpsvavP2/file16c4c48b9a490/figures/summary_plot.pdf
2025-02-03 21:34:02.437289 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpsvavP2/file16c4c48b9a490/figures
2025-02-03 21:34:02.439438 INFO::Plotting associations from most to least significant, grouped by metadata
2025-02-03 21:34:02.44493 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-02-03 21:34:03.525592 INFO::Applying z-score to standardize continuous metadata
2025-02-03 21:34:03.535207 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-02-03 21:34:03.536076 INFO::Bypass z-score application to metadata
2025-02-03 21:34:03.538535 INFO::Bypass z-score application to metadata
2025-02-03 21:34:03.563786 INFO::Determining format of input files
2025-02-03 21:34:03.564895 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-03 21:34:03.566307 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-02-03 21:34:03.579916 INFO::Determining format of input files
2025-02-03 21:34:03.5831 INFO::Input format is data samples as columns and metadata samples as rows
2025-02-03 21:34:03.585269 INFO::Input format is feature_specific_covariate samples as columns
2025-02-03 21:34:03.595003 INFO::Determining format of input files
2025-02-03 21:34:03.596016 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-03 21:34:03.596971 INFO::Input format is feature_specific_covariate samples as columns
2025-02-03 21:34:03.598972 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-02-03 21:34:03.600083 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-02-03 21:34:03.617605 INFO::Running selected transform method: LOG
2025-02-03 21:34:03.619351 INFO::Creating output feature tables folder
2025-02-03 21:34:03.620708 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpsvavP2/file16c4c39d0d51a/features/data_transformed.tsv
2025-02-03 21:34:03.625619 INFO::Running selected transform method: LOG
2025-02-03 21:34:03.626799 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpsvavP2/file16c4c39d0d51a/features/data_transformed.tsv
2025-02-03 21:34:03.631126 INFO::Running selected transform method: PLOG
2025-02-03 21:34:03.633344 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpsvavP2/file16c4c39d0d51a/features/data_transformed.tsv
2025-02-03 21:34:03.637912 INFO::Running selected transform method: NONE
2025-02-03 21:34:03.639075 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpsvavP2/file16c4c39d0d51a/features/data_transformed.tsv
2025-02-03 21:34:03.647932 INFO::Running the linear model component
2025-02-03 21:34:03.652919 INFO::Fitting model to feature number 1, a
2025-02-03 21:34:03.65744 INFO::Fitting model to feature number 2, b
2025-02-03 21:34:03.663033 INFO::Fitting model to feature number 3, c
2025-02-03 21:34:03.673042 INFO::Counting total values for each feature
2025-02-03 21:34:03.675505 INFO::Running the logistic model component
2025-02-03 21:34:03.679781 INFO::Fitting model to feature number 1, a
2025-02-03 21:34:03.687743 INFO::Fitting model to feature number 2, b
2025-02-03 21:34:03.695009 INFO::Fitting model to feature number 3, c
2025-02-03 21:34:03.707217 INFO::Counting total values for each feature
2025-02-03 21:34:03.710311 INFO::Re-running abundances for warn_prevalence
2025-02-03 21:34:03.711804 INFO::Running selected normalization method: TSS
2025-02-03 21:34:03.714099 INFO::Running selected transform method: LOG
2025-02-03 21:34:03.718485 INFO::Fitting model to feature number 1, a
2025-02-03 21:34:03.724228 INFO::Fitting model to feature number 2, b
2025-02-03 21:34:03.729814 INFO::Fitting model to feature number 3, c
2025-02-03 21:34:03.848227 INFO::Creating output folder
2025-02-03 21:34:03.849481 INFO::Creating fits folder
2025-02-03 21:34:03.850582 INFO::Writing residuals to file /tmp/RtmpsvavP2/file16c4c3d56bb9d/fits/residuals_linear.rds
2025-02-03 21:34:03.851962 INFO::Writing fitted values to file /tmp/RtmpsvavP2/file16c4c3d56bb9d/fits/fitted_linear.rds
2025-02-03 21:34:03.853232 INFO::Writing residuals to file /tmp/RtmpsvavP2/file16c4c3d56bb9d/fits/residuals_logistic.rds
2025-02-03 21:34:03.854917 INFO::Writing fitted values to file /tmp/RtmpsvavP2/file16c4c3d56bb9d/fits/fitted_logistic.rds
2025-02-03 21:34:03.858195 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpsvavP2/file16c4c3d56bb9d/all_results.tsv
2025-02-03 21:34:03.860459 INFO::Writing the significant results without errors (those which have joint q-values less than or equal to the threshold of 0.100000 ) to file (ordered by increasing individual q-values): /tmp/RtmpsvavP2/file16c4c3d56bb9d/significant_results.tsv
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 89 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 89 ]
> 
> 
> proc.time()
   user  system elapsed 
163.601   4.411 169.122

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin321.573 0.99422.778
maaslin_check_arguments0.2100.0050.216
maaslin_check_formula0.1770.0100.190
maaslin_compute_formula0.1970.0130.214
maaslin_contrast_test19.683 0.99020.874
maaslin_filter0.6640.1090.805
maaslin_fit14.144 0.71714.966
maaslin_log_arguments0.1910.0090.203
maaslin_normalize0.3980.0430.446
maaslin_plot_results40.283 1.21841.812
maaslin_plot_results_from_output39.795 1.23541.372
maaslin_process_metadata0.6310.0390.677
maaslin_read_data0.1800.0090.191
maaslin_reorder_data0.1960.0110.211
maaslin_transform0.7560.0610.823
maaslin_write_results15.525 0.55816.211
maaslin_write_results_lefse_format17.666 0.81018.590
preprocess_dna_mtx0.0040.0000.004