Multiple platform build/check report for BioC 3.21 - CHECK results for maaslin3 on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4720
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4482
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4493
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4446
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*

CHECK results for maaslin3 on palomino7

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: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:maaslin3.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings maaslin3_0.99.4.tar.gz

StartedAt: 2025-02-15 02:37:20 -0500 (Sat, 15 Feb 2025)

EndedAt: 2025-02-15 02:48:24 -0500 (Sat, 15 Feb 2025)

EllapsedTime: 663.3 seconds

RetCode: 0

Status: OK

CheckDir: maaslin3.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:maaslin3.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings maaslin3_0.99.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/maaslin3.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 '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 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_from_output   46.16   2.45   48.86
maaslin_plot_results               45.75   2.00   47.76
maaslin3                           27.94   1.26   29.37
maaslin_contrast_test              23.98   1.44   25.44
maaslin_write_results_lefse_format 22.00   1.62   23.63
maaslin_write_results              21.00   2.07   23.11
maaslin_fit                        18.34   1.57   19.91
* 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:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL maaslin3
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/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) (2025-01-21 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(maaslin3)
> 
> test_check("maaslin3")
2025-02-15 02:45:00.862557 WARNING::Fitting problem for feature 50 returning NA
2025-02-15 02:45:00.990421 WARNING::Fitting problem for feature 62 returning NA
2025-02-15 02:45:01.145004 WARNING::Fitting problem for feature 74 returning NA
2025-02-15 02:45:01.183022 WARNING::Fitting problem for feature 78 returning NA
2025-02-15 02:45:01.242413 WARNING::Fitting problem for feature 84 returning NA
2025-02-15 02:45:01.347277 WARNING::Fitting problem for feature 96 returning NA
2025-02-15 02:45:01.354074 WARNING::Fitting problem for feature 97 returning NA
2025-02-15 02:45:01.368716 WARNING::Fitting problem for feature 99 returning NA
2025-02-15 02:45:01.490844 WARNING::Fitting problem for feature 114 returning NA
2025-02-15 02:45:01.501066 WARNING::Fitting problem for feature 115 returning NA
2025-02-15 02:45:01.570298 WARNING::Fitting problem for feature 123 returning NA
2025-02-15 02:45:01.641258 WARNING::Fitting problem for feature 130 returning NA
2025-02-15 02:45:01.660889 WARNING::Fitting problem for feature 132 returning NA
2025-02-15 02:45:01.709601 WARNING::Fitting problem for feature 139 returning NA
2025-02-15 02:45:01.800402 WARNING::Fitting problem for feature 150 returning NA
2025-02-15 02:45:23.076654 WARNING::Fitting problem for feature 50 returning NA
2025-02-15 02:45:23.190142 WARNING::Fitting problem for feature 62 returning NA
2025-02-15 02:45:23.341609 WARNING::Fitting problem for feature 74 returning NA
2025-02-15 02:45:23.380905 WARNING::Fitting problem for feature 78 returning NA
2025-02-15 02:45:23.45079 WARNING::Fitting problem for feature 84 returning NA
2025-02-15 02:45:23.607953 WARNING::Fitting problem for feature 96 returning NA
2025-02-15 02:45:23.620073 WARNING::Fitting problem for feature 97 returning NA
2025-02-15 02:45:23.646327 WARNING::Fitting problem for feature 99 returning NA
2025-02-15 02:45:23.844816 WARNING::Fitting problem for feature 114 returning NA
2025-02-15 02:45:23.857382 WARNING::Fitting problem for feature 115 returning NA
2025-02-15 02:45:23.981442 WARNING::Fitting problem for feature 123 returning NA
2025-02-15 02:45:24.061089 WARNING::Fitting problem for feature 130 returning NA
2025-02-15 02:45:24.085585 WARNING::Fitting problem for feature 132 returning NA
2025-02-15 02:45:24.166073 WARNING::Fitting problem for feature 139 returning NA
2025-02-15 02:45:24.299936 WARNING::Fitting problem for feature 150 returning NA
2025-02-15 02:45:49.711176 WARNING::Fitting problem for feature 50 returning NA
2025-02-15 02:45:49.850398 WARNING::Fitting problem for feature 62 returning NA
2025-02-15 02:45:49.987099 WARNING::Fitting problem for feature 74 returning NA
2025-02-15 02:45:50.029759 WARNING::Fitting problem for feature 78 returning NA
2025-02-15 02:45:50.095775 WARNING::Fitting problem for feature 84 returning NA
2025-02-15 02:45:50.244185 WARNING::Fitting problem for feature 96 returning NA
2025-02-15 02:45:50.255724 WARNING::Fitting problem for feature 97 returning NA
2025-02-15 02:45:50.280856 WARNING::Fitting problem for feature 99 returning NA
2025-02-15 02:45:50.460196 WARNING::Fitting problem for feature 114 returning NA
2025-02-15 02:45:50.474796 WARNING::Fitting problem for feature 115 returning NA
2025-02-15 02:45:50.581649 WARNING::Fitting problem for feature 123 returning NA
2025-02-15 02:45:50.671665 WARNING::Fitting problem for feature 130 returning NA
2025-02-15 02:45:50.697142 WARNING::Fitting problem for feature 132 returning NA
2025-02-15 02:45:50.782221 WARNING::Fitting problem for feature 139 returning NA
2025-02-15 02:45:50.913923 WARNING::Fitting problem for feature 150 returning NA
2025-02-15 02:46:06.921238 WARNING::Fitting problem for feature 50 returning NA
2025-02-15 02:46:07.009464 WARNING::Fitting problem for feature 62 returning NA
2025-02-15 02:46:07.161917 WARNING::Fitting problem for feature 74 returning NA
2025-02-15 02:46:07.207746 WARNING::Fitting problem for feature 78 returning NA
2025-02-15 02:46:07.278942 WARNING::Fitting problem for feature 84 returning NA
2025-02-15 02:46:07.434289 WARNING::Fitting problem for feature 96 returning NA
2025-02-15 02:46:07.446227 WARNING::Fitting problem for feature 97 returning NA
2025-02-15 02:46:07.471074 WARNING::Fitting problem for feature 99 returning NA
2025-02-15 02:46:07.694478 WARNING::Fitting problem for feature 114 returning NA
2025-02-15 02:46:07.705959 WARNING::Fitting problem for feature 115 returning NA
2025-02-15 02:46:07.801306 WARNING::Fitting problem for feature 123 returning NA
2025-02-15 02:46:07.877593 WARNING::Fitting problem for feature 130 returning NA
2025-02-15 02:46:07.90093 WARNING::Fitting problem for feature 132 returning NA
2025-02-15 02:46:07.977487 WARNING::Fitting problem for feature 139 returning NA
2025-02-15 02:46:08.11103 WARNING::Fitting problem for feature 150 returning NA
2025-02-15 02:46:08.411541 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928206e2d8f/fits/residuals_linear.rds
2025-02-15 02:46:08.463522 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928206e2d8f/fits/fitted_linear.rds
2025-02-15 02:46:08.537978 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928206e2d8f/fits/residuals_logistic.rds
2025-02-15 02:46:08.896058 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928206e2d8f/fits/fitted_logistic.rds
2025-02-15 02:46:31.767209 WARNING::Fitting problem for feature 50 returning NA
2025-02-15 02:46:31.899443 WARNING::Fitting problem for feature 62 returning NA
2025-02-15 02:46:32.027688 WARNING::Fitting problem for feature 74 returning NA
2025-02-15 02:46:32.06686 WARNING::Fitting problem for feature 78 returning NA
2025-02-15 02:46:32.128863 WARNING::Fitting problem for feature 84 returning NA
2025-02-15 02:46:32.271397 WARNING::Fitting problem for feature 96 returning NA
2025-02-15 02:46:32.28319 WARNING::Fitting problem for feature 97 returning NA
2025-02-15 02:46:32.307767 WARNING::Fitting problem for feature 99 returning NA
2025-02-15 02:46:32.494132 WARNING::Fitting problem for feature 114 returning NA
2025-02-15 02:46:32.507567 WARNING::Fitting problem for feature 115 returning NA
2025-02-15 02:46:32.600688 WARNING::Fitting problem for feature 123 returning NA
2025-02-15 02:46:32.681994 WARNING::Fitting problem for feature 130 returning NA
2025-02-15 02:46:32.713105 WARNING::Fitting problem for feature 132 returning NA
2025-02-15 02:46:33.85611 WARNING::Fitting problem for feature 139 returning NA
2025-02-15 02:46:33.98329 WARNING::Fitting problem for feature 150 returning NA
2025-02-15 02:46:50.424348 WARNING::Fitting problem for feature 50 returning NA
2025-02-15 02:46:50.577426 WARNING::Fitting problem for feature 62 returning NA
2025-02-15 02:46:50.733706 WARNING::Fitting problem for feature 74 returning NA
2025-02-15 02:46:50.779203 WARNING::Fitting problem for feature 78 returning NA
2025-02-15 02:46:50.851715 WARNING::Fitting problem for feature 84 returning NA
2025-02-15 02:46:50.981777 WARNING::Fitting problem for feature 96 returning NA
2025-02-15 02:46:50.993687 WARNING::Fitting problem for feature 97 returning NA
2025-02-15 02:46:51.019168 WARNING::Fitting problem for feature 99 returning NA
2025-02-15 02:46:51.181121 WARNING::Fitting problem for feature 114 returning NA
2025-02-15 02:46:51.189868 WARNING::Fitting problem for feature 115 returning NA
2025-02-15 02:46:51.288598 WARNING::Fitting problem for feature 123 returning NA
2025-02-15 02:46:51.369482 WARNING::Fitting problem for feature 130 returning NA
2025-02-15 02:46:51.39342 WARNING::Fitting problem for feature 132 returning NA
2025-02-15 02:46:51.47306 WARNING::Fitting problem for feature 139 returning NA
2025-02-15 02:46:51.653371 WARNING::Fitting problem for feature 150 returning NA
2025-02-15 02:46:51.996326 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928206e2d8f/fits/residuals_linear.rds
2025-02-15 02:46:52.073919 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928206e2d8f/fits/fitted_linear.rds
2025-02-15 02:46:52.150947 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928206e2d8f/fits/residuals_logistic.rds
2025-02-15 02:46:52.452651 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928206e2d8f/fits/fitted_logistic.rds
2025-02-15 02:47:15.51564 WARNING::Fitting problem for feature 50 returning NA
2025-02-15 02:47:15.635307 WARNING::Fitting problem for feature 62 returning NA
2025-02-15 02:47:15.769902 WARNING::Fitting problem for feature 74 returning NA
2025-02-15 02:47:15.81273 WARNING::Fitting problem for feature 78 returning NA
2025-02-15 02:47:15.873728 WARNING::Fitting problem for feature 84 returning NA
2025-02-15 02:47:15.976619 WARNING::Fitting problem for feature 96 returning NA
2025-02-15 02:47:15.983748 WARNING::Fitting problem for feature 97 returning NA
2025-02-15 02:47:15.999083 WARNING::Fitting problem for feature 99 returning NA
2025-02-15 02:47:16.118961 WARNING::Fitting problem for feature 114 returning NA
2025-02-15 02:47:16.127945 WARNING::Fitting problem for feature 115 returning NA
2025-02-15 02:47:16.190049 WARNING::Fitting problem for feature 123 returning NA
2025-02-15 02:47:16.246421 WARNING::Fitting problem for feature 130 returning NA
2025-02-15 02:47:16.269969 WARNING::Fitting problem for feature 132 returning NA
2025-02-15 02:47:16.350844 WARNING::Fitting problem for feature 139 returning NA
2025-02-15 02:47:16.488103 WARNING::Fitting problem for feature 150 returning NA
2025-02-15 02:47:32.0465 WARNING::Fitting problem for feature 50 returning NA
2025-02-15 02:47:32.185484 WARNING::Fitting problem for feature 62 returning NA
2025-02-15 02:47:32.322576 WARNING::Fitting problem for feature 74 returning NA
2025-02-15 02:47:32.370116 WARNING::Fitting problem for feature 78 returning NA
2025-02-15 02:47:32.434432 WARNING::Fitting problem for feature 84 returning NA
2025-02-15 02:47:32.538848 WARNING::Fitting problem for feature 96 returning NA
2025-02-15 02:47:32.546147 WARNING::Fitting problem for feature 97 returning NA
2025-02-15 02:47:32.56178 WARNING::Fitting problem for feature 99 returning NA
2025-02-15 02:47:32.701296 WARNING::Fitting problem for feature 114 returning NA
2025-02-15 02:47:32.713364 WARNING::Fitting problem for feature 115 returning NA
2025-02-15 02:47:32.786886 WARNING::Fitting problem for feature 123 returning NA
2025-02-15 02:47:32.840439 WARNING::Fitting problem for feature 130 returning NA
2025-02-15 02:47:32.864688 WARNING::Fitting problem for feature 132 returning NA
2025-02-15 02:47:32.944124 WARNING::Fitting problem for feature 139 returning NA
2025-02-15 02:47:33.080125 WARNING::Fitting problem for feature 150 returning NA
2025-02-15 02:47:33.326859 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928206e2d8f/fits/residuals_linear.rds
2025-02-15 02:47:33.379397 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928206e2d8f/fits/fitted_linear.rds
2025-02-15 02:47:33.433364 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928206e2d8f/fits/residuals_logistic.rds
2025-02-15 02:47:33.698624 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928206e2d8f/fits/fitted_logistic.rds
2025-02-15 02:47:54.101505 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-02-15 02:47:54.120476 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-02-15 02:47:54.131058 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-02-15 02:47:54.212539 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-02-15 02:47:54.232008 ERROR::Effect name not found in metadata: d
2025-02-15 02:47:54.242472 ERROR::No user formula provided
2025-02-15 02:47:54.290318 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-02-15 02:47:54.301056 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-02-15 02:47:58.299601 INFO::Writing function arguments to log file
2025-02-15 02:47:58.341109 INFO::Verifying options selected are valid
2025-02-15 02:48:00.661437 INFO::Writing function arguments to log file
2025-02-15 02:48:00.703225 INFO::Verifying options selected are valid
2025-02-15 02:48:00.705095 INFO::Determining format of input files
2025-02-15 02:48:00.706877 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-15 02:48:00.711734 INFO::Running selected normalization method: TSS
2025-02-15 02:48:00.714207 INFO::Creating output feature tables folder
2025-02-15 02:48:00.716439 INFO::Writing normalized data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928671c4959/features/data_norm.tsv
2025-02-15 02:48:00.720152 INFO::Filter data based on min abundance and min prevalence
2025-02-15 02:48:00.721868 INFO::Total samples in data: 16
2025-02-15 02:48:00.723729 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-02-15 02:48:00.72756 INFO::Total filtered features: 0
2025-02-15 02:48:00.72958 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-15 02:48:00.732719 INFO::Total features filtered by non-zero variance filtering: 0
2025-02-15 02:48:00.735335 INFO::Filtered feature names from variance filtering:
2025-02-15 02:48:00.737149 INFO::Writing filtered data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928671c4959/features/filtered_data.tsv
2025-02-15 02:48:00.740099 INFO::Running selected transform method: LOG
2025-02-15 02:48:00.742274 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928671c4959/features/data_transformed.tsv
2025-02-15 02:48:00.745802 INFO::Applying z-score to standardize continuous metadata
2025-02-15 02:48:00.751967 INFO::Running the linear model component
2025-02-15 02:48:00.760688 INFO::Fitting model to feature number 1, a
2025-02-15 02:48:00.767669 INFO::Fitting model to feature number 2, b
2025-02-15 02:48:00.773849 INFO::Fitting model to feature number 3, c
2025-02-15 02:48:00.783281 INFO::Counting total values for each feature
2025-02-15 02:48:00.78651 INFO::Running the logistic model component
2025-02-15 02:48:00.797061 INFO::Fitting model to feature number 1, a
2025-02-15 02:48:00.811106 INFO::Fitting model to feature number 2, b
2025-02-15 02:48:00.820495 INFO::Fitting model to feature number 3, c
2025-02-15 02:48:00.831085 INFO::Counting total values for each feature
2025-02-15 02:48:00.834125 INFO::Re-running abundances for warn_prevalence
2025-02-15 02:48:00.835859 INFO::Running selected normalization method: TSS
2025-02-15 02:48:00.838123 INFO::Running selected transform method: LOG
2025-02-15 02:48:00.845521 INFO::Fitting model to feature number 1, a
2025-02-15 02:48:00.851841 INFO::Fitting model to feature number 2, b
2025-02-15 02:48:00.857969 INFO::Fitting model to feature number 3, c
2025-02-15 02:48:01.004272 INFO::Creating fits folder
2025-02-15 02:48:01.007838 INFO::Writing residuals to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928671c4959/fits/residuals_linear.rds
2025-02-15 02:48:01.011407 INFO::Writing fitted values to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928671c4959/fits/fitted_linear.rds
2025-02-15 02:48:01.014841 INFO::Writing residuals to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928671c4959/fits/residuals_logistic.rds
2025-02-15 02:48:01.017254 INFO::Writing fitted values to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928671c4959/fits/fitted_logistic.rds
2025-02-15 02:48:01.020806 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928671c4959/all_results.tsv
2025-02-15 02:48:01.02382 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): E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928671c4959/significant_results.tsv
2025-02-15 02:48:01.026435 INFO::Creating output figures folder
2025-02-15 02:48:01.028786 INFO::Writing summary plot of significant
                        results to file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928671c4959/figures/summary_plot.pdf
2025-02-15 02:48:02.264785 INFO::Writing association plots (one for each significant association) to output folder: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928671c4959/figures
2025-02-15 02:48:02.268457 INFO::Plotting associations from most to least significant, grouped by metadata
2025-02-15 02:48:02.277412 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-02-15 02:48:02.743432 INFO::Writing summary plot of
                        significant results to file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928671c4959/figures/summary_plot.pdf
2025-02-15 02:48:04.324976 INFO::Writing association plots (one for each significant association) to output folder: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928671c4959/figures
2025-02-15 02:48:04.327003 INFO::Plotting associations from most to least significant, grouped by metadata
2025-02-15 02:48:04.333282 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-02-15 02:48:04.852509 INFO::Running the linear model component
2025-02-15 02:48:04.864812 INFO::Fitting model to feature number 1, a
2025-02-15 02:48:04.874154 INFO::Fitting model to feature number 2, b
2025-02-15 02:48:04.88341 INFO::Fitting model to feature number 3, c
2025-02-15 02:48:04.896502 INFO::Counting total values for each feature
2025-02-15 02:48:04.899825 INFO::Running the logistic model component
2025-02-15 02:48:04.91202 INFO::Fitting model to feature number 1, a
2025-02-15 02:48:04.924139 INFO::Fitting model to feature number 2, b
2025-02-15 02:48:04.93572 INFO::Fitting model to feature number 3, c
2025-02-15 02:48:04.951501 INFO::Counting total values for each feature
2025-02-15 02:48:04.955399 INFO::Re-running abundances for warn_prevalence
2025-02-15 02:48:04.957098 INFO::Running selected normalization method: TSS
2025-02-15 02:48:04.959646 INFO::Running selected transform method: LOG
2025-02-15 02:48:04.970348 INFO::Fitting model to feature number 1, a
2025-02-15 02:48:04.978401 INFO::Fitting model to feature number 2, b
2025-02-15 02:48:04.986087 INFO::Fitting model to feature number 3, c
2025-02-15 02:48:05.128916 INFO::Creating output folder
2025-02-15 02:48:05.131385 INFO::Creating output figures folder
2025-02-15 02:48:05.134308 INFO::Writing summary plot of significant
                        results to file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file139285b401513/figures/summary_plot.pdf
2025-02-15 02:48:06.749038 INFO::Writing association plots (one for each significant association) to output folder: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file139285b401513/figures
2025-02-15 02:48:06.75187 INFO::Plotting associations from most to least significant, grouped by metadata
2025-02-15 02:48:06.760061 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-02-15 02:48:08.064058 INFO::Applying z-score to standardize continuous metadata
2025-02-15 02:48:08.072513 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-02-15 02:48:08.073705 INFO::Bypass z-score application to metadata
2025-02-15 02:48:08.07671 INFO::Bypass z-score application to metadata
2025-02-15 02:48:08.134142 INFO::Determining format of input files
2025-02-15 02:48:08.136544 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-15 02:48:08.138997 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-02-15 02:48:08.154232 INFO::Determining format of input files
2025-02-15 02:48:08.156975 INFO::Input format is data samples as columns and metadata samples as rows
2025-02-15 02:48:08.160187 INFO::Input format is feature_specific_covariate samples as columns
2025-02-15 02:48:08.192052 INFO::Determining format of input files
2025-02-15 02:48:08.194135 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-15 02:48:08.196403 INFO::Input format is feature_specific_covariate samples as columns
2025-02-15 02:48:08.199661 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-02-15 02:48:08.201336 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-02-15 02:48:08.221732 INFO::Running selected transform method: LOG
2025-02-15 02:48:08.224132 INFO::Creating output feature tables folder
2025-02-15 02:48:08.226918 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928328a1405/features/data_transformed.tsv
2025-02-15 02:48:08.234827 INFO::Running selected transform method: LOG
2025-02-15 02:48:08.237422 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928328a1405/features/data_transformed.tsv
2025-02-15 02:48:08.252181 INFO::Running selected transform method: PLOG
2025-02-15 02:48:08.255521 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928328a1405/features/data_transformed.tsv
2025-02-15 02:48:08.261329 INFO::Running selected transform method: NONE
2025-02-15 02:48:08.263306 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file13928328a1405/features/data_transformed.tsv
2025-02-15 02:48:08.278762 INFO::Running the linear model component
2025-02-15 02:48:08.290733 INFO::Fitting model to feature number 1, a
2025-02-15 02:48:08.299807 INFO::Fitting model to feature number 2, b
2025-02-15 02:48:08.308792 INFO::Fitting model to feature number 3, c
2025-02-15 02:48:08.319048 INFO::Counting total values for each feature
2025-02-15 02:48:08.32128 INFO::Running the logistic model component
2025-02-15 02:48:08.328004 INFO::Fitting model to feature number 1, a
2025-02-15 02:48:08.335462 INFO::Fitting model to feature number 2, b
2025-02-15 02:48:08.342531 INFO::Fitting model to feature number 3, c
2025-02-15 02:48:08.352541 INFO::Counting total values for each feature
2025-02-15 02:48:08.354988 INFO::Re-running abundances for warn_prevalence
2025-02-15 02:48:08.356109 INFO::Running selected normalization method: TSS
2025-02-15 02:48:08.357809 INFO::Running selected transform method: LOG
2025-02-15 02:48:08.364715 INFO::Fitting model to feature number 1, a
2025-02-15 02:48:08.37036 INFO::Fitting model to feature number 2, b
2025-02-15 02:48:08.376254 INFO::Fitting model to feature number 3, c
2025-02-15 02:48:08.517375 INFO::Creating output folder
2025-02-15 02:48:08.519912 INFO::Creating fits folder
2025-02-15 02:48:08.522229 INFO::Writing residuals to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file1392833742638/fits/residuals_linear.rds
2025-02-15 02:48:08.524961 INFO::Writing fitted values to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file1392833742638/fits/fitted_linear.rds
2025-02-15 02:48:08.527685 INFO::Writing residuals to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file1392833742638/fits/residuals_logistic.rds
2025-02-15 02:48:08.530413 INFO::Writing fitted values to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file1392833742638/fits/fitted_logistic.rds
2025-02-15 02:48:08.535226 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file1392833742638/all_results.tsv
2025-02-15 02:48:08.539209 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): E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4cHw4d\file1392833742638/significant_results.tsv
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 89 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 89 ]
> 
> 
> proc.time()
   user  system elapsed 
 195.48    7.10  203.17

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

name	user	system	elapsed
maaslin3	27.94	1.26	29.37
maaslin_check_arguments	0.33	0.00	0.33
maaslin_check_formula	0.27	0.00	0.28
maaslin_compute_formula	0.22	0.02	0.23
maaslin_contrast_test	23.98	1.44	25.44
maaslin_filter	2.19	0.15	2.34
maaslin_fit	18.34	1.57	19.91
maaslin_log_arguments	0.22	0.00	0.22
maaslin_normalize	0.89	0.03	0.94
maaslin_plot_results	45.75	2.00	47.76
maaslin_plot_results_from_output	46.16	2.45	48.86
maaslin_process_metadata	1.58	0.05	1.66
maaslin_read_data	0.29	0.01	0.31
maaslin_reorder_data	0.33	0.02	0.36
maaslin_transform	2.05	0.12	2.17
maaslin_write_results	21.00	2.07	23.11
maaslin_write_results_lefse_format	22.00	1.62	23.63
preprocess_dna_mtx	0.02	0.00	0.01