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"	4716
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4478
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4489
kjohnson3	macOS 13.7.1 Ventura	arm64	R 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*

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: 2025-02-04 02:56:39 -0500 (Tue, 04 Feb 2025)

EndedAt: 2025-02-04 03:07:41 -0500 (Tue, 04 Feb 2025)

EllapsedTime: 662.1 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               48.13   2.54   50.68
maaslin_plot_results_from_output   47.14   2.38   49.53
maaslin3                           28.00   1.22   29.68
maaslin_contrast_test              24.00   1.56   25.56
maaslin_write_results              21.93   1.51   23.54
maaslin_write_results_lefse_format 21.35   1.44   22.76
maaslin_fit                        20.25   1.58   21.85
* 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")
2025-02-04 03:04:22.48299 WARNING::Fitting problem for feature 50 returning NA
2025-02-04 03:04:23.278149 WARNING::Fitting problem for feature 62 returning NA
2025-02-04 03:04:23.387014 WARNING::Fitting problem for feature 74 returning NA
2025-02-04 03:04:23.415506 WARNING::Fitting problem for feature 78 returning NA
2025-02-04 03:04:23.460351 WARNING::Fitting problem for feature 84 returning NA
2025-02-04 03:04:23.56931 WARNING::Fitting problem for feature 96 returning NA
2025-02-04 03:04:23.580772 WARNING::Fitting problem for feature 97 returning NA
2025-02-04 03:04:23.602565 WARNING::Fitting problem for feature 99 returning NA
2025-02-04 03:04:23.757545 WARNING::Fitting problem for feature 114 returning NA
2025-02-04 03:04:23.771215 WARNING::Fitting problem for feature 115 returning NA
2025-02-04 03:04:23.84996 WARNING::Fitting problem for feature 123 returning NA
2025-02-04 03:04:23.900809 WARNING::Fitting problem for feature 130 returning NA
2025-02-04 03:04:23.915341 WARNING::Fitting problem for feature 132 returning NA
2025-02-04 03:04:23.963484 WARNING::Fitting problem for feature 139 returning NA
2025-02-04 03:04:24.043666 WARNING::Fitting problem for feature 150 returning NA
2025-02-04 03:04:44.216393 WARNING::Fitting problem for feature 50 returning NA
2025-02-04 03:04:44.329181 WARNING::Fitting problem for feature 62 returning NA
2025-02-04 03:04:44.424348 WARNING::Fitting problem for feature 74 returning NA
2025-02-04 03:04:44.452094 WARNING::Fitting problem for feature 78 returning NA
2025-02-04 03:04:44.495791 WARNING::Fitting problem for feature 84 returning NA
2025-02-04 03:04:44.640896 WARNING::Fitting problem for feature 96 returning NA
2025-02-04 03:04:44.652874 WARNING::Fitting problem for feature 97 returning NA
2025-02-04 03:04:44.680897 WARNING::Fitting problem for feature 99 returning NA
2025-02-04 03:04:44.878411 WARNING::Fitting problem for feature 114 returning NA
2025-02-04 03:04:44.890405 WARNING::Fitting problem for feature 115 returning NA
2025-02-04 03:04:44.964366 WARNING::Fitting problem for feature 123 returning NA
2025-02-04 03:04:45.016923 WARNING::Fitting problem for feature 130 returning NA
2025-02-04 03:04:45.032631 WARNING::Fitting problem for feature 132 returning NA
2025-02-04 03:04:45.101239 WARNING::Fitting problem for feature 139 returning NA
2025-02-04 03:04:45.183112 WARNING::Fitting problem for feature 150 returning NA
2025-02-04 03:05:07.903577 WARNING::Fitting problem for feature 50 returning NA
2025-02-04 03:05:08.876497 WARNING::Fitting problem for feature 62 returning NA
2025-02-04 03:05:08.987446 WARNING::Fitting problem for feature 74 returning NA
2025-02-04 03:05:09.023444 WARNING::Fitting problem for feature 78 returning NA
2025-02-04 03:05:09.085691 WARNING::Fitting problem for feature 84 returning NA
2025-02-04 03:05:09.225003 WARNING::Fitting problem for feature 96 returning NA
2025-02-04 03:05:09.236347 WARNING::Fitting problem for feature 97 returning NA
2025-02-04 03:05:09.260719 WARNING::Fitting problem for feature 99 returning NA
2025-02-04 03:05:09.425152 WARNING::Fitting problem for feature 114 returning NA
2025-02-04 03:05:09.438366 WARNING::Fitting problem for feature 115 returning NA
2025-02-04 03:05:09.537719 WARNING::Fitting problem for feature 123 returning NA
2025-02-04 03:05:09.618146 WARNING::Fitting problem for feature 130 returning NA
2025-02-04 03:05:09.642198 WARNING::Fitting problem for feature 132 returning NA
2025-02-04 03:05:09.723745 WARNING::Fitting problem for feature 139 returning NA
2025-02-04 03:05:09.836766 WARNING::Fitting problem for feature 150 returning NA
2025-02-04 03:05:27.822912 WARNING::Fitting problem for feature 50 returning NA
2025-02-04 03:05:27.918538 WARNING::Fitting problem for feature 62 returning NA
2025-02-04 03:05:28.063116 WARNING::Fitting problem for feature 74 returning NA
2025-02-04 03:05:28.107937 WARNING::Fitting problem for feature 78 returning NA
2025-02-04 03:05:28.158186 WARNING::Fitting problem for feature 84 returning NA
2025-02-04 03:05:28.269617 WARNING::Fitting problem for feature 96 returning NA
2025-02-04 03:05:28.281889 WARNING::Fitting problem for feature 97 returning NA
2025-02-04 03:05:28.302764 WARNING::Fitting problem for feature 99 returning NA
2025-02-04 03:05:28.477719 WARNING::Fitting problem for feature 114 returning NA
2025-02-04 03:05:28.489502 WARNING::Fitting problem for feature 115 returning NA
2025-02-04 03:05:28.583852 WARNING::Fitting problem for feature 123 returning NA
2025-02-04 03:05:28.645525 WARNING::Fitting problem for feature 130 returning NA
2025-02-04 03:05:28.661526 WARNING::Fitting problem for feature 132 returning NA
2025-02-04 03:05:28.714358 WARNING::Fitting problem for feature 139 returning NA
2025-02-04 03:05:28.807176 WARNING::Fitting problem for feature 150 returning NA
2025-02-04 03:05:29.132701 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea75819b65324/fits/residuals_linear.rds
2025-02-04 03:05:29.209434 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea75819b65324/fits/fitted_linear.rds
2025-02-04 03:05:29.28054 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea75819b65324/fits/residuals_logistic.rds
2025-02-04 03:05:29.56813 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea75819b65324/fits/fitted_logistic.rds
2025-02-04 03:05:50.177826 WARNING::Fitting problem for feature 50 returning NA
2025-02-04 03:05:50.303879 WARNING::Fitting problem for feature 62 returning NA
2025-02-04 03:05:50.3964 WARNING::Fitting problem for feature 74 returning NA
2025-02-04 03:05:50.429672 WARNING::Fitting problem for feature 78 returning NA
2025-02-04 03:05:50.504781 WARNING::Fitting problem for feature 84 returning NA
2025-02-04 03:05:50.631516 WARNING::Fitting problem for feature 96 returning NA
2025-02-04 03:05:50.639352 WARNING::Fitting problem for feature 97 returning NA
2025-02-04 03:05:50.658648 WARNING::Fitting problem for feature 99 returning NA
2025-02-04 03:05:50.848322 WARNING::Fitting problem for feature 114 returning NA
2025-02-04 03:05:50.86211 WARNING::Fitting problem for feature 115 returning NA
2025-02-04 03:05:50.964352 WARNING::Fitting problem for feature 123 returning NA
2025-02-04 03:05:51.075713 WARNING::Fitting problem for feature 130 returning NA
2025-02-04 03:05:51.098347 WARNING::Fitting problem for feature 132 returning NA
2025-02-04 03:05:51.173704 WARNING::Fitting problem for feature 139 returning NA
2025-02-04 03:05:51.301967 WARNING::Fitting problem for feature 150 returning NA
2025-02-04 03:06:08.898561 WARNING::Fitting problem for feature 50 returning NA
2025-02-04 03:06:09.053432 WARNING::Fitting problem for feature 62 returning NA
2025-02-04 03:06:09.166896 WARNING::Fitting problem for feature 74 returning NA
2025-02-04 03:06:09.194544 WARNING::Fitting problem for feature 78 returning NA
2025-02-04 03:06:09.260441 WARNING::Fitting problem for feature 84 returning NA
2025-02-04 03:06:09.423741 WARNING::Fitting problem for feature 96 returning NA
2025-02-04 03:06:09.43847 WARNING::Fitting problem for feature 97 returning NA
2025-02-04 03:06:09.464737 WARNING::Fitting problem for feature 99 returning NA
2025-02-04 03:06:09.659487 WARNING::Fitting problem for feature 114 returning NA
2025-02-04 03:06:09.671737 WARNING::Fitting problem for feature 115 returning NA
2025-02-04 03:06:09.818472 WARNING::Fitting problem for feature 123 returning NA
2025-02-04 03:06:09.897731 WARNING::Fitting problem for feature 130 returning NA
2025-02-04 03:06:09.921785 WARNING::Fitting problem for feature 132 returning NA
2025-02-04 03:06:09.999124 WARNING::Fitting problem for feature 139 returning NA
2025-02-04 03:06:10.129448 WARNING::Fitting problem for feature 150 returning NA
2025-02-04 03:06:10.405864 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea75819b65324/fits/residuals_linear.rds
2025-02-04 03:06:10.456953 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea75819b65324/fits/fitted_linear.rds
2025-02-04 03:06:10.509719 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea75819b65324/fits/residuals_logistic.rds
2025-02-04 03:06:10.769329 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea75819b65324/fits/fitted_logistic.rds
2025-02-04 03:06:31.207255 WARNING::Fitting problem for feature 50 returning NA
2025-02-04 03:06:31.334994 WARNING::Fitting problem for feature 62 returning NA
2025-02-04 03:06:31.473098 WARNING::Fitting problem for feature 74 returning NA
2025-02-04 03:06:31.516719 WARNING::Fitting problem for feature 78 returning NA
2025-02-04 03:06:31.572879 WARNING::Fitting problem for feature 84 returning NA
2025-02-04 03:06:31.71451 WARNING::Fitting problem for feature 96 returning NA
2025-02-04 03:06:31.726628 WARNING::Fitting problem for feature 97 returning NA
2025-02-04 03:06:31.752254 WARNING::Fitting problem for feature 99 returning NA
2025-02-04 03:06:31.913091 WARNING::Fitting problem for feature 114 returning NA
2025-02-04 03:06:31.925147 WARNING::Fitting problem for feature 115 returning NA
2025-02-04 03:06:31.989736 WARNING::Fitting problem for feature 123 returning NA
2025-02-04 03:06:32.04222 WARNING::Fitting problem for feature 130 returning NA
2025-02-04 03:06:32.058262 WARNING::Fitting problem for feature 132 returning NA
2025-02-04 03:06:32.110646 WARNING::Fitting problem for feature 139 returning NA
2025-02-04 03:06:32.204217 WARNING::Fitting problem for feature 150 returning NA
2025-02-04 03:06:48.586439 WARNING::Fitting problem for feature 50 returning NA
2025-02-04 03:06:48.731468 WARNING::Fitting problem for feature 62 returning NA
2025-02-04 03:06:48.868295 WARNING::Fitting problem for feature 74 returning NA
2025-02-04 03:06:48.909823 WARNING::Fitting problem for feature 78 returning NA
2025-02-04 03:06:48.976219 WARNING::Fitting problem for feature 84 returning NA
2025-02-04 03:06:49.104821 WARNING::Fitting problem for feature 96 returning NA
2025-02-04 03:06:49.1119 WARNING::Fitting problem for feature 97 returning NA
2025-02-04 03:06:49.128727 WARNING::Fitting problem for feature 99 returning NA
2025-02-04 03:06:49.255476 WARNING::Fitting problem for feature 114 returning NA
2025-02-04 03:06:49.266526 WARNING::Fitting problem for feature 115 returning NA
2025-02-04 03:06:49.358192 WARNING::Fitting problem for feature 123 returning NA
2025-02-04 03:06:49.414362 WARNING::Fitting problem for feature 130 returning NA
2025-02-04 03:06:49.437649 WARNING::Fitting problem for feature 132 returning NA
2025-02-04 03:06:49.51521 WARNING::Fitting problem for feature 139 returning NA
2025-02-04 03:06:49.648079 WARNING::Fitting problem for feature 150 returning NA
2025-02-04 03:06:49.944686 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea75819b65324/fits/residuals_linear.rds
2025-02-04 03:06:50.004276 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea75819b65324/fits/fitted_linear.rds
2025-02-04 03:06:50.058827 WARNING::Deleting existing residuals file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea75819b65324/fits/residuals_logistic.rds
2025-02-04 03:06:50.384141 WARNING::Deleting existing fitted file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea75819b65324/fits/fitted_logistic.rds
2025-02-04 03:07:09.72811 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-02-04 03:07:09.746171 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-02-04 03:07:09.756418 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-02-04 03:07:09.827684 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-02-04 03:07:09.847237 ERROR::Effect name not found in metadata: d
2025-02-04 03:07:09.857993 ERROR::No user formula provided
2025-02-04 03:07:09.925479 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-02-04 03:07:09.935942 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-02-04 03:07:14.264453 INFO::Writing function arguments to log file
2025-02-04 03:07:14.302271 INFO::Verifying options selected are valid
2025-02-04 03:07:16.87724 INFO::Writing function arguments to log file
2025-02-04 03:07:16.916547 INFO::Verifying options selected are valid
2025-02-04 03:07:16.918355 INFO::Determining format of input files
2025-02-04 03:07:16.920149 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-04 03:07:16.92434 INFO::Running selected normalization method: TSS
2025-02-04 03:07:16.926641 INFO::Creating output feature tables folder
2025-02-04 03:07:16.928896 INFO::Writing normalized data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea758b9b6a71/features/data_norm.tsv
2025-02-04 03:07:16.931795 INFO::Filter data based on min abundance and min prevalence
2025-02-04 03:07:16.93424 INFO::Total samples in data: 16
2025-02-04 03:07:16.936862 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-02-04 03:07:16.941005 INFO::Total filtered features: 0
2025-02-04 03:07:16.94376 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-04 03:07:16.946782 INFO::Total features filtered by non-zero variance filtering: 0
2025-02-04 03:07:16.949525 INFO::Filtered feature names from variance filtering:
2025-02-04 03:07:16.952151 INFO::Writing filtered data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea758b9b6a71/features/filtered_data.tsv
2025-02-04 03:07:16.956443 INFO::Running selected transform method: LOG
2025-02-04 03:07:16.959723 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea758b9b6a71/features/data_transformed.tsv
2025-02-04 03:07:16.964396 INFO::Applying z-score to standardize continuous metadata
2025-02-04 03:07:16.974559 INFO::Running the linear model component
2025-02-04 03:07:16.987675 INFO::Fitting model to feature number 1, a
2025-02-04 03:07:16.997696 INFO::Fitting model to feature number 2, b
2025-02-04 03:07:17.007317 INFO::Fitting model to feature number 3, c
2025-02-04 03:07:17.021327 INFO::Counting total values for each feature
2025-02-04 03:07:17.025615 INFO::Running the logistic model component
2025-02-04 03:07:17.037545 INFO::Fitting model to feature number 1, a
2025-02-04 03:07:17.046287 INFO::Fitting model to feature number 2, b
2025-02-04 03:07:17.055301 INFO::Fitting model to feature number 3, c
2025-02-04 03:07:17.066959 INFO::Counting total values for each feature
2025-02-04 03:07:17.070611 INFO::Re-running abundances for warn_prevalence
2025-02-04 03:07:17.072557 INFO::Running selected normalization method: TSS
2025-02-04 03:07:17.075084 INFO::Running selected transform method: LOG
2025-02-04 03:07:17.083037 INFO::Fitting model to feature number 1, a
2025-02-04 03:07:17.089936 INFO::Fitting model to feature number 2, b
2025-02-04 03:07:17.099382 INFO::Fitting model to feature number 3, c
2025-02-04 03:07:17.233316 INFO::Creating fits folder
2025-02-04 03:07:17.236092 INFO::Writing residuals to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea758b9b6a71/fits/residuals_linear.rds
2025-02-04 03:07:17.238837 INFO::Writing fitted values to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea758b9b6a71/fits/fitted_linear.rds
2025-02-04 03:07:17.242416 INFO::Writing residuals to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea758b9b6a71/fits/residuals_logistic.rds
2025-02-04 03:07:17.24597 INFO::Writing fitted values to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea758b9b6a71/fits/fitted_logistic.rds
2025-02-04 03:07:17.252333 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea758b9b6a71/all_results.tsv
2025-02-04 03:07:17.257421 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\Rtmp4QLOAG\filea758b9b6a71/significant_results.tsv
2025-02-04 03:07:17.261582 INFO::Creating output figures folder
2025-02-04 03:07:17.265403 INFO::Writing summary plot of significant
                        results to file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea758b9b6a71/figures/summary_plot.pdf
2025-02-04 03:07:18.896995 INFO::Writing association plots (one for each significant association) to output folder: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea758b9b6a71/figures
2025-02-04 03:07:18.901015 INFO::Plotting associations from most to least significant, grouped by metadata
2025-02-04 03:07:18.910928 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-02-04 03:07:19.434931 INFO::Writing summary plot of
                        significant results to file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea758b9b6a71/figures/summary_plot.pdf
2025-02-04 03:07:21.082157 INFO::Writing association plots (one for each significant association) to output folder: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea758b9b6a71/figures
2025-02-04 03:07:21.084947 INFO::Plotting associations from most to least significant, grouped by metadata
2025-02-04 03:07:21.093923 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-02-04 03:07:21.604223 INFO::Running the linear model component
2025-02-04 03:07:21.615995 INFO::Fitting model to feature number 1, a
2025-02-04 03:07:21.624939 INFO::Fitting model to feature number 2, b
2025-02-04 03:07:21.633848 INFO::Fitting model to feature number 3, c
2025-02-04 03:07:21.649629 INFO::Counting total values for each feature
2025-02-04 03:07:21.652954 INFO::Running the logistic model component
2025-02-04 03:07:21.662697 INFO::Fitting model to feature number 1, a
2025-02-04 03:07:21.674493 INFO::Fitting model to feature number 2, b
2025-02-04 03:07:21.686323 INFO::Fitting model to feature number 3, c
2025-02-04 03:07:21.699579 INFO::Counting total values for each feature
2025-02-04 03:07:21.70345 INFO::Re-running abundances for warn_prevalence
2025-02-04 03:07:21.70526 INFO::Running selected normalization method: TSS
2025-02-04 03:07:21.707985 INFO::Running selected transform method: LOG
2025-02-04 03:07:21.71934 INFO::Fitting model to feature number 1, a
2025-02-04 03:07:21.72825 INFO::Fitting model to feature number 2, b
2025-02-04 03:07:21.736189 INFO::Fitting model to feature number 3, c
2025-02-04 03:07:21.870716 INFO::Creating output folder
2025-02-04 03:07:21.872569 INFO::Creating output figures folder
2025-02-04 03:07:21.87523 INFO::Writing summary plot of significant
                        results to file: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea7582d9f5094/figures/summary_plot.pdf
2025-02-04 03:07:23.487444 INFO::Writing association plots (one for each significant association) to output folder: E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea7582d9f5094/figures
2025-02-04 03:07:23.489199 INFO::Plotting associations from most to least significant, grouped by metadata
2025-02-04 03:07:23.494358 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-02-04 03:07:24.847008 INFO::Applying z-score to standardize continuous metadata
2025-02-04 03:07:24.860263 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-02-04 03:07:24.862199 INFO::Bypass z-score application to metadata
2025-02-04 03:07:24.867039 INFO::Bypass z-score application to metadata
2025-02-04 03:07:24.95826 INFO::Determining format of input files
2025-02-04 03:07:24.959578 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-04 03:07:24.960702 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-02-04 03:07:24.9686 INFO::Determining format of input files
2025-02-04 03:07:24.969971 INFO::Input format is data samples as columns and metadata samples as rows
2025-02-04 03:07:24.971564 INFO::Input format is feature_specific_covariate samples as columns
2025-02-04 03:07:24.981189 INFO::Determining format of input files
2025-02-04 03:07:24.982576 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-04 03:07:24.983941 INFO::Input format is feature_specific_covariate samples as columns
2025-02-04 03:07:24.985947 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-02-04 03:07:24.986982 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-02-04 03:07:25.026669 INFO::Running selected transform method: LOG
2025-02-04 03:07:25.029172 INFO::Creating output feature tables folder
2025-02-04 03:07:25.031831 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea7581b6b39e7/features/data_transformed.tsv
2025-02-04 03:07:25.039536 INFO::Running selected transform method: LOG
2025-02-04 03:07:25.041987 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea7581b6b39e7/features/data_transformed.tsv
2025-02-04 03:07:25.048923 INFO::Running selected transform method: PLOG
2025-02-04 03:07:25.052153 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea7581b6b39e7/features/data_transformed.tsv
2025-02-04 03:07:25.068396 INFO::Running selected transform method: NONE
2025-02-04 03:07:25.070569 INFO::Writing normalized, filtered, transformed data to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea7581b6b39e7/features/data_transformed.tsv
2025-02-04 03:07:25.127653 INFO::Running the linear model component
2025-02-04 03:07:25.140239 INFO::Fitting model to feature number 1, a
2025-02-04 03:07:25.149704 INFO::Fitting model to feature number 2, b
2025-02-04 03:07:25.159792 INFO::Fitting model to feature number 3, c
2025-02-04 03:07:25.174132 INFO::Counting total values for each feature
2025-02-04 03:07:25.177934 INFO::Running the logistic model component
2025-02-04 03:07:25.189136 INFO::Fitting model to feature number 1, a
2025-02-04 03:07:25.200705 INFO::Fitting model to feature number 2, b
2025-02-04 03:07:25.212353 INFO::Fitting model to feature number 3, c
2025-02-04 03:07:25.229278 INFO::Counting total values for each feature
2025-02-04 03:07:25.233382 INFO::Re-running abundances for warn_prevalence
2025-02-04 03:07:25.235274 INFO::Running selected normalization method: TSS
2025-02-04 03:07:25.238162 INFO::Running selected transform method: LOG
2025-02-04 03:07:25.25037 INFO::Fitting model to feature number 1, a
2025-02-04 03:07:25.260006 INFO::Fitting model to feature number 2, b
2025-02-04 03:07:25.26867 INFO::Fitting model to feature number 3, c
2025-02-04 03:07:25.410108 INFO::Creating output folder
2025-02-04 03:07:25.412347 INFO::Creating fits folder
2025-02-04 03:07:25.414407 INFO::Writing residuals to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea7583f942dc/fits/residuals_linear.rds
2025-02-04 03:07:25.416891 INFO::Writing fitted values to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea7583f942dc/fits/fitted_linear.rds
2025-02-04 03:07:25.419271 INFO::Writing residuals to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea7583f942dc/fits/residuals_logistic.rds
2025-02-04 03:07:25.421654 INFO::Writing fitted values to file E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea7583f942dc/fits/fitted_logistic.rds
2025-02-04 03:07:25.425879 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4QLOAG\filea7583f942dc/all_results.tsv
2025-02-04 03:07:25.429385 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\Rtmp4QLOAG\filea7583f942dc/significant_results.tsv
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 89 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 89 ]
> 
> 
> proc.time()
   user  system elapsed 
 188.90    7.06  196.42

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

name	user	system	elapsed
maaslin3	28.00	1.22	29.68
maaslin_check_arguments	0.33	0.00	0.33
maaslin_check_formula	0.17	0.02	0.21
maaslin_compute_formula	0.34	0.00	0.35
maaslin_contrast_test	24.00	1.56	25.56
maaslin_filter	1.44	0.03	1.48
maaslin_fit	20.25	1.58	21.85
maaslin_log_arguments	0.33	0.00	0.36
maaslin_normalize	0.84	0.13	0.97
maaslin_plot_results	48.13	2.54	50.68
maaslin_plot_results_from_output	47.14	2.38	49.53
maaslin_process_metadata	1.71	0.04	1.75
maaslin_read_data	0.26	0.04	0.31
maaslin_reorder_data	0.27	0.03	0.30
maaslin_transform	2.19	0.14	2.34
maaslin_write_results	21.93	1.51	23.54
maaslin_write_results_lefse_format	21.35	1.44	22.76
preprocess_dna_mtx	0.01	0.00	0.02