William Nickols
| Snapshot Date: 2025-08-10 13:45 -0400 (Sun, 10 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: ed6ae28 |
| git_last_commit_date: 2025-04-15 13:45:33 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-11 12:11 -0400 (Mon, 11 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4532 |
| 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 1147/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.1.0 (landing page) William Nickols
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| Package: maaslin3 |
| Version: 1.1.0 |
| 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_1.1.0.tar.gz |
| StartedAt: 2025-08-10 20:04:53 -0400 (Sun, 10 Aug 2025) |
| EndedAt: 2025-08-10 20:09:18 -0400 (Sun, 10 Aug 2025) |
| EllapsedTime: 265.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.1.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘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 13.805 0.537 14.413
maaslin_plot_results 13.576 0.638 14.325
maaslin3 8.189 0.463 8.682
maaslin_contrast_test 7.127 0.631 8.080
maaslin_write_results_lefse_format 5.805 0.420 6.252
maaslin_write_results 5.209 0.364 5.577
maaslin_fit 4.998 0.563 5.672
* 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
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-arm64/Resources/library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.1.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (maaslin3)
maaslin3.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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")
2025-08-10 20:07:13.645756 WARNING::Fitting problem for feature 50 returning NA
2025-08-10 20:07:13.672326 WARNING::Fitting problem for feature 62 returning NA
2025-08-10 20:07:13.702918 WARNING::Fitting problem for feature 74 returning NA
2025-08-10 20:07:13.711111 WARNING::Fitting problem for feature 78 returning NA
2025-08-10 20:07:13.730841 WARNING::Fitting problem for feature 84 returning NA
2025-08-10 20:07:13.757585 WARNING::Fitting problem for feature 96 returning NA
2025-08-10 20:07:13.759593 WARNING::Fitting problem for feature 97 returning NA
2025-08-10 20:07:13.763727 WARNING::Fitting problem for feature 99 returning NA
2025-08-10 20:07:13.801823 WARNING::Fitting problem for feature 114 returning NA
2025-08-10 20:07:13.803911 WARNING::Fitting problem for feature 115 returning NA
2025-08-10 20:07:13.82123 WARNING::Fitting problem for feature 123 returning NA
2025-08-10 20:07:13.83508 WARNING::Fitting problem for feature 130 returning NA
2025-08-10 20:07:13.839394 WARNING::Fitting problem for feature 132 returning NA
2025-08-10 20:07:13.853038 WARNING::Fitting problem for feature 139 returning NA
2025-08-10 20:07:13.88115 WARNING::Fitting problem for feature 150 returning NA
2025-08-10 20:07:20.258583 WARNING::Fitting problem for feature 50 returning NA
2025-08-10 20:07:20.286729 WARNING::Fitting problem for feature 62 returning NA
2025-08-10 20:07:20.313863 WARNING::Fitting problem for feature 74 returning NA
2025-08-10 20:07:20.321963 WARNING::Fitting problem for feature 78 returning NA
2025-08-10 20:07:20.334628 WARNING::Fitting problem for feature 84 returning NA
2025-08-10 20:07:20.364696 WARNING::Fitting problem for feature 96 returning NA
2025-08-10 20:07:20.380404 WARNING::Fitting problem for feature 97 returning NA
2025-08-10 20:07:20.384754 WARNING::Fitting problem for feature 99 returning NA
2025-08-10 20:07:20.418601 WARNING::Fitting problem for feature 114 returning NA
2025-08-10 20:07:20.420618 WARNING::Fitting problem for feature 115 returning NA
2025-08-10 20:07:20.438216 WARNING::Fitting problem for feature 123 returning NA
2025-08-10 20:07:20.452041 WARNING::Fitting problem for feature 130 returning NA
2025-08-10 20:07:20.456243 WARNING::Fitting problem for feature 132 returning NA
2025-08-10 20:07:20.470358 WARNING::Fitting problem for feature 139 returning NA
2025-08-10 20:07:20.494566 WARNING::Fitting problem for feature 150 returning NA
2025-08-10 20:07:21.713 R[15504:499415817] XType: Using static font registry.
2025-08-10 20:07:27.783473 WARNING::Fitting problem for feature 50 returning NA
2025-08-10 20:07:27.817583 WARNING::Fitting problem for feature 62 returning NA
2025-08-10 20:07:27.842198 WARNING::Fitting problem for feature 74 returning NA
2025-08-10 20:07:27.849665 WARNING::Fitting problem for feature 78 returning NA
2025-08-10 20:07:27.861219 WARNING::Fitting problem for feature 84 returning NA
2025-08-10 20:07:27.886911 WARNING::Fitting problem for feature 96 returning NA
2025-08-10 20:07:27.888889 WARNING::Fitting problem for feature 97 returning NA
2025-08-10 20:07:27.893021 WARNING::Fitting problem for feature 99 returning NA
2025-08-10 20:07:27.9264 WARNING::Fitting problem for feature 114 returning NA
2025-08-10 20:07:27.928536 WARNING::Fitting problem for feature 115 returning NA
2025-08-10 20:07:27.981044 WARNING::Fitting problem for feature 123 returning NA
2025-08-10 20:07:27.994772 WARNING::Fitting problem for feature 130 returning NA
2025-08-10 20:07:27.998797 WARNING::Fitting problem for feature 132 returning NA
2025-08-10 20:07:28.012668 WARNING::Fitting problem for feature 139 returning NA
2025-08-10 20:07:28.036277 WARNING::Fitting problem for feature 150 returning NA
2025-08-10 20:07:33.482544 WARNING::Fitting problem for feature 50 returning NA
2025-08-10 20:07:33.508535 WARNING::Fitting problem for feature 62 returning NA
2025-08-10 20:07:33.533623 WARNING::Fitting problem for feature 74 returning NA
2025-08-10 20:07:33.541485 WARNING::Fitting problem for feature 78 returning NA
2025-08-10 20:07:33.553546 WARNING::Fitting problem for feature 84 returning NA
2025-08-10 20:07:33.579906 WARNING::Fitting problem for feature 96 returning NA
2025-08-10 20:07:33.581962 WARNING::Fitting problem for feature 97 returning NA
2025-08-10 20:07:33.586186 WARNING::Fitting problem for feature 99 returning NA
2025-08-10 20:07:33.623087 WARNING::Fitting problem for feature 114 returning NA
2025-08-10 20:07:33.625296 WARNING::Fitting problem for feature 115 returning NA
2025-08-10 20:07:33.643858 WARNING::Fitting problem for feature 123 returning NA
2025-08-10 20:07:33.658467 WARNING::Fitting problem for feature 130 returning NA
2025-08-10 20:07:33.663057 WARNING::Fitting problem for feature 132 returning NA
2025-08-10 20:07:33.678076 WARNING::Fitting problem for feature 139 returning NA
2025-08-10 20:07:33.703716 WARNING::Fitting problem for feature 150 returning NA
2025-08-10 20:07:33.793057 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c905b4dd5ba/fits/residuals_linear.rds
2025-08-10 20:07:33.825703 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c905b4dd5ba/fits/fitted_linear.rds
2025-08-10 20:07:33.859563 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c905b4dd5ba/fits/residuals_logistic.rds
2025-08-10 20:07:34.026697 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c905b4dd5ba/fits/fitted_logistic.rds
2025-08-10 20:07:40.451725 WARNING::Fitting problem for feature 50 returning NA
2025-08-10 20:07:40.477949 WARNING::Fitting problem for feature 62 returning NA
2025-08-10 20:07:40.503832 WARNING::Fitting problem for feature 74 returning NA
2025-08-10 20:07:40.511393 WARNING::Fitting problem for feature 78 returning NA
2025-08-10 20:07:40.522959 WARNING::Fitting problem for feature 84 returning NA
2025-08-10 20:07:40.548601 WARNING::Fitting problem for feature 96 returning NA
2025-08-10 20:07:40.550603 WARNING::Fitting problem for feature 97 returning NA
2025-08-10 20:07:40.554674 WARNING::Fitting problem for feature 99 returning NA
2025-08-10 20:07:40.587879 WARNING::Fitting problem for feature 114 returning NA
2025-08-10 20:07:40.589876 WARNING::Fitting problem for feature 115 returning NA
2025-08-10 20:07:40.607016 WARNING::Fitting problem for feature 123 returning NA
2025-08-10 20:07:40.620733 WARNING::Fitting problem for feature 130 returning NA
2025-08-10 20:07:40.62499 WARNING::Fitting problem for feature 132 returning NA
2025-08-10 20:07:40.638971 WARNING::Fitting problem for feature 139 returning NA
2025-08-10 20:07:40.663398 WARNING::Fitting problem for feature 150 returning NA
2025-08-10 20:07:46.107564 WARNING::Fitting problem for feature 50 returning NA
2025-08-10 20:07:46.130467 WARNING::Fitting problem for feature 62 returning NA
2025-08-10 20:07:46.152699 WARNING::Fitting problem for feature 74 returning NA
2025-08-10 20:07:46.159413 WARNING::Fitting problem for feature 78 returning NA
2025-08-10 20:07:46.169862 WARNING::Fitting problem for feature 84 returning NA
2025-08-10 20:07:46.193492 WARNING::Fitting problem for feature 96 returning NA
2025-08-10 20:07:46.195331 WARNING::Fitting problem for feature 97 returning NA
2025-08-10 20:07:46.199044 WARNING::Fitting problem for feature 99 returning NA
2025-08-10 20:07:46.229001 WARNING::Fitting problem for feature 114 returning NA
2025-08-10 20:07:46.230966 WARNING::Fitting problem for feature 115 returning NA
2025-08-10 20:07:46.247757 WARNING::Fitting problem for feature 123 returning NA
2025-08-10 20:07:46.261681 WARNING::Fitting problem for feature 130 returning NA
2025-08-10 20:07:46.266176 WARNING::Fitting problem for feature 132 returning NA
2025-08-10 20:07:46.280438 WARNING::Fitting problem for feature 139 returning NA
2025-08-10 20:07:46.304361 WARNING::Fitting problem for feature 150 returning NA
2025-08-10 20:07:46.380552 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c905b4dd5ba/fits/residuals_linear.rds
2025-08-10 20:07:46.411091 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c905b4dd5ba/fits/fitted_linear.rds
2025-08-10 20:07:46.442213 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c905b4dd5ba/fits/residuals_logistic.rds
2025-08-10 20:07:46.598655 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c905b4dd5ba/fits/fitted_logistic.rds
2025-08-10 20:07:52.827125 WARNING::Fitting problem for feature 50 returning NA
2025-08-10 20:07:52.853529 WARNING::Fitting problem for feature 62 returning NA
2025-08-10 20:07:52.879169 WARNING::Fitting problem for feature 74 returning NA
2025-08-10 20:07:52.886817 WARNING::Fitting problem for feature 78 returning NA
2025-08-10 20:07:52.898864 WARNING::Fitting problem for feature 84 returning NA
2025-08-10 20:07:52.925121 WARNING::Fitting problem for feature 96 returning NA
2025-08-10 20:07:52.92714 WARNING::Fitting problem for feature 97 returning NA
2025-08-10 20:07:52.931264 WARNING::Fitting problem for feature 99 returning NA
2025-08-10 20:07:52.965358 WARNING::Fitting problem for feature 114 returning NA
2025-08-10 20:07:52.967534 WARNING::Fitting problem for feature 115 returning NA
2025-08-10 20:07:52.985533 WARNING::Fitting problem for feature 123 returning NA
2025-08-10 20:07:52.999544 WARNING::Fitting problem for feature 130 returning NA
2025-08-10 20:07:53.003761 WARNING::Fitting problem for feature 132 returning NA
2025-08-10 20:07:53.032951 WARNING::Fitting problem for feature 139 returning NA
2025-08-10 20:07:53.056289 WARNING::Fitting problem for feature 150 returning NA
2025-08-10 20:07:58.046332 WARNING::Fitting problem for feature 50 returning NA
2025-08-10 20:07:58.072591 WARNING::Fitting problem for feature 62 returning NA
2025-08-10 20:07:58.098654 WARNING::Fitting problem for feature 74 returning NA
2025-08-10 20:07:58.10656 WARNING::Fitting problem for feature 78 returning NA
2025-08-10 20:07:58.118907 WARNING::Fitting problem for feature 84 returning NA
2025-08-10 20:07:58.146021 WARNING::Fitting problem for feature 96 returning NA
2025-08-10 20:07:58.148108 WARNING::Fitting problem for feature 97 returning NA
2025-08-10 20:07:58.152377 WARNING::Fitting problem for feature 99 returning NA
2025-08-10 20:07:58.189551 WARNING::Fitting problem for feature 114 returning NA
2025-08-10 20:07:58.191933 WARNING::Fitting problem for feature 115 returning NA
2025-08-10 20:07:58.211729 WARNING::Fitting problem for feature 123 returning NA
2025-08-10 20:07:58.228522 WARNING::Fitting problem for feature 130 returning NA
2025-08-10 20:07:58.233692 WARNING::Fitting problem for feature 132 returning NA
2025-08-10 20:07:58.250962 WARNING::Fitting problem for feature 139 returning NA
2025-08-10 20:07:58.277282 WARNING::Fitting problem for feature 150 returning NA
2025-08-10 20:07:58.378746 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c905b4dd5ba/fits/residuals_linear.rds
2025-08-10 20:07:58.410953 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c905b4dd5ba/fits/fitted_linear.rds
2025-08-10 20:07:58.443998 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c905b4dd5ba/fits/residuals_logistic.rds
2025-08-10 20:07:58.611169 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c905b4dd5ba/fits/fitted_logistic.rds
2025-08-10 20:08:04.996992 WARNING::Fitting problem for feature 50 returning NA
2025-08-10 20:08:05.023643 WARNING::Fitting problem for feature 62 returning NA
2025-08-10 20:08:05.049838 WARNING::Fitting problem for feature 74 returning NA
2025-08-10 20:08:05.057999 WARNING::Fitting problem for feature 78 returning NA
2025-08-10 20:08:05.070873 WARNING::Fitting problem for feature 84 returning NA
2025-08-10 20:08:05.097736 WARNING::Fitting problem for feature 96 returning NA
2025-08-10 20:08:05.099711 WARNING::Fitting problem for feature 97 returning NA
2025-08-10 20:08:05.103813 WARNING::Fitting problem for feature 99 returning NA
2025-08-10 20:08:05.154832 WARNING::Fitting problem for feature 114 returning NA
2025-08-10 20:08:05.157282 WARNING::Fitting problem for feature 115 returning NA
2025-08-10 20:08:05.174403 WARNING::Fitting problem for feature 123 returning NA
2025-08-10 20:08:05.188772 WARNING::Fitting problem for feature 130 returning NA
2025-08-10 20:08:05.19328 WARNING::Fitting problem for feature 132 returning NA
2025-08-10 20:08:05.207511 WARNING::Fitting problem for feature 139 returning NA
2025-08-10 20:08:05.233501 WARNING::Fitting problem for feature 150 returning NA
2025-08-10 20:08:10.212551 WARNING::Fitting problem for feature 50 returning NA
2025-08-10 20:08:10.261976 WARNING::Fitting problem for feature 62 returning NA
2025-08-10 20:08:10.287885 WARNING::Fitting problem for feature 74 returning NA
2025-08-10 20:08:10.295663 WARNING::Fitting problem for feature 78 returning NA
2025-08-10 20:08:10.307804 WARNING::Fitting problem for feature 84 returning NA
2025-08-10 20:08:10.334888 WARNING::Fitting problem for feature 96 returning NA
2025-08-10 20:08:10.337137 WARNING::Fitting problem for feature 97 returning NA
2025-08-10 20:08:10.341655 WARNING::Fitting problem for feature 99 returning NA
2025-08-10 20:08:10.376223 WARNING::Fitting problem for feature 114 returning NA
2025-08-10 20:08:10.37855 WARNING::Fitting problem for feature 115 returning NA
2025-08-10 20:08:10.395313 WARNING::Fitting problem for feature 123 returning NA
2025-08-10 20:08:10.40915 WARNING::Fitting problem for feature 130 returning NA
2025-08-10 20:08:10.413357 WARNING::Fitting problem for feature 132 returning NA
2025-08-10 20:08:10.427399 WARNING::Fitting problem for feature 139 returning NA
2025-08-10 20:08:10.451199 WARNING::Fitting problem for feature 150 returning NA
2025-08-10 20:08:17.767687 WARNING::Fitting problem for feature 124 returning NA
2025-08-10 20:08:21.682964 WARNING::Fitting problem for feature 124 returning NA
2025-08-10 20:08:29.429222 WARNING::Fitting problem for feature 124 returning NA
2025-08-10 20:08:33.073962 WARNING::Fitting problem for feature 124 returning NA
2025-08-10 20:08:33.304096 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c9043271de3/fits/residuals_linear.rds
2025-08-10 20:08:33.33675 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c9043271de3/fits/fitted_linear.rds
2025-08-10 20:08:33.35931 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c9043271de3/fits/residuals_logistic.rds
2025-08-10 20:08:33.400566 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c9043271de3/fits/fitted_logistic.rds
2025-08-10 20:08:40.617971 WARNING::Fitting problem for feature 124 returning NA
2025-08-10 20:08:43.241272 WARNING::Fitting problem for feature 124 returning NA
2025-08-10 20:08:43.341303 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c9043271de3/fits/residuals_linear.rds
2025-08-10 20:08:43.374599 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c9043271de3/fits/fitted_linear.rds
2025-08-10 20:08:43.397562 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c9043271de3/fits/residuals_logistic.rds
2025-08-10 20:08:43.438475 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c9043271de3/fits/fitted_logistic.rds
2025-08-10 20:08:49.809441 WARNING::Fitting problem for feature 124 returning NA
2025-08-10 20:08:51.945666 WARNING::Fitting problem for feature 124 returning NA
2025-08-10 20:08:52.060559 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c9043271de3/fits/residuals_linear.rds
2025-08-10 20:08:52.09353 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c9043271de3/fits/fitted_linear.rds
2025-08-10 20:08:52.115981 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c9043271de3/fits/residuals_logistic.rds
2025-08-10 20:08:52.156285 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c9043271de3/fits/fitted_logistic.rds
2025-08-10 20:08:57.907671 WARNING::Fitting problem for feature 50 returning NA
2025-08-10 20:08:57.935627 WARNING::Fitting problem for feature 62 returning NA
2025-08-10 20:08:57.962205 WARNING::Fitting problem for feature 74 returning NA
2025-08-10 20:08:57.969845 WARNING::Fitting problem for feature 78 returning NA
2025-08-10 20:08:57.98172 WARNING::Fitting problem for feature 84 returning NA
2025-08-10 20:08:58.007979 WARNING::Fitting problem for feature 96 returning NA
2025-08-10 20:08:58.010001 WARNING::Fitting problem for feature 97 returning NA
2025-08-10 20:08:58.014115 WARNING::Fitting problem for feature 99 returning NA
2025-08-10 20:08:58.047585 WARNING::Fitting problem for feature 114 returning NA
2025-08-10 20:08:58.049659 WARNING::Fitting problem for feature 115 returning NA
2025-08-10 20:08:58.067063 WARNING::Fitting problem for feature 123 returning NA
2025-08-10 20:08:58.08124 WARNING::Fitting problem for feature 130 returning NA
2025-08-10 20:08:58.085746 WARNING::Fitting problem for feature 132 returning NA
2025-08-10 20:08:58.120534 WARNING::Fitting problem for feature 139 returning NA
2025-08-10 20:08:58.144858 WARNING::Fitting problem for feature 150 returning NA
2025-08-10 20:09:03.110033 WARNING::Fitting problem for feature 50 returning NA
2025-08-10 20:09:03.133342 WARNING::Fitting problem for feature 62 returning NA
2025-08-10 20:09:03.155625 WARNING::Fitting problem for feature 74 returning NA
2025-08-10 20:09:03.162444 WARNING::Fitting problem for feature 78 returning NA
2025-08-10 20:09:03.173016 WARNING::Fitting problem for feature 84 returning NA
2025-08-10 20:09:03.195907 WARNING::Fitting problem for feature 96 returning NA
2025-08-10 20:09:03.197649 WARNING::Fitting problem for feature 97 returning NA
2025-08-10 20:09:03.20121 WARNING::Fitting problem for feature 99 returning NA
2025-08-10 20:09:03.229734 WARNING::Fitting problem for feature 114 returning NA
2025-08-10 20:09:03.231573 WARNING::Fitting problem for feature 115 returning NA
2025-08-10 20:09:03.246255 WARNING::Fitting problem for feature 123 returning NA
2025-08-10 20:09:03.258264 WARNING::Fitting problem for feature 130 returning NA
2025-08-10 20:09:03.26196 WARNING::Fitting problem for feature 132 returning NA
2025-08-10 20:09:03.274382 WARNING::Fitting problem for feature 139 returning NA
2025-08-10 20:09:03.296142 WARNING::Fitting problem for feature 150 returning NA
2025-08-10 20:09:03.378447 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c9043271de3/fits/residuals_linear.rds
2025-08-10 20:09:03.410473 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c9043271de3/fits/fitted_linear.rds
2025-08-10 20:09:03.443477 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c9043271de3/fits/residuals_logistic.rds
2025-08-10 20:09:03.598028 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c9043271de3/fits/fitted_logistic.rds
2025-08-10 20:09:09.767975 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-08-10 20:09:09.773213 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-08-10 20:09:09.776774 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-08-10 20:09:09.792572 ERROR::No fixed, group, or
ordered effects included in formula.
2025-08-10 20:09:09.797743 ERROR::Effect name not found in metadata: d
2025-08-10 20:09:09.801252 ERROR::No user formula provided
2025-08-10 20:09:09.810375 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-08-10 20:09:09.813947 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-08-10 20:09:10.807461 INFO::Writing function arguments to log file
2025-08-10 20:09:10.812598 INFO::Verifying options selected are valid
2025-08-10 20:09:11.482 INFO::Writing function arguments to log file
2025-08-10 20:09:11.486068 INFO::Verifying options selected are valid
2025-08-10 20:09:11.486425 INFO::Determining format of input files
2025-08-10 20:09:11.486727 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-10 20:09:11.487517 INFO::Running selected normalization method: TSS
2025-08-10 20:09:11.488034 INFO::Creating output feature tables folder
2025-08-10 20:09:11.488434 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c90fd05c8c/features/data_norm.tsv
2025-08-10 20:09:11.489033 INFO::Filter data based on min abundance and min prevalence
2025-08-10 20:09:11.489331 INFO::Total samples in data: 16
2025-08-10 20:09:11.48961 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-08-10 20:09:11.490238 INFO::Total filtered features: 0
2025-08-10 20:09:11.490573 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-10 20:09:11.490951 INFO::Total features filtered by non-zero variance filtering: 0
2025-08-10 20:09:11.491256 INFO::Filtered feature names from variance filtering:
2025-08-10 20:09:11.491541 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c90fd05c8c/features/filtered_data.tsv
2025-08-10 20:09:11.492085 INFO::Running selected transform method: LOG
2025-08-10 20:09:11.492473 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c90fd05c8c/features/data_transformed.tsv
2025-08-10 20:09:11.493066 INFO::Applying z-score to standardize continuous metadata
2025-08-10 20:09:11.495233 INFO::Running the linear model component
2025-08-10 20:09:11.50053 INFO::Fitting model to feature number 1, a
2025-08-10 20:09:11.502001 INFO::Fitting model to feature number 2, b
2025-08-10 20:09:11.503273 INFO::Fitting model to feature number 3, c
2025-08-10 20:09:11.505568 INFO::Counting total values for each feature
2025-08-10 20:09:11.506178 INFO::Running the logistic model component
2025-08-10 20:09:11.510971 INFO::Fitting model to feature number 1, a
2025-08-10 20:09:11.512909 INFO::Fitting model to feature number 2, b
2025-08-10 20:09:11.51472 INFO::Fitting model to feature number 3, c
2025-08-10 20:09:11.517394 INFO::Counting total values for each feature
2025-08-10 20:09:11.518106 INFO::Re-running abundances for warn_prevalence
2025-08-10 20:09:11.518416 INFO::Running selected normalization method: TSS
2025-08-10 20:09:11.518892 INFO::Running selected transform method: LOG
2025-08-10 20:09:11.52377 INFO::Fitting model to feature number 1, a
2025-08-10 20:09:11.525073 INFO::Fitting model to feature number 2, b
2025-08-10 20:09:11.526314 INFO::Fitting model to feature number 3, c
2025-08-10 20:09:11.551422 INFO::Creating fits folder
2025-08-10 20:09:11.551962 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c90fd05c8c/fits/residuals_linear.rds
2025-08-10 20:09:11.552441 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c90fd05c8c/fits/fitted_linear.rds
2025-08-10 20:09:11.552858 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c90fd05c8c/fits/residuals_logistic.rds
2025-08-10 20:09:11.553282 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c90fd05c8c/fits/fitted_logistic.rds
2025-08-10 20:09:11.554178 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c90fd05c8c/all_results.tsv
2025-08-10 20:09:11.55482 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): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c90fd05c8c/significant_results.tsv
2025-08-10 20:09:11.555329 INFO::Creating output figures folder
2025-08-10 20:09:11.555789 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c90fd05c8c/figures/summary_plot.pdf
2025-08-10 20:09:12.023363 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c90fd05c8c/figures
2025-08-10 20:09:12.024104 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-10 20:09:12.025972 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-10 20:09:12.173417 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c90fd05c8c/figures/summary_plot.pdf
2025-08-10 20:09:12.63988 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c90fd05c8c/figures
2025-08-10 20:09:12.640464 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-10 20:09:12.642311 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-10 20:09:12.792776 INFO::Running the linear model component
2025-08-10 20:09:12.795526 INFO::Fitting model to feature number 1, a
2025-08-10 20:09:12.796928 INFO::Fitting model to feature number 2, b
2025-08-10 20:09:12.798137 INFO::Fitting model to feature number 3, c
2025-08-10 20:09:12.800346 INFO::Counting total values for each feature
2025-08-10 20:09:12.800873 INFO::Running the logistic model component
2025-08-10 20:09:12.803324 INFO::Fitting model to feature number 1, a
2025-08-10 20:09:12.805152 INFO::Fitting model to feature number 2, b
2025-08-10 20:09:12.807055 INFO::Fitting model to feature number 3, c
2025-08-10 20:09:12.809678 INFO::Counting total values for each feature
2025-08-10 20:09:12.810301 INFO::Re-running abundances for warn_prevalence
2025-08-10 20:09:12.810525 INFO::Running selected normalization method: TSS
2025-08-10 20:09:12.81092 INFO::Running selected transform method: LOG
2025-08-10 20:09:12.813537 INFO::Fitting model to feature number 1, a
2025-08-10 20:09:12.814964 INFO::Fitting model to feature number 2, b
2025-08-10 20:09:12.816127 INFO::Fitting model to feature number 3, c
2025-08-10 20:09:12.842211 INFO::Creating output folder
2025-08-10 20:09:12.842629 INFO::Creating output figures folder
2025-08-10 20:09:12.843045 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c9019d37954/figures/summary_plot.pdf
2025-08-10 20:09:13.314109 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c9019d37954/figures
2025-08-10 20:09:13.314681 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-10 20:09:13.316383 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-10 20:09:13.65353 INFO::Applying z-score to standardize continuous metadata
2025-08-10 20:09:13.656011 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-08-10 20:09:13.656261 INFO::Bypass z-score application to metadata
2025-08-10 20:09:13.656961 INFO::Bypass z-score application to metadata
2025-08-10 20:09:13.662941 INFO::Determining format of input files
2025-08-10 20:09:13.66323 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-10 20:09:13.663469 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-08-10 20:09:13.665481 INFO::Determining format of input files
2025-08-10 20:09:13.665782 INFO::Input format is data samples as columns and metadata samples as rows
2025-08-10 20:09:13.666142 INFO::Input format is feature_specific_covariate samples as columns
2025-08-10 20:09:13.668383 INFO::Determining format of input files
2025-08-10 20:09:13.668658 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-10 20:09:13.668959 INFO::Input format is feature_specific_covariate samples as columns
2025-08-10 20:09:13.66941 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-08-10 20:09:13.669622 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-08-10 20:09:13.673006 INFO::Running selected transform method: LOG
2025-08-10 20:09:13.673349 INFO::Creating output feature tables folder
2025-08-10 20:09:13.673709 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c904855f26a/features/data_transformed.tsv
2025-08-10 20:09:13.675019 INFO::Running selected transform method: LOG
2025-08-10 20:09:13.675337 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c904855f26a/features/data_transformed.tsv
2025-08-10 20:09:13.67644 INFO::Running selected transform method: PLOG
2025-08-10 20:09:13.676902 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c904855f26a/features/data_transformed.tsv
2025-08-10 20:09:13.677751 INFO::Running selected transform method: NONE
2025-08-10 20:09:13.677978 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c904855f26a/features/data_transformed.tsv
2025-08-10 20:09:13.680439 INFO::Running the linear model component
2025-08-10 20:09:13.683021 INFO::Fitting model to feature number 1, a
2025-08-10 20:09:13.684381 INFO::Fitting model to feature number 2, b
2025-08-10 20:09:13.685562 INFO::Fitting model to feature number 3, c
2025-08-10 20:09:13.68784 INFO::Counting total values for each feature
2025-08-10 20:09:13.688403 INFO::Running the logistic model component
2025-08-10 20:09:13.690885 INFO::Fitting model to feature number 1, a
2025-08-10 20:09:13.692754 INFO::Fitting model to feature number 2, b
2025-08-10 20:09:13.694434 INFO::Fitting model to feature number 3, c
2025-08-10 20:09:13.697039 INFO::Counting total values for each feature
2025-08-10 20:09:13.697666 INFO::Re-running abundances for warn_prevalence
2025-08-10 20:09:13.69789 INFO::Running selected normalization method: TSS
2025-08-10 20:09:13.698282 INFO::Running selected transform method: LOG
2025-08-10 20:09:13.700768 INFO::Fitting model to feature number 1, a
2025-08-10 20:09:13.701967 INFO::Fitting model to feature number 2, b
2025-08-10 20:09:13.703079 INFO::Fitting model to feature number 3, c
2025-08-10 20:09:13.728203 INFO::Creating output folder
2025-08-10 20:09:13.728582 INFO::Creating fits folder
2025-08-10 20:09:13.728889 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c9029e3240/fits/residuals_linear.rds
2025-08-10 20:09:13.729315 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c9029e3240/fits/fitted_linear.rds
2025-08-10 20:09:13.729668 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c9029e3240/fits/residuals_logistic.rds
2025-08-10 20:09:13.730021 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c9029e3240/fits/fitted_logistic.rds
2025-08-10 20:09:13.730842 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c9029e3240/all_results.tsv
2025-08-10 20:09:13.731391 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): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmprOipoq/file3c9029e3240/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
119.046 5.113 124.576
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 8.189 | 0.463 | 8.682 | |
| maaslin_check_arguments | 0.059 | 0.002 | 0.062 | |
| maaslin_check_formula | 0.055 | 0.003 | 0.058 | |
| maaslin_compute_formula | 0.056 | 0.002 | 0.059 | |
| maaslin_contrast_test | 7.127 | 0.631 | 8.080 | |
| maaslin_filter | 0.225 | 0.044 | 0.308 | |
| maaslin_fit | 4.998 | 0.563 | 5.672 | |
| maaslin_log_arguments | 0.053 | 0.003 | 0.057 | |
| maaslin_normalize | 0.123 | 0.014 | 0.137 | |
| maaslin_plot_results | 13.576 | 0.638 | 14.325 | |
| maaslin_plot_results_from_output | 13.805 | 0.537 | 14.413 | |
| maaslin_process_metadata | 0.220 | 0.025 | 0.245 | |
| maaslin_read_data | 0.053 | 0.003 | 0.057 | |
| maaslin_reorder_data | 0.052 | 0.004 | 0.055 | |
| maaslin_transform | 0.261 | 0.021 | 0.282 | |
| maaslin_write_results | 5.209 | 0.364 | 5.577 | |
| maaslin_write_results_lefse_format | 5.805 | 0.420 | 6.252 | |
| preprocess_dna_mtx | 0.001 | 0.000 | 0.002 | |
| preprocess_taxa_mtx | 0.001 | 0.000 | 0.001 | |